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Sample records for intraspecific phylogeographic genomics

  1. Identification of chloroplast genome loci suitable for high-resolution phylogeographic studies of Colocasia esculenta (L.) Schott (Araceae) and closely related taxa.

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    Ahmed, Ibrar; Matthews, Peter J; Biggs, Patrick J; Naeem, Muhammad; McLenachan, Patricia A; Lockhart, Peter J

    2013-09-01

    Recently, we reported the chloroplast genome-wide association of oligonucleotide repeats, indels and nucleotide substitutions in aroid chloroplast genomes. We hypothesized that the distribution of oligonucleotide repeat sequences in a single representative genome can be used to identify mutational hotspots and loci suitable for population genetic, phylogenetic and phylogeographic studies. Using information on the location of oligonucleotide repeats in the chloroplast genome of taro (Colocasia esculenta), we designed 30 primer pairs to amplify and sequence polymorphic loci. The primers have been tested in a range of intra-specific to intergeneric comparisons, including ten taro samples (Colocasia esculenta) from diverse geographical locations, four other Colocasia species (C. affinis, C. fallax, C. formosana, C. gigantea) and three other aroid genera (represented by Remusatia vivipara, Alocasia brisbanensis and Amorphophallus konjac). Multiple sequence alignments for the intra-specific comparison revealed nucleotide substitutions (point mutations) at all 30 loci and microsatellite polymorphisms at 14 loci. The primer pairs reported here reveal levels of genetic variation suitable for high-resolution phylogeographic and evolutionary studies of taro and other closely related aroids. Our results confirm that information on repeat distribution can be used to identify loci suitable for such studies, and we expect that this approach can be used in other plant groups. © 2013 John Wiley & Sons Ltd.

  2. Phylogeographic, genomic, and meropenem susceptibility analysis of Burkholderia ubonensis.

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    Erin P Price

    2017-09-01

    Full Text Available The bacterium Burkholderia ubonensis is commonly co-isolated from environmental specimens harbouring the melioidosis pathogen, Burkholderia pseudomallei. B. ubonensis has been reported in northern Australia and Thailand but not North America, suggesting similar geographic distribution to B. pseudomallei. Unlike most other Burkholderia cepacia complex (Bcc species, B. ubonensis is considered non-pathogenic, although its virulence potential has not been tested. Antibiotic resistance in B. ubonensis, particularly towards drugs used to treat the most severe B. pseudomallei infections, has also been poorly characterised. This study examined the population biology of B. ubonensis, and includes the first reported isolates from the Caribbean. Phylogenomic analysis of 264 B. ubonensis genomes identified distinct clades that corresponded with geographic origin, similar to B. pseudomallei. A small proportion (4% of strains lacked the 920kb chromosome III replicon, with discordance of presence/absence amongst genetically highly related strains, demonstrating that the third chromosome of B. ubonensis, like other Bcc species, probably encodes for a nonessential pC3 megaplasmid. Multilocus sequence typing using the B. pseudomallei scheme revealed that one-third of strains lack the "housekeeping" narK locus. In comparison, all strains could be genotyped using the Bcc scheme. Several strains possessed high-level meropenem resistance (≥32 μg/mL, a concern due to potential transmission of this phenotype to B. pseudomallei. In silico analysis uncovered a high degree of heterogeneity among the lipopolysaccharide O-antigen cluster loci, with at least 35 different variants identified. Finally, we show that Asian B. ubonensis isolate RF23-BP41 is avirulent in the BALB/c mouse model via a subcutaneous route of infection. Our results provide several new insights into the biology of this understudied species.

  3. Complete mitochondrial genome phylogeographic analysis of killer whales (Orcinus orca) indicates multiple species.

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    Morin, Phillip A; Archer, Frederick I; Foote, Andrew D; Vilstrup, Julia; Allen, Eric E; Wade, Paul; Durban, John; Parsons, Kim; Pitman, Robert; Li, Lewyn; Bouffard, Pascal; Abel Nielsen, Sandra C; Rasmussen, Morten; Willerslev, Eske; Gilbert, M Thomas P; Harkins, Timothy

    2010-07-01

    Killer whales (Orcinus orca) currently comprise a single, cosmopolitan species with a diverse diet. However, studies over the last 30 yr have revealed populations of sympatric "ecotypes" with discrete prey preferences, morphology, and behaviors. Although these ecotypes avoid social interactions and are not known to interbreed, genetic studies to date have found extremely low levels of diversity in the mitochondrial control region, and few clear phylogeographic patterns worldwide. This low level of diversity is likely due to low mitochondrial mutation rates that are common to cetaceans. Using killer whales as a case study, we have developed a method to readily sequence, assemble, and analyze complete mitochondrial genomes from large numbers of samples to more accurately assess phylogeography and estimate divergence times. This represents an important tool for wildlife management, not only for killer whales but for many marine taxa. We used high-throughput sequencing to survey whole mitochondrial genome variation of 139 samples from the North Pacific, North Atlantic, and southern oceans. Phylogenetic analysis indicated that each of the known ecotypes represents a strongly supported clade with divergence times ranging from approximately 150,000 to 700,000 yr ago. We recommend that three named ecotypes be elevated to full species, and that the remaining types be recognized as subspecies pending additional data. Establishing appropriate taxonomic designations will greatly aid in understanding the ecological impacts and conservation needs of these important marine predators. We predict that phylogeographic mitogenomics will become an important tool for improved statistical phylogeography and more precise estimates of divergence times.

  4. Complete mitochondrial genome phylogeographic analysis of killer whales (Orcinus orca) indicates multiple species

    DEFF Research Database (Denmark)

    Morin, Phillip A; Archer, Frederick I.; Foote, Andrew David

    2010-01-01

    Killer whales (Orcinus orca) currently comprise a single, cosmopolitan species with a diverse diet. However, studies over the last 30 yr have revealed populations of sympatric "ecotypes" with discrete prey preferences, morphology, and behaviors. Although these ecotypes avoid social interactions...... as a case study, we have developed a method to readily sequence, assemble, and analyze complete mitochondrial genomes from large numbers of samples to more accurately assess phylogeography and estimate divergence times. This represents an important tool for wildlife management, not only for killer whales...... impacts and conservation needs of these important marine predators. We predict that phylogeographic mitogenomics will become an important tool for improved statistical phylogeography and more precise estimates of divergence times....

  5. Genomic and Genotypic Characterization of Cylindrospermopsis raciborskii: Toward an Intraspecific Phylogenetic Evaluation by Comparative Genomics

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    Vinicius A. C. Abreu

    2018-02-01

    Full Text Available Cylindrospermopsis raciborskii is a freshwater cyanobacterial species with increasing bloom reports worldwide that are likely due to factors related to climate change. In addition to the deleterious effects of blooms on aquatic ecosystems, the majority of ecotypes can synthesize toxic secondary metabolites causing public health issues. To overcome the harmful effects of C. raciborskii blooms, it is important to advance knowledge of diversity, genetic variation, and evolutionary processes within populations. An efficient approach to exploring this diversity and understanding the evolution of C. raciborskii is to use comparative genomics. Here, we report two new draft genomes of C. raciborskii (strains CENA302 and CENA303 from Brazilian isolates of different origins and explore their molecular diversity, phylogeny, and evolutionary diversification by comparing their genomes with sequences from other strains available in public databases. The results obtained by comparing seven C. raciborskii and the Raphidiopsis brookii D9 genomes revealed a set of conserved core genes and a variable set of accessory genes, such as those involved in the biosynthesis of natural products, heterocyte glycolipid formation, and nitrogen fixation. Gene cluster arrangements related to the biosynthesis of the antifungal cyclic glycosylated lipopeptide hassallidin were identified in four C. raciborskii genomes, including the non-nitrogen fixing strain CENA303. Shifts in gene clusters involved in toxin production according to geographic origins were observed, as well as a lack of nitrogen fixation (nif and heterocyte glycolipid (hgl gene clusters in some strains. Single gene phylogeny (16S rRNA sequences was congruent with phylogeny based on 31 concatenated housekeeping protein sequences, and both analyses have shown, with high support values, that the species C. raciborskii is monophyletic. This comparative genomics study allowed a species-wide view of the biological

  6. Pneumocystis diversity as a phylogeographic tool

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    S Derouiche

    2009-02-01

    Full Text Available Parasites are increasingly used to complement the evolutionary and ecological adaptation history of their hosts. Pneumocystis pathogenic fungi, which are transmitted from host-to-host via an airborne route, have been shown to constitute genuine host markers of evolution. These parasites can also provide valuable information about their host ecology. Here, we suggest that parasites can be used as phylogeographic markers to understand the geographical distribution of intra-specific host genetic variants. To test our hypothesis, we characterised Pneumocystis isolates from wild bats living in different areas. Bats comprise a wide variety of species; some of them are able to migrate. Thus, bat chorology and migration behaviour can be approached using Pneumocystis as phylogeographic markers. In the present work, we find that the genetic polymorphisms of bat-derived Pneumocystis are structured by host chorology. Therefore, Pneumocystis intra-specific genetic diversity may constitute a useful and relevant phylogeographic tool.

  7. Stabilizing selection on genome size in a population of Festuca pallens under conditions of intensive intraspecific competition.

    Science.gov (United States)

    Smarda, Petr; Horová, Lucie; Bures, Petr; Hralová, Ivana; Marková, Michaela

    2010-09-01

    *Stabilizing selection is a key evolutionary mechanism for which there is relatively little experimental evidence. To date, stabilizing selection has never been observed at the whole-genome level. *We tested the effect of selection on genome size in a field experiment using seeds collected in a population of Festuca pallens with a highly variable genome size. Using flow cytometry, we measured the genome size in germinating seedlings and juvenile plants grown with or without high intraspecific competition (908 individuals). Above-ground biomass and leaf number were used as measurements of individual vegetative performance. The possible confounding effect of seed weight was controlled for in a separate experiment. *Growth under high competition had a significant stabilizing effect on genome size. Because no relationship was observed between genome size and vegetative performance, we assume that the elimination of plants with extreme genome sizes was the result of decreased survival as a consequence of some unrecognized stress. *Our results indicate that genome size may be under direct selection. The equal disadvantaging of either large or small genomes indicates that the selection for optimum genome size in species may be fully context dependent. This study demonstrates the power of competition experiments for the detection of weak selection processes.

  8. Advancing the STMS genomic resources for defining new locations on the intraspecific genetic linkage map of chickpea (Cicer arietinum L.

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    Shokeen Bhumika

    2011-02-01

    Full Text Available Abstract Background Chickpea (Cicer arietinum L. is an economically important cool season grain legume crop that is valued for its nutritive seeds having high protein content. However, several biotic and abiotic stresses and the low genetic variability in the chickpea genome have continuously hindered the chickpea molecular breeding programs. STMS (Sequence Tagged Microsatellite Sites markers which are preferred for the construction of saturated linkage maps in several crop species, have also emerged as the most efficient and reliable source for detecting allelic diversity in chickpea. However, the number of STMS markers reported in chickpea is still limited and moreover exhibit low rates of both inter and intraspecific polymorphism, thereby limiting the positions of the SSR markers especially on the intraspecific linkage maps of chickpea. Hence, this study was undertaken with the aim of developing additional STMS markers and utilizing them for advancing the genetic linkage map of chickpea which would have applications in QTL identification, MAS and for de novo assembly of high throughput whole genome sequence data. Results A microsatellite enriched library of chickpea (enriched for (GT/CAn and (GA/CTn repeats was constructed from which 387 putative microsatellite containing clones were identified. From these, 254 STMS primers were designed of which 181 were developed as functional markers. An intraspecific mapping population of chickpea, [ICCV-2 (single podded × JG-62 (double podded] and comprising of 126 RILs, was genotyped for mapping. Of the 522 chickpea STMS markers (including the double-podding trait, screened for parental polymorphism, 226 (43.3% were polymorphic in the parents and were used to genotype the RILs. At a LOD score of 3.5, eight linkage groups defining the position of 138 markers were obtained that spanned 630.9 cM with an average marker density of 4.57 cM. Further, based on the common loci present between the current map

  9. Advancing the STMS genomic resources for defining new locations on the intraspecific genetic linkage map of chickpea (Cicer arietinum L.).

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    Gaur, Rashmi; Sethy, Niroj K; Choudhary, Shalu; Shokeen, Bhumika; Gupta, Varsha; Bhatia, Sabhyata

    2011-02-17

    Chickpea (Cicer arietinum L.) is an economically important cool season grain legume crop that is valued for its nutritive seeds having high protein content. However, several biotic and abiotic stresses and the low genetic variability in the chickpea genome have continuously hindered the chickpea molecular breeding programs. STMS (Sequence Tagged Microsatellite Sites) markers which are preferred for the construction of saturated linkage maps in several crop species, have also emerged as the most efficient and reliable source for detecting allelic diversity in chickpea. However, the number of STMS markers reported in chickpea is still limited and moreover exhibit low rates of both inter and intraspecific polymorphism, thereby limiting the positions of the SSR markers especially on the intraspecific linkage maps of chickpea. Hence, this study was undertaken with the aim of developing additional STMS markers and utilizing them for advancing the genetic linkage map of chickpea which would have applications in QTL identification, MAS and for de novo assembly of high throughput whole genome sequence data. A microsatellite enriched library of chickpea (enriched for (GT/CA)n and (GA/CT)n repeats) was constructed from which 387 putative microsatellite containing clones were identified. From these, 254 STMS primers were designed of which 181 were developed as functional markers. An intraspecific mapping population of chickpea, [ICCV-2 (single podded) × JG-62 (double podded)] and comprising of 126 RILs, was genotyped for mapping. Of the 522 chickpea STMS markers (including the double-podding trait, screened for parental polymorphism, 226 (43.3%) were polymorphic in the parents and were used to genotype the RILs. At a LOD score of 3.5, eight linkage groups defining the position of 138 markers were obtained that spanned 630.9 cM with an average marker density of 4.57 cM. Further, based on the common loci present between the current map and the previously published chickpea

  10. The genomic distribution of intraspecific and interspecific sequence divergence of human segmental duplications relative to human/chimpanzee chromosomal rearrangements

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    Eichler Evan E

    2008-08-01

    Full Text Available Abstract Background It has been suggested that chromosomal rearrangements harbor the molecular footprint of the biological phenomena which they induce, in the form, for instance, of changes in the sequence divergence rates of linked genes. So far, all the studies of these potential associations have focused on the relationship between structural changes and the rates of evolution of single-copy DNA and have tried to exclude segmental duplications (SDs. This is paradoxical, since SDs are one of the primary forces driving the evolution of structure and function in our genomes and have been linked not only with novel genes acquiring new functions, but also with overall higher DNA sequence divergence and major chromosomal rearrangements. Results Here we take the opposite view and focus on SDs. We analyze several of the features of SDs, including the rates of intraspecific divergence between paralogous copies of human SDs and of interspecific divergence between human SDs and chimpanzee DNA. We study how divergence measures relate to chromosomal rearrangements, while considering other factors that affect evolutionary rates in single copy DNA. Conclusion We find that interspecific SD divergence behaves similarly to divergence of single-copy DNA. In contrast, old and recent paralogous copies of SDs do present different patterns of intraspecific divergence. Also, we show that some relatively recent SDs accumulate in regions that carry inversions in sister lineages.

  11. Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes

    DEFF Research Database (Denmark)

    Gilbert, M Thomas P; Drautz, Daniela I; Lesk, Arthur M

    2008-01-01

    We report five new complete mitochondrial DNA (mtDNA) genomes of Siberian woolly mammoth (Mammuthus primigenius), sequenced with up to 73-fold coverage from DNA extracted from hair shaft material. Three of the sequences present the first complete mtDNA genomes of mammoth clade II. Analysis...... to indicate any important functional difference between genomes belonging to the two clades, suggesting that the loss of clade II more likely is due to genetic drift than a selective sweep....

  12. Comparative mapping in intraspecific populations uncovers a high degree of macrosynteny between A- and B-genome diploid species of peanut

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    Guo Yufang

    2012-11-01

    Full Text Available Abstract Background Cultivated peanut or groundnut (Arachis hypogaea L. is an important oilseed crop with an allotetraploid genome (AABB, 2n = 4x = 40. Both the low level of genetic variation within the cultivated gene pool and its polyploid nature limit the utilization of molecular markers to explore genome structure and facilitate genetic improvement. Nevertheless, a wealth of genetic diversity exists in diploid Arachis species (2n = 2x = 20, which represent a valuable gene pool for cultivated peanut improvement. Interspecific populations have been used widely for genetic mapping in diploid species of Arachis. However, an intraspecific mapping strategy was essential to detect chromosomal rearrangements among species that could be obscured by mapping in interspecific populations. To develop intraspecific reference linkage maps and gain insights into karyotypic evolution within the genus, we comparatively mapped the A- and B-genome diploid species using intraspecific F2 populations. Exploring genome organization among diploid peanut species by comparative mapping will enhance our understanding of the cultivated tetraploid peanut genome. Moreover, new sources of molecular markers that are highly transferable between species and developed from expressed genes will be required to construct saturated genetic maps for peanut. Results A total of 2,138 EST-SSR (expressed sequence tag-simple sequence repeat markers were developed by mining a tetraploid peanut EST assembly including 101,132 unigenes (37,916 contigs and 63,216 singletons derived from 70,771 long-read (Sanger and 270,957 short-read (454 sequences. A set of 97 SSR markers were also developed by mining 9,517 genomic survey sequences of Arachis. An SSR-based intraspecific linkage map was constructed using an F2 population derived from a cross between K 9484 (PI 298639 and GKBSPSc 30081 (PI 468327 in the B-genome species A. batizocoi. A high degree of macrosynteny was observed

  13. Illumina based whole mitochondrial genome of Junonia iphita reveals minor intraspecific variation

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    Catherine Vanlalruati

    2015-12-01

    Full Text Available In the present study, the near complete mitochondrial genome (mitogenome of Junonia iphita (Lepidoptera: Nymphalidae: Nymphalinae was determined to be 14,892 bp. The gene order and orientation are identical to those in other butterfly species. The phylogenetic tree constructed from the whole mitogenomes using the 13 protein coding genes (PCGs defines the genetic relatedness of the two J. iphita species collected from two different regions. All the Junonia species clustered together, and were further subdivided into clade one consisting of J. almana and J. orithya and clade two comprising of the two J. iphita which were collected from Indo and Indochinese subregions separated by river barrier. Comparison between the two J. iphita sequences revealed minor variations and Single Nucleotide Polymorphisms were identified at 51 sites amounting to 0.4% of the entire mitochondrial genome.

  14. Intraspecific variations of Dekkera/Brettanomyces bruxellensis genome studied by capillary electrophoresis separation of the intron splice site profiles.

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    Vigentini, Ileana; De Lorenzis, Gabriella; Picozzi, Claudia; Imazio, Serena; Merico, Annamaria; Galafassi, Silvia; Piškur, Jure; Foschino, Roberto

    2012-06-15

    In enology, "Brett" character refers to the wine spoilage caused by the yeast Dekkera/Brettanomyces bruxellensis and its production of volatile phenolic off-flavours. However, the spoilage potential of this yeast is strain-dependent. Therefore, a rapid and reliable recognition at the strain level is a key point to avoid serious economic losses. The present work provides an operative tool to assess the genetic intraspecific variation in this species through the use of introns as molecular targets. Firstly, the available partial D./B. bruxellensis genome sequence was investigated in order to build primers annealing to introns 5' splice site sequence (ISS). This analysis allowed the detection of a non-random vocabulary flanking the site and, exploiting this feature, the creation of specific probes for strain discrimination. Secondly, the separation of the intron splice site PCR fragments was obtained throughout the set up of a capillary electrophoresis protocol, giving a 94% repeatability threshold in our experimental conditions. The comparison of results obtained with ISS-PCR/CE versus the ones performed by mtDNA RFLP revealed that the former protocol is more discriminating and allowed a reliable identification at strain level. Actually sixty D./B. bruxellensis isolates were recognised as unique strains, showing a level of similarity below 79% and confirming the high genetic polymorphism existing within the species. Two main clusters were grouped at similarity levels of about 46% and 47%, respectively, showing a poor correlation with the geographic area of isolation. Moreover, from the evolutionary point of view, the proposed technique could determine the frequency of the genome rearrangements that can occur in D./B. bruxellesis populations. Copyright © 2012 Elsevier B.V. All rights reserved.

  15. [RAPD analysis of the intraspecific and interspecific variation and phylogenetic relationships of Aegilops L. species with the U genome].

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    Goriunova, S V; Chikida, N N; Kochieva, E Z

    2010-07-01

    RAPD analysis was used to study the genetic variation and phylogenetic relationships of polyploid Aegilops species with the U genome. In total, 115 DNA samples of eight polyploid species containing the U genome and the diploid species Ae. umbellulata (U) were examined. Substantial interspecific polymorphism was observed for the majority of the polyploid species with the U genome (interspecific differences, 0.01-0,2; proportion of polymorphic loci, 56.6-88.2%). Aegilops triuncialis was identified as the only alloploid species with low interspecific polymorphism (interspecific differences, 0-0.01, P = 50%) in the U-genome group. The U-genome Aegilops species proved to be separated from other species of the genus. The phylogenetic relationships were established for the U-genome species. The greatest separation within the U-genome group was observed for the US-genome species Ae. kotschyi and Ae. variabilis. The tetraploid species Ae. triaristata and Ae. columnaris, which had the UX genome, and the hexaploid species Ae. recta (UXN) were found to be related to each other and separate from the UM-genome species. A similarity was observed between the U M-genome species Ae. ovata and Ae. biuncialis, which had the UM genome, and the ancestral diploid U-genome species Ae. umbellulata. The UC-genome species Ae. triuncialis was rather separate and slightly similar to the UX-genome species.

  16. Genome-wide analysis of intraspecific DNA polymorphism in 'Micro-Tom', a model cultivar of tomato (Solanum lycopersicum).

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    Kobayashi, Masaaki; Nagasaki, Hideki; Garcia, Virginie; Just, Daniel; Bres, Cécile; Mauxion, Jean-Philippe; Le Paslier, Marie-Christine; Brunel, Dominique; Suda, Kunihiro; Minakuchi, Yohei; Toyoda, Atsushi; Fujiyama, Asao; Toyoshima, Hiromi; Suzuki, Takayuki; Igarashi, Kaori; Rothan, Christophe; Kaminuma, Eli; Nakamura, Yasukazu; Yano, Kentaro; Aoki, Koh

    2014-02-01

    Tomato (Solanum lycopersicum) is regarded as a model plant of the Solanaceae family. The genome sequencing of the tomato cultivar 'Heinz 1706' was recently completed. To accelerate the progress of tomato genomics studies, systematic bioresources, such as mutagenized lines and full-length cDNA libraries, have been established for the cultivar 'Micro-Tom'. However, these resources cannot be utilized to their full potential without the completion of the genome sequencing of 'Micro-Tom'. We undertook the genome sequencing of 'Micro-Tom' and here report the identification of single nucleotide polymorphisms (SNPs) and insertion/deletions (indels) between 'Micro-Tom' and 'Heinz 1706'. The analysis demonstrated the presence of 1.23 million SNPs and 0.19 million indels between the two cultivars. The density of SNPs and indels was high in chromosomes 2, 5 and 11, but was low in chromosomes 6, 8 and 10. Three known mutations of 'Micro-Tom' were localized on chromosomal regions where the density of SNPs and indels was low, which was consistent with the fact that these mutations were relatively new and introgressed into 'Micro-Tom' during the breeding of this cultivar. We also report SNP analysis for two 'Micro-Tom' varieties that have been maintained independently in Japan and France, both of which have served as standard lines for 'Micro-Tom' mutant collections. Approximately 28,000 SNPs were identified between these two 'Micro-Tom' lines. These results provide high-resolution DNA polymorphic information on 'Micro-Tom' and represent a valuable contribution to the 'Micro-Tom'-based genomics resources.

  17. The complete mitochondrial genome of the land snail Cornu aspersum (Helicidae: Mollusca: intra-specific divergence of protein-coding genes and phylogenetic considerations within Euthyneura.

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    Juan Diego Gaitán-Espitia

    Full Text Available The complete sequences of three mitochondrial genomes from the land snail Cornu aspersum were determined. The mitogenome has a length of 14050 bp, and it encodes 13 protein-coding genes, 22 transfer RNA genes and two ribosomal RNA genes. It also includes nine small intergene spacers, and a large AT-rich intergenic spacer. The intra-specific divergence analysis revealed that COX1 has the lower genetic differentiation, while the most divergent genes were NADH1, NADH3 and NADH4. With the exception of Euhadra herklotsi, the structural comparisons showed the same gene order within the family Helicidae, and nearly identical gene organization to that found in order Pulmonata. Phylogenetic reconstruction recovered Basommatophora as polyphyletic group, whereas Eupulmonata and Pulmonata as paraphyletic groups. Bayesian and Maximum Likelihood analyses showed that C. aspersum is a close relative of Cepaea nemoralis, and with the other Helicidae species form a sister group of Albinaria caerulea, supporting the monophyly of the Stylommatophora clade.

  18. Transposable elements in phytopathogenic Verticillium spp.: insights into genome evolution and inter- and intra-specific diversification

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    Amyotte Stefan G

    2012-07-01

    Full Text Available Abstract Background Verticillium dahliae (Vd and Verticillium albo-atrum (Va are cosmopolitan soil fungi causing very disruptive vascular diseases on a wide range of crop plants. To date, no sexual stage has been identified in either microorganism suggesting that somatic mutation is a major force in generating genetic diversity. Whole genome comparative analysis of the recently sequenced strains VdLs.17 and VaMs.102 revealed that non-random insertions of transposable elements (TEs have contributed to the generation of four lineage-specific (LS regions in VdLs.17. Results We present here a detailed analysis of Class I retrotransposons and Class II “cut-and-paste” DNA elements detected in the sequenced Verticillium genomes. We report also of their distribution in other Vd and Va isolates from various geographic origins. In VdLs.17, we identified and characterized 56 complete retrotransposons of the Gypsy-, Copia- and LINE-like types, as well as 34 full-length elements of the “cut-and-paste” superfamilies Tc1/mariner, Activator and Mutator. While Copia and Tc1/mariner were present in multiple identical copies, Activator and Mutator sequences were highly divergent. Most elements comprised complete ORFs, had matching ESTs and showed active transcription in response to stress treatment. Noticeably, we found evidences of repeat-induced point mutation (RIP only in some of the Gypsy retroelements. While Copia-, Gypsy- and Tc1/mariner-like transposons were prominent, a large variation in presence of the other types of mobile elements was detected in the other Verticillium spp. strains surveyed. In particular, neither complete nor defective “cut-and-paste” TEs were found in VaMs.102. Conclusions Copia-, Gypsy- and Tc1/mariner-like transposons are the most wide-spread TEs in the phytopathogens V. dahliae and V. albo-atrum. In VdLs.17, we identified several retroelements and “cut-and-paste” transposons still potentially active. Some of these

  19. Intraspecific chromosomal and genetic polymorphism in Brassica ...

    Indian Academy of Sciences (India)

    2014-04-16

    Apr 16, 2014 ... A. V., Lemesh V. A. and Muravenko O. V. 2014 Intraspecific chromosomal and genetic polymorphism in Brassica napus L. detected by cytogenetic and molecular markers. J. Genet. ...... Howell E. C., Kearsey M. J., Jones G. H., King G. J. and Armstrong. S. J. 2008 A and C genome distinction and ...

  20. Phylogeographical analysis of mtDNA data indicates postglacial expansion from multiple glacial refugia in woodland caribou (Rangifer tarandus caribou.

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    Cornelya F C Klütsch

    Full Text Available Glacial refugia considerably shaped the phylogeographical structure of species and may influence intra-specific morphological, genetic, and adaptive differentiation. However, the impact of the Quaternary ice ages on the phylogeographical structure of North American temperate mammalian species is not well-studied. Here, we surveyed ~1600 individuals of the widely distributed woodland caribou (Rangifer tarandus caribou using mtDNA control region sequences to investigate if glacial refugia contributed to the phylogeographical structure in this subspecies. Phylogenetic tree reconstruction, a median-joining network, and mismatch distributions supported postglacial expansions of woodland caribou from three glacial refugia dating back to 13544-22005 years. These three lineages consisted almost exclusively of woodland caribou mtDNA haplotypes, indicating that phylogeographical structure was mainly shaped by postglacial expansions. The putative centres of these lineages are geographically separated; indicating disconnected glacial refugia in the Rocky Mountains, east of the Mississippi, and the Appalachian Mountains. This is in congruence with the fossil record that caribou were distributed in these areas during the Pleistocene. Our results suggest that the last glacial maximum substantially shaped the phylogeographical structure of this large mammalian North American species that will be affected by climatic change. Therefore, the presented results will be essential for future conservation planning in woodland caribou.

  1. Comparative population genomics of the Borrelia burgdorferi species complex reveals high degree of genetic isolation among species and underscores benefits and constraints to studying intra-specific epidemiological processes.

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    Maude Jacquot

    Full Text Available Lyme borreliosis, one of the most frequently contracted zoonotic diseases in the Northern Hemisphere, is caused by bacteria belonging to different genetic groups within the Borrelia burgdorferi species complex, which are transmitted by ticks among various wildlife reservoirs, such as small mammals and birds. These features make the Borrelia burgdorferi species complex an attractive biological model that can be used to study the diversification and the epidemiology of endemic bacterial pathogens. We investigated the potential of population genomic approaches to study these processes. Sixty-three strains belonging to three species within the Borrelia burgdorferi complex were isolated from questing ticks in Alsace (France, a region where Lyme disease is highly endemic. We first aimed to characterize the degree of genetic isolation among the species sampled. Phylogenetic and coalescent-based analyses revealed clear delineations: there was a ∼50 fold difference between intra-specific and inter-specific recombination rates. We then investigated whether the population genomic data contained information of epidemiological relevance. In phylogenies inferred using most of the genome, conspecific strains did not cluster in clades. These results raise questions about the relevance of different strategies when investigating pathogen epidemiology. For instance, here, both classical analytic approaches and phylodynamic simulations suggested that population sizes and migration rates were higher in B. garinii populations, which are normally associated with birds, than in B. burgdorferi s.s. populations. The phylogenetic analyses of the infection-related ospC gene and its flanking region provided additional support for this finding. Traces of recombination among the B. burgdorferi s.s. lineages and lineages associated with small mammals were found, suggesting that they shared the same hosts. Altogether, these results provide baseline evidence that can be used

  2. Comparative Population Genomics of the Borrelia burgdorferi Species Complex Reveals High Degree of Genetic Isolation among Species and Underscores Benefits and Constraints to Studying Intra-Specific Epidemiological Processes

    Science.gov (United States)

    Jacquot, Maude; Gonnet, Mathieu; Ferquel, Elisabeth; Abrial, David; Claude, Alexandre; Gasqui, Patrick; Choumet, Valérie; Charras-Garrido, Myriam; Garnier, Martine; Faure, Benjamin; Sertour, Natacha; Dorr, Nelly; De Goër, Jocelyn; Vourc'h, Gwenaël; Bailly, Xavier

    2014-01-01

    Lyme borreliosis, one of the most frequently contracted zoonotic diseases in the Northern Hemisphere, is caused by bacteria belonging to different genetic groups within the Borrelia burgdorferi species complex, which are transmitted by ticks among various wildlife reservoirs, such as small mammals and birds. These features make the Borrelia burgdorferi species complex an attractive biological model that can be used to study the diversification and the epidemiology of endemic bacterial pathogens. We investigated the potential of population genomic approaches to study these processes. Sixty-three strains belonging to three species within the Borrelia burgdorferi complex were isolated from questing ticks in Alsace (France), a region where Lyme disease is highly endemic. We first aimed to characterize the degree of genetic isolation among the species sampled. Phylogenetic and coalescent-based analyses revealed clear delineations: there was a ∼50 fold difference between intra-specific and inter-specific recombination rates. We then investigated whether the population genomic data contained information of epidemiological relevance. In phylogenies inferred using most of the genome, conspecific strains did not cluster in clades. These results raise questions about the relevance of different strategies when investigating pathogen epidemiology. For instance, here, both classical analytic approaches and phylodynamic simulations suggested that population sizes and migration rates were higher in B. garinii populations, which are normally associated with birds, than in B. burgdorferi s.s. populations. The phylogenetic analyses of the infection-related ospC gene and its flanking region provided additional support for this finding. Traces of recombination among the B. burgdorferi s.s. lineages and lineages associated with small mammals were found, suggesting that they shared the same hosts. Altogether, these results provide baseline evidence that can be used to formulate

  3. Estimating intraspecific genetic diversity from community DNA metabarcoding data

    Directory of Open Access Journals (Sweden)

    Vasco Elbrecht

    2018-04-01

    Full Text Available Background DNA metabarcoding is used to generate species composition data for entire communities. However, sequencing errors in high-throughput sequencing instruments are fairly common, usually requiring reads to be clustered into operational taxonomic units (OTUs, losing information on intraspecific diversity in the process. While Cytochrome c oxidase subunit I (COI haplotype information is limited in resolving intraspecific diversity it is nevertheless often useful e.g. in a phylogeographic context, helping to formulate hypotheses on taxon distribution and dispersal. Methods This study combines sequence denoising strategies, normally applied in microbial research, with additional abundance-based filtering to extract haplotype information from freshwater macroinvertebrate metabarcoding datasets. This novel approach was added to the R package “JAMP” and can be applied to COI amplicon datasets. We tested our haplotyping method by sequencing (i a single-species mock community composed of 31 individuals with 15 different haplotypes spanning three orders of magnitude in biomass and (ii 18 monitoring samples each amplified with four different primer sets and two PCR replicates. Results We detected all 15 haplotypes of the single specimens in the mock community with relaxed filtering and denoising settings. However, up to 480 additional unexpected haplotypes remained in both replicates. Rigorous filtering removes most unexpected haplotypes, but also can discard expected haplotypes mainly from the small specimens. In the monitoring samples, the different primer sets detected 177–200 OTUs, each containing an average of 2.40–3.30 haplotypes per OTU. The derived intraspecific diversity data showed population structures that were consistent between replicates and similar between primer pairs but resolution depended on the primer length. A closer look at abundant taxa in the dataset revealed various population genetic patterns, e.g. the stonefly

  4. Intraspecific sequence comparisons reveal similar rates of non-collinear gene insertion in the B and D genomes of bread wheat

    Czech Academy of Sciences Publication Activity Database

    Bartoš, Jan; Vlček, Čestmír; Choulet, F.; Džunková, Mária; Cviková, Kateřina; Šafář, Jan; Šimková, Hana; Pačes, Jan; Strnad, Hynek; Sourdille, P.; Berges, H.; Cattonaro, F.; Feuillet, C.; Doležel, Jaroslav

    2012-01-01

    Roč. 12, č. 155 (2012), s. 1-10 ISSN 1471-2229 R&D Projects: GA ČR GAP501/10/1778 Grant - others:GA MŠk(CZ) ED0007/01/01 Program:ED Institutional research plan: CEZ:AV0Z50380511; CEZ:AV0Z50520514 Keywords : Wheat * BAC sequencing * Homoeologous genomes Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.354, year: 2012

  5. Complete mitochondrial genome sequences ofBrassica rapa(Chinese cabbage and mizuna), and intraspecific differentiation of cytoplasm inB. rapaandBrassica juncea.

    Science.gov (United States)

    Hatono, Saki; Nishimura, Kaori; Murakami, Yoko; Tsujimura, Mai; Yamagishi, Hiroshi

    2017-09-01

    The complete sequence of the mitochondrial genome was determined for two cultivars of Brassica rapa . After determining the sequence of a Chinese cabbage variety, 'Oushou hakusai', the sequence of a mizuna variety, 'Chusei shiroguki sensuji kyomizuna', was mapped against the sequence of Chinese cabbage. The precise sequences where the two varieties demonstrated variation were ascertained by direct sequencing. It was found that the mitochondrial genomes of the two varieties are identical over 219,775 bp, with a single nucleotide polymorphism (SNP) between the genomes. Because B. rapa is the maternal species of an amphidiploid crop species, Brassica juncea , the distribution of the SNP was observed both in B. rapa and B. juncea . While the mizuna type SNP was restricted mainly to cultivars of mizuna (japonica group) in B. rapa , the mizuna type was widely distributed in B. juncea . The finding that the two Brassica species have these SNP types in common suggests that the nucleotide substitution occurred in wild B. rapa before both mitotypes were domesticated. It was further inferred that the interspecific hybridization between B. rapa and B. nigra took place twice and resulted in the two mitotypes of cultivated B. juncea .

  6. High density, genome-wide markers and intra-specific replication yield an unprecedented phylogenetic reconstruction of a globally significant, speciose lineage of Eucalyptus.

    Science.gov (United States)

    Jones, Rebecca C; Nicolle, Dean; Steane, Dorothy A; Vaillancourt, René E; Potts, Brad M

    2016-12-01

    We used genome-wide markers and an unprecedented scale of sampling to construct a phylogeny for a globally significant Eucalyptus lineage that has been impacted by hybridisation, recent radiation and morphological convergence. Our approach, using 3109 DArT markers distributed throughout the genome and 540 samples covering 185 terminal taxa in sections Maidenaria, Exsertaria, Latoangulatae and related smaller sections, with multiple geographically widespread samples per terminal taxon, produced a phylogeny that largely matched the morphological treatment of sections, though sections Exsertaria and Latoangulatae were polyphyletic. At lower levels there were numerous inconsistencies between the morphological treatment and the molecular phylogeny, and taxa within the three main sections were generally not monophyletic at the series (at least 62% polyphyly) or species (at least 52% polyphyly) level. Some of the discrepancies appear to be the result of morphological convergence or misclassifications, and we propose some taxonomic reassessments to address this. However, many inconsistencies appear to be the products of incomplete speciation and/or hybridisation. Our analysis represents a significant advance on previous phylogenies of these important eucalypt sections (which have mainly used single samples to represent each species), thus providing a robust phylogenetic framework for evolutionary and ecological studies. Copyright © 2016 Elsevier Inc. All rights reserved.

  7. Intraspecific chemical communication in microalgae

    Czech Academy of Sciences Publication Activity Database

    Venuleo, M.; Raven, J. A.; Giordano, Mario

    2017-01-01

    Roč. 215, č. 2 (2017), s. 516-530 ISSN 1469-8137 Institutional support: RVO:61388971 Keywords : evolution * infochemicals * intraspecific communication Subject RIV: EE - Microbiology, Virology OBOR OECD: Microbiology

  8. Distinct Phylogeographic Structures of Wild Radish (Raphanus sativus L. var. raphanistroides Makino in Japan.

    Directory of Open Access Journals (Sweden)

    Qingxiang Han

    Full Text Available Coastal plants with simple linear distribution ranges along coastlines provide a suitable system for improving our understanding of patterns of intra-specific distributional history and genetic variation. Due to the combination of high seed longevity and high dispersibility of seeds via seawater, we hypothesized that wild radish would poorly represent phylogeographic structure at the local scale. On the other hand, we also hypothesized that wild radish populations might be geographically differentiated, as has been exhibited by their considerable phenotypic variations along the islands of Japan. We conducted nuclear DNA microsatellite loci and chloroplast DNA haplotype analyses for 486 samples and 144 samples, respectively, from 18 populations to investigate the phylogeographic structure of wild radish in Japan. Cluster analysis supported the existence of differential genetic structures between the Ryukyu Islands and mainland Japan populations. A significant strong pattern of isolation by distance and significant evidence of a recent bottleneck were detected. The chloroplast marker analysis resulted in the generation of eight haplotypes, of which two haplotypes (A and B were broadly distributed in most wild radish populations. High levels of variation in microsatellite loci were identified, whereas cpDNA displayed low levels of genetic diversity within populations. Our results indicate that the Kuroshio Current would have contributed to the sculpting of the phylogeographic structure by shaping genetic gaps between isolated populations. In addition, the Tokara Strait would have created a geographic barrier between the Ryukyu Islands and mainland Japan. Finally, extant habitat disturbances (coastal erosion, migration patterns (linear expansion, and geographic characteristics (small islands and sea currents have influenced the expansion and historical population dynamics of wild radish. Our study is the first to record the robust phylogeographic

  9. Phylogeographical structure and temporal complexity in American sweetgum (Liquidambar styraciflua; Altingiaceae).

    Science.gov (United States)

    Morris, Ashley B; Ickert-Bond, Stefanie M; Brunson, D Burke; Soltis, Douglas E; Soltis, Pamela S

    2008-09-01

    Eastern North American plant biogeography has traditionally focused on two primary issues: (i) the location of temperate Pleistocene refugia and their proximity to the southern margin of the ice sheet during the last glacial maximum, and (ii) the origin of the temperate element of northern Latin America. While numerous population genetic and phylogeographical studies have focused on the first issue, few (if any) have considered the second. We addressed these issues by surveying 117 individuals from 24 populations of Liquidambar styraciflua (American sweetgum; Altingiaceae) across the southeastern USA, eastern Mexico, and Guatemala, using more than 2200 bp of chloroplast DNA sequence data. To specifically address the issue of timing, we estimated intraspecific divergence times on the basis of multiple fossil-based calibration points, using taxa from Altingiaceae (Liquidambar and Altingia) and Hammamelidaceae (Hamamelis) as outgroups. More than half of the sampled localities exhibited multiple haplotypes. Remarkably, the greatest variation was observed within the USA, with Mexico and Guatemala sharing widespread haplotypes with Texas, Mississippi, Kentucky, Ohio, and northern Virginia. This lack of differentiation suggests shared ancestral polymorphisms, and that the genetic signal we observed is older than the disjunction itself. Our data provide support for previously proposed hypotheses of Pleistocene refugia in peninsular Florida and along the eastern Atlantic, but also for deeper divergences (approximately 8 million years ago) within the USA. These patterns reflect a dynamic biogeographical history for eastern North American trees, and emphasize the importance of the inclusion of a temporal component in any phylogeographical study.

  10. Phylogeographic concordance factors quantify phylogeographic congruence among co-distributed species in the Sarracenia alata pitcher plant system.

    Science.gov (United States)

    Satler, Jordan D; Carstens, Bryan C

    2016-05-01

    Comparative phylogeographic investigations have identified congruent phylogeographic breaks in co-distributed species in nearly every region of the world. The qualitative assessments of phylogeographic patterns traditionally used to identify such breaks, however, are limited because they rely on identifying monophyletic groups across species and do not account for coalescent stochasticity. Only long-standing phylogeographic breaks are likely to be obvious; many species could have had a concerted response to more recent landscape events, yet possess subtle signs of phylogeographic congruence because ancestral polymorphism has not completely sorted. Here, we introduce Phylogeographic Concordance Factors (PCFs), a novel method for quantifying phylogeographic congruence across species. We apply this method to the Sarracenia alata pitcher plant system, a carnivorous plant with a diverse array of commensal organisms. We explore whether a group of ecologically associated arthropods have co-diversified with the host pitcher plant, and identify if there is a positive correlation between ecological interaction and PCFs. Results demonstrate that multiple arthropods share congruent phylogeographic breaks with S. alata, and provide evidence that the level of ecological association can be used to predict the degree of similarity in the phylogeographic pattern. This study outlines an approach for quantifying phylogeographic congruence, a central concept in biogeographic research. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

  11. The complete chloroplast genome sequence of Podocarpus lambertii: genome structure, evolutionary aspects, gene content and SSR detection.

    Directory of Open Access Journals (Sweden)

    Leila do Nascimento Vieira

    Full Text Available BACKGROUND: Podocarpus lambertii (Podocarpaceae is a native conifer from the Brazilian Atlantic Forest Biome, which is considered one of the 25 biodiversity hotspots in the world. The advancement of next-generation sequencing technologies has enabled the rapid acquisition of whole chloroplast (cp genome sequences at low cost. Several studies have proven the potential of cp genomes as tools to understand enigmatic and basal phylogenetic relationships at different taxonomic levels, as well as further probe the structural and functional evolution of plants. In this work, we present the complete cp genome sequence of P. lambertii. METHODOLOGY/PRINCIPAL FINDINGS: The P. lambertii cp genome is 133,734 bp in length, and similar to other sequenced cupressophytes, it lacks one of the large inverted repeat regions (IR. It contains 118 unique genes and one duplicated tRNA (trnN-GUU, which occurs as an inverted repeat sequence. The rps16 gene was not found, which was previously reported for the plastid genome of another Podocarpaceae (Nageia nagi and Araucariaceae (Agathis dammara. Structurally, P. lambertii shows 4 inversions of a large DNA fragment ∼20,000 bp compared to the Podocarpus totara cp genome. These unexpected characteristics may be attributed to geographical distance and different adaptive needs. The P. lambertii cp genome presents a total of 28 tandem repeats and 156 SSRs, with homo- and dipolymers being the most common and tri-, tetra-, penta-, and hexapolymers occurring with less frequency. CONCLUSION: The complete cp genome sequence of P. lambertii revealed significant structural changes, even in species from the same genus. These results reinforce the apparently loss of rps16 gene in Podocarpaceae cp genome. In addition, several SSRs in the P. lambertii cp genome are likely intraspecific polymorphism sites, which may allow highly sensitive phylogeographic and population structure studies, as well as phylogenetic studies of species of

  12. Diversification in a biodiversity hot spot: landscape correlates of phylogeographic patterns in the African spotted reed frog.

    Science.gov (United States)

    Lawson, Lucinda P

    2013-04-01

    The Eastern Afromontane Biodiversity Hotspot is known for microendemism and exceptional population genetic structure. The region's landscape heterogeneity is thought to limit gene flow between fragmented populations and create opportunities for regional adaptation, but the processes involved are poorly understood. Using a combination of phylogeographic analyses and circuit theory, I investigate how characteristics of landscape heterogeneity including regional distributions of slope, rivers and streams, habitat and hydrological basins (drainages) impact genetic distance among populations of the endemic spotted reed frog (Hyperolius substriatus), identifying corridors of connectivity as well as barriers to dispersal. Results show that genetic distance among populations is most strongly correlated to regional and local hydrologic structure and the distribution of suitable habitat corridors, not isolation by distance. Contrary to expectations, phylogeographic structure is not coincident with the two montane systems, but instead corresponds to the split between the region's two major hydrological basins (Zambezi and East Central Coastal). This results in a paraphyletic relationship for the Malawian Highlands populations with respect to the Eastern Arc Mountains and implies that the northern Malawian Highlands are the diversity centre for H. substriatus. Although the Malawian Highlands collectively hold the greatest genetic diversity, individual populations have lower diversity than their Eastern Arc counterparts, with an overall pattern of decreasing population diversity from north to south. Through the study of intraspecific differentiation across a mosaic of ecosystem and geographic heterogeneity, we gain insight into the processes of diversification and a broader understanding of the role of landscape in evolution. © 2013 Blackwell Publishing Ltd.

  13. The ecological importance of intraspecific variation.

    Science.gov (United States)

    Des Roches, Simone; Post, David M; Turley, Nash E; Bailey, Joseph K; Hendry, Andrew P; Kinnison, Michael T; Schweitzer, Jennifer A; Palkovacs, Eric P

    2018-01-01

    Human activity is causing wild populations to experience rapid trait change and local extirpation. The resulting effects on intraspecific variation could have substantial consequences for ecological processes and ecosystem services. Although researchers have long acknowledged that variation among species influences the surrounding environment, only recently has evidence accumulated for the ecological importance of variation within species. We conducted a meta-analysis comparing the ecological effects of variation within a species (intraspecific effects) with the effects of replacement or removal of that species (species effects). We evaluated direct and indirect ecological responses, including changes in abundance (or biomass), rates of ecological processes and changes in community composition. Our results show that intraspecific effects are often comparable to, and sometimes stronger than, species effects. Species effects tend to be larger for direct ecological responses (for example, through consumption), whereas intraspecific effects and species effects tend to be similar for indirect responses (for example, through trophic cascades). Intraspecific effects are especially strong when indirect interactions alter community composition. Our results summarize data from the first generation of studies examining the relative ecological effects of intraspecific variation. Our conclusions can help inform the design of future experiments and the formulation of strategies to quantify and conserve biodiversity.

  14. Intraspecific diversity regulates fungal productivity and respiration.

    Directory of Open Access Journals (Sweden)

    Anna Wilkinson

    2010-09-01

    Full Text Available Individuals and not just species are key components of biodiversity, yet the relationship between intraspecific diversity and ecosystem functioning in microbial systems remains largely untested. This limits our ability to understand and predict the effects of altered genetic diversity in regulating key ecosystem processes and functions. Here, we use a model fungal system to test the hypothesis that intraspecific genotypic richness of Paxillus obscurosporus stimulates biomass and CO(2 efflux, but that this is dependent on nitrogen supply. Using controlled experimental microcosms, we show that populations containing several genotypes (maximum 8 of the fungus had greater productivity and produced significantly more CO(2 than those with fewer genotypes. Moreover, intraspecific diversity had a much stronger effect than a four-fold manipulation of the carbon:nitrogen ratio of the growth medium. The effects of intraspecific diversity were underpinned by strong roles of individuals, but overall intraspecific diversity increased the propensity of populations to over-yield, indicating that both complementarity and selection effects can operate within species. Our data demonstrate the importance of intraspecific diversity over a range of nitrogen concentrations, and the need to consider fine scale phylogenetic information of microbial communities in understanding their contribution to ecosystem processes.

  15. Quantitative Phylogenomics of Within-Species Mitogenome Variation: Monte Carlo and Non-Parametric Analysis of Phylogeographic Structure among Discrete Transatlantic Breeding Areas of Harp Seals (Pagophilus groenlandicus).

    Science.gov (United States)

    Carr, Steven M; Duggan, Ana T; Stenson, Garry B; Marshall, H Dawn

    2015-01-01

    Phylogenomic analysis of highly-resolved intraspecific phylogenies obtained from complete mitochondrial DNA genomes has had great success in clarifying relationships within and among human populations, but has found limited application in other wild species. Analytical challenges include assessment of random versus non-random phylogeographic distributions, and quantification of differences in tree topologies among populations. Harp Seals (Pagophilus groenlandicus Erxleben, 1777) have a biogeographic distribution based on four discrete trans-Atlantic breeding and whelping populations located on "fast ice" attached to land in the White Sea, Greenland Sea, the Labrador ice Front, and Southern Gulf of St Lawrence. This East to West distribution provides a set of a priori phylogeographic hypotheses. Outstanding biogeographic questions include the degree of genetic distinctiveness among these populations, in particular between the Greenland Sea and White Sea grounds. We obtained complete coding-region DNA sequences (15,825 bp) for 53 seals. Each seal has a unique mtDNA genome sequence, which differ by 6 ~ 107 substitutions. Six major clades / groups are detectable by parsimony, neighbor-joining, and Bayesian methods, all of which are found in breeding populations on either side of the Atlantic. The species coalescent is at 180 KYA; the most recent clade, which accounts for 66% of the diversity, reflects an expansion during the mid-Wisconsinan glaciation 40~60 KYA. FST is significant only between the White Sea and Greenland Sea or Ice Front populations. Hierarchal AMOVA of 2-, 3-, or 4-island models identifies small but significant ΦSC among populations within groups, but not among groups. A novel Monte-Carlo simulation indicates that the observed distribution of individuals within breeding populations over the phylogenetic tree requires significantly fewer dispersal events than random expectation, consistent with island or a priori East to West 2- or 3-stepping

  16. Phylogeographic history of grey wolves in Europe.

    Science.gov (United States)

    Pilot, Małgorzata; Branicki, Wojciech; Jedrzejewski, Włodzimierz; Goszczyński, Jacek; Jedrzejewska, Bogumiła; Dykyy, Ihor; Shkvyrya, Maryna; Tsingarska, Elena

    2010-04-21

    While it is generally accepted that patterns of intra-specific genetic differentiation are substantially affected by glacial history, population genetic processes occurring during Pleistocene glaciations are still poorly understood. In this study, we address the question of the genetic consequences of Pleistocene glaciations for European grey wolves. Combining our data with data from published studies, we analysed phylogenetic relationships and geographic distribution of mitochondrial DNA haplotypes for 947 contemporary European wolves. We also compared the contemporary wolf sequences with published sequences of 24 ancient European wolves. We found that haplotypes representing two haplogroups, 1 and 2, overlap geographically, but substantially differ in frequency between populations from south-western and eastern Europe. A comparison between haplotypes from Europe and other continents showed that both haplogroups are spread throughout Eurasia, while only haplogroup 1 occurs in contemporary North American wolves. All ancient wolf samples from western Europe that dated from between 44,000 and 1,200 years B.P. belonged to haplogroup 2, suggesting the long-term predominance of this haplogroup in this region. Moreover, a comparison of current and past frequencies and distributions of the two haplogroups in Europe suggested that haplogroup 2 became outnumbered by haplogroup 1 during the last several thousand years. Parallel haplogroup replacement, with haplogroup 2 being totally replaced by haplogroup 1, has been reported for North American grey wolves. Taking into account the similarity of diets reported for the late Pleistocene wolves from Europe and North America, the correspondence between these haplogroup frequency changes may suggest that they were associated with ecological changes occurring after the Last Glacial Maximum.

  17. Contrasting phylogeographic patterns in Sphagnum fimbriatum and Sphagnum squarrosum (Bryophyta, Sphagnopsida) in Europe.

    Science.gov (United States)

    Szövényi, Péter; Hock, Zsófia; Urmi, Edwin; Schneller, Jakob J

    2006-01-01

    The chloroplast phylogeography of two peat mosses (Sphagnum fimbriatum and Sphagnum squarrosum) with similar distributions but different life history characteristics was investigated in Europe. Our main aim was to test whether similar distributions reflect similar phylogeographic and phylodemographic processes. Accessions covering the European distributions of the species were collected and approx. 2000 bp of the chloroplast genome of each species was sequenced. Maximum parsimony, statistical parsimony and phylodemographic analyses were used to address the question of whether these species with similar distributions show evidence of similar phylogeographic and phylodemographic processes. The chloroplast haplotypes of the currently spreading species S. fimbriatum showed strong geographic structure, whereas those of S. squarrosum, which has stable historical population sizes, showed only very weak geographic affinity and were widely distributed. We hypothesize that S. fimbriatum survived the last glaciations along the Atlantic coast of Europe, whereas S. squarrosum had numerous, scattered refugia in Europe. The dominance of one haplotype of S. fimbriatum across almost all of Europe suggests rapid colonization after the last glacial maximum. We hypothesize that high colonizing ability is an inherent characteristic of the species and its recent expansion in Europe is a response to climate change.

  18. Phylogeographic evidence for two mesic refugia in a biodiversity hotspot

    Science.gov (United States)

    Nistelberger, H; Gibson, N; Macdonald, B; Tapper, S-L; Byrne, M

    2014-01-01

    Phylogeographic studies of flora in species-rich south-western Australia point to complex evolutionary histories, reflecting patterns of persistence and resilience to climatic changes during the Pleistocene. We asked whether coastal areas of the mid-west and south, as well as granite outcrops and inland ranges, have acted as major refugia within this region during Pleistocene climatic fluctuations by analysing phylogeographic patterns in the shrub Calothamnus quadrifidus R.Br. (Myrtaceae). We determined variation in chloroplast DNA data for 41 populations across the geographic range. Relationships and major clades were resolved using parsimony and Bayesian analyses. We tested for demographic and spatial expansion of the major clades and estimated clade divergence dates using an uncorrelated, lognormal relaxed clock based on two conservative chloroplast mutation rates. Two distinct phylogeographic clades were identified showing divergence during the Pleistocene, consistent with other phylogeographic studies of south-west Australian flora, emphasising the impact of climatic oscillations in driving divergence in this landscape. The southern clade was more diverse, having higher haplotype diversity and greater genetic structure, while the northern clade showed evidence of fluctuation in population size. Regions of high haplotype diversity with adjacent areas of low diversity observed in each clade indicated the locations of two coastal refugia: one on the south coast and another along the mid-west coast. This is the first evidence for major Pleistocene refugia using chloroplast genetic data in a common, widespread species from this region. PMID:24984607

  19. A trans-Amazonian screening of mtDNA reveals deep intraspecific divergence in forest birds and suggests a vast underestimation of species diversity.

    Directory of Open Access Journals (Sweden)

    Borja Milá

    Full Text Available The Amazonian avifauna remains severely understudied relative to that of the temperate zone, and its species richness is thought to be underestimated by current taxonomy. Recent molecular systematic studies using mtDNA sequence reveal that traditionally accepted species-level taxa often conceal genetically divergent subspecific lineages found to represent new species upon close taxonomic scrutiny, suggesting that intraspecific mtDNA variation could be useful in species discovery. Surveys of mtDNA variation in Holarctic species have revealed patterns of variation that are largely congruent with species boundaries. However, little information exists on intraspecific divergence in most Amazonian species. Here we screen intraspecific mtDNA genetic variation in 41 Amazonian forest understory species belonging to 36 genera and 17 families in 6 orders, using 758 individual samples from Ecuador and French Guiana. For 13 of these species, we also analyzed trans-Andean populations from the Ecuadorian Chocó. A consistent pattern of deep intraspecific divergence among trans-Amazonian haplogroups was found for 33 of the 41 taxa, and genetic differentiation and genetic diversity among them was highly variable, suggesting a complex range of evolutionary histories. Mean sequence divergence within families was the same as that found in North American birds (13%, yet mean intraspecific divergence in Neotropical species was an order of magnitude larger (2.13% vs. 0.23%, with mean distance between intraspecific lineages reaching 3.56%. We found no clear relationship between genetic distances and differentiation in plumage color. Our results identify numerous genetically and phenotypically divergent lineages which may result in new species-level designations upon closer taxonomic scrutiny and thorough sampling, although lineages in the tropical region could be older than those in the temperate zone without necessarily representing separate species. In

  20. Characterization and intraspecific variation of Fusarium semitectum ...

    African Journals Online (AJOL)

    A total of 79 isolates of Fusarium semitectum were characterized by morphological and IGS-RFLP analysis to assess its intraspecific variation. Based on morphological characteristics, the isolates of F. semitectum were classified into 2 distinct groups, morphotypes I and II. Morphotype I was characterized by longer ...

  1. Molecular markers unravel intraspecific and interspecific genetic ...

    Indian Academy of Sciences (India)

    Molecular markers unravel intraspecific and interspecific genetic variability in Plantago ovata and some of its wild allies. Shivanjali Kotwal, Manoj K. Dhar, Balbir Kour, Kuldeep Raj and Sanjana Kaul. J. Genet. 92, 293–298. Table 1. Jaccard's similarity matrix of AFLP analysis of Plantago species. P. coronopus P. lanceolata ...

  2. Introduction and evolution of dengue virus type 2 in Pakistan: a phylogeographic analysis.

    Science.gov (United States)

    Akram, Madiha; Fatima, Zareen; Purdy, Mike A; Sue, Amanda; Saleem, Sana; Amin, Irum; Shahid, Muhammad; Idrees, Muhammad; Nawaz, Rabia

    2015-09-22

    Pattern of Dengue periodic epidemics through the years along with sporadic cases of Dengue hemorrhagic fever followed by a severe 2011 epidemic of Dengue fever in Pakistan make Pakistan a Dengue endemic country. To study the entry and evolution of dengue virus serotype 2 (DENV-2) in Pakistan, we sequenced three full length genomes and 24 complete envelope sequences of DENV-2 from the years 2010, 2011 and 2013 collected from Punjab province of Pakistan. Phylogenetic and Bayesian phylogeographic analyses was applied to three full genome sequences as well as 24 envelope sequences to study the spatiotemporal dynamics of DENV-2 in Pakistan. Most of the DENV-2 viruses from the years 2008 to 2013 formed a monophyletic Pakistani clade in IVb sublineage of cosmopolitan genotype except one 2008 DENV-2 strain. Phylogeographic analysis revealed that this 2008 DENV-2 strain was rooted to India 25.4 years ago with a location probability of 0.88. However Pakistani clade rooted back to Sri Lanka 12.6 years ago with a location probability of 0.57. DENV-2 genotype IV was introduced in Pakistan in two time events. First event was introduction from India to Pakistan in the late 1980s (around 1986), and second event was introduction from Sri Lanka to Pakistan around 2000. The later introduction event was responsible for major outbreaks in the Punjab region of Pakistan, including major 2011 outbreak. After the second Introduction event, DENV-2 circulated locally in the region forming a distinct Sublineage within the IVb cosmopolitan genotype of DENV-2.

  3. Intraspecific plant-soil feedback and intraspecific overyielding in Arabidopsis thaliana.

    Science.gov (United States)

    Bukowski, Alexandra R; Petermann, Jana S

    2014-06-01

    Understanding the mechanisms of community coexistence and ecosystem functioning may help to counteract the current biodiversity loss and its potentially harmful consequences. In recent years, plant-soil feedback that can, for example, be caused by below-ground microorganisms has been suggested to play a role in maintaining plant coexistence and to be a potential driver of the positive relationship between plant diversity and ecosystem functioning. Most of the studies addressing these topics have focused on the species level. However, in addition to interspecific interactions, intraspecific interactions might be important for the structure of natural communities. Here, we examine intraspecific coexistence and intraspecific diversity effects using 10 natural accessions of the model species Arabidopsis thaliana (L.) Heynh. We assessed morphological intraspecific diversity by measuring several above- and below-ground traits. We performed a plant-soil feedback experiment that was based on these trait differences between the accessions in order to determine whether A. thaliana experiences feedback at intraspecific level as a result of trait differences. We also experimentally tested the diversity-productivity relationship at intraspecific level. We found strong differences in above- and below-ground traits between the A. thaliana accessions. Overall, plant-soil feedback occurred at intraspecific level. However, accessions differed in the direction and strength of this feedback: Some accessions grew better on their own soils, some on soils from other accessions. Furthermore, we found positive diversity effects within A. thaliana: Accession mixtures produced a higher total above-ground biomass than accession monocultures. Differences between accessions in their feedback response could not be explained by morphological traits. Therefore, we suggest that they might have been caused by accession-specific accumulated soil communities, by root exudates, or by accession

  4. Phylogeographic inferences concerning evolution of Brazilian Passiflora actinia and P. elegans (Passifloraceae) based on ITS (nrDNA) variation.

    Science.gov (United States)

    Lorenz-Lemke, Aline P; Muschner, Valéria C; Bonatto, Sandro L; Cervi, Armando C; Salzano, Francisco M; Freitas, Loreta B

    2005-04-01

    Passiflora actinia and P. elegans, two markedly parapatric species, have their southern and northern distribution limits, respectively, in the most southern part of the Brazilian Atlantic Rain Forest. Despite the fact that they are classified in different taxonomic series, previous phylogenetic studies of this genus revealed a high genetic similarity between them. The aim of the present work was to analyse in more detail their geographical range in this region of overlap, to investigate intraspecific genetic variability and phylogeographic structure, and to search for possible hybrids. Eighty-two localities were searched for these species, and nuclear internal transcribed spacer (ITS) sequences were investigated for 32 individuals of P. actinia, 20 of P. elegans and one putative interspecific hybrid. Plastid trnL-trnF and psbA-trnH were examined for 12 plants of each species and the putative hybrid. Both species showed a high level of intraspecific and intra-individual ITS variability. Network analysis revealed a north-south geographic gradient in their intra and interspecific relationships. Mismatch analyses suggested a recent population expansion of P. elegans. The plastid markers showed restricted variability but, together with the nuclear data, they contributed to the identification of an interspecific hybrid of intermediate morphology at the border of the distribution of these two species. Both genetic and morphological data indicate the absence of an extensive hybridization zone between these species. Gene flow between lineages is the possible cause for the presence of different ITS sequences within a given plant, the absence of homogenization being due to the high degree of vegetative reproduction in the two species. Differentiation of P. actinia into geographic groups and the origin of P. elegans may have been influenced by the Atlantic Forest migration towards southern Brazil. The genetic pattern of the interspecific hybrid indicates that plastid

  5. Phylogeographic patterns of Armillaria ostoyae in the western United States

    Science.gov (United States)

    J. W. Hanna; N. B. Klopfenstein; M. -S. Kim; G. I. McDonald; J. A. Moore

    2007-01-01

    Nuclear ribosomal DNA regions (i.e. large subunit, internal transcribed spacer, 5.8S and intergenic spacer) were sequenced using a direct-polymerase chain reaction method from Armillaria ostoyae genets collected from the western USA. Many of the A. ostoyae genets contained heterogeneity among rDNA repeats, indicating intragenomic variation and likely intraspecific...

  6. Intraspecific variation in aerobic and anaerobic locomotion

    DEFF Research Database (Denmark)

    Svendsen, Jon Christian; Tirsgård, Bjørn; Cordero, Gerardo A.

    2015-01-01

    Intraspecific variation and trade-off in aerobic and anaerobic traits remain poorly understood in aquatic locomotion. Using gilthead sea bream (Sparus aurata) and Trinidadian guppy (Poecilia reticulata), both axial swimmers, this study tested four hypotheses: (1) gait transition from steady...... to unsteady (i.e., burst-assisted) swimming is associated with anaerobic metabolism evidenced as excess post exercise oxygen consumption (EPOC); (2) variation in swimming performance (critical swimming speed; U crit) correlates with metabolic scope (MS) or anaerobic capacity (i.e., maximum EPOC); (3...

  7. Phylogeographical disjunction in abundant high-dispersal littoral gastropods.

    Science.gov (United States)

    Waters, J M; King, T M; O'Loughlin, P M; Spencer, H G

    2005-08-01

    Abstract Phylogeographical disjunctions in high-dispersal marine taxa are variously ascribed to palaeogeographical conditions or contemporary ecological factors. Associated biogeographical studies, however, seldom incorporate the sampling design required to confidently discriminate among such competing hypotheses. In the current study, over 7800 gastropod specimens were examined for operculum colour, and 129 specimens genetically, to test ecological and historical biogeographical hypotheses relating to biogeographical disjunction in the Southern Hemisphere, and to southern Australia in particular. Mitochondrial DNA sequence analysis of the high-dispersal intertidal gastropod Nerita atramentosa in southern Australia (88 specimens; 18 localities) revealed an east-west phylogeographical split involving two highly divergent clades (26.0 +/- 1.9%) exhibiting minimal geographical overlap in the southeast. The eastern clade of Nerita atramentosa is also widespread in northern New Zealand (43 specimens, 10 localities), but no significant genetic differentiation is explained by the Tasman Sea, a 2000-km-wide oceanic barrier. Spatial genetic structure was not detected within either clade, consistent with the species' dispersive planktotrophic phase lasting for 5-6 months. Digital analysis of operculum colouration revealed substantial differences between eastern (tan) and western (black) specimens. Genetic analysis and visual inspection of 88 Australian specimens revealed a completely nonrandom association between mtDNA data and operculum colouration. Independent examination of a further 7822 specimens from 14 sites in southern Australia revealed both colour morphs at all localities, but reinforced the phylogeographical data by indicating a marked turnover in colour morph abundance associated with a palaeogeographical barrier: Wilsons Promontory. This sharp biogeographical disjunction is in marked contrast to the species' high dispersal abilities. The genetic similarity of

  8. Genomes

    National Research Council Canada - National Science Library

    Brown, T. A. (Terence A.)

    2002-01-01

    ... of genome expression and replication processes, and transcriptomics and proteomics. This text is richly illustrated with clear, easy-to-follow, full color diagrams, which are downloadable from the book's website...

  9. Variation in the relative magnitude of intraspecific and interspecific ...

    Indian Academy of Sciences (India)

    While there was considerable variation in the relative magnitude of intraspecific and interspecific competitive effects over generations, among both populations and environments, there was no clear evidence supporting the genetic feedback hypothesis. Intraspecific and interspecific competitive effects on population growth ...

  10. Exploring Phylogeographic Congruence in a Continental Island System

    Directory of Open Access Journals (Sweden)

    Julia Goldberg

    2011-08-01

    Full Text Available A prediction in phylogeographic studies is that patterns of lineage diversity and timing will be similar within the same landscape under the assumption that these lineages have responded to past environmental changes in comparable ways. Eight invertebrate taxa from four different orders were included in this study of mainland New Zealand and Chatham Islands lineages to explore outcomes of island colonization. These comprised two orthopteran genera, one an endemic forest-dwelling genus of cave weta (Rhaphidophoridae, Talitropsis and the other a grasshopper (Acrididae, Phaulacridum that inhabits open grassland; four genera of Coleoptera including carabid beetles (Mecodema, stag beetles (Geodorcus, weevils (Hadramphus and clickbeetles (Amychus; the widespread earwig genus Anisolabis (Dermaptera that is common on beaches in New Zealand and the Chatham Islands, and an endemic and widespread cockroach genus Celatoblatta (Blattodea. Mitochondrial DNA data were used to reconstruct phylogeographic hypotheses to compare among these taxa. Strikingly, despite a maximum age of the Chathams of ~4 million years there is no concordance among these taxa, in the extent of genetic divergence and partitioning between Chatham and Mainland populations. Some Chatham lineages are represented by insular endemics and others by haplotypes shared with mainland populations. These diverse patterns suggest that combinations of intrinsic (taxon ecology and extrinsic (extinction and dispersal factors can result in apparently very different biogeographic outcomes.

  11. The conditions for speciation through intraspecific competition.

    Science.gov (United States)

    Bürger, Reinhard; Schneider, Kristan A; Willensdorfer, Martin

    2006-11-01

    It has been shown theoretically that sympatric speciation can occur if intraspecific competition is strong enough to induce disruptive selection. However, the plausibility of the involved processes is under debate, and many questions on the conditions for speciation remain unresolved. For instance, is strong disruptive selection sufficient for speciation? Which roles do genetic architecture and initial composition of the population play? How strong must assortative mating be before a population can split in two? These are some of the issues we address here. We investigate a diploid multilocus model of a quantitative trait that is under frequency-dependent selection caused by a balance of intraspecific competition and frequency-independent stabilizing selection. This trait also acts as mating character for assortment. It has been established previously that speciation can occur only if competition is strong enough to induce disruptive selection. We find that speciation becomes more difficult for very strong competition, because then extremely strong assortment is required. Thus, speciation is most likely for intermediate strengths of competition, where it requires strong, but not extremely strong, assortment. For this range of parameters, however, it is not obvious how assortment can evolve from low to high levels, because with moderately strong assortment less genetic variation is maintained than under weak or strong assortment-sometimes none at all. In addition to the strength of frequency-dependent competition and assortative mating, the roles of the number of loci, the distribution of allelic effects, the initial conditions, costs to being choosy, the strength of stabilizing selection, and the particular choice of the fitness function are explored. A multitude of possible evolutionary outcomes is observed, including loss of all genetic variation, splitting in two to five species, as well as very short and extremely long stable limit cycles. On the methodological

  12. Limited phylogeographic structure for five bathyal ophiuroids at continental scales

    Science.gov (United States)

    O'Hara, Timothy D.; England, Phillip R.; Gunasekera, Rasanthi M.; Naughton, Kate M.

    2014-02-01

    There have been comparatively few large-scale studies on spatial genetic structure of bathyal seafloor fauna, despite the importance of these data to the successful management of the world's oceans. We use a comparative analysis of mitochondrial DNA from five bathyal (200-3500 m) species of brittle-stars (Ophiuroidea) to assess phylogeographic structure along an extensive (8000 km) longitudinal gradient at temperate latitudes (28-56°S) from south-west Australia (113°E) to seamounts east of New Zealand (175°W). We found no evidence of a genetic discontinuity between Australia and New Zealand, either across the temperate Tasman Sea or across the Southern Ocean between the South Tasman Rise and the Macquarie Ridge. However, there were latitudinal phylogeographical breaks between tropical, temperate and polar regions; longitudinal breaks across the eastern Indian Ocean; and a bathymetric break at approximately 1700 m. Although there was limited regional structure in the frequency of haplotype distributions within the major clades, and no clade appeared to be strictly panmictic, the regional structure in general was not concordant with a simple isolation-by-distance model. Demographic structure varied with three clades having a simplified haplotype network, low effective population sizes and no evidence of significant population expansion, and two clades having a high diversity of haplotypes, relatively high effective population sizes and signs of recent population expansion. These results are discussed with respect to putative dispersal strategies. We hypothesise that the 'brooding' species produce both brooded young and pelagic larvae, allowing for both the maintenance of local populations and long-distance dispersal.

  13. Egg size matching by an intraspecific brood parasite

    OpenAIRE

    Patrick R. Lemons; James S. Sedinger

    2011-01-01

    Avian brood parasitism provides an ideal system with which to understand animal recognition and its affect on fitness. This phenomenon of laying eggs in the nests of other individuals has classically been framed from the perspective of interspecific brood parasitism and host recognition of parasitic eggs. Few examples exist of strategies adopted by intraspecific brood parasites to maximize success of parasitic eggs. Intraspecific brood parasitism within precocial birds can be a risky strategy...

  14. Intraspecific competition delays recovery of population structure.

    Science.gov (United States)

    Liess, Matthias; Foit, Kaarina

    2010-04-01

    Ecotoxicological field studies have shown that total abundance and biomass often recover shortly after pulsed toxicant stress. In contrast, population structure showed comparatively long-term alterations before reaching pre-treatment conditions. We investigated two mechanisms that may explain the prolonged recovery of population structure: latent toxicant effects on life-history traits on the individual level and competition on the population level. To test these hypotheses we exposed populations of Daphnia magna to a pulse of the pyrethroid Fenvalerate. For several generations the populations were kept at two different degrees of competition: strong competition at carrying capacity and reduced competition maintained by simulated predation. After disturbance due to Fenvalerate exposure, biomass recovered after 14-17 days. In contrast, size structure characterised by a lack of large and dominance of small organisms recovered after 43 days in populations with strong competition. Size structure recovered twice faster in populations with reduced competition. We explain this as follows: due to toxicant induced mortality, food availability and consequently birth rate increased and populations were dominated by small individuals. In populations without predation, these cohorts grew and eventually exerted high intraspecific competition that (i) stopped further growth of juveniles and (ii) increased mortality of adults. These demographic processes were mainly responsible for the prolonged recovery of size structure. In contrast, for populations with predation, the regular harvest of individuals reduced competition. Juveniles developed continuously, allowing a fast recovery of size structure in these dynamic populations. In risk assessment the duration for populations to recover from (toxicant) stress, is crucial for the determination of ecological acceptable effects. We conclude that competition needs to be considered in order to understand and predict recovery of size

  15. Profound Climatic Effects on Two East Asian Black-Throated Tits (Ave: Aegithalidae), Revealed by Ecological Niche Models and Phylogeographic Analysis

    Science.gov (United States)

    Wang, Wenjuan; Lin, Congtian; Gao, Bin; Yang, Xiaojun; Zhang, Zhengwang; Lei, Fumin

    2011-01-01

    Although a number of studies have assessed the effects of geological and climatic changes on species distributions in East Asian, we still have limited knowledge of how these changes have impacted avian species in south-western and southern China. Here, we aim to study paleo-climatic effects on an East Asian bird, two subspecies of black-throated tit (A. c. talifuensis–concinnus) with the combined analysis of phylogeography and Ecological Niche Models (ENMs). We sequenced three mitochondrial DNA markers from 32 populations (203 individuals) and used phylogenetic inferences to reconstruct the intra-specific relationships among haplotypes. Population genetic analyses were undertaken to gain insight into the demographic history of these populations. We used ENMs to predict the distribution of target species during three periods; last inter-glacial (LIG), last glacial maximum (LGM) and present. We found three highly supported, monophyletic MtDNA lineages and different historical demography among lineages in A. c. talifuensis–concinnus. These lineages formed a narrowly circumscribed intra-specific contact zone. The estimated times of lineage divergences were about 2.4 Ma and 0.32 Ma respectively. ENMs predictions were similar between present and LGM but substantially reduced during LIG. ENMs reconstructions and molecular dating suggest that Pleistocene climate changes had triggered and shaped the genetic structure of black-throated tit. Interestingly, in contrast to profound impacts of other glacial cycles, ENMs and phylogeographic analysis suggest that LGM had limited effect on these two subspecies. ENMs also suggest that Pleistocene climatic oscillations enabled the formation of the contact zone and thus support the refuge theory. PMID:22195047

  16. Profound climatic effects on two East Asian black-throated tits (Ave: Aegithalidae), revealed by ecological niche models and phylogeographic analysis.

    Science.gov (United States)

    Dai, Chuanyin; Zhao, Na; Wang, Wenjuan; Lin, Congtian; Gao, Bin; Yang, Xiaojun; Zhang, Zhengwang; Lei, Fumin

    2011-01-01

    Although a number of studies have assessed the effects of geological and climatic changes on species distributions in East Asian, we still have limited knowledge of how these changes have impacted avian species in south-western and southern China. Here, we aim to study paleo-climatic effects on an East Asian bird, two subspecies of black-throated tit (A. c. talifuensis-concinnus) with the combined analysis of phylogeography and Ecological Niche Models (ENMs). We sequenced three mitochondrial DNA markers from 32 populations (203 individuals) and used phylogenetic inferences to reconstruct the intra-specific relationships among haplotypes. Population genetic analyses were undertaken to gain insight into the demographic history of these populations. We used ENMs to predict the distribution of target species during three periods; last inter-glacial (LIG), last glacial maximum (LGM) and present. We found three highly supported, monophyletic MtDNA lineages and different historical demography among lineages in A. c. talifuensis-concinnus. These lineages formed a narrowly circumscribed intra-specific contact zone. The estimated times of lineage divergences were about 2.4 Ma and 0.32 Ma respectively. ENMs predictions were similar between present and LGM but substantially reduced during LIG. ENMs reconstructions and molecular dating suggest that Pleistocene climate changes had triggered and shaped the genetic structure of black-throated tit. Interestingly, in contrast to profound impacts of other glacial cycles, ENMs and phylogeographic analysis suggest that LGM had limited effect on these two subspecies. ENMs also suggest that Pleistocene climatic oscillations enabled the formation of the contact zone and thus support the refuge theory.

  17. Identifying designatable units for intraspecific conservation prioritization: a hierarchical approach applied to the lake whitefish species complex (Coregonus spp.).

    Science.gov (United States)

    Mee, Jonathan A; Bernatchez, Louis; Reist, Jim D; Rogers, Sean M; Taylor, Eric B

    2015-06-01

    The concept of the designatable unit (DU) affords a practical approach to identifying diversity below the species level for conservation prioritization. However, its suitability for defining conservation units in ecologically diverse, geographically widespread and taxonomically challenging species complexes has not been broadly evaluated. The lake whitefish species complex (Coregonus spp.) is geographically widespread in the Northern Hemisphere, and it contains a great deal of variability in ecology and evolutionary legacy within and among populations, as well as a great deal of taxonomic ambiguity. Here, we employ a set of hierarchical criteria to identify DUs within the Canadian distribution of the lake whitefish species complex. We identified 36 DUs based on (i) reproductive isolation, (ii) phylogeographic groupings, (iii) local adaptation and (iv) biogeographic regions. The identification of DUs is required for clear discussion regarding the conservation prioritization of lake whitefish populations. We suggest conservation priorities among lake whitefish DUs based on biological consequences of extinction, risk of extinction and distinctiveness. Our results exemplify the need for extensive genetic and biogeographic analyses for any species with broad geographic distributions and the need for detailed evaluation of evolutionary history and adaptive ecological divergence when defining intraspecific conservation units.

  18. Bayesian population structure analysis reveals presence of phylogeographically specific sublineages within previously ill-defined T group of Mycobacterium tuberculosis

    Science.gov (United States)

    Reynaud, Yann; Zheng, Chao; Wu, Guihui; Sun, Qun; Rastogi, Nalin

    2017-01-01

    Mycobacterium tuberculosis genetic structure, and evolutionary history have been studied for years by several genotyping approaches, but delineation of a few sublineages remains controversial and needs better characterization. This is particularly the case of T group within lineage 4 (L4) which was first described using spoligotyping to pool together a number of strains with ill-defined signatures. Although T strains were not traditionally considered as a real phylogenetic group, they did contain a few phylogenetically meaningful sublineages as shown using SNPs. We therefore decided to investigate if this observation could be corroborated using other robust genetic markers. We consequently made a first assessment of genetic structure using 24-loci MIRU-VNTRs data extracted from the SITVIT2 database (n = 607 clinical isolates collected in Russia, Albania, Turkey, Iraq, Brazil and China). Combining Minimum Spanning Trees and Bayesian population structure analyses (using STRUCTURE and TESS softwares), we distinctly identified eight tentative phylogenetic groups (T1-T8) with a remarkable correlation with geographical origin. We further compared the present structure observed with other L4 sublineages (n = 416 clinical isolates belonging to LAM, Haarlem, X, S sublineages), and showed that 5 out of 8 T groups seemed phylogeographically well-defined as opposed to the remaining 3 groups that partially mixed with other L4 isolates. These results provide with novel evidence about phylogeographically specificity of a proportion of ill-defined T group of M. tuberculosis. The genetic structure observed will now be further validated on an enlarged worldwide dataset using Whole Genome Sequencing (WGS). PMID:28166309

  19. Bayesian population structure analysis reveals presence of phylogeographically specific sublineages within previously ill-defined T group of Mycobacterium tuberculosis.

    Directory of Open Access Journals (Sweden)

    Yann Reynaud

    Full Text Available Mycobacterium tuberculosis genetic structure, and evolutionary history have been studied for years by several genotyping approaches, but delineation of a few sublineages remains controversial and needs better characterization. This is particularly the case of T group within lineage 4 (L4 which was first described using spoligotyping to pool together a number of strains with ill-defined signatures. Although T strains were not traditionally considered as a real phylogenetic group, they did contain a few phylogenetically meaningful sublineages as shown using SNPs. We therefore decided to investigate if this observation could be corroborated using other robust genetic markers. We consequently made a first assessment of genetic structure using 24-loci MIRU-VNTRs data extracted from the SITVIT2 database (n = 607 clinical isolates collected in Russia, Albania, Turkey, Iraq, Brazil and China. Combining Minimum Spanning Trees and Bayesian population structure analyses (using STRUCTURE and TESS softwares, we distinctly identified eight tentative phylogenetic groups (T1-T8 with a remarkable correlation with geographical origin. We further compared the present structure observed with other L4 sublineages (n = 416 clinical isolates belonging to LAM, Haarlem, X, S sublineages, and showed that 5 out of 8 T groups seemed phylogeographically well-defined as opposed to the remaining 3 groups that partially mixed with other L4 isolates. These results provide with novel evidence about phylogeographically specificity of a proportion of ill-defined T group of M. tuberculosis. The genetic structure observed will now be further validated on an enlarged worldwide dataset using Whole Genome Sequencing (WGS.

  20. Phylogeographic and Demographic Analysis of the Asian Black Bear (Ursus thibetanus) Based on Mitochondrial DNA

    Science.gov (United States)

    Wu, Jiaqi; Kohno, Naoki; Mano, Shuhei; Fukumoto, Yukio; Tanabe, Hideyuki; Hasegawa, Masami; Yonezawa, Takahiro

    2015-01-01

    The Asian black bear Ursus thibetanus is widely distributed in Asia and is adapted to broad-leaved deciduous forests, playing an important ecological role in the natural environment. Several subspecies of U. thibetanus have been recognized, one of which, the Japanese black bear, is distributed in the Japanese archipelago. Recent molecular phylogeographic studies clarified that this subspecies is genetically distantly related to continental subspecies, suggesting an earlier origin. However, the evolutionary relationship between the Japanese and continental subspecies remained unclear. To understand the evolution of the Asian black bear in relation to geological events such as climatic and transgression-regression cycles, a reliable time estimation is also essential. To address these issues, we determined and analyzed the mt-genome of the Japanese subspecies. This indicates that the Japanese subspecies initially diverged from other Asian black bears in around 1.46Ma. The Northern continental population (northeast China, Russia, Korean peninsula) subsequently evolved, relatively recently, from the Southern continental population (southern China and Southeast Asia). While the Japanese black bear has an early origin, the tMRCAs and the dynamics of population sizes suggest that it dispersed relatively recently in the main Japanese islands: during the late Middle and Late Pleistocene, probably during or soon after the extinction of the brown bear in Honshu in the same period. Our estimation that the population size of the Japanese subspecies increased rapidly during the Late Pleistocene is the first evidential signal of a niche exchange between brown bears and black bears in the Japanese main islands. This interpretation seems plausible but was not corroborated by paleontological evidence that fossil record of the Japanese subspecies limited after the Late Pleistocene. We also report here a new fossil record of the oldest Japanese black bear from the Middle Pleistocene

  1. Phylogeographic and Demographic Analysis of the Asian Black Bear (Ursus thibetanus) Based on Mitochondrial DNA.

    Science.gov (United States)

    Wu, Jiaqi; Kohno, Naoki; Mano, Shuhei; Fukumoto, Yukio; Tanabe, Hideyuki; Hasegawa, Masami; Yonezawa, Takahiro

    2015-01-01

    The Asian black bear Ursus thibetanus is widely distributed in Asia and is adapted to broad-leaved deciduous forests, playing an important ecological role in the natural environment. Several subspecies of U. thibetanus have been recognized, one of which, the Japanese black bear, is distributed in the Japanese archipelago. Recent molecular phylogeographic studies clarified that this subspecies is genetically distantly related to continental subspecies, suggesting an earlier origin. However, the evolutionary relationship between the Japanese and continental subspecies remained unclear. To understand the evolution of the Asian black bear in relation to geological events such as climatic and transgression-regression cycles, a reliable time estimation is also essential. To address these issues, we determined and analyzed the mt-genome of the Japanese subspecies. This indicates that the Japanese subspecies initially diverged from other Asian black bears in around 1.46Ma. The Northern continental population (northeast China, Russia, Korean peninsula) subsequently evolved, relatively recently, from the Southern continental population (southern China and Southeast Asia). While the Japanese black bear has an early origin, the tMRCAs and the dynamics of population sizes suggest that it dispersed relatively recently in the main Japanese islands: during the late Middle and Late Pleistocene, probably during or soon after the extinction of the brown bear in Honshu in the same period. Our estimation that the population size of the Japanese subspecies increased rapidly during the Late Pleistocene is the first evidential signal of a niche exchange between brown bears and black bears in the Japanese main islands. This interpretation seems plausible but was not corroborated by paleontological evidence that fossil record of the Japanese subspecies limited after the Late Pleistocene. We also report here a new fossil record of the oldest Japanese black bear from the Middle Pleistocene

  2. Phylogeographic and Demographic Analysis of the Asian Black Bear (Ursus thibetanus Based on Mitochondrial DNA.

    Directory of Open Access Journals (Sweden)

    Jiaqi Wu

    Full Text Available The Asian black bear Ursus thibetanus is widely distributed in Asia and is adapted to broad-leaved deciduous forests, playing an important ecological role in the natural environment. Several subspecies of U. thibetanus have been recognized, one of which, the Japanese black bear, is distributed in the Japanese archipelago. Recent molecular phylogeographic studies clarified that this subspecies is genetically distantly related to continental subspecies, suggesting an earlier origin. However, the evolutionary relationship between the Japanese and continental subspecies remained unclear. To understand the evolution of the Asian black bear in relation to geological events such as climatic and transgression-regression cycles, a reliable time estimation is also essential. To address these issues, we determined and analyzed the mt-genome of the Japanese subspecies. This indicates that the Japanese subspecies initially diverged from other Asian black bears in around 1.46Ma. The Northern continental population (northeast China, Russia, Korean peninsula subsequently evolved, relatively recently, from the Southern continental population (southern China and Southeast Asia. While the Japanese black bear has an early origin, the tMRCAs and the dynamics of population sizes suggest that it dispersed relatively recently in the main Japanese islands: during the late Middle and Late Pleistocene, probably during or soon after the extinction of the brown bear in Honshu in the same period. Our estimation that the population size of the Japanese subspecies increased rapidly during the Late Pleistocene is the first evidential signal of a niche exchange between brown bears and black bears in the Japanese main islands. This interpretation seems plausible but was not corroborated by paleontological evidence that fossil record of the Japanese subspecies limited after the Late Pleistocene. We also report here a new fossil record of the oldest Japanese black bear from the

  3. Phylogeographic analysis of rabies viruses in the Philippines.

    Science.gov (United States)

    Tohma, Kentaro; Saito, Mariko; Kamigaki, Taro; Tuason, Laarni T; Demetria, Catalino S; Orbina, Jun Ryan C; Manalo, Daria L; Miranda, Mary E; Noguchi, Akira; Inoue, Satoshi; Suzuki, Akira; Quiambao, Beatriz P; Oshitani, Hitoshi

    2014-04-01

    Rabies still remains a public health threat in the Philippines. A significant number of human rabies cases, about 200-300 cases annually, have been reported, and the country needs an effective strategy for rabies control. To develop an effective control strategy, it is important to understand the transmission patterns of the rabies viruses. We conducted phylogenetic analyses by considering the temporal and spatial evolution of rabies viruses to reveal the transmission dynamics in the Philippines. After evaluating the molecular clock and phylogeographic analysis, we estimated that the Philippine strains were introduced from China around the beginning of 20th century. Upon this introduction, the rabies viruses evolved within the Philippines to form three major clades, and there was no indication of introduction of other rabies viruses from any other country. However, within the Philippines, island-to-island migrations were observed. Since then, the rabies viruses have diffused and only evolved within each island group. The evolutionary pattern of these viruses was strongly shaped by geographical boundaries. The association index statistics demonstrated a strong spatial structure within the island group, indicating that the seas were a significant geographical barrier for viral dispersal. Strong spatial structure was also observed even at a regional level, and most of the viral migrations (79.7% of the total median number) in Luzon were observed between neighboring regions. Rabies viruses were genetically clustered at a regional level, and this strong spatial structure suggests a geographical clustering of transmission chains and the potential effectiveness of rabies control that targets geographical clustering. Dog vaccination campaigns have been conducted independently by local governments in the Philippines, but it could be more effective to implement a coordinated vaccination campaign among neighboring areas to eliminate geographically-clustered rabies

  4. Phylogeographic analysis of severe fever with thrombocytopenia syndrome virus from Zhoushan Islands, China: implication for transmission across the ocean.

    Science.gov (United States)

    Fu, Yongfeng; Li, Shibo; Zhang, Zhao; Man, Suqin; Li, Xueping; Zhang, Wenhong; Zhang, Chiyu; Cheng, Xunjia

    2016-01-25

    From June 2011 to August 2014, 21 cases of infection by severe fever with thrombocytopenia syndrome bunyavirus (SFTSV) were confirmed in Zhoushan Islands in the Eastern coast of China. To identify the source of SFTSV in Zhoushan Islands, the whole SFTSV genomes were amplified and sequenced from 17 of 21 patients. The L, M, and S genomic segments of these SFTSV strains were phylogenetically analyzed together with those of 188 SFTSV strains available from GenBank. Phylogenetic analysis demonstrated SFTSV could be classified into six genotypes. The genotypes F, A, and D were dominant in mainland China. Additionally, seven types of SFTSV genetic reassortants (abbreviated as AFA, CCD, DDF, DFD, DFF, FAF, and FFA for the L, M and S segments) were identified from 10 strains in mainland China. Genotype B was dominant in Zhoushan Islands, Japan and South Korea, but not found in mainland China. Phylogeographic analysis also revealed South Korea possible be the origin area for genotype B and transmitted into Japan and Zhoushan islands in the later part of 20(th) century. Therefore, we propose that genotype B isolates were probable transmitted from South Korea to Japan and Zhoushan Islands.

  5. Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer.

    Science.gov (United States)

    Pearson, Talima; Giffard, Philip; Beckstrom-Sternberg, Stephen; Auerbach, Raymond; Hornstra, Heidie; Tuanyok, Apichai; Price, Erin P; Glass, Mindy B; Leadem, Benjamin; Beckstrom-Sternberg, James S; Allan, Gerard J; Foster, Jeffrey T; Wagner, David M; Okinaka, Richard T; Sim, Siew Hoon; Pearson, Ofori; Wu, Zaining; Chang, Jean; Kaul, Rajinder; Hoffmaster, Alex R; Brettin, Thomas S; Robison, Richard A; Mayo, Mark; Gee, Jay E; Tan, Patrick; Currie, Bart J; Keim, Paul

    2009-11-18

    Phylogeographic reconstruction of some bacterial populations is hindered by low diversity coupled with high levels of lateral gene transfer. A comparison of recombination levels and diversity at seven housekeeping genes for eleven bacterial species, most of which are commonly cited as having high levels of lateral gene transfer shows that the relative contributions of homologous recombination versus mutation for Burkholderia pseudomallei is over two times higher than for Streptococcus pneumoniae and is thus the highest value yet reported in bacteria. Despite the potential for homologous recombination to increase diversity, B. pseudomallei exhibits a relative lack of diversity at these loci. In these situations, whole genome genotyping of orthologous shared single nucleotide polymorphism loci, discovered using next generation sequencing technologies, can provide very large data sets capable of estimating core phylogenetic relationships. We compared and searched 43 whole genome sequences of B. pseudomallei and its closest relatives for single nucleotide polymorphisms in orthologous shared regions to use in phylogenetic reconstruction. Bayesian phylogenetic analyses of >14,000 single nucleotide polymorphisms yielded completely resolved trees for these 43 strains with high levels of statistical support. These results enable a better understanding of a separate analysis of population differentiation among >1,700 B. pseudomallei isolates as defined by sequence data from seven housekeeping genes. We analyzed this larger data set for population structure and allele sharing that can be attributed to lateral gene transfer. Our results suggest that despite an almost panmictic population, we can detect two distinct populations of B. pseudomallei that conform to biogeographic patterns found in many plant and animal species. That is, separation along Wallace's Line, a biogeographic boundary between Southeast Asia and Australia. We describe an Australian origin for B

  6. Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer

    Science.gov (United States)

    Pearson, T.; Giffard, P.; Beckstrom-Sternberg, S.; Auerbach, R.; Hornstra, H.; Tuanyok, A.; Price, E.P.; Glass, M.B.; Leadem, B.; Beckstrom-Sternberg, J. S.; Allan, G.J.; Foster, J.T.; Wagner, D.M.; Okinaka, R.T.; Sim, S.H.; Pearson, O.; Wu, Z.; Chang, J.; Kaul, R.; Hoffmaster, A.R.; Brettin, T.S.; Robison, R.A.; Mayo, M.; Gee, J.E.; Tan, P.; Currie, B.J.; Keim, P.

    2009-01-01

    Background: Phylogeographic reconstruction of some bacterial populations is hindered by low diversity coupled with high levels of lateral gene transfer. A comparison of recombination levels and diversity at seven housekeeping genes for eleven bacterial species, most of which are commonly cited as having high levels of lateral gene transfer shows that the relative contributions of homologous recombination versus mutation for Burkholderia pseudomallei is over two times higher than for Streptococcus pneumoniae and is thus the highest value yet reported in bacteria. Despite the potential for homologous recombination to increase diversity, B. pseudomallei exhibits a relative lack of diversity at these loci. In these situations, whole genome genotyping of orthologous shared single nucleotide polymorphism loci, discovered using next generation sequencing technologies, can provide very large data sets capable of estimating core phylogenetic relationships. We compared and searched 43 whole genome sequences of B. pseudomallei and its closest relatives for single nucleotide polymorphisms in orthologous shared regions to use in phylogenetic reconstruction. Results: Bayesian phylogenetic analyses of >14,000 single nucleotide polymorphisms yielded completely resolved trees for these 43 strains with high levels of statistical support. These results enable a better understanding of a separate analysis of population differentiation among >1,700 B. pseudomallei isolates as defined by sequence data from seven housekeeping genes. We analyzed this larger data set for population structure and allele sharing that can be attributed to lateral gene transfer. Our results suggest that despite an almost panmictic population, we can detect two distinct populations of B. pseudomallei that conform to biogeographic patterns found in many plant and animal species. That is, separation along Wallace's Line, a biogeographic boundary between Southeast Asia and Australia. Conclusion: We describe an

  7. Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer

    Directory of Open Access Journals (Sweden)

    Kaul Rajinder

    2009-11-01

    Full Text Available Abstract Background Phylogeographic reconstruction of some bacterial populations is hindered by low diversity coupled with high levels of lateral gene transfer. A comparison of recombination levels and diversity at seven housekeeping genes for eleven bacterial species, most of which are commonly cited as having high levels of lateral gene transfer shows that the relative contributions of homologous recombination versus mutation for Burkholderia pseudomallei is over two times higher than for Streptococcus pneumoniae and is thus the highest value yet reported in bacteria. Despite the potential for homologous recombination to increase diversity, B. pseudomallei exhibits a relative lack of diversity at these loci. In these situations, whole genome genotyping of orthologous shared single nucleotide polymorphism loci, discovered using next generation sequencing technologies, can provide very large data sets capable of estimating core phylogenetic relationships. We compared and searched 43 whole genome sequences of B. pseudomallei and its closest relatives for single nucleotide polymorphisms in orthologous shared regions to use in phylogenetic reconstruction. Results Bayesian phylogenetic analyses of >14,000 single nucleotide polymorphisms yielded completely resolved trees for these 43 strains with high levels of statistical support. These results enable a better understanding of a separate analysis of population differentiation among >1,700 B. pseudomallei isolates as defined by sequence data from seven housekeeping genes. We analyzed this larger data set for population structure and allele sharing that can be attributed to lateral gene transfer. Our results suggest that despite an almost panmictic population, we can detect two distinct populations of B. pseudomallei that conform to biogeographic patterns found in many plant and animal species. That is, separation along Wallace's Line, a biogeographic boundary between Southeast Asia and Australia

  8. Intraspecific hybridization studies in three wild strains of ...

    African Journals Online (AJOL)

    There were no significant (P > 0.05) differences in the weight of the three parental strains and the six intraspecific hybrids at hatching and six weeks of rearing indoor aquaria and outdoor concrete tanks. The best survival value of 96% was recorded for the Jos strain followed by that of the hybrid cross involving female Jos ...

  9. Hypothalamically Induced Intraspecific Aggressive Behaviour in the Rat

    NARCIS (Netherlands)

    Koolhaas, J.M.

    1978-01-01

    The effects of electrical stimulation of the lateral hypothalamus (LH) of rats on intraspecific aggressive behaviour were studied. In order to investigate the specificity of the stimulation effects, each experimental animal was stimulated in a number of different social situations. Stimulation of

  10. Intraspecific competition increases toxicant effects in outdoor pond microcosms.

    Science.gov (United States)

    Knillmann, Saskia; Stampfli, Nathalie C; Beketov, Mikhail A; Liess, Matthias

    2012-10-01

    Competition is a ubiquitous factor in natural populations and has been reported to alter the ecological impact of xenobiotics. We investigated conditions that mirror the natural variation of environmental factors. For this, different treatments were applied to 96 outdoor pond microcosms by shading the ponds and harvesting the communities. Then, the effect of esfenvalerate (0.03, 0.3, and 3 μg/L) on populations of Daphnia spp. was investigated. The pesticide effect and the sensitivity of Daphnia spp. in the context of a zooplankton community was increased by intraspecific competition 11 days after contamination. This relationship was most pronounced at 0.03 and 0.3 μg/L esfenvalerate, which were the concentrations that led to partial mortality. In contrast, interspecific interaction did not significantly alter the effect of the toxicant on Daphnia spp. Modelled concentration-response curves showed that the negative effects of the pesticide differed by a factor of up to 100 depending on the strength of intraspecific competition. In addition, a wider range of concentrations led to negative effects at high levels of intraspecific competition than at low levels. We argue that increased intraspecific competition reduces the availability of resources at the individual level and thereby increases the effect of contaminants. This knowledge about the interaction between competition and the response to toxicants is important in assessing the effects of these factors under field conditions.

  11. Variation in the relative magnitude of intraspecific and interspecific ...

    Indian Academy of Sciences (India)

    Administrator

    Models of competitor coevolution, especially the genetic feedback hypothesis, suggest that a negative correlation be- tween intraspecific and interspecific competitive effects may be important in sustaining competitor coexistence, and can give rise to oscillatory dynamics with repeated reversals of competitive superiority.

  12. Intraspecific prey choice of bushmeat hunters outside the Serengeti ...

    African Journals Online (AJOL)

    In this study we investigated intraspecific prey choice of illegal bushmeat hunters outside the Serengeti National Park, Tanzania. During the study 151 animals belonging to 12 species were reported killed. The majority, 76%, of prey species were migratory herbivores. Night hunting with dogs was the most common hunting ...

  13. Intraspecific genetic variation and species coexistence in plant communities.

    Science.gov (United States)

    Ehlers, Bodil K; Damgaard, Christian F; Laroche, Fabien

    2016-01-01

    Many studies report that intraspecific genetic variation in plants can affect community composition and coexistence. However, less is known about which traits are responsible and the mechanisms by which variation in these traits affect the associated community. Focusing on plant-plant interactions, we review empirical studies exemplifying how intraspecific genetic variation in functional traits impacts plant coexistence. Intraspecific variation in chemical and architectural traits promotes species coexistence, by both increasing habitat heterogeneity and altering competitive hierarchies. Decomposing species interactions into interactions between genotypes shows that genotype × genotype interactions are often intransitive. The outcome of plant-plant interactions varies with local adaptation to the environment and with dominant neighbour genotypes, and some plants can recognize the genetic identity of neighbour plants if they have a common history of coexistence. Taken together, this reveals a very dynamic nature of coexistence. We outline how more traits mediating plant-plant interactions may be identified, and how future studies could use population genetic surveys of genotype distribution in nature and methods from trait-based ecology to better quantify the impact of intraspecific genetic variation on plant coexistence. © 2016 The Author(s).

  14. Intraspecific genetic diversity of Drechslera tritici-repentis as detected by random amplified polymorphic DNA analysis

    Directory of Open Access Journals (Sweden)

    Ana Maria Pujol Vieira dos Santos

    2002-01-01

    Full Text Available The phytopathogenic fungus Drechslera tritici-repentis causes tan spot, an important disease of wheat in the southern Brazilian state of Rio Grande do Sul. Twelve D. tritici-repentis isolates were obtained from wheat seeds from different locations in the state. Their colony morphology on potato dextrose agar and polymorphisms in genomic DNA by the random amplified polymorphic DNA (RAPD method were investigated. For the RAPD method, 23 primers were tested of which nine were selected for use in the study of D. tritici-repentis polymorphisms. The degree of similarity between isolates was calculated using a simple matching coefficient and dendrograms constructed by the unweighted pair-group method with arithmetical averages (UPGMA. The morphological and RAPD analyses showed intraspecific polymorphisms within the isolates, but it was not possible to establish a relationship between these polymorphisms and the geographical regions from where the host seeds were collected.

  15. Thesis Abstract Morphological and phylogeographic analysis of Brazilian tortoises (Testudinidae).

    Science.gov (United States)

    Silva, T L; Venancio, L P R; Bonini-Domingos, C R

    2015-12-29

    distribution of C. carbonarius can partially be explained by the fact that all the morphotypes are considered as a single taxonomic unit. Behavioral aspects such as intraspecific communication may be as reliable as morphological or molecular data for inferring evolutionary relationships. Analysis of the physical characteristics of vocalization [fundamental frequency (Hz), interval between notes (s), duration of each note (s), and number of notes from each vocalization] between C. carbonarius and morphotype 1 revealed statistically significant differences in the interval between notes (s) (P = 0.0000); duration of each note (s) (P = 0.0000); frequency of notes (Hz) (P = 0.0009); and number of notes (P = 0.0002). The results of preference experiments using sound stimulus were inconclusive with respect to species-specific vocalization preference; only females of C. carbonarius showed intraspecific vocalization preference, indicating possible reproductive isolation mechanisms. To explore the presence of sexual dimorphism and morphological differences between C. denticulatus, C. carbonarius, and morphotype 1, descriptive statistics to analyze the data obtained for the investigated measures were used. Two sets of analysis were conducted - the first for each group, to compare the sexes; and the second for each sex, to compare the groups. To examine the interspecific variation in size and shape, a correlation matrix inprincipal component analysis was used. Next, I used factor analysis to rank the features showing >0.75 correlation in the differentiation between the sexes. The results were consistent with the hypothesis that morphotype 1 corresponds to a new species, because it differs from the species pattern in terms of morphology, coloring, and sexual dimorphism. The results of classical cytogenetic analysis - to differentiate C. denticulatus, C. carbonarius, and morphotype 1 - revealed no consistent data that would enable its use as a taxonomic parameter. Conventional Giemsa

  16. Climate oscillations, range shifts and phylogeographic patterns of North Atlantic Fucaceae

    NARCIS (Netherlands)

    Neiva, João; Serrão, Ester A.; Assis, Jorge; Pearson, Gareth A.; Coyer, James; Olsen, Jeanine; Hoarau, Galice; Valero, Myriam; Hu, Zi-Min; Fraser, Ceridwen

    2016-01-01

    Members of the seaweed family Fucaceae have been recurrent models in North Atlantic phylogeographic research; numerous studies have been published since 2000, and this review synthesizes their major findings. Fucoid species exhibited diverse responses to glacial–interglacial cycles, but evidence

  17. Contrasting demographic history and phylogeographical patterns in two Indo-Pacific gastropods.

    Science.gov (United States)

    Crandall, Eric D; Frey, Melissa A; Grosberg, Richard K; Barber, Paul H

    2008-01-01

    Marine species with ranges that span the Indo-Australian Archipelago (IAA) exhibit a range of phylogeographical patterns, most of which are interpreted in the context of vicariance between Indian and Pacific Ocean populations during Pliocene and Pleistocene low sea-level stands. However, patterns often vary among ecologically similar taxa, sometimes even within genera. This study compares phylogeographical patterns in two species of highly dispersive neritid gastropod, Nerita albicilla and Nerita plicata, with nearly sympatric ranges that span the Indo-Pacific. Mitochondrial COI sequences from >1000 individuals from 97 sites reveal similar phylogenies in both species (two divergent clades differing by 3.2% and 2.3%, for N. albicilla and N. plicata, respectively). However, despite ecological similarity and congeneric status, the two species exhibit phylogeographical discordance. N. albicilla has maintained reciprocal monophyly of Indian and Pacific Ocean populations, while N. plicata is panmictic between oceans, but displays a genetic cline in the Central Pacific. Although this difference might be explained by qualitatively different demographic histories, parameter estimates from three coalescent models indicate that both species have high levels of gene flow between demes (2Nem>75), and share a common history of population expansion that is likely associated with cyclical flooding of continental shelves and island lagoons following low sea-level stands. Results indicate that ecologically similar, codistributed species may respond very differently to shared environmental processes, suggesting that relatively minor differences in traits such as pelagic larval duration or microhabitat association may profoundly impact phylogeographical structure.

  18. Genomic and Genotypic Characterization of Cylindrospermopsis raciborskii: Toward an Intraspecific Phylogenetic Evaluation by Comparative Genomics

    OpenAIRE

    Vinicius A. C. Abreu; Rafael V. Popin; Danillo O. Alvarenga; Danillo O. Alvarenga; Patricia D. C. Schaker; Caroline Hoff-Risseti; Alessandro M. Varani; Marli F. Fiore

    2018-01-01

    Cylindrospermopsis raciborskii is a freshwater cyanobacterial species with increasing bloom reports worldwide that are likely due to factors related to climate change. In addition to the deleterious effects of blooms on aquatic ecosystems, the majority of ecotypes can synthesize toxic secondary metabolites causing public health issues. To overcome the harmful effects of C. raciborskii blooms, it is important to advance knowledge of diversity, genetic variation, and evolutionary processes with...

  19. Intraspecific competition in Tridacna crocea, a burrowing bivalve.

    Science.gov (United States)

    Hamner, W M

    1978-01-01

    Intraspecific competition for space and light occurred when Tridacna crocea burrowed into coralline substratum of boulders on leeward coral reefs in the central Great Barrier Reef near Townsville, Australia. Intensity of competition was linearly related to clam density. Above about 200 clams/m 2 , all clams physically contacted one another and all shells sustained damage. Mortality in isolated populations due to intraspecific competition was estimated at 40%. Principles of intraspecific competition in plants were tested for applicability to T. crocea populations. Juvenile mortality due to competitive stress was density dependent. Aggregated distributions of one year old clams changed to random or regular distribution of adults. Normal size-frequency distribution for juveniles became skewed for older groups. A bimodal size-frequency distribution of the population was related to selective mortality in 1-3 year old clams. Adult mortality due to crowding was less severe but significant. Growth rates were inhibited by competition. Deformations in morphology resulted from crowding. Intraspecific competition for space and light by adults inhibited recruitment of young. Animal adaptations to reduce mortality under crowded conditions were also important. Larvae aggregated on settling and oriented with posterior ends pointed away from nearest neighbors. Positional alignment within the substratum was selectively advantageous. Burrowing posteriorly was preferential, but anterior and sideways burrowing as well as twisting within the burrow were also observed. Movement within substratum served to reduce local damage to the shell. Proteinaceous deposits secreted through perforations in the shell reduced subsequent damage. T. crocea populations exhibited many animal adaptations that reduced mortality during the first years of life, but as cohorts matured, plant-like patterns of competitive interaction became more significant.

  20. Intraspecific Competition and Population Dynamics of Aedes aegypti

    Science.gov (United States)

    Paixão, C. A.; Charret, I. C.; Lima, R. R.

    2012-04-01

    We report computational simulations for the evolution of the population of the dengue vector, Aedes aegypti mosquitoes. The results suggest that controlling the mosquito population, on the basis of intraspecific competition at the larval stage, can be an efficient mechanism for controlling the spread of the epidemic. The results also show the presence of a kind of genetic evolution in vector population, which results mainly in increasing the average lifespan of individuals in adulthood.

  1. Intraspecific hybridization, developmental stability and fitness in Drosophila mercatorum

    DEFF Research Database (Denmark)

    Andersen, DH; Pertoldi, C; Scali, V

    2002-01-01

    One of the possible effects of intraspecific hybridization is outbreeding depression, due to a breakdown of coadapted gene complexes, which can lead to reduced fitness and decreased developmental stability in hybrids. Alternatively, increased fitness and increased developmental stability in hybrids...... (hybrid vigour) may be a result of hybridization, probably due to increased heterozygosity. Developmental stability is assumed to be correlated with fitness and is commonly measured as fluctuating asymmetry or phenotypic variance. Drosophila mercatorum is capable of reproducing sexually, but also...

  2. Egg size matching by an intraspecific brood parasite

    Science.gov (United States)

    Lemons, Patrick R.; Sedinger, James S.

    2011-01-01

    Avian brood parasitism provides an ideal system with which to understand animal recognition and its affect on fitness. This phenomenon of laying eggs in the nests of other individuals has classically been framed from the perspective of interspecific brood parasitism and host recognition of parasitic eggs. Few examples exist of strategies adopted by intraspecific brood parasites to maximize success of parasitic eggs. Intraspecific brood parasitism within precocial birds can be a risky strategy in that hatch synchrony is essential to reproductive success. Given that egg size is positively correlated with incubation time, parasitic birds would benefit by recognizing and selecting hosts with a similar egg size. Intraspecific brood parasitism is an alternative reproductive strategy in black brant (Branta bernicla nigricans), a colonial nesting goose with precocial young. Based on a randomization test, parasitic eggs in this study differed less in size from eggs in their host's nests than did random eggs placed in random nests. Parasitic eggs were remarkably similar in size to hosts’ eggs, differing by parasitic brant match the egg size of hosts in our study supports our hypothesis that brant match egg size of hosts, thereby maximizing hatching success of their parasitic eggs.

  3. Intraspecific competition, not predation, drives lizard tail loss on islands.

    Science.gov (United States)

    Itescu, Yuval; Schwarz, Rachel; Meiri, Shai; Pafilis, Panayiotis

    2017-01-01

    Tail autotomy is mainly considered an antipredator mechanism. Theory suggests that predation pressure relaxes on islands, subsequently reducing autotomy rates. Intraspecific aggression, which may also cause tail loss, probably intensifies on islands due to the higher abundance. We studied whether tail autotomy is mostly affected by predation pressure or by intraspecific competition. We further studied whether predator abundance or predator richness is more important in this context. To test our predictions, we examined multiple populations of two gecko species: Kotschy's gecko (Mediodactylus kotschyi; mainland and 41 islands) and the Mediterranean house gecko (Hemidactylus turcicus; mainland and 17 islands), and estimated their abundance together with five indices of predation. In both species, autotomy rates are higher on islands and decline with most predation indices, in contrast with common wisdom, and increase with gecko abundance. In M. kotschyi, tail-loss rates are higher on predator and viper-free islands, but increase with viper abundance. We suggest that autotomy is not simply, or maybe even mainly, an antipredatory mechanism. Rather, such defence mechanisms are a response to complex direct and indirect biotic interactions and perhaps, in the case of tail autotomy in insular populations, chiefly to intraspecific aggression. © 2016 The Authors. Journal of Animal Ecology © 2016 British Ecological Society.

  4. Phylogeny and intraspecific variability of holoparasitic Orobanche (Orobanchaceae) inferred from plastid rbcL sequences.

    Science.gov (United States)

    Manen, Jean-François; Habashi, Christine; Jeanmonod, Daniel; Park, Jeong-Mi; Schneeweiss, Gerald M

    2004-11-01

    The rbcL sequences of 106 specimens representing 28 species of the four recognized sections of Orobanche were analyzed and compared. Most sequences represent pseudogenes with premature stop codons. This study confirms that the American lineage (sects. Gymnocaulis and Myzorrhiza) contains potentially functional rbcL-copies with intact open reading frames and low rates of non-synonymous substitutions. For the first time, this is also shown for a member of the Eurasian lineage, O. coerulescens of sect. Orobanche, while all other investigated species of sects. Orobanche and Trionychon contain pseudogenes with distorted reading frames and significantly higher rates of non-synonymous substitutions. Phylogenetic analyses of the rbcL sequences give equivocal results concerning the monophyly of Orobanche, and the American lineage might be more closely related to Boschniakia and Cistanche than to the other sections of Orobanche. Additionally, species of sect. Trionychon phylogenetically nest in sect. Orobanche. This is in concordance with results from other plastid markers (rps2 and matK), but in disagreement with other molecular (nuclear ITS), morphological, and karyological data. This might indicate that the ancestor of sect. Trionychon has captured the plastid genome, or parts of it, of a member of sect. Orobanche. Apart from the phylogenetically problematic position of sect. Trionychon, the phylogenetic relationships within sect. Orobanche are similar to those inferred from nuclear ITS data and are close to the traditional groupings traditionally recognized based on morphology. The intraspecific variation of rbcL is low and is neither correlated with intraspecific morphological variability nor with host range. Ancestral character reconstruction using parsimony suggests that the ancestor of O. sect. Orobanche had a narrow host range.

  5. Extinction risks forced by climatic change and intraspecific variation in the thermal physiology of a tropical lizard.

    Science.gov (United States)

    Pontes-da-Silva, Emerson; Magnusson, William E; Sinervo, Barry; Caetano, Gabriel H; Miles, Donald B; Colli, Guarino R; Diele-Viegas, Luisa M; Fenker, Jessica; Santos, Juan C; Werneck, Fernanda P

    2018-04-01

    Temperature increases can impact biodiversity and predicting their effects is one of the main challenges facing global climate-change research. Ectotherms are sensitive to temperature change and, although predictions indicate that tropical species are highly vulnerable to global warming, they remain one of the least studied groups with respect to the extent of physiological variation and local extinction risks. We model the extinction risks for a tropical heliothermic teiid lizard (Kentropyx calcarata) integrating previously obtained information on intraspecific phylogeographic structure, eco-physiological traits and contemporary species distributions in the Amazon rainforest and its ecotone to the Cerrado savannah. We also investigated how thermal-biology traits vary throughout the species' geographic range and the consequences of such variation for lineage vulnerability. We show substantial variation in thermal tolerance of individuals among thermally distinct sites. Thermal critical limits were highly correlated with operative environmental temperatures. Our physiological/climatic model predicted relative extinction risks for local populations within clades of K. calcarata for 2050 ranging between 26.1% and 70.8%, while for 2070, extinction risks ranged from 52.8% to 92.8%. Our results support the hypothesis that tropical-lizard taxa are at high risk of local extinction caused by increasing temperatures. However, the thermo-physiological differences found across the species' distribution suggest that local adaptation may allow persistence of this tropical ectotherm in global warming scenarios. These results will serve as basis to further research to investigate the strength of local adaptation to climate change. Persistence of Kentropyx calcarata also depends on forest preservation, but the Amazon rainforest is currently under high deforestation rates. We argue that higher conservation priority is necessary so the Amazon rainforest can fulfill its capacity to

  6. Mitochondrial genomics in the Genus Phytophthora with a focus on Phytophthora ramorum

    Science.gov (United States)

    Frank N. Martin; Paul Richardson

    2008-01-01

    The mitochondrial genomes of Phytophthora infestans, P. ramorum and P. sojae have been sequenced and comparative genomics has provided an opportunity to examine the processes involved with genome evolution in the genus Phytophthora. This approach can also be useful in assessing intraspecific...

  7. Transcriptome analysis of intraspecific competition in Arabidopsis thaliana reveals organ-specific signatures related to nutrient acquisition and general stress response pathways.

    Science.gov (United States)

    Masclaux, Frédéric G; Bruessow, Friederike; Schweizer, Fabian; Gouhier-Darimont, Caroline; Keller, Laurent; Reymond, Philippe

    2012-11-29

    Plants are sessile and therefore have to perceive and adjust to changes in their environment. The presence of neighbours leads to a competitive situation where resources and space will be limited. Complex adaptive responses to such situation are poorly understood at the molecular level. Using microarrays, we analysed whole-genome expression changes in Arabidopsis thaliana plants subjected to intraspecific competition. The leaf and root transcriptome was strongly altered by competition. Differentially expressed genes were enriched in genes involved in nutrient deficiency (mainly N, P, K), perception of light quality, and responses to abiotic and biotic stresses. Interestingly, performance of the generalist insect Spodoptera littoralis on densely grown plants was significantly reduced, suggesting that plants under competition display enhanced resistance to herbivory. This study provides a comprehensive list of genes whose expression is affected by intraspecific competition in Arabidopsis. The outcome is a unique response that involves genes related to light, nutrient deficiency, abiotic stress, and defence responses.

  8. Phylogeographic Investigations of the Widespread, Arid-Adapted Antlion Brachynemurus sackeni Hagen (Neuroptera: Myrmeleontidae

    Directory of Open Access Journals (Sweden)

    Joseph S. Wilson

    2010-01-01

    Full Text Available Several recent studies investigating patterns of diversification in widespread desert-adapted vertebrates have associated major periods of genetic differentiation to late Neogene mountain-building events; yet few projects have addressed these patterns in widespread invertebrates. We examine phylogeographic patterns in the widespread antlion species Brachynemurus sackeni Hagen (Neuroptera: Myrmeleontidae using a region of the mitochondrial gene cytochrome oxidase I (COI. We then use a molecular clock to estimate divergence dates for the major lineages. Our analyses resulted in a phylogeny that shows two distinct lineages, both of which are likely distinct species. This reveals the first cryptic species-complex in Myrmeleontidae. The genetic split between lineages dates to about 3.8–4.7 million years ago and may be associated with Neogene mountain building. The phylogeographic pattern does not match patterns found in other taxa. Future analyses within this species-complex may uncover a unique evolutionary history in this group.

  9. Phylogeographic Investigations of the Widespread, Arid-Adapted Antlion Brachynemurus sackeni Hagen (Neuroptera: Myrmeleontidae)

    OpenAIRE

    Wilson, Joseph S.; Williams, Kevin A.; Gunnell, Clayton F.; Pitts, James P.

    2010-01-01

    Several recent studies investigating patterns of diversification in widespread desert-adapted vertebrates have associated major periods of genetic differentiation to late Neogene mountain-building events; yet few projects have addressed these patterns in widespread invertebrates. We examine phylogeographic patterns in the widespread antlion species Brachynemurus sackeni Hagen (Neuroptera: Myrmeleontidae) using a region of the mitochondrial gene cytochrome oxidase I (COI). We then use a mole...

  10. Discongruence of Mhc and cytochrome b phylogeographical patterns in Myodes glareolus (Rodentia: Cricetidae)

    OpenAIRE

    Malé, P.-J. G.; Martin, J.-F.; Galan, M.; Deffontaine, V.; Bryja, J.; Cosson, J.-F.; Michaux, Johan; Charbonnel, N.

    2012-01-01

    In the present study, a phylogeographical approach was developed to analyse the influence of selection and history on a major histocompatibility complex (Mhc) class II gene polymorphism in European bank vole (Myodes glareolus) populations. We focused on exon 2 of the Dqa gene because it is highly variable in a large array of species and appears to evolve under pathogen-mediated selection in several rodent species. Using single-strand conformation polymorphism analysis and sequencing technique...

  11. Intraspecific hybridization, developmental stability and fitness in Drosophila mercatorum

    DEFF Research Database (Denmark)

    Andersen, DH; Pertoldi, C; Scali, V

    2002-01-01

    (hybrid vigour) may be a result of hybridization, probably due to increased heterozygosity. Developmental stability is assumed to be correlated with fitness and is commonly measured as fluctuating asymmetry or phenotypic variance. Drosophila mercatorum is capable of reproducing sexually, but also....... Intraspecific hybridization between a parthenogenetic and a sexually reproducing strain of Drosophila mercatorum resulted in significant changes in fecundity as well as fluctuating asymmetry and phenotypic variance for the number of sternopleural bristles and in the length of two wing traits over three...

  12. Deep divergences and extensive phylogeographic structure in a clade of lowland tropical salamanders

    Directory of Open Access Journals (Sweden)

    Rovito Sean M

    2012-12-01

    Full Text Available Abstract Background The complex geological history of Mesoamerica provides the opportunity to study the impact of multiple biogeographic barriers on population differentiation. We examine phylogeographic patterns in a clade of lowland salamanders (Bolitoglossa subgenus Nanotriton using two mitochondrial genes and one nuclear gene. We use several phylogeographic analyses to infer the history of this clade and test hypotheses regarding the geographic origin of species and location of genetic breaks within species. We compare our results to those for other taxa to determine if historical events impacted different species in a similar manner. Results Deep genetic divergence between species indicates that they are relatively old, and two of the three widespread species show strong phylogeographic structure. Comparison of mtDNA and nuclear gene trees shows no evidence of hybridization or introgression between species. Isolated populations of Bolitoglossa rufescens from Los Tuxtlas region constitute a separate lineage based on molecular data and morphology, and divergence between Los Tuxtlas and other areas appears to predate the arrival of B. rufescens in other areas west of the Isthmus of Tehuantepec. The Isthmus appears responsible for Pliocene vicariance within B. rufescens, as has been shown for other taxa. The Motagua-Polochic fault system does not appear to have caused population vicariance, unlike in other systems. Conclusions Species of Nanotriton have responded to some major geological events in the same manner as other taxa, particularly in the case of the Isthmus of Tehuantepec. The deep divergence of the Los Tuxtlas populations of B. rufescens from other populations highlights the contribution of this volcanic system to patterns of regional endemism, and morphological differences observed in the Los Tuxtlas populations suggests that they may represent an undescribed species of Bolitoglossa. The absence of phylogeographic structure in B

  13. Intraspecific larval competition in the olive fruit fly (Diptera: tephritidae).

    Science.gov (United States)

    Burrack, Hannah Joy; Fornell, Angela M; Connell, Joseph H; O'Connell, Neil V; Phillips, Phil A; Vossen, Paul M; Zalom, Frank G

    2009-10-01

    Olive fruit flies [Bactrocera oleae (Gmelin)] occur at densities in California that can result in intraspecific larval competition within infested fruit. Larval B. oleae densities tracked in the field at six location were found to be highly variable and related to the proportion of fruit infested and adult densities. Egg and larval distribution within the field was generally aggregated early in the season and trended toward random and uniform as the season progressed. To determine whether B. oleae experienced fitness consequences at a range of larval densities observed in the field, olive fruits were infested with one, two, four, and six eggs, and larval and pupal developmental time, pupal weight, and pupal yield were compared. At the highest egg density, all measures of performance were negatively impacted, resulting in fewer and lighter pupae that took longer to pupate and emerge as adults, and even when only two larvae was present per olive, resulting pupae were significantly smaller. Density did not impact the sex ratio of the resulting flies or survive to adults. As field surveys showed, larval densities ranged from 1 to 11 B. oleae per fruit at some sites, and our results suggest that, at high densities, B. oleae do experience competition for larval resources. The impact of intraspecific larval competition North American in field populations of B. oleae is unknown, but the potential for competition is present.

  14. Intraspecific genetic variation and competition interact to influence niche expansion.

    Science.gov (United States)

    Agashe, Deepa; Bolnick, Daniel I

    2010-10-07

    Theory and empirical evidence show that intraspecific competition can drive selection favouring the use of novel resources (i.e. niche expansion). The evolutionary response to such selection depends on genetic variation for resource use. However, while genetic variation might facilitate niche expansion, genetically diverse groups may also experience weaker competition, reducing density-dependent selection on resource use. Therefore, genetic variation for fitness on different resources could directly facilitate, or indirectly retard, niche expansion. To test these alternatives, we factorially manipulated both the degree of genetic variation and population density in flour beetles (Tribolium castaneum) exposed to both novel and familiar food resources. Using stable carbon isotope analysis, we measured temporal change and individual variation in beetle diet across eight generations. Intraspecific competition and genetic variation acted on different components of niche evolution: competition facilitated niche expansion, while genetic variation increased individual variation in niche use. In addition, genetic variation and competition together facilitated niche expansion, but all these impacts were temporally variable. Thus, we show that the interaction between genetic variation and competition can also determine niche evolution at different time scales.

  15. Effects of temperature on intraspecific competition in ectotherms.

    Science.gov (United States)

    Amarasekare, Priyanga; Coutinho, Renato M

    2014-09-01

    Understanding how temperature influences population regulation through its effects on intraspecific competition is an important question for which there is currently little theory or data. Here we develop a theoretical framework for elucidating temperature effects on competition that integrates mechanistic descriptions of life-history trait responses to temperature with population models that realistically capture the variable developmental delays that characterize ectotherm life cycles. This framework yields testable comparative predictions about how intraspecific competition affects reproduction, development, and mortality under alternative hypotheses about the temperature dependence of competition. The key finding is that ectotherm population regulation in seasonal environments depends crucially on the mechanisms by which temperature affects competition. When competition is strongest at temperatures optimal for reproduction, effects of temperature and competition act antagonistically, leading to more complex dynamics than when competition is temperature independent. When the strength of competition increases with temperature past the optimal temperature for reproduction, effects of temperature and competition act synergistically, leading to dynamics qualitatively similar to those when competition is temperature independent. Paradoxically, antagonistic effects yield a higher population floor despite greater fluctuations. These findings have important implications for predicting effects of climate warming on population regulation. Synergistic effects of temperature and competition can predispose populations to stochastic extinction by lowering minimum population sizes, while antagonistic effects can increase the potential for population outbreaks through greater fluctuations in abundance.

  16. DNA Methylation Alterations at 5'-CCGG Sites in the Interspecific and Intraspecific Hybridizations Derived from Brassica rapa and B. napus.

    Directory of Open Access Journals (Sweden)

    Wanshan Xiong

    Full Text Available DNA methylation is an important regulatory mechanism for gene expression that involved in the biological processes of development and differentiation in plants. To investigate the association of DNA methylation with heterosis in Brassica, a set of intraspecific hybrids in Brassica rapa and B. napus and interspecific hybrids between B. rapa and B. napus, together with parental lines, were used to monitor alterations in cytosine methylation at 5'-CCGG sites in seedlings and buds by methylation-sensitive amplification polymorphism analysis. The methylation status of approximately a quarter of the methylation sites changed between seedlings and buds. These alterations were related closely to the genomic structure and heterozygous status among accessions. The methylation status in the majority of DNA methylation sites detected in hybrids was the same as that in at least one of the parental lines in both seedlings and buds. However, the association between patterns of cytosine methylation and heterosis varied among different traits and between tissues in hybrids of Brassica, although a few methylation loci were associated with heterosis. Our data suggest that changes in DNA methylation at 5'-CCGG sites are not associated simply with heterosis in the interspecific and intraspecific hybridizations derived from B. rapa and B. napus.

  17. The genetic architecture of ecological adaptation: intraspecific variation in host plant use by the lepidopteran crop pest Chloridea virescens.

    Science.gov (United States)

    Oppenheim, Sara J; Gould, Fred; Hopper, Keith R

    2018-03-01

    Intraspecific variation in ecologically important traits is a cornerstone of Darwin's theory of evolution by natural selection. The evolution and maintenance of this variation depends on genetic architecture, which in turn determines responses to natural selection. Some models suggest that traits with complex architectures are less likely to respond to selection than those with simple architectures, yet rapid divergence has been observed in such traits. The simultaneous evolutionary lability and genetic complexity of host plant use in the Lepidopteran subfamily Heliothinae suggest that architecture may not constrain ecological adaptation in this group. Here we investigate the response of Chloridea virescens, a generalist that feeds on diverse plant species, to selection for performance on a novel host, Physalis angulata (Solanaceae). P. angulata is the preferred host of Chloridea subflexa, a narrow specialist on the genus Physalis. In previous experiments, we found that the performance of C. subflexa on P. angulata depends on many loci of small effect distributed throughout the genome, but whether the same architecture would be involved in the generalist's adoption of P. angulata was unknown. Here we report a rapid response to selection in C. virescens for performance on P. angulata, and establish that the genetic architecture of intraspecific variation is quite similar to that of the interspecific differences in terms of the number, distribution, and effect sizes of the QTL involved. We discuss the impact of genetic architecture on the ability of Heliothine moths to respond to varying ecological selection pressures.

  18. Effects of intraspecific variation in white cabbage (Brassica oleracea var. Capitata) on soil ogranisms

    NARCIS (Netherlands)

    Kabouw, P.; Putten, van der W.H.; Dam, van N.M.; Biere, A.

    2010-01-01

    Intraspecific variation in plants can affect soil organisms. However, little is known about whether the magnitude of the effect depends on the degree of interaction with the roots. We analyzed effects of plant intraspecific variation on root herbivores and other soil organisms that interact directly

  19. Concordance between phylogeographical and biogeographical patterns in the Brazilian Cerrado: diversification of the endemic tree Dalbergia miscolobium (Fabaceae).

    Science.gov (United States)

    Novaes, Renan Milagres Lage; Ribeiro, Renata Acácio; Lemos-Filho, José Pires; Lovato, Maria Bernadete

    2013-01-01

    Few studies have addressed the phylogeography of species of the Cerrado, the largest savanna biome of South America. Here we aimed to investigate the phylogeographical structure of Dalbergia miscolobium, a widespread tree from the Cerrado, and to verify its concordance with plant phylogeographical and biogeographical patterns so far described. A total of 287 individuals from 32 populations were analyzed by sequencing the trnL intron of the chloroplast DNA and the internal transcribed spacer of the nuclear ribosomal DNA. Analysis of population structure and tests of population expansion were performed and the time of divergence of haplotypes was estimated. Twelve and 27 haplotypes were identified in the cpDNA and nrDNA data, respectively. The star-like network configuration and the mismatch distributions indicated a recent spatial and demographic expansion of the species. Consistent with previous tree phylogeographical studies of Cerrado trees, the cpDNA also suggested a recent expansion towards the southern Cerrado. The diversity of D. miscolobium was widespread but high levels of genetic diversity were found in the Central Eastern and in the southern portion of Central Western Cerrado. The combined analysis of cpDNA and nrDNA supported a phylogeographic structure into seven groups. The phylogeographical pattern showed many concordances with biogeographical and phylogeographical studies in the Cerrado, mainly with the Cerrado phytogeographic provinces superimposed to our sampling area. The data reinforced the uniqueness of Northeastern and Southeastern Cerrados and the differentiation between Eastern and Western Central Cerrados. The recent diversification of the species (estimated between the Pliocene and the Pleistocene) and the 'genealogical concordances' suggest that a shared and persistent pattern of species diversification might have been present in the Cerrado over time. This is the first time that an extensive 'genealogical concordance' between

  20. Tracing hepatitis B virus (HBV genotype B5 (formerly B6 evolutionary history in the circumpolar Arctic through phylogeographic modelling

    Directory of Open Access Journals (Sweden)

    Remco Bouckaert

    2017-08-01

    Full Text Available Background Indigenous populations of the circumpolar Arctic are considered to be endemically infected (>2% prevalence with hepatitis B virus (HBV, with subgenotype B5 (formerly B6 unique to these populations. The distinctive properties of HBV/B5, including high nucleotide diversity yet no significant liver disease, suggest virus adaptation through long-term host-pathogen association. Methods To investigate the origin and evolutionary spread of HBV/B5 into the circumpolar Arctic, fifty-seven partial and full genome sequences from Alaska, Canada and Greenland, having known location and sampling dates spanning 40 years, were phylogeographically investigated by Bayesian analysis (BEAST 2 using a reversible-jump-based substitution model and a clock rate estimated at 4.1 × 10−5 substitutions/site/year. Results Following an initial divergence from an Asian viral ancestor approximately 1954 years before present (YBP; 95% highest probability density interval [1188, 2901], HBV/B5 coalescence occurred almost 1000 years later. Surprisingly, the HBV/B5 ancestor appears to locate first to Greenland in a rapid coastal route progression based on the landscape aware geographic model, with subsequent B5 evolution and spread westward. Bayesian skyline plot analysis demonstrated an HBV/B5 population expansion occurring approximately 400 YBP, coinciding with the disruption of the Neo-Eskimo Thule culture into more heterogeneous and regionally distinct Inuit populations throughout the North American Arctic. Discussion HBV/B5 origin and spread appears to occur coincident with the movement of Neo-Eskimo (Inuit populations within the past 1000 years, further supporting the hypothesis of HBV/host co-expansion, and illustrating the concept of host-pathogen adaptation and balance.

  1. Phylogeographic Analyses of American Black Bears (Ursus americanus) Suggest Four Glacial Refugia and Complex Patterns of Postglacial Admixture.

    Science.gov (United States)

    Puckett, Emily E; Etter, Paul D; Johnson, Eric A; Eggert, Lori S

    2015-09-01

    Studies of species with continental distributions continue to identify intraspecific lineages despite continuous habitat. Lineages may form due to isolation by distance, adaptation, divergence across barriers, or genetic drift following range expansion. We investigated lineage diversification and admixture within American black bears (Ursus americanus) across their range using 22 k single nucleotide polymorphisms and mitochondrial DNA sequences. We identified three subcontinental nuclear clusters which we further divided into nine geographic regions: Alaskan (Alaska-East), eastern (Central Interior Highlands, Great Lakes, Northeast, Southeast), and western (Alaska-West, West, Pacific Coast, Southwest). We estimated that the western cluster diverged 67 ka, before eastern and Alaskan divergence 31 ka; these divergence dates contrasted with those from the mitochondrial genome where clades A and B diverged 1.07 Ma, and clades A-east and A-west diverged 169 ka. We combined estimates of divergence timing with hindcast species distribution models to infer glacial refugia for the species in Beringia, Pacific Northwest, Southwest, and Southeast. Our results show a complex arrangement of admixture due to expansion out of multiple refugia. The delineation of the genomic population clusters was inconsistent with the ranges for 16 previously described subspecies. Ranges for U. a. pugnax and U. a. cinnamomum were concordant with admixed clusters, calling into question how to order taxa below the species level. Additionally, our finding that U. a. floridanus has not diverged from U. a. americanus also suggests that morphology and genetics should be reanalyzed to assess taxonomic designations relevant to the conservation management of the species. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved.For permissions please email: journals.permissions@oup.com.

  2. The reciprocal relationship between competition and intraspecific trait variation

    DEFF Research Database (Denmark)

    A Bennett, Jonathan; Riibak, Kersti; Tamme, Riin

    2016-01-01

    with larger leaves and lower specific leaf area than their neighbours. Switching to more stress tolerant strategies by increasing root diameter and leaf tissue density also reduced competition. However, dissimilarity in root tissue density also minimized competition, consistent with limiting similarity...... outcomes, we grew 15 species alone, in monoculture, and in mixture. We measured traits relating to leaf and root tissue morphology as well as biomass allocation and related competition induced changes in these traits to intra- and interspecific competition using multi-model inference. Additionally, we...... to both intra- and interspecific competition, frequently affecting competitive hierarchies. Intraspecific competition was lower for species that limited competition-induced increases in root allocation and had less variability in this trait overall. Interspecific competition was lower for species...

  3. Comparative phylogeographic analyses illustrate the complex evolutionary history of threatened cloud forests of northern Mesoamerica.

    Science.gov (United States)

    Ornelas, Juan Francisco; Sosa, Victoria; Soltis, Douglas E; Daza, Juan M; González, Clementina; Soltis, Pamela S; Gutiérrez-Rodríguez, Carla; de los Monteros, Alejandro Espinosa; Castoe, Todd A; Bell, Charles; Ruiz-Sanchez, Eduardo

    2013-01-01

    Comparative phylogeography can elucidate the influence of historical events on current patterns of biodiversity and can identify patterns of co-vicariance among unrelated taxa that span the same geographic areas. Here we analyze temporal and spatial divergence patterns of cloud forest plant and animal species and relate them to the evolutionary history of naturally fragmented cloud forests--among the most threatened vegetation types in northern Mesoamerica. We used comparative phylogeographic analyses to identify patterns of co-vicariance in taxa that share geographic ranges across cloud forest habitats and to elucidate the influence of historical events on current patterns of biodiversity. We document temporal and spatial genetic divergence of 15 species (including seed plants, birds and rodents), and relate them to the evolutionary history of the naturally fragmented cloud forests. We used fossil-calibrated genealogies, coalescent-based divergence time inference, and estimates of gene flow to assess the permeability of putative barriers to gene flow. We also used the hierarchical Approximate Bayesian Computation (HABC) method implemented in the program msBayes to test simultaneous versus non-simultaneous divergence of the cloud forest lineages. Our results show shared phylogeographic breaks that correspond to the Isthmus of Tehuantepec, Los Tuxtlas, and the Chiapas Central Depression, with the Isthmus representing the most frequently shared break among taxa. However, dating analyses suggest that the phylogeographic breaks corresponding to the Isthmus occurred at different times in different taxa. Current divergence patterns are therefore consistent with the hypothesis of broad vicariance across the Isthmus of Tehuantepec derived from different mechanisms operating at different times. This study, coupled with existing data on divergence cloud forest species, indicates that the evolutionary history of contemporary cloud forest lineages is complex and often lineage

  4. Comparative phylogeographic analyses illustrate the complex evolutionary history of threatened cloud forests of northern Mesoamerica.

    Directory of Open Access Journals (Sweden)

    Juan Francisco Ornelas

    Full Text Available Comparative phylogeography can elucidate the influence of historical events on current patterns of biodiversity and can identify patterns of co-vicariance among unrelated taxa that span the same geographic areas. Here we analyze temporal and spatial divergence patterns of cloud forest plant and animal species and relate them to the evolutionary history of naturally fragmented cloud forests--among the most threatened vegetation types in northern Mesoamerica. We used comparative phylogeographic analyses to identify patterns of co-vicariance in taxa that share geographic ranges across cloud forest habitats and to elucidate the influence of historical events on current patterns of biodiversity. We document temporal and spatial genetic divergence of 15 species (including seed plants, birds and rodents, and relate them to the evolutionary history of the naturally fragmented cloud forests. We used fossil-calibrated genealogies, coalescent-based divergence time inference, and estimates of gene flow to assess the permeability of putative barriers to gene flow. We also used the hierarchical Approximate Bayesian Computation (HABC method implemented in the program msBayes to test simultaneous versus non-simultaneous divergence of the cloud forest lineages. Our results show shared phylogeographic breaks that correspond to the Isthmus of Tehuantepec, Los Tuxtlas, and the Chiapas Central Depression, with the Isthmus representing the most frequently shared break among taxa. However, dating analyses suggest that the phylogeographic breaks corresponding to the Isthmus occurred at different times in different taxa. Current divergence patterns are therefore consistent with the hypothesis of broad vicariance across the Isthmus of Tehuantepec derived from different mechanisms operating at different times. This study, coupled with existing data on divergence cloud forest species, indicates that the evolutionary history of contemporary cloud forest lineages is complex

  5. Intraspecific functional and genetic diversity ofPetriella setifera.

    Science.gov (United States)

    Pertile, Giorgia; Panek, Jacek; Oszust, Karolina; Siczek, Anna; Frąc, Magdalena

    2018-01-01

    The aim of the study was an analysis of the intraspecific genetic and functional diversity of the new isolated fungal strains of P. setifera . This is the first report concerning the genetic and metabolic diversity of Petriella setifera strains isolated from industrial compost and the first description of a protocol for AFLP fingerprinting analysis optimised for these fungal species. The results showed a significant degree of variability among the isolates, which was demonstrated by the clearly subdivision of all the isolates into two clusters with 51% and 62% similarity, respectively. For the metabolic diversity, the BIOLOG system was used and this analysis revealed clearly different patterns of carbon substrates utilization between the isolates resulting in a clear separation of the five isolates into three clusters with 0%, 42% and 54% of similarity, respectively. These results suggest that genetic diversity does not always match the level of functional diversity, which may be useful in discovering the importance of this fungus to ecosystem functioning. The results indicated that P. setifera strains were able to degrade substrates produced in the degradation of hemicellulose (D-Arabinose, L-Arabinose, D-Glucuronic Acid, Xylitol, γ-Amino-Butyric Acid, D-Mannose, D-Xylose and L-Rhamnose), cellulose (α-D-Glucose and D-Cellobiose) and the synthesis of lignin (Quinic Acid) at a high level, showing their importance in ecosystem services as a decomposer of carbon compounds and as organisms, which make a significant contribution to carbon cycling in the ecosystem.The results showed for the first time that the use of molecular biology techniques (such as AFLP and BIOLOG analyses) may allow for the identification of intraspecific diversity of as yet poorly investigated fungal species with favourable consequences for our understanding their ecosystem function.

  6. Does intraspecific competition promote variation? A test via synthesis.

    Science.gov (United States)

    Jones, Andrew W; Post, David M

    2016-03-01

    Competitive diversification, that is, when increasing intraspecific competition promotes population niche expansion, is commonly invoked in evolutionary studies and currently plays a central role in how we conceptualize the process of adaptive diversification. Despite the frequency with which this idea is cited, the empirical evidence for the process is somewhat limited, and the findings of these studies have yet to be weighed objectively through synthesis. Here, we sought to fill this gap by reviewing the existing literature and collecting the data necessary to assess the evidence for competition as a diversifying force. Additionally, we sought to test a more recent hypothesis, which suggests that competition can act to both promote and inhibit dietary diversification depending on the degree to which a consumer depletes its resources. The surprising result of this synthesis was that increasing competition did not have a mean positive effect on population-level diet breadth or the degree of individual specialization. Instead, we found that increasing intraspecific competition had a restricting effect on population-level diet breadth in as many cases as it had a diversifying effect. This wide disparity in the effect of competition on consumer diet variation was negatively related to a metric for consumer resource depletion. Altogether, these findings call into question a long-standing assumption of basic evolutionary models and lend some support to recent theoretical predictions. Specifically, these findings support the idea that competition is primarily diversifying for species with a small effect (per unit biomass) on their resources and that resource depletion limits the diversifying effect of competition for consumers with larger ecological effects.

  7. Revisiting Coleoptera a + T-rich region: structural conservation, phylogenetic and phylogeographic approaches in mitochondrial control region of bioluminescent Elateridae species (Coleoptera).

    Science.gov (United States)

    Amaral, Danilo T; Mitani, Yasuo; Oliveira, Gabriela; Ohmiya, Yoshihiro; Viviani, Vadim R

    2017-09-01

    The control region (CR) or A + T-rich region in Coleoptera mt genome is poorly characterized, including the Elateroidea bioluminescent species. Here, we provided the first attempt to characterize and compare the structure and organization of the CR of different species within Elateridae. We also revisited some sequenced Coleoptera CR and observed consensus T-stretches, non-conserved sequences near the stem-loop and unusual inner tRNAs-like sequences. All these features are probably involved in the replication start of the mt genome. The phylogenetic relationships in Elateridae bioluminescent groups using partial sequence of CR showed the monophyly of Pyrearinus pumilus group and Pyrearinus as a polyphyletic genus, corroborating our previous results. The wider genetic variation obtained by CR analysis could separate two different lineages that occur within P. termitilluminans populations. In Elateridae, the CR exhibited high polymorphism within and between populations, which was also observed in other Coleoptera species, suggesting that the CR could be described as a suitable molecular marker to be applied in phylogenetic and phylogeographic studies.

  8. A range-wide synthesis and timeline for phylogeographic events in the red fox (Vulpes vulpes).

    Science.gov (United States)

    Kutschera, Verena E; Lecomte, Nicolas; Janke, Axel; Selva, Nuria; Sokolov, Alexander A; Haun, Timm; Steyer, Katharina; Nowak, Carsten; Hailer, Frank

    2013-06-05

    Many boreo-temperate mammals have a Pleistocene fossil record throughout Eurasia and North America, but only few have a contemporary distribution that spans this large area. Examples of Holarctic-distributed carnivores are the brown bear, grey wolf, and red fox, all three ecological generalists with large dispersal capacity and a high adaptive flexibility. While the two former have been examined extensively across their ranges, no phylogeographic study of the red fox has been conducted across its entire Holarctic range. Moreover, no study included samples from central Asia, leaving a large sampling gap in the middle of the Eurasian landmass. Here we provide the first mitochondrial DNA sequence data of red foxes from central Asia (Siberia), and new sequences from several European populations. In a range-wide synthesis of 729 red fox mitochondrial control region sequences, including 677 previously published and 52 newly obtained sequences, this manuscript describes the pattern and timing of major phylogeographic events in red foxes, using a Bayesian coalescence approach with multiple fossil tip and root calibration points. In a 335 bp alignment we found in total 175 unique haplotypes. All newly sequenced individuals belonged to the previously described Holarctic lineage. Our analyses confirmed the presence of three Nearctic- and two Japan-restricted lineages that were formed since the Mid/Late Pleistocene. The phylogeographic history of red foxes is highly similar to that previously described for grey wolves and brown bears, indicating that climatic fluctuations and habitat changes since the Pleistocene had similar effects on these highly mobile generalist species. All three species originally diversified in Eurasia and later colonized North America and Japan. North American lineages persisted through the last glacial maximum south of the ice sheets, meeting more recent colonizers from Beringia during postglacial expansion into the northern Nearctic. Both brown

  9. Scandinavian Oncophorus (Bryopsida, Oncophoraceae: species, cryptic species, and intraspecific variation

    Directory of Open Access Journals (Sweden)

    Lars Hedenäs

    2017-05-01

    Full Text Available Scandinavian members of the acrocarpous moss genus Oncophorus were revised after field observations had suggested unrecognized diversity. Based on molecular (nuclear: internal transcribed spacers 1 and 2, ITS; plastid: trnGUCC G2 intron, trnG, rps4 gene + trnS-rps4 spacer, rps4 and morphological evidence, four morphologically distinguishable species are recognized, Oncophorus elongatus (I.Hagen Hedenäs, O. integerrimus Hedenäs sp. nov. (syn. O. virens var. elongatus Limpr., O. virens (Hedw. Brid., and O. wahlenbergii Brid. (O. sardous Herzog, syn. nov.. Oncophorus elongatus was earlier recognized, but much of its variation was hidden within O. wahlenbergii. Its circumscription is here expanded to include plants with long leaves having mostly denticulate or sharply denticulate upper margins and with long and narrow marginal cells in the basal portion of the sheathing leaf lamina. The new species O. integerrimus sp. nov. differs from O. virens in having more loosely incurved leaves and entire or almost entire upper leaf margins. Besides these characters, the species in the respective pairs differ in quantitative features of the leaf lamina cells. Several cryptic entities were found, in several cases as molecularly distinct as some of the morphologically recognizable species, and phylogeographic structure is present within O. elongatus and O. virens.

  10. The Phylogeographic History of the New World Screwworm Fly, Inferred by Approximate Bayesian Computation Analysis

    Science.gov (United States)

    Azeredo-Espin, Ana Maria L.

    2013-01-01

    Insect pest phylogeography might be shaped both by biogeographic events and by human influence. Here, we conducted an approximate Bayesian computation (ABC) analysis to investigate the phylogeography of the New World screwworm fly, Cochliomyia hominivorax, with the aim of understanding its population history and its order and time of divergence. Our ABC analysis supports that populations spread from North to South in the Americas, in at least two different moments. The first split occurred between the North/Central American and South American populations in the end of the Last Glacial Maximum (15,300-19,000 YBP). The second split occurred between the North and South Amazonian populations in the transition between the Pleistocene and the Holocene eras (9,100-11,000 YBP). The species also experienced population expansion. Phylogenetic analysis likewise suggests this north to south colonization and Maxent models suggest an increase in the number of suitable areas in South America from the past to present. We found that the phylogeographic patterns observed in C. hominivorax cannot be explained only by climatic oscillations and can be connected to host population histories. Interestingly we found these patterns are very coincident with general patterns of ancient human movements in the Americas, suggesting that humans might have played a crucial role in shaping the distribution and population structure of this insect pest. This work presents the first hypothesis test regarding the processes that shaped the current phylogeographic structure of C. hominivorax and represents an alternate perspective on investigating the problem of insect pests. PMID:24098436

  11. Contemporary patterns in a historical context: phylogeographic history of the pipevine swallowtail, Battus philenor (Papilionidae).

    Science.gov (United States)

    Fordyce, James A; Nice, Chris C

    2003-05-01

    We examined mitochondrial DNA (mtDNA) variation in pipevine swallowtail butterflies (Battus philenor) from throughout its extant range to provide a historical, phylogeographical context for ecological studies of the disjunct population in California. We evaluate current hypotheses regarding host plant use, behavior, and mimetic relationships of B. philenor populations and generate alternative hypotheses. Compared to populations throughout the rest of the species' range, California populations are ecologically distinct in that they lack mimics, lay significantly larger clutches of eggs, and exclusively use a unique, endemic larval host plant. Analysis of molecular variance, tests of population differentiation, and nested clade analysis of mtDNA variation indicate that, despite low levels of population genetic structure across the species' range, there is evidence of recent range expansion from presumed Pleistocene refuge(s) in southeastern North America. Colonization of California appears to have been a recent event. This phylogeographic investigation also suggests that the evolution of life-history adaptations to a novel larval host has occurred rapidly in California and the lack of mimics in California may be attributable to the recency of colonization.

  12. Construction and Comparative Analyses of Highly Dense Linkage Maps of Two Sweet Cherry Intra-Specific Progenies of Commercial Cultivars

    Science.gov (United States)

    Quero-García, José; Guzmán, Alejandra; Mansur, Levi; Gratacós, Eduardo; Silva, Herman; Rosyara, Umesh R.; Iezzoni, Amy; Meisel, Lee A.; Dirlewanger, Elisabeth

    2013-01-01

    Despite the agronomical importance and high synteny with other Prunus species, breeding improvements for cherry have been slow compared to other temperate fruits, such as apple or peach. However, the recent release of the peach genome v1.0 by the International Peach Genome Initiative and the sequencing of cherry accessions to identify Single Nucleotide Polymorphisms (SNPs) provide an excellent basis for the advancement of cherry genetic and genomic studies. The availability of dense genetic linkage maps in phenotyped segregating progenies would be a valuable tool for breeders and geneticists. Using two sweet cherry (Prunus avium L.) intra-specific progenies derived from crosses between ‘Black Tartarian’ × ‘Kordia’ (BT×K) and ‘Regina’ × ‘Lapins’(R×L), high-density genetic maps of the four parental lines and the two segregating populations were constructed. For BT×K and R×L, 89 and 121 F1 plants were used for linkage mapping, respectively. A total of 5,696 SNP markers were tested in each progeny. As a result of these analyses, 723 and 687 markers were mapped into eight linkage groups (LGs) in BT×K and R×L, respectively. The resulting maps spanned 752.9 and 639.9 cM with an average distance of 1.1 and 0.9 cM between adjacent markers in BT×K and R×L, respectively. The maps displayed high synteny and co-linearity between each other, with the Prunus bin map, and with the peach genome v1.0 for all eight LGs (LG1–LG8). These maps provide a useful tool for investigating traits of interest in sweet cherry and represent a qualitative advance in the understanding of the cherry genome and its synteny with other members of the Rosaceae family. PMID:23382953

  13. Intraspecific variation of the interparietal suture closure in Siberian roe deer Capreolus pygargus from Jeju Island.

    Science.gov (United States)

    Oh, Jinwoo; Oh, Hong-Shik; Kimura, Junpei; Koyabu, Daisuke

    2017-12-22

    The sequence of cranial suture closure among cervids is reported to be generally species-specific and highly conservative within species. On the other hand, it is known that intraspecific variation often exists to some extent in other mammalian taxa. Here we studied the cranial suture closures of Capreolus pygargus from Jeju Island and compared it with other cervid species. We found that the timing of the interparietal suture closure is highly variable within C. pygargus. Capreolus capreolus similarly shows intraspecific variation of the interparietal suture closure, whereas other cervid species studied to date do not show any intraspecific variation in the sequence of cranial suture closure. Such high intraspecific variation of the interparietal suture may be a derived character for Capreolus.

  14. Plant movements and climate warming: intraspecific variation in growth responses to nonlocal soils

    Czech Academy of Sciences Publication Activity Database

    De Frenne, P.; Coomes, D. A.; De Schrijver, A.; Staelens, J.; Alexander, J. M.; Bernhardt-Römermann, M.; Brunet, J.; Chabrerie, O.; Chiarucci, A.; den Ouden, J.; Eckstein, R. L.; Graae, B. J.; Gruwez, R.; Hédl, Radim; Hermy, M.; Kolb, A.; Marell, A.; Mullender, S. M.; Olsen, S. L.; Orczewska, A.; Peterken, G.; Petřík, Petr; Plue, J.; Simonson, W. D.; Tomescu, C. V.; Vangansbeke, P.; Verstraeten, G.; Vesterdal, L.; Wulf, M.; Verheyen, K.

    2014-01-01

    Roč. 202, č. 2 (2014), s. 431-441 ISSN 0028-646X Institutional support: RVO:67985939 Keywords : climate change * intraspecific variability * soil chemism Subject RIV: EF - Botanics Impact factor: 7.672, year: 2014

  15. Spatial Heterogeneity in Light Supply Affects Intraspecific Competition of a Stoloniferous Clonal Plant

    OpenAIRE

    Wang, Pu; Lei, Jing-Pin; Li, Mai-He; Yu, Fei-Hai

    2012-01-01

    Spatial heterogeneity in light supply is common in nature. Many studies have examined the effects of heterogeneous light supply on growth, morphology, physiology and biomass allocation of clonal plants, but few have tested those effects on intraspecific competition. In a greenhouse experiment, we grew one (no competition) or nine ramets (with intraspecific competition) of a stoloniferous clonal plant, Duchesnea indica, in three homogeneous light conditions (high, medium and low light intensit...

  16. Intra-specific pelage color variation in a South American small rodent species

    OpenAIRE

    Sandoval Salinas,M. L.; Barquez,R. M.; Colombo,E. M.; Sandoval,J. D.

    2017-01-01

    Abstract Intra-specific color variation is often underestimated by researchers, and among mammals, intra-specific differences in coloration are poorly documented for most species. The main goal of this study was to apply an objective color measurement methodology to the study of a specific problem: the detection, if any, of patterns of changes in the fur color of specimens of Akodon budini in relation to biological (i.e., sex) and environmental (i.e., season) variables. We hypothesize that co...

  17. Intra-specific pelage color variation in a South American small rodent species

    OpenAIRE

    Sandoval Salinas, M. L.; Barquez, R. M.; Colombo, E. M.; Sandoval, J. D.

    2016-01-01

    Abstract Intra-specific color variation is often underestimated by researchers, and among mammals, intra-specific differences in coloration are poorly documented for most species. The main goal of this study was to apply an objective color measurement methodology to the study of a specific problem: the detection, if any, of patterns of changes in the fur color of specimens of Akodon budini in relation to biological (i.e., sex) and environmental (i.e., season) variables. We hypothesize that co...

  18. Intraspecific diet shift in Talitrus saltator inhabiting exposed sandy beaches

    Science.gov (United States)

    Olabarria, Celia; Incera, Mónica; Garrido, Josefina; Rodil, Iván F.; Rossi, Francesca

    2009-09-01

    Talitrid amphipods are the most abundant herbivores on exposed sandy beaches. Despite their important role as trophic intermediates between macrophytes and higher levels (i.e. insect and bird) of beach food webs, very little information is available on their feeding patterns. The main aim of this study was to investigate intraspecific differences in the feeding behaviour of Talitrus saltator. We tested the hypotheses that: (1) adult females and males showed different isotope signatures and therefore relied on different sources of food; and (2) patterns of variation of isotope signatures of juveniles differed from those of adult specimens, evidencing a diet shift during the development. We used stable isotope signatures and tested for differences upon the level on the shore, times of the year and beaches experiencing similar morpho-dynamic and environmental conditions. Finally, we investigated the trophic significance of macrophyte detritus in the diet of males, females and juveniles. Results showed that adult males had a more variable diet than females and juveniles (inferred from δ 13C and δ 15N values). Dual-isotope graphs suggested that Sargassum muticum and Cystoseira baccata wrack could be among the main food sources for both juvenile and adult stage.

  19. Intraspecific competition reduces niche width in experimental populations.

    Science.gov (United States)

    Parent, Christine E; Agashe, Deepa; Bolnick, Daniel I

    2014-10-01

    Intraspecific competition is believed to drive niche expansion, because otherwise suboptimal resources can provide a refuge from competition for preferred resources. Competitive niche expansion is well supported by empirical observations, experiments, and theory, and is often invoked to explain phenotypic diversification within populations, some forms of speciation, and adaptive radiation. However, some foraging models predict the opposite outcome, and it therefore remains unclear whether competition will promote or inhibit niche expansion. We conducted experiments to test whether competition changes the fitness landscape to favor niche expansion, and if competition indeed drives niche expansion as expected. Using Tribolium castaneum flour beetles fed either wheat (their ancestral resource), corn (a novel resource) or mixtures of both resources, we show that fitness is maximized on a mixed diet. Next, we show that at higher population density, the optimal diet shifts toward greater use of corn, favoring niche expansion. In stark contrast, when beetles were given a choice of resources, we found that competition caused niche contraction onto the ancestral resource. This presents a puzzling mismatch between how competition alters the fitness landscape, versus competition's effects on resource use. We discuss several explanations for this mismatch, highlighting potential reasons why optimality models might be misleading.

  20. Spatial heterogeneity in light supply affects intraspecific competition of a stoloniferous clonal plant.

    Science.gov (United States)

    Wang, Pu; Lei, Jing-Pin; Li, Mai-He; Yu, Fei-Hai

    2012-01-01

    Spatial heterogeneity in light supply is common in nature. Many studies have examined the effects of heterogeneous light supply on growth, morphology, physiology and biomass allocation of clonal plants, but few have tested those effects on intraspecific competition. In a greenhouse experiment, we grew one (no competition) or nine ramets (with intraspecific competition) of a stoloniferous clonal plant, Duchesnea indica, in three homogeneous light conditions (high, medium and low light intensity) and two heterogeneous ones differing in patch size (large and small patch treatments). The total light in the two heterogeneous treatments was the same as that in the homogeneous medium light treatment. Both decreasing light intensity and intraspecific competition significantly decreased the growth (biomass, number of ramets and total stolon length) of D. indica. As compared with the homogeneous medium light treatment, the large patch treatment significantly increased the growth of D. indica without intraspecific competition. However, the growth of D. indica with competition did not differ among the homogeneous medium light, the large and the small patch treatments. Consequently, light heterogeneity significantly increased intraspecific competition intensity, as measured by the decreased log response ratio. These results suggest that spatial heterogeneity in light supply can alter intraspecific interactions of clonal plants.

  1. Spatial heterogeneity in light supply affects intraspecific competition of a stoloniferous clonal plant.

    Directory of Open Access Journals (Sweden)

    Pu Wang

    Full Text Available Spatial heterogeneity in light supply is common in nature. Many studies have examined the effects of heterogeneous light supply on growth, morphology, physiology and biomass allocation of clonal plants, but few have tested those effects on intraspecific competition. In a greenhouse experiment, we grew one (no competition or nine ramets (with intraspecific competition of a stoloniferous clonal plant, Duchesnea indica, in three homogeneous light conditions (high, medium and low light intensity and two heterogeneous ones differing in patch size (large and small patch treatments. The total light in the two heterogeneous treatments was the same as that in the homogeneous medium light treatment. Both decreasing light intensity and intraspecific competition significantly decreased the growth (biomass, number of ramets and total stolon length of D. indica. As compared with the homogeneous medium light treatment, the large patch treatment significantly increased the growth of D. indica without intraspecific competition. However, the growth of D. indica with competition did not differ among the homogeneous medium light, the large and the small patch treatments. Consequently, light heterogeneity significantly increased intraspecific competition intensity, as measured by the decreased log response ratio. These results suggest that spatial heterogeneity in light supply can alter intraspecific interactions of clonal plants.

  2. The Near East as a cradle of biodiversity: A phylogeography of banded newts (genus Ommatotriton) reveals extensive inter- and intraspecific genetic differentiation.

    Science.gov (United States)

    van Riemsdijk, Isolde; Arntzen, Jan W; Bogaerts, Sergé; Franzen, Michael; Litvinchuk, Spartak N; Olgun, Kurtuluş; Wielstra, Ben

    2017-09-01

    The banded newt (genus Ommatotriton) is widely distributed in the Near East (Anatolia, Caucasus and the Levant) - an understudied region from the perspective of phylogeography. The genus is polytypic, but the number of species included and the phylogenetic relationships between them are not settled. We sequenced two mitochondrial and two nuclear DNA markers throughout the range of Ommatotriton. For mtDNA we constructed phylogenetic trees, estimated divergence times using fossil calibration, and investigated changes in effective population size with Bayesian skyline plots and mismatch analyses. For nuDNA we constructed phylogenetic trees and haplotype networks. Species trees were constructed for all markers and nuDNA only. Species distribution models were projected on current and Last Glacial Maximum climate layers. We confirm the presence of three Ommatotriton species: O. nesterovi, O. ophryticus and O. vittatus. These species are genetically distinct and their most recent common ancestor was dated at ∼25Ma (Oligocene). No evidence of recent gene flow between species was found. The species show deep intraspecific genetic divergence, represented by geographically structured clades, with crown nodes of species dated ∼8-13Ma (Miocene to Early Quaternary); evidence of long-term in situ evolution and survival in multiple glacial refugia. While a species tree based on nuDNA suggested a sister species relationship between O. vittatus and O. ophryticus, when mtDNA was included, phylogenetic relationships were unresolved, and we refrain from accepting a particular phylogenetic hypothesis at this stage. While species distribution models suggest reduced and fragmented ranges during the Last Glacial Maximum, we found no evidence for strong population bottlenecks. We discuss our results in the light of other phylogeographic studies from the Near East. Our study underlines the important role of the Near East in generating and sustaining biodiversity. Copyright © 2017

  3. Phylogeographical analysis reveals multiple conservation units in brook lampreys Lampetra planeri of Portuguese streams.

    Science.gov (United States)

    Pereira, A M; Robalo, J I; Freyhof, J; Maia, C; Fonseca, J P; Valente, A; Almada, V C

    2010-08-01

    The populations of brook lamprey Lampetra planeri of Portuguese Rivers were analysed phylogeographically using a fragment of 644 bp of the mitochondrial control region of 158 individuals from six populations. Samples representing L. planeri and migratory lampreys Lampetra fluviatilis of rivers draining to the North Sea and the Baltic Sea were also included to assess the relationships of Portuguese samples. The data support a clear differentiation of all the populations studied. Several populations, which are isolated among themselves and also from the migratory lampreys, proved to be entirely composed of private haplotypes, a finding that supports some time of independent evolutionary history for these populations. This, combined with the geographic confinement to small water bodies, justifies the recognition of at least four conservation units in the Portuguese rivers Sado, São Pedro, Nabão and Inha.

  4. The phylogeographic history of the new world screwworm fly, inferred by approximate bayesian computation analysis.

    Directory of Open Access Journals (Sweden)

    Pablo Fresia

    Full Text Available Insect pest phylogeography might be shaped both by biogeographic events and by human influence. Here, we conducted an approximate Bayesian computation (ABC analysis to investigate the phylogeography of the New World screwworm fly, Cochliomyia hominivorax, with the aim of understanding its population history and its order and time of divergence. Our ABC analysis supports that populations spread from North to South in the Americas, in at least two different moments. The first split occurred between the North/Central American and South American populations in the end of the Last Glacial Maximum (15,300-19,000 YBP. The second split occurred between the North and South Amazonian populations in the transition between the Pleistocene and the Holocene eras (9,100-11,000 YBP. The species also experienced population expansion. Phylogenetic analysis likewise suggests this north to south colonization and Maxent models suggest an increase in the number of suitable areas in South America from the past to present. We found that the phylogeographic patterns observed in C. hominivorax cannot be explained only by climatic oscillations and can be connected to host population histories. Interestingly we found these patterns are very coincident with general patterns of ancient human movements in the Americas, suggesting that humans might have played a crucial role in shaping the distribution and population structure of this insect pest. This work presents the first hypothesis test regarding the processes that shaped the current phylogeographic structure of C. hominivorax and represents an alternate perspective on investigating the problem of insect pests.

  5. Phylogeographical Studies of Ascaris spp. Based on Ribosomal and Mitochondrial DNA Sequences

    Science.gov (United States)

    Cavallero, Serena; Snabel, Viliam; Pacella, Francesca; Perrone, Vitantonio; D'Amelio, Stefano

    2013-01-01

    Background The taxonomic distinctiveness of Ascaris lumbricoides and A. suum, two of the world's most significant nematodes, still represents a much-debated scientific issue. Previous studies have described two different scenarios in transmission patterns, explained by two hypotheses: (1) separated host-specific transmission cycles in highly endemic regions, (2) a single pool of infection shared by humans and pigs in non-endemic regions. Recently, A. suum has been suggested as an important cause of human ascariasis in endemic areas such as China, where cross-infections and hybridization have also been reported. The main aims of the present study were to investigate the molecular epidemiology of human and pig Ascaris from non-endemic regions and, with reference to existing data, to infer the phylogenetic and phylogeographic relationships among the samples. Methodology 151 Ascaris worms from pigs and humans were characterized using PCR-RFLP on nuclear ITS rDNA. Representative geographical sub-samples were also analysed by sequencing a portion of the mitochondrial cox1 gene, to infer the extent of variability at population level. Sequence data were compared to GenBank sequences from endemic and non-endemic regions. Principal Findings No fixed differences between human and pig Ascaris were evident, with the exception of the Slovak population, which displays significant genetic differentiation. The RFLP analysis confirmed pig as a source of human infection in non-endemic regions and as a corridor for the promulgation of hybrid genotypes. Epidemiology and host-affiliation seem not to be relevant in shaping molecular variance. Phylogenetic and phylogeographical analyses described a complex scenario, involving multiple hosts, sporadic contact between forms and an ancestral taxon referable to A. suum. Conclusions/Significance These results suggest the existence of homogenizing gene flow between the two taxa, which appear to be variants of a single polytypic species. This

  6. Desert springs: deep phylogeographic structure in an ancient endemic crustacean (Phreatomerus latipes.

    Directory of Open Access Journals (Sweden)

    Michelle T Guzik

    Full Text Available Desert mound springs of the Great Artesian Basin in central Australia maintain an endemic fauna that have historically been considered ubiquitous throughout all of the springs. Recent studies, however, have shown that several endemic invertebrate species are genetically highly structured and contain previously unrecognised species, suggesting that individuals may be geographically 'stranded in desert islands'. Here we further tested the generality of this hypothesis by conducting genetic analyses of the obligate aquatic phreatoicid isopod Phreatomerus latipes. Phylogenetic and phylogeographic relationships amongst P. latipes individuals were examined using a multilocus approach comprising allozymes and mtDNA sequence data. From the Lake Eyre region in South Australia we collected data for 476 individuals from 69 springs for the mtDNA gene COI; in addition, allozyme electrophoresis was conducted on 331 individuals from 19 sites for 25 putative loci. Phylogenetic and population genetic analyses showed three major clades in both allozyme and mtDNA data, with a further nine mtDNA sub-clades, largely supported by the allozymes. Generally, each of these sub-clades was concordant with a traditional geographic grouping known as spring complexes. We observed a coalescent time between ∼2-15 million years ago for haplotypes within each of the nine mtDNA sub-clades, whilst an older total time to coalescence (>15 mya was observed for the three major clades. Overall we observed that multiple layers of phylogeographic history are exemplified by Phreatomerus, suggesting that major climate events and their impact on the landscape have shaped the observed high levels of diversity and endemism. Our results show that this genus reflects a diverse fauna that existed during the early Miocene and appears to have been regionally restricted. Subsequent aridification events have led to substantial contraction of the original habitat, possibly over repeated Pleistocene

  7. Phylogeographical studies of Ascaris spp. based on ribosomal and mitochondrial DNA sequences.

    Science.gov (United States)

    Cavallero, Serena; Snabel, Viliam; Pacella, Francesca; Perrone, Vitantonio; D'Amelio, Stefano

    2013-01-01

    The taxonomic distinctiveness of Ascaris lumbricoides and A. suum, two of the world's most significant nematodes, still represents a much-debated scientific issue. Previous studies have described two different scenarios in transmission patterns, explained by two hypotheses: (1) separated host-specific transmission cycles in highly endemic regions, (2) a single pool of infection shared by humans and pigs in non-endemic regions. Recently, A. suum has been suggested as an important cause of human ascariasis in endemic areas such as China, where cross-infections and hybridization have also been reported. The main aims of the present study were to investigate the molecular epidemiology of human and pig Ascaris from non-endemic regions and, with reference to existing data, to infer the phylogenetic and phylogeographic relationships among the samples. 151 Ascaris worms from pigs and humans were characterized using PCR-RFLP on nuclear ITS rDNA. Representative geographical sub-samples were also analysed by sequencing a portion of the mitochondrial cox1 gene, to infer the extent of variability at population level. Sequence data were compared to GenBank sequences from endemic and non-endemic regions. No fixed differences between human and pig Ascaris were evident, with the exception of the Slovak population, which displays significant genetic differentiation. The RFLP analysis confirmed pig as a source of human infection in non-endemic regions and as a corridor for the promulgation of hybrid genotypes. Epidemiology and host-affiliation seem not to be relevant in shaping molecular variance. Phylogenetic and phylogeographical analyses described a complex scenario, involving multiple hosts, sporadic contact between forms and an ancestral taxon referable to A. suum. These results suggest the existence of homogenizing gene flow between the two taxa, which appear to be variants of a single polytypic species. This conclusion has implications on the systematics, transmission and

  8. Desert Springs: Deep Phylogeographic Structure in an Ancient Endemic Crustacean (Phreatomerus latipes)

    Science.gov (United States)

    Guzik, Michelle T.; Adams, Mark A.; Murphy, Nicholas P.; Cooper, Steven J. B.; Austin, Andrew D.

    2012-01-01

    Desert mound springs of the Great Artesian Basin in central Australia maintain an endemic fauna that have historically been considered ubiquitous throughout all of the springs. Recent studies, however, have shown that several endemic invertebrate species are genetically highly structured and contain previously unrecognised species, suggesting that individuals may be geographically ‘stranded in desert islands’. Here we further tested the generality of this hypothesis by conducting genetic analyses of the obligate aquatic phreatoicid isopod Phreatomerus latipes. Phylogenetic and phylogeographic relationships amongst P. latipes individuals were examined using a multilocus approach comprising allozymes and mtDNA sequence data. From the Lake Eyre region in South Australia we collected data for 476 individuals from 69 springs for the mtDNA gene COI; in addition, allozyme electrophoresis was conducted on 331 individuals from 19 sites for 25 putative loci. Phylogenetic and population genetic analyses showed three major clades in both allozyme and mtDNA data, with a further nine mtDNA sub-clades, largely supported by the allozymes. Generally, each of these sub-clades was concordant with a traditional geographic grouping known as spring complexes. We observed a coalescent time between ∼2–15 million years ago for haplotypes within each of the nine mtDNA sub-clades, whilst an older total time to coalescence (>15 mya) was observed for the three major clades. Overall we observed that multiple layers of phylogeographic history are exemplified by Phreatomerus, suggesting that major climate events and their impact on the landscape have shaped the observed high levels of diversity and endemism. Our results show that this genus reflects a diverse fauna that existed during the early Miocene and appears to have been regionally restricted. Subsequent aridification events have led to substantial contraction of the original habitat, possibly over repeated Pleistocene ice age

  9. Population genetic structure and phylogeographical pattern of rice grasshopper, Oxya hyla intricata, across Southeast Asia.

    Science.gov (United States)

    Li, Tao; Zhang, Min; Qu, Yanhua; Ren, Zhumei; Zhang, Jianzhen; Guo, Yaping; Heong, K L; Villareal, Bong; Zhong, Yang; Ma, Enbo

    2011-04-01

    The rice grasshopper, Oxya hyla intricata, is a rice pest in Southeast Asia. In this study, population genetic diversity and structure of this Oxya species was examined using both DNA sequences and AFLP technology. The samples of 12 populations were collected from four Southeast Asian countries, among which 175 individuals were analysed using mitochondrial DNA cytochrome c oxidase subunit I (COI) sequences, and 232 individuals were examined using amplified fragment length polymorphisms (AFLP) to test whether the phylogeographical pattern and population genetics of this species are related to past geological events and/or climatic oscillations. No obvious trend of genetic diversity was found along a latitude/longitude gradient among different geographical groups. Phylogenetic analysis indicated three deep monophyletic clades that approximately correspond to three geographical regions separated by high mountains and a deep strait, and TCS analysis also revealed three disconnected networks, suggesting that spatial and temporal separations by vicariance, which were also supported by AMOVA as a source of the molecular variance presented among groups. Gene flow analysis showed that there had been frequent historical gene flow among local populations in different regions, but the networks exhibited no shared haplotype among populations. In conclusion, the past geological events and climatic fluctuations are the most important factor on the phylogeographical structure and genetic patterns of O. hyla intricata in Southeast Asia. Habitat, vegetation, and anthropogenic effect may also contribute to gene flow and introgression of this species. Moreover, temperature, abundant rainfall and a diversity of graminaceous species are beneficial for the migration of O. hyla intricata. High haplotype diversity, deep phylogenetic division, negative Fu's F (s) values and unimodal and multimodal distribution shapes all suggest a complicated demographic expansion pattern of these O. hyla

  10. Deep phylogeographical structure and parallel host range evolution in the leaf beetle Agelasa nigriceps.

    Science.gov (United States)

    Kohyama, Tetsuo I; Matsumoto, Kazuma; Katakura, Haruo

    2014-02-01

    To understand the mechanisms behind the diversification of herbivorous insects through insect-plant interactions, it is important to know how the insects change their diet breadth in response to environmental changes. In this study, we investigated the phylogeographical pattern of the leaf beetle Agelasa nigriceps to infer the evolutionary history of its host range. While this beetle commonly uses Actinidia arguta (Actinidiaceae) as a host plant, it has been recorded recently on Pterostyrax hispidus (Styracaceae), which is now increasing in abundance at some localities in Japan due to the indirect effects of high population size of a mammalian herbivore. Considerable variation among populations in the ability of Ag. nigriceps to use P. hispidus suggests that P. hispidus is a newly acquired host plant for this beetle. Phylogenetic analyses using mitochondrial DNA sequences and amplified fragment length polymorphism (AFLP) revealed a high degree of phylogeographical structure in Ag. nigriceps throughout Japan, which is consistent with the hypothesis that several glacial refugia existed in the Japanese archipelago. In contrast, no genetic structure associated with the host plants was detected. Both the mitochondrial DNA and AFLP analyses showed that populations that can use P. hispidus are polyphyletic. These results and geographical variation in host use suggest that the host range expansion to a novel host, P. hispidus, is a very recent and possibly ongoing phenomenon and has occurred independently in several regions. Our study illustrates that the host range of herbivorous insects can evolve repeatedly in response to similar environmental changes. © 2013 John Wiley & Sons Ltd.

  11. Functional genetics of intraspecific ecological interactions in Arabidopsis thaliana.

    Science.gov (United States)

    Wolf, Jason B; Mutic, Joshua J; Kover, Paula X

    2011-05-12

    Studying the genetic basis of traits involved in ecological interactions is a fundamental part of elucidating the connections between evolutionary and ecological processes. Such knowledge allows one to link genetic models of trait evolution with ecological models describing interactions within and between species. Previous work has shown that connections between genetic and ecological processes in Arabidopsis thaliana may be mediated by the fact that quantitative trait loci (QTL) with 'direct' effects on traits of individuals also have pleiotropic 'indirect' effects on traits expressed in neighbouring plants. Here, we further explore these connections by examining functional relationships between traits affected directly and indirectly by the same QTL. We develop a novel approach using structural equation models (SEMs) to determine whether observed pleiotropic effects result from traits directly affected by the QTL in focal individuals causing the changes in the neighbours' phenotypes. This hypothesis was assessed using SEMs to test whether focal plant phenotypes appear to mediate the connection between the focal plants' genotypes and the phenotypes of their neighbours, or alternatively, whether the connection between the focal plants' genotypes and the neighbours' phenotypes is mediated by unmeasured traits. We implement this analysis using a QTL of major effect that maps to the well-characterized flowering locus, FRIGIDA. The SEMs support the hypothesis that the pleiotropic indirect effects of this locus arise from size and developmental timing-related traits in focal plants affecting the expression of developmental traits in their neighbours. Our findings provide empirical insights into the genetics and nature of intraspecific ecological interactions. Our technique holds promise in directing future work into the genetic basis and functional relationship of traits mediating and responding to ecological interactions.

  12. Intraspecific functional diversity of common species enhances community stability.

    Science.gov (United States)

    Wood, Connor M; McKinney, Shawn T; Loftin, Cynthia S

    2017-03-01

    Common species are fundamental to the structure and function of their communities and may enhance community stability through intraspecific functional diversity (iFD). We measured among-habitat and within-habitat iFD (i.e., among- and within-plant community types) of two common small mammal species using stable isotopes and functional trait dendrograms, determined whether iFD was related to short-term population stability and small mammal community stability, and tested whether spatially explicit trait filters helped explain observed patterns of iFD. Southern red-backed voles ( Myodes gapperi ) had greater iFD than deer mice ( Peromyscus maniculatus ), both among habitats, and within the plant community in which they were most abundant (their "primary habitat"). Peromyscus maniculatus populations across habitats differed significantly between years and declined 78% in deciduous forests, their primary habitat, as did the overall deciduous forest small mammal community. Myodes gapperi populations were stable across habitats and within coniferous forest, their primary habitat, as was the coniferous forest small mammal community. Generalized linear models representing internal trait filters (e.g., competition), which increase within-habitat type iFD, best explained variation in M. gapperi diet, while models representing internal filters and external filters (e.g., climate), which suppress within-habitat iFD, best explained P. maniculatus diet. This supports the finding that M. gapperi had higher iFD than P. maniculatus and is consistent with the theory that internal trait filters are associated with higher iFD than external filters. Common species with high iFD can impart a stabilizing influence on their communities, information that can be important for conserving biodiversity under environmental change.

  13. Intraspecific maternal competition induces summer diapause in insect parasitoids.

    Science.gov (United States)

    Tougeron, Kévin; Hraoui, George; Le Lann, Cécile; van Baaren, Joan; Brodeur, Jacques

    2017-06-15

    , by considering intraspecific competition. © 2017 Institute of Zoology, Chinese Academy of Sciences.

  14. Intraspecific variability and systematics in South American Syrotrigoniinae (Trigoniida, Bivalvia)

    Science.gov (United States)

    Echevarría, Javier; Damborenea, Susana E.; Manceñido, Miguel O.

    2015-04-01

    The systematics of the genus Syrotrigonia is revised in the light of the intraspecific variability of a large sample of Syrotrigonia sigeli from the Valanginian from Neuquén Basin, Argentina. The genus can be recognized by the presence of concentric or subconcentric costae surrounding the umbo, later on developing an inflection and finally resulting in a set of anterior horizontal to commarginal costae and another set of posterior sub-vertical costae. The anterior part of the area bears transverse, usually anteriorly concave, costae which direct towards the umbo on the escutcheon; initially they are continuous with those on the flank, but later on they usually alternate. General shell shape, the presence of an antecarinal sulcus, the junction pattern between both sets of costae and the number of horizontal costae relative to vertical costae are variable among species, while costae width or density and the development of horizontal vs. commarginal costae may vary highly within species. The presence of commarginal rugae developed on the whole surface of the shell is interpreted as a result of environmental perturbations. A brief biogeographical interpretation of the family Buchotrigoniidae is also outlined. Syrotrigonia probably originated in North America in the Tithonian, being widespread in the Pacific coast of South America by Early Cretaceous times; at least six (probably seven) South American species could be recognized. By Aptian times the taxon reached the Tethyan realm, its last record being Aptian or Albian in age. The frequent presence of different species in marginal marine deposits suggests a euryhaline lineage adapted to salinity variations, this may also be the cause of the frequent presence of commarginal rugae. Considering the high variability displayed in the analyzed material, large samples are needed to characterize new species within the group.

  15. Intraspecific functional diversity of common species enhances community stability

    Science.gov (United States)

    Wood, Connor M.; McKinney, Shawn T.; Loftin, Cynthia S.

    2017-01-01

    Common species are fundamental to the structure and function of their communities and may enhance community stability through intraspecific functional diversity (iFD). We measured among-habitat and within-habitat iFD (i.e., among- and within-plant community types) of two common small mammal species using stable isotopes and functional trait dendrograms, determined whether iFD was related to short-term population stability and small mammal community stability, and tested whether spatially explicit trait filters helped explain observed patterns of iFD. Southern red-backed voles (Myodes gapperi) had greater iFD than deer mice (Peromyscus maniculatus), both among habitats, and within the plant community in which they were most abundant (their “primary habitat”). Peromyscus maniculatus populations across habitats differed significantly between years and declined 78% in deciduous forests, their primary habitat, as did the overall deciduous forest small mammal community. Myodes gapperi populations were stable across habitats and within coniferous forest, their primary habitat, as was the coniferous forest small mammal community. Generalized linear models representing internal trait filters (e.g., competition), which increase within-habitat type iFD, best explained variation in M. gapperidiet, while models representing internal filters and external filters (e.g., climate), which suppress within-habitat iFD, best explained P. maniculatus diet. This supports the finding that M. gapperi had higher iFD than P. maniculatus and is consistent with the theory that internal trait filters are associated with higher iFD than external filters. Common species with high iFD can impart a stabilizing influence on their communities, information that can be important for conserving biodiversity under environmental change.

  16. Revisiting Darwin's hypothesis: Does greater intraspecific variability increase species' ecological breadth?

    Science.gov (United States)

    Sides, Colby B; Enquist, Brian J; Ebersole, James J; Smith, Marielle N; Henderson, Amanda N; Sloat, Lindsey L

    2014-01-01

    Darwin first proposed that species with larger ecological breadth have greater phenotypic variation. We tested this hypothesis by comparing intraspecific variation in specific leaf area (SLA) to species' local elevational range and by assessing how external (abiotic) filters may influence observed differences in ecological breadth among species. Understanding the patterns of individual variation within and between populations will help evaluate differing hypotheses for structuring of communities and distribution of species. We selected 21 species with varying elevational ranges and compared the coefficient of variation of SLA for each species against its local elevational range. We examined the influence of external filters on local trait composition by determining if intraspecific changes in SLA with elevation have the same direction and similar rates of change as the change in community mean SLA value. In support of Darwin's hypothesis, we found a positive relationship between species' coefficient of variation for SLA with species' local elevational range. Intraspecific changes in SLA had the same sign, but generally lower magnitude than the community mean SLA. The results indicate that wide-ranging species are indeed characterized by greater intraspecific variation and that species' phenotypes shift along environmental gradients in the same direction as the community phenotypes. However, across species, the rate of intraspecific trait change, reflecting plastic and/or adaptive changes across populations, is limited and prevents species from adjusting to environmental gradients as quickly as interspecific changes resulting from community assembly.

  17. Plague in the genomic area.

    Science.gov (United States)

    Drancourt, M

    2012-03-01

    With plague being not only a subject of interest for historians, but still a disease of public health concern in several countries, mainly in Africa, there were hopes that analyses of the Yersinia pestis genomes would put an end to this deadly epidemic pathogen. Genomics revealed that Y. pestis isolates evolved from Yersinia pseudotuberculosis in Central Asia some millennia ago, after the acquisition of two Y. pestis-specific plasmids balanced genomic reduction parallel with the expansion of insertion sequences, illustrating the modern concept that, except for the acquisition of plasmid-borne toxin-encoding genes, the increased virulence of Y. pestis resulted from gene loss rather than gene acquisition. The telluric persistence of Y. pestis reminds us of this close relationship, and matters in terms of plague epidemiology. Whereas biotype Orientalis isolates spread worldwide, the Antiqua and Medievalis isolates showed more limited expansion. In addition to animal ectoparasites, human ectoparasites such as the body louse may have participated in this expansion and in devastating historical epidemics. The recent analysis of a Black Death genome indicated that it was more closely related to the Orientalis branch than to the Medievalis branch. Modern Y. pestis isolates grossly exhibit the same gene content, but still undergo micro-evolution in geographically limited areas by differing in the genome architecture, owing to inversions near insertion sequences and the stabilization of the YpfPhi prophage in Orientalis biotype isolates. Genomics have provided several new molecular tools for the genotyping and phylogeographical tracing of isolates and description of plague foci. However, genomics and post-genomics approaches have not yet provided new tools for the prevention, diagnosis and management of plague patients and the plague epidemics still raging in some sub-Saharan countries. © 2012 The Author. Clinical Microbiology and Infection © 2012 European Society of

  18. Species coexistence under resource competition with intraspecific and interspecific direct competition in a chemostat.

    Science.gov (United States)

    Saito, Yasuhisa; Miki, Takeshi

    2010-11-01

    Competition theory has developed separately for direct competition and for exploitative competition. However, the combined effects of the two types of competition on species coexistence remain unclear. To examine how intraspecific and interspecific direct competition contributes to the coexistence of species competing for a single resource, we constructed a chemostat-type resource competition model. With general functions for intraspecific and interspecific direct competition, we derived necessary and sufficient conditions (except for a critical case that rarely occurs in a biological sense) that determine the number of stably coexisting species. From these conditions, we found that the number of coexisting species is determined just by the invasibility of each species into subcommunities with a smaller number of species. In addition, using a combination of rigorous mathematical theory and a simple graphical method, we can demonstrate how the stronger intraspecific direct competition facilitates species invasion, leading to a larger number of coexisting species. Copyright 2010 Elsevier Inc. All rights reserved.

  19. Inter- and intraspecific variations of cadmium accumulation of 13 leafy vegetable species in a greenhouse experiment.

    Science.gov (United States)

    Wang, Junli; Fang, Wei; Yang, Zhongyi; Yuan, Jiangang; Zhu, Yun; Yu, Hui

    2007-10-31

    Leafy vegetables are among the crop species that are most vulnerable to heavy metal pollution. This study investigated inter- and intraspecific variations of cadmium accumulation in 13 species with a total of 39 cultivars of leafy vegetables under two levels of soil Cd stress (1.5 and 7.7 mg kg (-1)). Intraspecific variations of shoot biomass and Cd concentration of the tested leafy vegetables were significantly larger than interspecific variations under both Cd treatments and were also more significantly correlated between two Cd stress levels when grouped by cultivar than grouped by species. These results indicate that cultivar is a more reliable taxa level for screening pollutant-safe leafy vegetables than species. Any screening for pollutant hypoaccumulator species, or other similar species-based concepts, without considering intraspecific variation should be avoided.

  20. Phylodynamic and Phylogeographic Profiles of Subtype B HIV-1 Epidemics in South Spain.

    Directory of Open Access Journals (Sweden)

    Santiago Pérez-Parra

    Full Text Available Since 1982, HIV-1 epidemics have evolved to different scenarios in terms of transmission routes, subtype distribution and characteristics of transmission clusters. We investigated the evolutionary history of HIV-1 subtype B in south Spain.We studied all newly diagnosed HIV-1 subtype B patients in East Andalusia during the 2005-2012 period. For the analysis, we used the reverse transcriptase and protease sequences from baseline resistance, and the Trugene® HIV Genotyping kit (Siemens, Barcelona, Spain. Subtyping was done with REGA v3.0. The maximum likelihood trees constructed with RAxML were used to study HIV-1 clustering. Phylogeographic and phylodynamic profiles were studied by Bayesian inference methods with BEAST v1.7.5 and SPREAD v1.0.6.Of the 493 patients infected with HIV-1 subtype B, 234 grouped into 55 clusters, most of which were small (44 clusters ≤ 5 patients, 31 with 2 patients, 13 with 3. The rest (133/234 were grouped into 11 clusters with ≥ 5 patients, and most (82%, 109/133 were men who have sex with men (MSM grouped into 8 clusters. The association with clusters was more frequent in Spanish (p = 0.02 men (p< 0.001, MSM (p<0.001 younger than 35 years (p = 0.001 and with a CD4+ T-cell count above 350 cells/ul (p<0.001. We estimated the date of HIV-1 subtype B regional epidemic diversification around 1970 (95% CI: 1965-1987, with an evolutionary rate of 2.4 (95%CI: 1.7-3.1 x 10-3 substitutions/site/year. Most clusters originated in the 1990s in MSMs. We observed exponential subtype B HIV-1 growth in 1980-1990 and 2005-2008. The most significant migration routes for subtype B went from inland cities to seaside locations.We provide the first data on the phylodynamic and phylogeographic profiles of HIV-1 subtype B in south Spain. Our findings of transmission clustering among MSMs should alert healthcare managers to enhance preventive measures in this risk group in order to prevent future outbreaks.

  1. Intraspecific Trait Variation and Coordination: Root and Leaf Economics Spectra in Coffee across Environmental Gradients.

    Science.gov (United States)

    Isaac, Marney E; Martin, Adam R; de Melo Virginio Filho, Elias; Rapidel, Bruno; Roupsard, Olivier; Van den Meersche, Karel

    2017-01-01

    Hypotheses on the existence of a universal "Root Economics Spectrum" (RES) have received arguably the least attention of all trait spectra, despite the key role root trait variation plays in resource acquisition potential. There is growing interest in quantifying intraspecific trait variation (ITV) in plants, but there are few studies evaluating (i) the existence of an intraspecific RES within a plant species, or (ii) how a RES may be coordinated with other trait spectra within species, such as a leaf economics spectrum (LES). Using Coffea arabica (Rubiaceae) as a model species, we measured seven morphological and chemical traits of intact lateral roots, which were paired with information on four key LES traits. Field collections were completed across four nested levels of biological organization. The intraspecific trait coefficient of variation (cv) ranged from 25 to 87% with root diameter and specific root tip density showing the lowest and highest cv, respectively. Between 27 and 68% of root ITV was explained by site identity alone for five of the seven traits measured. A single principal component explained 56.2% of root trait covariation, with plants falling along a RES from resource acquiring to conserving traits. Multiple factor analysis revealed significant orthogonal relationships between root and leaf spectra. RES traits were strongly orthogonal with respect to LES traits, suggesting these traits vary independently from one another in response to environmental cues. This study provides among the first evidence that plants from the same species differentiate from one another along an intraspecific RES. We find that in one of the world's most widely cultivated crops, an intraspecific RES is orthogonal to an intraspecific LES, indicating that above and belowground responses of plants to managed (or natural) environmental gradients are likely to occur independently from one another.

  2. What triggers the rising of an intraspecific biodiversity hotspot? Hints from the agile frog.

    Science.gov (United States)

    Canestrelli, Daniele; Bisconti, Roberta; Sacco, Florinda; Nascetti, Giuseppe

    2014-05-23

    Hotspots of genetic diversity are regions of utmost importance for species survival and conservation, and their intimate link with the geographic location of glacial refugia has been well established. Nonetheless, the microevolutionary processes underlying the generation of hotspots in such regions have only recently become a fervent field of research. We investigated the phylogeographic and population genetic structure of the agile frog, Rana dalmatina, within its putative refugium in peninsular Italy. We found this region to harbour far more diversity, phylogeographic structure, and lineages of ancient origin than that by the rest of the species' range in Europe. This pattern appeared to be well explained by climate-driven microevolutionary processes that occurred during both glacial and interglacial epochs. Therefore, the inferred evolutionary history of R. dalmatina in Italy supports a view of glacial refugia as 'factories' rather than as repositories of genetic diversity, with significant implications for conservation strategies for hotspots.

  3. Transcriptome analysis of intraspecific competition in Arabidopsis thaliana reveals organ-specific signatures related to nutrient acquisition and general stress response pathways

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    Masclaux Frédéric G

    2012-11-01

    Full Text Available Abstract Background Plants are sessile and therefore have to perceive and adjust to changes in their environment. The presence of neighbours leads to a competitive situation where resources and space will be limited. Complex adaptive responses to such situation are poorly understood at the molecular level. Results Using microarrays, we analysed whole-genome expression changes in Arabidopsis thaliana plants subjected to intraspecific competition. The leaf and root transcriptome was strongly altered by competition. Differentially expressed genes were enriched in genes involved in nutrient deficiency (mainly N, P, K, perception of light quality, and responses to abiotic and biotic stresses. Interestingly, performance of the generalist insect Spodoptera littoralis on densely grown plants was significantly reduced, suggesting that plants under competition display enhanced resistance to herbivory. Conclusions This study provides a comprehensive list of genes whose expression is affected by intraspecific competition in Arabidopsis. The outcome is a unique response that involves genes related to light, nutrient deficiency, abiotic stress, and defence responses.

  4. Unequal contribution of native South African phylogeographic lineages to the invasion of the African clawed frog, Xenopus laevis, in Europe

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    Charlotte De Busschere

    2016-02-01

    Full Text Available Due to both deliberate and accidental introductions, invasive African Clawed Frog (Xenopus laevis populations have become established worldwide. In this study, we investigate the geographic origins of invasive X. laevis populations in France and Portugal using the phylogeographic structure of X. laevis in its native South African range. In total, 80 individuals from the whole area known to be invaded in France and Portugal were analysed for two mitochondrial and three nuclear genes, allowing a comparison with 185 specimens from the native range. Our results show that native phylogeographic lineages have contributed differently to invasive European X. laevis populations. In Portugal, genetic and historical data suggest a single colonization event involving a small number of individuals from the south-western Cape region in South Africa. In contrast, French invasive X. laevis encompass two distinct native phylogeographic lineages, i.e., one from the south-western Cape region and one from the northern regions of South Africa. The French X. laevis population is the first example of a X. laevis invasion involving multiple lineages. Moreover, the lack of population structure based on nuclear DNA suggests a potential role for admixture within the invasive French population.

  5. Inter- and intraspecific sexual discrimination in the flour beetles Tribolium castaneum and Tribolium confusum.

    Science.gov (United States)

    Serrano, J M; Castro, L; Toro, M A; López-Fanjul, C

    2000-08-01

    In Tribolium castaneum (CS) and T. confusum (CF), intra- and interspecific rates of homosexual mounting have been measured. The intraspecific results are compatible with the hypothesis of both species being sexually indiscriminate. However, the CF intraspecific rates were very high (35%-53% of mountings were homosexual), suggesting a lower sexual attractiveness, or a stronger rejection to being mounted, of CF females relative to conspecific males. CS males discriminate between species but, in interspecific contacts, preferentially mounted CF males rather than CF females. CF males do not discriminate between species, but the loss of sexual attractiveness of CF females, or their rejection to being mounted, may act as a precopulatory isolation mechanism.

  6. PHYLOGEOrec: A QGIS plugin for spatial phylogeographic reconstruction from phylogenetic tree and geographical information data

    Science.gov (United States)

    Nashrulloh, Maulana Malik; Kurniawan, Nia; Rahardi, Brian

    2017-11-01

    The increasing availability of genetic sequence data associated with explicit geographic and environment (including biotic and abiotic components) information offers new opportunities to study the processes that shape biodiversity and its patterns. Developing phylogeography reconstruction, by integrating phylogenetic and biogeographic knowledge, provides richer and deeper visualization and information on diversification events than ever before. Geographical information systems such as QGIS provide an environment for spatial modeling, analysis, and dissemination by which phylogenetic models can be explicitly linked with their associated spatial data, and subsequently, they will be integrated with other related georeferenced datasets describing the biotic and abiotic environment. We are introducing PHYLOGEOrec, a QGIS plugin for building spatial phylogeographic reconstructions constructed from phylogenetic tree and geographical information data based on QGIS2threejs. By using PHYLOGEOrec, researchers can integrate existing phylogeny and geographical information data, resulting in three-dimensional geographic visualizations of phylogenetic trees in the Keyhole Markup Language (KML) format. Such formats can be overlaid on a map using QGIS and finally, spatially viewed in QGIS by means of a QGIS2threejs engine for further analysis. KML can also be viewed in reputable geobrowsers with KML-support (i.e., Google Earth).

  7. Strong phylogeographic structure in a sedentary seabird, the Stewart Island Shag (Leucocarbo chalconotus.

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    Nicolas J Rawlence

    Full Text Available New Zealand's endemic Stewart Island Shag (Leucocarbo chalconotus comprises two regional groups (Otago and Foveaux Strait that show consistent differentiation in relative frequencies of pied versus dark-bronze morphotypes, the extent of facial carunculation, body size and breeding time. We used modern and ancient DNA (mitochondrial DNA control region one, and morphometric approaches to investigate the phylogeography and taxonomy of L. chalconotus and its closely related sister species, the endemic Chatham Island Shag (L. onslowi. Our analysis shows Leucocarbo shags in southern New Zealand comprise two well-supported clades, each containing both pied and dark-bronze morphs. However, the combined monophyly of these populations is not supported, with the L. chalconotus Otago lineage sister to L. onslowi. Morphometric analysis indicates that Leucocarbo shags from Otago are larger on average than those from Foveaux Strait. Principal co-ordinate analysis of morphometric data showed substantial morphological differentiation between the Otago and Foveaux Strait clades, and L. onslowi. The phylogeographic partitioning detected within L. chalconotus is marked, and such strong structure is rare for phalacrocoracid species. Our phylogenetic results, together with consistent differences in relative proportions of plumage morphs and facial carunculation, and concordant differentiation in body size and breeding time, suggest several alternative evolutionary hypotheses that require further investigation to determine the level of taxonomic distinctiveness that best represents the L. chalconotus Otago and Foveaux Strait clades.

  8. First DNA sequences from Asian cave bear fossils reveal deep divergences and complex phylogeographic patterns.

    Science.gov (United States)

    Knapp, Michael; Rohland, Nadin; Weinstock, Jacobo; Baryshnikov, Gennady; Sher, Andrei; Nagel, Doris; Rabeder, Gernot; Pinhasi, Ron; Schmidt, Heiko A; Hofreiter, Michael

    2009-03-01

    Until recently, cave bears were believed to have only inhabited Europe. However, recent morphological evidence suggests that cave bears' geographic range extended as far east as Transbaikalia, Eastern Siberia. These Asian cave bears were morphologically distinct from European cave bears. However, how they related to European lineages remains unclear, stressing the need to assess the phylogenetic and phylogeographic relationship between Asian cave bears and their European relatives. In this work, we address this issue using a 227 base-pair fragment of the mitochondrial control region obtained from nine fossil bone samples from eight sites from the Urals, Caucasus, Altai Mountains, Ukraine and Yana River region in Eastern Siberia. Results of the phylogenetic analyses indicate that (i) the cave bear from the Yana River is most closely related to cave bears from the Caucasus region; (ii) the Caucasus/Yana group of bears is genetically very distinct from both European cave bears and brown bears, suggesting that these bears could represent an independent species; and (iii) the Western European cave bear lineage reached at least temporarily to the Altai Mountains, 7000 km east of their known centre of distribution. These results suggest that the diversity of cave bears was greater than previously believed, and that they could survive in a much wider range of ecological conditions than previously assumed. They also agree with recent studies on other extinct and extant species, such as wolves, hyenas and steppe bison, which have also revealed higher genetic and ecological diversity in Pleistocene populations than previously known.

  9. A Phylogeographic Assessment of the Malagasy Giant Chameleons (Furcifer verrucosus and Furcifer oustaleti.

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    Antonia M Florio

    Full Text Available The Malagasy giant chameleons (Furcifer oustaleti and Furcifer verrucosus are sister species that are both broadly distributed in Madagascar, and also endemic to the island. These species are also morphologically similar and, because of this, have been frequently misidentified in the field. Previous studies have suggested that cryptic species are nested within this chameleon group, and two subspecies have been described in F. verrucosus. In this study, we utilized a phylogeographic approach to assess genetic diversification within these chameleons. This was accomplished by (1 identifying clades within each species supported by both mitochondrial and nuclear DNA, (2 assessing divergence times between clades, and (3 testing for niche divergence or conservatism. We found that both F. oustaleti and F. verrucosus could be readily identified based on genetic data, and within each species, there are two well-supported clades. However, divergence times are not contemporary and spatial patterns are not congruent. Diversification within F. verrucosus occurred during the Plio-Pleistocene, and there is evidence for niche divergence between a southwestern and southeastern clade, in a region of Madagascar that shows no obvious landscape barriers to dispersal. Diversification in F. oustaleti occurred earlier in the Pliocene or Miocene, and niche conservatism is supported with two genetically distinct clades separated at the Sofia River in northwestern Madagascar. Divergence within F. verrucosus is most consistent with patterns expected from ecologically mediated speciation, whereas divergence in F. oustaleti most strongly matches the patterns expected from the riverine barrier hypothesis.

  10. A Phylogeographic Assessment of the Malagasy Giant Chameleons (Furcifer verrucosus and Furcifer oustaleti)

    Science.gov (United States)

    Raxworthy, Christopher J.

    2016-01-01

    The Malagasy giant chameleons (Furcifer oustaleti and Furcifer verrucosus) are sister species that are both broadly distributed in Madagascar, and also endemic to the island. These species are also morphologically similar and, because of this, have been frequently misidentified in the field. Previous studies have suggested that cryptic species are nested within this chameleon group, and two subspecies have been described in F. verrucosus. In this study, we utilized a phylogeographic approach to assess genetic diversification within these chameleons. This was accomplished by (1) identifying clades within each species supported by both mitochondrial and nuclear DNA, (2) assessing divergence times between clades, and (3) testing for niche divergence or conservatism. We found that both F. oustaleti and F. verrucosus could be readily identified based on genetic data, and within each species, there are two well-supported clades. However, divergence times are not contemporary and spatial patterns are not congruent. Diversification within F. verrucosus occurred during the Plio-Pleistocene, and there is evidence for niche divergence between a southwestern and southeastern clade, in a region of Madagascar that shows no obvious landscape barriers to dispersal. Diversification in F. oustaleti occurred earlier in the Pliocene or Miocene, and niche conservatism is supported with two genetically distinct clades separated at the Sofia River in northwestern Madagascar. Divergence within F. verrucosus is most consistent with patterns expected from ecologically mediated speciation, whereas divergence in F. oustaleti most strongly matches the patterns expected from the riverine barrier hypothesis. PMID:27257819

  11. Intraspecific trait variation and the leaf economics spectrum across resource gradients and levels of organization.

    Science.gov (United States)

    Fajardo, Alex; Siefert, Andrew

    2018-03-30

    Understanding patterns of functional trait variation across environmental gradients offers an opportunity to increase inference in the mechanistic causes of plant community assembly. The leaf economics spectrum (LES) predicts global tradeoffs in leaf traits and trait-environment relationships, but few studies have examined whether these predictions hold across different levels of organization, particularly within species. Here, we asked (1) whether the main assumptions of the LES (expected trait relationships and shifts in trait values across resource gradients) hold at the intraspecific level, and (2) how within-species trait correlations scale up to interspecific or among-community levels. We worked with leaf traits of saplings of woody species growing across light and soil N and P availability gradients in temperate rainforests of southern Chile. We found that ITV accounted for a large proportion of community-level variation in leaf traits (e.g., LMA and leaf P) and played an important role in driving community-level shifts in leaf traits across environmental gradients. Additionally, intraspecific leaf trait relationships were generally consistent with interspecific and community-level trait relationships and with LES predictions-e.g., a strong negative intraspecific LMA-leaf N correlation-although, most trait relationships varied significantly among species, suggesting idiosyncrasies in the LES at the intraspecific level. © 2018 by the Ecological Society of America.

  12. Isolation and identification of 4-a-rhamnosyloxy benzyl glucosinolate in Noccaea caerulescens showing intraspecific variation

    NARCIS (Netherlands)

    Graaf, de R.M.; Krosse, S.; Swolfs, A.E.M.; Brinke, te E.; Prill, N.; Leimu, R.; Galen, van P.M.; Wang, Y.; Aarts, M.G.M.; Dam, van N.M.

    2015-01-01

    Glucosinolates are secondary plant compounds typically found in members of the Brassicaceae and a few other plant families. Usually each plant species contains a specific subset of the ~130 different glucosinolates identified to date. However, intraspecific variation in glucosinolate profiles is

  13. Field manipulations of resources mediate the transition from intraspecific competition to facilitation.

    Science.gov (United States)

    Svanfeldt, Karin; Monro, Keyne; Marshall, Dustin J

    2017-05-01

    Population density affects individual performance, though its effects are often mixed. For sessile species, increases in population density typically reduce performance. Still, cases of positive density-dependence do occur in sessile systems and demand explanation. The stress gradient hypothesis (SGH) predicts that under stressful conditions, positive effects of facilitation may outweigh the negative effects of competition. While some elements of the SGH are well studied, its potential to explain intraspecific facilitation has received little attention. Further, there have been questions regarding whether the SGH holds if the stressor is a resource. Most studies of interactions between the environment and intraspecific facilitation have relied on natural environmental gradients; manipulative studies are much rarer. To test the effects of intraspecific density and resources, we manipulated resource availability over natural population densities for the marine bryozoan Watersipora subtorquata. We found negative effects of density on colony performance in low resource environments, but mainly positive density-dependence in high resource environments. By adding resources, competition effects were reduced and the positive effects of facilitation were revealed. Our results suggest that resource availability mediates the relative strength of competition and facilitation in our system. We also suggest that intraspecific facilitation is more common than may be appreciated and that environmental variation may mediate the balance between negative and positive density-dependence. © 2017 The Authors. Journal of Animal Ecology © 2017 British Ecological Society.

  14. Growth and intraspecific competitive abilities of the dioecious Lindera melissifolia (Lauraceae) in varied flooding regimes

    Science.gov (United States)

    Tracy S. Hawkins; Nathan M. Schiff; Theodor D. Leininger; Emile S Gardiner; Margaret S. Devall; Paul B. Hamel; A. Dan Wilson; Kristina F. Connor

    2009-01-01

    Forest Service, Southern Research Station, Stoneville, MS 38776). Growth and intraspecific competitive abilities of the dioecious Lindera melissifolia (Lauraceae) in varied flooding regimes. J. Torrey Bot. Soc. 136: 91–101. 2009.—The contribution of sexual dimorphism to malebiased colony ratios observed in field populations of the federally...

  15. Dynamical role of the degree of intraspecific cooperation: A simple model for prebiotic replicators and ecosystems

    Science.gov (United States)

    Fontich, Ernest; Sardanyés, Josep

    2009-05-01

    We present a simple mean field model to analyze the dynamics of competition between two populations of replicators in terms of the degree of intraspecific cooperation (i.e., autocatalysis) in one of these populations. The first population can only replicate with Malthusian kinetics while the second one can reproduce with Malthusian or autocatalytic replication or with a combination of both reproducing strategies. The model consists of two coupled, nonlinear, autonomous ordinary differential equations. We investigate analytically and numerically the phase plane dynamics and the bifurcation scenarios of this ecologically coupled system, focusing on the outcome of competition for several degrees of intraspecific cooperation, σ, in the second population of replicators. We demonstrate that the dynamics of both populations can not be governed by a limit cycle, and also that once cooperation is considered, the topology of phase space does not allow for coexistence. Even for low values of the degree of intraspecific cooperation, for large enough autocatalytic replication rates, the second population of replicators is able to outcompete the first one, having a wide basin of attraction in state space. We characterize the same power law dependence between the outcompetition extinction times, τ, and the degree of intraspecific cooperation for both populations, given by τ˜ciσ-1. Our results suggest that, under some kinetic conditions, the appearance of autocatalysis might be favorable in a population of replicators growing with Malthusian kinetics competing with another population also reproducing exponentially.

  16. Hierarchical analysis of taxonomic variation in intraspecific competition across fish species.

    Science.gov (United States)

    Foss-Grant, Andrew P; Zipkin, Elise F; Thorson, James T; Jensen, Olaf P; Fagan, William F

    2016-07-01

    The nature and intensity of intraspecific competition can vary greatly among taxa, yet similarities in these interactions can lead to similar population dynamics among related organisms. Variation along the spectrum of intraspecific competition, with contest and scramble competition as endpoints, leads to vastly different responses to population density. Here we investigated the diversity of intraspecific competition among fish species, predicting that functional forms of density-dependent reproduction would be conserved in related taxa. Using a hierarchical model that links stock-recruitment parameters among populations, species, and orders, we found that the strength of overcompensation, and therefore the type of intraspecific competition, is tightly clustered within taxonomic groupings, as species within an order share similar degrees of compensation. Specifically, species within the orders Salmoniformes and Pleuronectiformes exhibited density dependence indicative of scramble competition (overcompensation) while the orders Clupeiformes, Gadiformes, Perciformes, and Scorpaeniformes exhibited dynamics consistent with contest competition (compensation). Maximum potential recruitment also varied among orders, but with less clustering across species. We also tested whether stock-recruitment parameters correlated with maximum body length among species, but found no strong relationship. Our results suggest that much of the variation in the form of density-dependent reproduction among fish species may be predicted taxonomically due to evolved life history traits and reproductive behaviors. © 2016 by the Ecological Society of America.

  17. Consequences of intraspecific seed-size variation in Sparganium emersum for dispersal by fish

    NARCIS (Netherlands)

    Pollux, B.J.A.; Ouborg, J.; Van Groenendael, J.M.; Klaassen, M.R.J.

    2007-01-01

    The potential for seed dispersal by fish (ichthyochory) is likely to vary within aquatic plant species, depending on intraspecific variation in phenotypic seed traits. 2. We studied the effect of seed size variation within the unbranched burreed (Sparganium emersum) on the potential for internal

  18. Can we predict diatoms herbicide sensitivities with phylogeny? Influence of intraspecific and interspecific variability.

    Science.gov (United States)

    Esteves, Sara M; Keck, François; Almeida, Salomé F P; Figueira, Etelvina; Bouchez, Agnès; Rimet, Frédéric

    2017-10-01

    Diatoms are used as indicators of freshwater ecosystems integrity. Developing diatom-based tools to assess impact of herbicide pollution is expected by water managers. But, defining sensitivities of all species to multiple herbicides would be unattainable. The existence of a phylogenetic signal of herbicide sensitivity was shown among diatoms and should enable prediction of new species sensitivity. However, diatoms present a cryptic diversity that may lead to variation in their sensitivity to herbicides that would need to be taken into account. Using bioassays, the sensitivity to four herbicides (Atrazine, Terbutryn, Diuron, Isoproturon) was evaluated for 11 freshwater diatom taxa and intraspecific variability was assessed for two of them (Nitzschia palea and Achnanthidium spp.). Intraspecific variability of herbicide sensitivity was always smaller than interspecific variability, but intraspecific variability was more important in N. palea than in Achnanthidium spp. Indeed, one species showed no intraspecific phylogenetic signal (N. palea) whereas the other did (Achnanthidium spp.). On one hand, species boundaries are not set properly for Achnanthidium spp. which encompass several taxa. On the other hand, there is a higher phenotypic plasticity for N. palea. Finally, a phylogenetic signal of herbicide sensitivity was measured at the interspecific level, opening up prospects for setting up reliable biomonitoring tools based on sensitivity prediction, insofar as species boundaries are correctly defined.

  19. Sizing ocean giants: patterns of intraspecific size variation in marine megafauna.

    Science.gov (United States)

    McClain, Craig R; Balk, Meghan A; Benfield, Mark C; Branch, Trevor A; Chen, Catherine; Cosgrove, James; Dove, Alistair D M; Gaskins, Lindsay C; Helm, Rebecca R; Hochberg, Frederick G; Lee, Frank B; Marshall, Andrea; McMurray, Steven E; Schanche, Caroline; Stone, Shane N; Thaler, Andrew D

    2015-01-01

    What are the greatest sizes that the largest marine megafauna obtain? This is a simple question with a difficult and complex answer. Many of the largest-sized species occur in the world's oceans. For many of these, rarity, remoteness, and quite simply the logistics of measuring these giants has made obtaining accurate size measurements difficult. Inaccurate reports of maximum sizes run rampant through the scientific literature and popular media. Moreover, how intraspecific variation in the body sizes of these animals relates to sex, population structure, the environment, and interactions with humans remains underappreciated. Here, we review and analyze body size for 25 ocean giants ranging across the animal kingdom. For each taxon we document body size for the largest known marine species of several clades. We also analyze intraspecific variation and identify the largest known individuals for each species. Where data allows, we analyze spatial and temporal intraspecific size variation. We also provide allometric scaling equations between different size measurements as resources to other researchers. In some cases, the lack of data prevents us from fully examining these topics and instead we specifically highlight these deficiencies and the barriers that exist for data collection. Overall, we found considerable variability in intraspecific size distributions from strongly left- to strongly right-skewed. We provide several allometric equations that allow for estimation of total lengths and weights from more easily obtained measurements. In several cases, we also quantify considerable geographic variation and decreases in size likely attributed to humans.

  20. Intraspecific variation of seed floating ability in Sparganium emersum suggests a bimodal dispersal strategy

    NARCIS (Netherlands)

    Pollux, B.J.A.; Verbruggen, E.; Van Groenendael, J.M.; Ouborg, N.J.

    2009-01-01

    Water-mediated spread of seeds (hydrochory) plays an important role in the dispersal of aquatic plants. In this study we investigate intraspecific variation in floating ability and germination capacity of Sparganium emersum seeds in relation to seed mass, within three natural populations along the

  1. Utilizing intraspecific variation in phenotypic plasticity to bolster agricultural and forest productivity under climate change.

    Science.gov (United States)

    Aspinwall, Michael J; Loik, Michael E; Resco de Dios, Victor; Tjoelker, Mark G; Payton, Paxton R; Tissue, David T

    2015-09-01

    Climate change threatens the ability of agriculture and forestry to meet growing global demands for food, fibre and wood products. Information gathered from genotype-by-environment interactions (G × E), which demonstrate intraspecific variation in phenotypic plasticity (the ability of a genotype to alter its phenotype in response to environmental change), may prove important for bolstering agricultural and forest productivity under climate change. Nonetheless, very few studies have explicitly quantified genotype plasticity-productivity relationships in agriculture or forestry. Here, we conceptualize the importance of intraspecific variation in agricultural and forest species plasticity, and discuss the physiological and genetic factors contributing to intraspecific variation in phenotypic plasticity. Our discussion highlights the need for an integrated understanding of the mechanisms of G × E, more extensive assessments of genotypic responses to climate change under field conditions, and explicit testing of genotype plasticity-productivity relationships. Ultimately, further investigation of intraspecific variation in phenotypic plasticity in agriculture and forestry may prove important for identifying genotypes capable of increasing or sustaining productivity under more extreme climatic conditions. © 2014 John Wiley & Sons Ltd.

  2. Inter- and intraspecific variation in leaf economic traits in wheat and maize.

    Science.gov (United States)

    Martin, Adam R; Hale, Christine E; Cerabolini, Bruno E L; Cornelissen, Johannes H C; Craine, Joseph; Gough, William A; Kattge, Jens; Tirona, Cairan K F

    2018-02-01

    Leaf Economics Spectrum (LES) trait variation underpins multiple agroecological processes and many prominent crop yield models. While there are numerous independent studies assessing trait variation in crops, to date there have been no comprehensive assessments of intraspecific trait variation (ITV) in LES traits for wheat and maize: the world's most widespread crops. Using trait databases and peer-reviewed literature, we compiled over 700 records of specific leaf area (SLA), maximum photosynthetic rates ( A max ) and leaf nitrogen (N) concentrations, for wheat and maize. We evaluated intraspecific LES trait variation, and intraspecific trait-environment relationships. While wheat and maize occupy the upper 90th percentile of LES trait values observed across a global species pool, ITV ranged widely across the LES in wheat and maize. Fertilization treatments had strong impacts on leaf N, while plant developmental stage (here standardized as the number of days since planting) had strong impacts on A max ; days since planting, N fertilization and irrigation all influenced SLA. When controlling for these factors, intraspecific responses to temperature and precipitation explained 39.4 and 43.7 % of the variation in A max and SLA, respectively, but only 5.4 % of the variation in leaf N. Despite a long history of domestication in these species, ITV in wheat and maize among and within cultivars remains large. Intraspecific trait variation is a critical consideration to refine regional to global models of agroecosystem structure, function and food security. Considerable opportunities and benefits exist for consolidating a crop trait database for a wider range of domesticated plant species.

  3. Time-lagged intraspecific competition in temporally separated cohorts of a generalist insect.

    Science.gov (United States)

    Barnes, Elizabeth E; Murphy, Shannon M

    2018-03-01

    Competition can have far-reaching consequences for insect fitness and dispersion. Time-lagged interspecific competition is known to negatively affect fitness, yet time-lagged intraspecific competition is rarely studied outside of outbreak conditions. We tested the impact of competition between larval cohorts of the western tent caterpillar (Malacosoma californicum) feeding on chokecherry (Prunus virginiana). We reared larvae on host plants that either had or did not have feeding damage from tent caterpillars the previous season to test the bottom-up fitness effects of intraspecific competition. We measured host-plant quality to test potential mechanisms for bottom-up effects and conducted field oviposition surveys to determine if female adult tent caterpillars avoided host plants with evidence of prior tent caterpillar presence. We found that time-lagged intraspecific competition impacted tent caterpillar fitness by reducing female pupal mass, which is a predictor of lifetime fitness. We found that plants that had been fed upon by tent caterpillars the previous season had leaves that were significantly tougher than plants that had not been fed upon by tent caterpillars, which may explain why female tent caterpillars suffered reduced fitness on these plants. Finally, we found that there were fewer tent caterpillar egg masses on plants that had tent caterpillars earlier in the season than plants without tent caterpillars, which suggests that adult females avoid these plants for oviposition. Our results confirm that intraspecific competition occurs among tent caterpillars and suggests that time-lagged intraspecific competition has been overlooked as an important component of insect fitness.

  4. Length polymorphism scanning is an efficient approach for revealing chloroplast DNA variation.

    Science.gov (United States)

    Matthew E. Horning; Richard C. Cronn

    2006-01-01

    Phylogeographic and population genetic screens of chloroplast DNA (cpDNA) provide insights into seedbased gene flow in angiosperms, yet studies are frequently hampered by the low mutation rate of this genome. Detection methods for intraspecific variation can be either direct (DNA sequencing) or indirect (PCR-RFLP), although no single method incorporates the best...

  5. Phylogeographic surveys and apomictic genetic connectivity in the North Atlantic red seaweed Mastocarpus stellatus.

    Science.gov (United States)

    Li, Jing-Jing; Hu, Zi-Min; Liu, Ruo-Yu; Zhang, Jie; Liu, Shao-Lun; Duan, De-Lin

    2016-01-01

    The North Atlantic red alga Mastocarpus stellatus is characterized by two life histories (sexual-type and direct-type), which correspond to two geographically isolated breeding groups. These features enable M. stellatus to be an interesting model to investigate how environmental shift and apomictic propagation have influenced its population genetic structure, historical demography and distribution dynamic. To test these ideas, we obtained 456 specimens from 15 locations on both sides of the North Atlantic and sequenced portion of the nuclear internal transcribed spacer (ITS), mitochondrial cox2-3 region (COX) and plastid RuBisCo spacer (RLS). Median-joining networks and ML trees inferred from COX and RLS consistently revealed two gene lineages (mtDNA: CN, CS; cpDNA: RN, RS). The concatenated COX and RLS markers yielded three cytotypes: a northern CN-RN, a southern CS-RS and a mixed cytotype CS-RN, which enabled us to roughly separate samples into D (direct-type life-cycle) and S (sexual-type life-cycle) groups (northern CN-RN and mixed cytotype CS-RN=D; southern CS-RS=S). Pairwise FST analysis of the D group revealed a high level of genetic differentiation both along European coasts and across the Atlantic basin. Bayesian skyline plots (BSPs) and IMa analyses indicated that M. stellatus underwent slight demographic expansion at the late-Pleistocene, with the beginning of divergence between lineages dating to c. 0.189Ma (95%HPD: 0.083-0.385Ma). IMa analyses also revealed asymmetric genetic exchange among European populations and a predominant postglacial trans-Atlantic migration from Norway and Galway Bay to North America. Our study highlights the importance of phylogeographic approaches to discover the imprints of climate change, life histories and gene flow in driving population genetic connectivity and biogeographic distribution of intertidal seaweeds in the North Atlantic. Copyright © 2015 Elsevier Inc. All rights reserved.

  6. Microsatellite marker analysis reveals the complex phylogeographic history of Rhododendron ferrugineum (Ericaceae in the Pyrenees.

    Directory of Open Access Journals (Sweden)

    Olivia Charrier

    Full Text Available Genetic variation within plant species is determined by a number of factors such as reproductive mode, breeding system, life history traits and climatic events. In alpine regions, plants experience heterogenic abiotic conditions that influence the population's genetic structure. The aim of this study was to investigate the genetic structure and phylogeographic history of the subalpine shrub Rhododendron ferrugineum across the Pyrenees and the links between the populations in the Pyrenees, the Alps and Jura Mountains. We used 27 microsatellite markers to genotype 645 samples from 29 Pyrenean populations, three from the Alps and one from the Jura Mountains. These data were used to estimate population genetics statistics such as allelic richness, observed heterozygosity, expected heterozygosity, fixation index, inbreeding coefficient and number of migrants. Genetic diversity was found to be higher in the Alps than in the Pyrenees suggesting colonization waves from the Alps to the Pyrenees. Two separate genetic lineages were found in both the Alps and Pyrenees, with a substructure of five genetic clusters in the Pyrenees where a loss of genetic diversity was noted. The strong differentiation among clusters is maintained by low gene flow across populations. Moreover, some populations showed higher genetic diversity than others and presented rare alleles that may indicate the presence of alpine refugia. Two lineages of R. ferrugineum have colonized the Pyrenees from the Alps. Then, during glaciation events R. ferrugineum survived in the Pyrenees in different refugia such as lowland refugia at the eastern part of the chain and nunataks at high elevations leading to a clustered genetic pattern.

  7. Effects of Pleistocene climatic fluctuations on the phylogeographic and demographic histories of Pacific herring (Clupea pallasii).

    Science.gov (United States)

    Liu, Jin-Xian; Tatarenkov, Andrey; Beacham, Terry D; Gorbachev, Victor; Wildes, Sharon; Avise, John C

    2011-09-01

    We gathered mitochondrial DNA sequences (557 bp from the control region in 935 specimens and 668 bp of the cytochrome b gene in 139 specimens) of Pacific herring collected from 20 nearshore localities spanning the species' extensive range along the North Pacific coastlines of Asia and North America. Haplotype diversity and nucleotide diversity were high, and three major phylogeographic lineages (sequence divergences ca. 1.5%) were detected. Using a variety of phylogenetic methods, coalescent reasoning, and molecular dating interpreted in conjunction with paleoclimatic and physiographic evidence, we infer that the genetic make-up of extant populations of C. pallasii was shaped by Pleistocene environmental impacts on the historical demography of this species. A deep genealogical split that cleanly distinguishes populations in the western vs. eastern North Pacific probably originated as a vicariant separation associated with a glacial cycle that drove the species southward and isolated two ancestral populations in Asia and North America. Another deep genealogical split may have involved either a vicariant isolation of a third herring lineage (perhaps originally in the Gulf of California) or it may have resulted simply from the long coalescent times that are possible in large populations. Coalescent analyses showed that all the three evolutionary lineages of C. pallasii experienced major expansions in their most recent histories after having remained more stable in the preceding periods. Independent of the molecular calibration chosen, populations of C. pallasii appear to have remained stable or grown throughout the periods that covered at least two major glaciations, and probably more. © 2011 Blackwell Publishing Ltd.

  8. Phylogeographic structure in the bogus yucca moth Prodoxus quinquepunctellus (Prodoxidae): comparisons with coexisting pollinator yucca moths.

    Science.gov (United States)

    Althoff, D M; Groman, J D; Segraves, K A; Pellmyr, O

    2001-10-01

    The pollination mutualism between yucca moths and yuccas highlights the potential importance of host plant specificity in insect diversification. Historically, one pollinator moth species, Tegeticula yuccasella, was believed to pollinate most yuccas. Recent phylogenetic studies have revealed that it is a complex of at least 13 distinct species, eight of which are specific to one yucca species. Moths in the closely related genus Prodoxus also specialize on yuccas, but they do not pollinate and their larvae feed on different plant parts. Previous research demonstrated that the geographically widespread Prodoxus quinquepunctellus can rapidly specialize to its host plants and may harbor hidden species diversity. We examined the phylogeographic structure of P. quinquepunctellus across its range to compare patterns of diversification with six coexisting pollinator yucca moth species. Morphometric and mtDNA cytochrome oxidase I sequence data indicated that P. quinquepunctellus as currently described contains two species. There was a deep division between moth populations in the eastern and the western United States, with limited sympatry in central Texas; these clades are considered separate species and are redescribed as P. decipiens and P. quinquepunctellus (sensu stricto), respectively. Sequence data also showed a lesser division within P. quinquepunctellus s.s. between the western populations on the Colorado Plateau and those elsewhere. The divergence among the three emerging lineages corresponded with major biogeographic provinces, whereas AMOVA indicated that host plant specialization has been relatively unimportant in diversification. In comparison, the six pollinator species comprise three lineages, one eastern and two western. A pollinator species endemic to the Colorado Plateau has evolved in both of the western lineages. The east-west division and the separate evolution of two Colorado Plateau pollinator species suggest that similar biogeographic factors have

  9. A comparative phylogeographic study reveals discordant evolutionary histories of alpine ground beetles (Coleoptera, Carabidae).

    Science.gov (United States)

    Weng, Yi-Ming; Yang, Man-Miao; Yeh, Wen-Bin

    2016-04-01

    Taiwan, an island with three major mountain ranges, provides an ideal topography to study mountain-island effect on organisms that would be diversified in the isolation areas. Glaciations, however, might drive these organisms to lower elevations, causing gene flow among previously isolated populations. Two hypotheses have been proposed to depict the possible refugia for alpine organisms during glaciations. Nunatak hypothesis suggests that alpine species might have stayed in situ in high mountain areas during glaciations. Massif de refuge, on the other hand, proposes that alpine species might have migrated to lower ice-free areas. By sampling five sympatric carabid species of Nebria and Leistus, and using two mitochondrial genes and two nuclear genes, we evaluated the mountain-island effect on alpine carabids and tested the two proposed hypotheses with comparative phylogeographic method. Results from the phylogenetic relationships, network analysis, lineage calibration, and genetic structure indicate that the deep divergence among populations in all L. smetanai, N. formosana, and N. niitakana was subjected to long-term isolation, a phenomenon in agreement with the nunatak hypothesis. However, genetic admixture among populations of N. uenoiana and some populations of L. nokoensis complex suggests that gene flow occurred during glaciations, as a massif de refuge depicts. The speciation event in N. niitakana is estimated to have occurred before 1.89 million years ago (Mya), while differentiation among isolated populations in N. niitakana, N. formosana, L. smetanai, and L. nokoensis complex might have taken place during 0.65-1.65 Mya. While each of the alpine carabids arriving in Taiwan during different glaciation events acquired its evolutionary history, all of them had confronted the existing mountain ranges.

  10. Molecular surveillance of HIV-1 in Madrid, Spain: a phylogeographic analysis.

    Science.gov (United States)

    González-Alba, José M; Holguín, Africa; Garcia, Rosa; García-Bujalance, Silvia; Alonso, Roberto; Suárez, Avelina; Delgado, Rafael; Cardeñoso, Laura; González, Rosa; García-Bermejo, Isabel; Portero, Francisca; de Mendoza, Carmen; González-Candelas, Fernando; Galán, Juan-Carlos

    2011-10-01

    The molecular epidemiology of HIV-1 is constantly changing, mainly as a result of human migratory flows and the high adaptive ability of the virus. In recent years, Spain has become one of Europe's main destinations for immigrants and one of the western European countries with the highest rates of HIV-positive patients. Using a phylogeographic approach, we have analyzed the relationship between HIV-1 variants detected in immigrant and native populations of the urban area of Madrid. Our project was based on two coincidental facts. First, resistance tests were extended to naïve and newly diagnosed patients, and second, the Spanish government legislated the provision of legal status to many immigrants. This allowed us to obtain a large data set (n = 2,792) from 11 Madrid hospitals of viral pol sequences from the two populations, and with this unique material, we explored the impact of immigration in the epidemiological trends of HIV-1 variants circulating in the largest Spanish city. The prevalence of infections by non-B HIV-1 variants in the studied cohort was 9%, rising to 25% among native Spanish patients. Multiple transmission events involving different lineages and subsubtypes were observed in all the subtypes and recombinant forms studied. Our results also revealed strong social clustering among the most recent immigrant groups, such as Russians and Romanians, but not in those groups who have lived in Madrid for many years. Additionally, we document for the first time the presence of CRF47_BF and CRF38_BF in Europe, and a new BG recombinant form found in Spaniards and Africans is tentatively proposed. These results suggest that the HIV-1 epidemic will evolve toward a more complex epidemiological landscape.

  11. Phylogeographic and Feeding Ecological Effects on the Mustelid Faunal Assemblages in Japan

    Directory of Open Access Journals (Sweden)

    Jun J. Sato

    2013-04-01

    Full Text Available Phylogeographic and feeding ecological studies of seven terrestrial mustelid species (Carnivora, Mustelidae, the Japanese marten Martes melampus, the sable Martes zibellina, the Japanese badger Meles anakuma, the ermine or the stoat Mustela erminea, the Japanese weasel Mustela itatsi, the least weasel Mustela nivalis, and the Siberian weasel Mustela sibirica, representing four biogeographic patterns in the Japanese archipelagos (Hokkaido, Honshu-Shikoku-Kyushu, Tsushima, and Hokkaido-Honshu, were reviewed in order to clarify causes for the faunal assemblage processes of those mustelid species in Japan. Here, three main constraints were extracted as important factors on the mustelid assemblage. First, fundamental evolutionary differences maintained by niche conservatism in each ecologically diversified lineage (“evolutionary constraint” would enable the species to co-occur without any major problem (coexistence among Martes, Meles, and Mustela species. Second, “ecological constraints” would force two closely related species to be allopatric by competitive exclusion (Mu. itatsi and Mu. sibirica or to be sympatric by resource partitions (Mu. erminea and Mu. nivalis. Third and most importantly, “geological constraints” would allow specific species to be embraced by a particular geographic region, primarily deciding which species co-occurs. The allopatric distribution of two Martes species in Japan would have been established by the strong effect of the geological separation in Tsugaru Strait. Elucidating both phylogeny and ecology of co-existing species in a community assemblage is important to know which species possess distinct lineage and which ecological traits are adapted to local environments, fulfilling the requirement of the field of conservation biology that endemism and adaptation should both be considered. The Japanese archipelagos would, therefore, provide valuable insight into the conservation for small carnivoran species.

  12. Intraspecific niche models for ponderosa pine (Pinus ponderosa) suggest potential variability in population-level response to climate change

    Science.gov (United States)

    Maguire, Kaitlin C.; Shinneman, Douglas; Potter, Kevin M.; Hipkins, Valerie D.

    2018-01-01

    Unique responses to climate change can occur across intraspecific levels, resulting in individualistic adaptation or movement patterns among populations within a given species. Thus, the need to model potential responses among genetically distinct populations within a species is increasingly recognized. However, predictive models of future distributions are regularly fit at the species level, often because intraspecific variation is unknown or is identified only within limited sample locations. In this study, we considered the role of intraspecific variation to shape the geographic distribution of ponderosa pine (Pinus ponderosa), an ecologically and economically important tree species in North America. Morphological and genetic variation across the distribution of ponderosa pine suggest the need to model intraspecific populations: the two varieties (var. ponderosa and var. scopulorum) and several haplotype groups within each variety have been shown to occupy unique climatic niches, suggesting populations have distinct evolutionary lineages adapted to different environmental conditions. We utilized a recently-available, geographically-widespread dataset of intraspecific variation (haplotypes) for ponderosa pine and a recently-devised lineage distance modeling approach to derive additional, likely intraspecific occurrence locations. We confirmed the relative uniqueness of each haplotype-climate relationship using a niche-overlap analysis, and developed ecological niche models (ENMs) to project the distribution for two varieties and eight haplotypes under future climate forecasts. Future projections of haplotype niche distributions generally revealed greater potential range loss than predicted for the varieties. This difference may reflect intraspecific responses of distinct evolutionary lineages. However, directional trends are generally consistent across intraspecific levels, and include a loss of distributional area and an upward shift in elevation. Our results

  13. Manipulating duckweed through genome duplication.

    Science.gov (United States)

    Vunsh, R; Heinig, U; Malitsky, S; Aharoni, A; Avidov, A; Lerner, A; Edelman, M

    2015-01-01

    Significant inter- and intraspecific genetic variation exists in duckweed, thus the potential for genome plasticity and manipulation is high. Polyploidy is recognised as a major mechanism of adaptation and speciation in plants. We produced several genome-duplicated lines of Landoltia punctata (Spirodela oligorrhiza) from both whole plants and regenerating explants using a colchicine-based cocktail. These lines stably maintained an enlarged frond and root morphology. DNA ploidy levels determined by florescence-activated cell sorting indicated genome duplication. Line A4 was analysed after 75 biomass doublings. Frond area, fresh and dry weights, rhizoid number and length were significantly increased versus wild type, while the growth rate was unchanged. This resulted in accumulation of biomass 17-20% faster in the A4 plants. We sought to determine if specific differences in gene products are found in the genome duplicated lines. Non-targeted ultra performance LC-quadrupole time of flight mass spectrometry was employed to compare some of the lines and the wild type to seek identification of up-regulated metabolites. We putatively identified differential metabolites in Line A65 as caffeoyl hexoses. The combination of directed genome duplication and metabolic profiling might offer a path for producing stable gene expression, leading to altered production of secondary metabolites. © 2014 German Botanical Society and The Royal Botanical Society of the Netherlands.

  14. Shallow phylogeographic structure in the declining Mexican Lance-headed Rattlesnake, Crotalus polystictus (Serpentes: Viperidae

    Directory of Open Access Journals (Sweden)

    Jesse M. Meik

    2012-06-01

    Full Text Available We investigated matrilineal relationships among populations of the Mexican lance-headed rattlesnake (Crotalus polystictus, a pitviper inhabiting high-elevation valleys of the densely populated southernMexican Plateau. A fragment of the mitochondrial ATPase 8 and 6 genes (589 base pairs revealed comparatively low levels of genetic diversity, with few nucleotide polymorphisms across the portion of the geographic distribution sampled. The shallow intraspecificsequence divergence (1.0% in C. polystictus ATPase 8 and 6 genes contrasts with deep divergences (~1.0–14.1% observed within other montane rattlesnake lineages from the Mexican highlands, and is more typical of intraspecific variation observed in lowland rattlesnake species with similar distributional extents (e.g., C. tigris. We posit that the low genetic diversity in C. polystictus relative to that of other highland rattlesnakes may reflect ecological differences resulting in a different evolutionary response to Pleistocene climatic events. Our finding of apparently low genetic diversity in C. polystictus highlights the importance of conservation initiatives to protect high elevation grasslands in central Mexico.

  15. Molecular analysis of phylogeographic subspecies in three Ponto-Caspian sturgeon species

    Directory of Open Access Journals (Sweden)

    Andreea Dudu

    2014-09-01

    Full Text Available Sturgeons (Order Acipenseriformes represent an extremely valuable natural resource that is now facing depletion. In the current study we evaluate if the traditional classification in subspecies of Acipenser gueldenstaedtii, Acipenser stellatus and Huso huso, endemic to Ponto-Caspian region is sustained by molecular analysis and if these represent Evolutionary Significant Units (ESUs that should be managed separately in conservation programs. To examine the classification of taxonomic entities we sequenced a fragment of the mitochondrial control region in case of three sturgeon species that inhabit the North-western of Black Sea and migrate for reproduction in the Lower Danube. Beside these sequences, we used previously published sequences from sturgeon individuals sampled in the Black Sea, Azov Sea and Caspian Sea. We determined the genetic diversity and genetic differentiation, conducted a Population Aggregation Analysis (PAA and inferred an intraspecific molecular phylogeny and haplotype network. The results indicated a low level of genetic differentiation between the geographically designated subspecies and did not support a significant divergence or reciprocal monophyly between them. Our results confirm previous genetic studies with smaller samples sizes, but additional analyses including nuclear markers should be conducted for proper recommendations aiming at the development of conservation programs.

  16. Phylogeographic divergence in the widespread delicate skink (Lampropholis delicata) corresponds to dry habitat barriers in eastern Australia.

    Science.gov (United States)

    Chapple, David G; Hoskin, Conrad J; Chapple, Stephanie N J; Thompson, Michael B

    2011-07-04

    The mesic habitats of eastern Australia harbour a highly diverse fauna. We examined the impact of climatic oscillations and recognised biogeographic barriers on the evolutionary history of the delicate skink (Lampropholis delicata), a species that occurs in moist habitats throughout eastern Australia. The delicate skink is a common and widespread species whose distribution spans 26° of latitude and nine major biogeographic barriers in eastern Australia. Sequence data were obtained from four mitochondrial genes (ND2, ND4, 12SrRNA, 16SrRNA) for 238 individuals from 120 populations across the entire native distribution of the species. The evolutionary history and diversification of the delicate skink was investigated using a range of phylogenetic (Maximum Likelihood, Bayesian) and phylogeographic analyses (genetic diversity, ΦST, AMOVA, Tajima's D, Fu's F statistic). Nine geographically structured, genetically divergent clades were identified within the delicate skink. The main clades diverged during the late Miocene-Pliocene, coinciding with the decline and fragmentation of rainforest and other wet forest habitats in eastern Australia. Most of the phylogeographic breaks within the delicate skink were concordant with dry habitat or high elevation barriers, including several recognised biogeographic barriers in eastern Australia (Burdekin Gap, St Lawrence Gap, McPherson Range, Hunter Valley, southern New South Wales). Genetically divergent populations were also located in high elevation topographic isolates inland from the main range of L. delicata (Kroombit Tops, Blackdown Tablelands, Coolah Tops). The species colonised South Australia from southern New South Wales via an inland route, possibly along the Murray River system. There is evidence for recent expansion of the species range across eastern Victoria and into Tasmania, via the Bassian Isthmus, during the late Pleistocene. The delicate skink is a single widespread, but genetically variable, species. This study

  17. Genetic and Metabolic Intraspecific Biodiversity of Ganoderma lucidum

    Science.gov (United States)

    Pawlik, Anna; Janusz, Grzegorz; Dębska, Iwona; Siwulski, Marek; Frąc, Magdalena; Rogalski, Jerzy

    2015-01-01

    Fourteen Ganoderma lucidum strains from different geographic regions were identified using ITS region sequencing. Based on the sequences obtained, the genomic relationship between the analyzed strains was determined. All G. lucidum strains were also genetically characterized using the AFLP technique. G. lucidum strains included in the analysis displayed an AFLP profile similarity level in the range from 9.6 to 33.9%. Biolog FF MicroPlates were applied to obtain data on utilization of 95 carbon sources and mitochondrial activity. The analysis allowed comparison of functional diversity of the fungal strains. The substrate utilization profiles for the isolates tested revealed a broad variability within the analyzed G. lucidum species and proved to be a good profiling technology for studying the diversity in fungi. Significant differences have been demonstrated in substrate richness values. Interestingly, the analysis of growth and biomass production also differentiated the strains based on the growth rate on the agar and sawdust substrate. In general, the mycelial growth on the sawdust substrate was more balanced and the fastest fungal growth was observed for GRE3 and FCL192. PMID:25815332

  18. Genetic and Metabolic Intraspecific Biodiversity of Ganoderma lucidum

    Directory of Open Access Journals (Sweden)

    Anna Pawlik

    2015-01-01

    Full Text Available Fourteen Ganoderma lucidum strains from different geographic regions were identified using ITS region sequencing. Based on the sequences obtained, the genomic relationship between the analyzed strains was determined. All G. lucidum strains were also genetically characterized using the AFLP technique. G. lucidum strains included in the analysis displayed an AFLP profile similarity level in the range from 9.6 to 33.9%. Biolog FF MicroPlates were applied to obtain data on utilization of 95 carbon sources and mitochondrial activity. The analysis allowed comparison of functional diversity of the fungal strains. The substrate utilization profiles for the isolates tested revealed a broad variability within the analyzed G. lucidum species and proved to be a good profiling technology for studying the diversity in fungi. Significant differences have been demonstrated in substrate richness values. Interestingly, the analysis of growth and biomass production also differentiated the strains based on the growth rate on the agar and sawdust substrate. In general, the mycelial growth on the sawdust substrate was more balanced and the fastest fungal growth was observed for GRE3 and FCL192.

  19. Genomic Testing

    Science.gov (United States)

    ... Events and Multimedia Implementation Genetics 101 Family Health History Genomics and Diseases Genetic Counseling Genomic Testing Epidemiology Pathogen Genomics Resources Genomic Testing Recommend on Facebook Tweet Share Compartir Fact Sheet: Identifying Opportunities to ...

  20. Processes Underlying Rabies Virus Incursions across US-Canada Border as Revealed by Whole-Genome Phylogeography.

    Science.gov (United States)

    Trewby, Hannah; Nadin-Davis, Susan A; Real, Leslie A; Biek, Roman

    2017-09-01

    Disease control programs aim to constrain and reduce the spread of infection. Human disease interventions such as wildlife vaccination play a major role in determining the limits of a pathogen's spatial distribution. Over the past few decades, a raccoon-specific variant of rabies virus (RRV) has invaded large areas of eastern North America. Although expansion into Canada has been largely prevented through vaccination along the US border, several outbreaks have occurred in Canada. Applying phylogeographic approaches to 289 RRV whole-genome sequences derived from isolates collected in Canada and adjacent US states, we examined the processes underlying these outbreaks. RRV incursions were attributable predominantly to systematic virus leakage of local strains across areas along the border where vaccination has been conducted but also to single stochastic events such as long-distance translocations. These results demonstrate the utility of phylogeographic analysis of pathogen genomes for understanding transboundary outbreaks.

  1. Intra-specific Differences in Root and Shoot Glucosinolate Profiles among White Cabbage (Brassica oleracea var capitata)

    NARCIS (Netherlands)

    Kabouw, P.; Biere, A.; Putten, van der W.H.; Dam, van N.M.

    2010-01-01

    Shoot glucosinolate profiles of Brassicaceae are known to vary within species, across environmental conditions, and between developmental stages. Here we study whether root profiles follow the intra-specific, environmental, and developmental variation observed for aerial parts in white cabbage

  2. Species interactions and chemical stress combined effects of intraspecific and interspecific interactions and pyrene n Daphnia magna populations dynamics

    NARCIS (Netherlands)

    Viaene, K.P.J.; Laender, de F.; Rico, A.; Brink, van den P.J.; Guardo, Di A.; Morselli, M.; Janssen, C.R.

    2015-01-01

    Species interactions are often suggested as an important factor when assessing the effects of chemicals on higher levels of biological organization. Nevertheless, the contribution of intraspecific and interspecific interactions to chemical effects on populations is often overlooked. In the present

  3. The diverse effects of intraspecific competition on the selective advantage to resistance: A model and its predictions

    NARCIS (Netherlands)

    Weis, A.E.; Hochberg, M.E.

    2000-01-01

    We constructed a model to investigate conditions under which intraspecific competition amplifies or diminishes the selective advantage to resistance. The growth trajectories of competing individual plants were depicted by logistic difference equations that incorporated basic costs (lowered growth

  4. Intraspecific Variation in Maximum Ingested Food Size and Body Mass in Varecia rubra and Propithecus coquereli.

    Science.gov (United States)

    Hartstone-Rose, Adam; Perry, Jonathan M G

    2011-01-01

    In a recent study, we quantified the scaling of ingested food size (V(b))-the maximum size at which an animal consistently ingests food whole-and found that V(b) scaled isometrically between species of captive strepsirrhines. The current study examines the relationship between V(b) and body size within species with a focus on the frugivorous Varecia rubra and the folivorous Propithecus coquereli. We found no overlap in V(b) between the species (all V. rubra ingested larger pieces of food relative to those eaten by P. coquereli), and least-squares regression of V(b) and three different measures of body mass showed no scaling relationship within each species. We believe that this lack of relationship results from the relatively narrow intraspecific body size variation and seemingly patternless individual variation in V(b) within species and take this study as further evidence that general scaling questions are best examined interspecifically rather than intraspecifically.

  5. Intraspecific variation of body size in a gamasid mite Laelaps clethrionomydis: environment, geography and host dependence.

    Science.gov (United States)

    Korallo-Vinarskaya, Natalia P; Vinarski, Maxim V; Khokhlova, Irina S; Shenbrot, Georgy I; Krasnov, Boris R

    2015-10-01

    We investigated intraspecific variation in body size of an ectoparasitic gamasid mite, Laelaps clethrionomydis, across 12 localities in the Palearctic. We asked whether mites collected from the same host species in different localities or from different host species in the same locality vary in body size. Within host species, mites collected in different localities differed significantly in body size, tending to be larger in northern than in southern localities. In addition, mite body size correlated negatively with mean annual temperature in a locality. Mites collected from different hosts in the same locality differed significantly in body size when hosts belonged to different genera but did not differ when collected from congeneric hosts. We conclude that intraspecific variation in mite body size is caused by interplay of environmental and host-related factors.

  6. Intraspecific competition and high food availability are associated with insular gigantism in a lizard

    Science.gov (United States)

    Pafilis, Panayiotis; Meiri, Shai; Foufopoulos, Johannes; Valakos, Efstratios

    2009-09-01

    Resource availability, competition, and predation commonly drive body size evolution. We assess the impact of high food availability and the consequent increased intraspecific competition, as expressed by tail injuries and cannibalism, on body size in Skyros wall lizards ( Podarcis gaigeae). Lizard populations on islets surrounding Skyros (Aegean Sea) all have fewer predators and competitors than on Skyros but differ in the numbers of nesting seabirds. We predicted the following: (1) the presence of breeding seabirds (providing nutrients) will increase lizard population densities; (2) dense lizard populations will experience stronger intraspecific competition; and (3) such aggression, will be associated with larger average body size. We found a positive correlation between seabird and lizard densities. Cannibalism and tail injuries were considerably higher in dense populations. Increases in cannibalism and tail loss were associated with large body sizes. Adult cannibalism on juveniles may select for rapid growth, fuelled by high food abundance, setting thus the stage for the evolution of gigantism.

  7. Intraspecific Variation in Maximum Ingested Food Size and Body Mass in Varecia rubra and Propithecus coquereli

    Directory of Open Access Journals (Sweden)

    Adam Hartstone-Rose

    2011-01-01

    Full Text Available In a recent study, we quantified the scaling of ingested food size (Vb—the maximum size at which an animal consistently ingests food whole—and found that Vb scaled isometrically between species of captive strepsirrhines. The current study examines the relationship between Vb and body size within species with a focus on the frugivorous Varecia rubra and the folivorous Propithecus coquereli. We found no overlap in Vb between the species (all V. rubra ingested larger pieces of food relative to those eaten by P. coquereli, and least-squares regression of Vb and three different measures of body mass showed no scaling relationship within each species. We believe that this lack of relationship results from the relatively narrow intraspecific body size variation and seemingly patternless individual variation in Vb within species and take this study as further evidence that general scaling questions are best examined interspecifically rather than intraspecifically.

  8. Rare insights into intraspecific brood parasitism and apparent quasi–parasitism in black–capped chickadees

    OpenAIRE

    Otter, K. A.; Murray, B. W.; Holschuh, C. I.; Fort, K. T.

    2011-01-01

    Genetic analysis of passerine birds often finds evidence of extra–pair copulations within species, but genetic evidence of intraspecific brood parasitism (IBP) and quasi–parasitism (Q–P) are relatively rare. Further, it is even rarer for genetic patterns that might indicate quasi–parasitism (resident male sires offspring through extra–pair copulations, and allows the female to lay these within the male’s nest) to be coupled with observational evidence of this behavior. In this paper, we repor...

  9. Repeated intraspecific divergence in life span and aging of African annual fishes along an aridity gradient

    Czech Academy of Sciences Publication Activity Database

    Blažek, Radim; Polačik, Matej; Kačer, P.; Cellerino, A.; Řežucha, Radomil; Methling, Caroline; Tomášek, Oldřich; Syslová, K.; Terzibasi Tozzini, E.; Albrecht, Tomáš; Vrtílek, Milan; Reichard, Martin

    2017-01-01

    Roč. 71, č. 2 (2017), s. 386-402 ISSN 0014-3820 R&D Projects: GA ČR GA13-05872S; GA ČR(CZ) GA16-00291S Institutional support: RVO:68081766 Keywords : Intraspecific variation * life span * neoplasia * pace-of-life syndrome * parallel evolution * reproductive senescence Subject RIV: EG - Zoology OBOR OECD: Ecology Impact factor: 4.201, year: 2016

  10. Behavioral signature of intraspecific competition and density dependence in colony-breeding marine predators.

    Science.gov (United States)

    Breed, Greg A; Don Bowen, W; Leonard, Marty L

    2013-10-01

    In populations of colony-breeding marine animals, foraging around colonies can lead to intraspecific competition. This competition affects individual foraging behavior and can cause density-dependent population growth. Where behavioral data are available, it may be possible to infer the mechanism of intraspecific competition. If these mechanics are understood, they can be used to predict the population-level functional response resulting from the competition. Using satellite relocation and dive data, we studied the use of space and foraging behavior of juvenile and adult gray seals (Halichoerus grypus) from a large (over 200,000) and growing population breeding at Sable Island, Nova Scotia (44.0 (o)N 60.0 (o)W). These data were first analyzed using a behaviorally switching state-space model to infer foraging areas followed by randomization analysis of foraging region overlap of competing age classes. Patterns of habitat use and behavioral time budgets indicate that young-of-year juveniles (YOY) were likely displaced from foraging areas near (intraspecific competition between adults and juveniles, resulting in the currently observed decelerating logistic population growth. Competition theory predicts that intraspecific competition resulting in a clear losing competitor should cause compensatory population regulation. This functional response produces a smooth logistic growth curve as carrying capacity is approached, and is consistent with census data collected from this population over the past 50 years. The competitive mechanism causing compensatory regulation likely stems from the capital-breeding life-history strategy employed by gray seals. This strategy decouples reproductive success from resources available around breeding colonies and prevents females from competing with each other while young are dependent.

  11. Intraspecific variation in fruit-frugivore interactions: effects of fruiting neighborhood and consequences for seed dispersal.

    Science.gov (United States)

    Guerra, Tadeu J; Dayrell, Roberta L C; Arruda, André J; Dáttilo, Wesley; Teixido, Alberto L; Messeder, João V S; Silveira, Fernando A O

    2017-10-01

    The extent of specialization/generalization continuum in fruit-frugivore interactions at the individual level remains poorly explored. Here, we investigated the interactions between the Neotropical treelet Miconia irwinii (Melastomataceae) and its avian seed dispersers in Brazilian campo rupestre. We built an individual-based network to derive plant degree of interaction specialization regarding disperser species. Then, we explored how intraspecific variation in interaction niche breadth relates to fruit availability on individual plants in varying densities of fruiting conspecific neighbors, and how these factors affect the quantity of viable seeds dispersed. We predicted broader interaction niche breadths for individuals with larger fruit crops in denser fruiting neighborhoods. The downscaled network included nine bird species and 15 plants, which varied nearly five-fold in their degree of interaction specialization. We found positive effects of crop size on visitation and fruit removal rates, but not on degree of interaction specialization. Conversely, we found that an increase in the density of conspecific fruiting neighbors both increased visitation rate and reduced plant degree of interaction specialization. We suggest that tracking fruit-rich patches by avian frugivore species is the main driver of density-dependent intraspecific variation in plants' interaction niche breadth. Our study shed some light on the overlooked fitness consequences of intraspecific variation in interaction niches by showing that individuals along the specialization/generalization continuum may have their seed dispersed with similar effectiveness. Our study exemplifies how individual-based networks linking plants to frugivore species that differ in their seed dispersal effectiveness can advance our understanding of intraspecific variation in the outcomes of fruit-frugivore interactions.

  12. Effects of Intraspecific Competition and Host-Parasitoid Developmental Timing on Foraging Behaviour of a Parasitoid Wasp

    OpenAIRE

    Couchoux, Christelle; van Nouhuys, Saskya

    2014-01-01

    In a context where hosts are distributed in patches and susceptible to parasitism for a limited time, female parasitoids foraging for hosts might experience intraspecific competition. We investigated the effects of host and parasitoid developmental stage and intraspecific competition among foraging females on host-searching behaviour in the parasitoid wasp Hyposoter horticola. We found that H. horticola females have a pre-reproductive adult stage during which their eggs are not mature yet and...

  13. Genetic dissection of maize phenology using an intraspecific introgression library

    Directory of Open Access Journals (Sweden)

    Sanguineti Maria C

    2011-01-01

    Full Text Available Abstract Background Collections of nearly isogenic lines where each line carries a delimited portion of a donor source genome into a common recipient genetic background are known as introgression libraries and have already shown to be instrumental for the dissection of quantitative traits. By means of marker-assisted backcrossing, we have produced an introgression library using the extremely early-flowering maize (Zea mays L. variety Gaspé Flint and the elite line B73 as donor and recipient genotypes, respectively, and utilized this collection to investigate the genetic basis of flowering time and related traits of adaptive and agronomic importance in maize. Results The collection includes 75 lines with an average Gaspé Flint introgression length of 43.1 cM. The collection was evaluated for flowering time, internode length, number of ears, number of nodes (phytomeres, number of nodes above the ear, number and proportion of nodes below the ear and plant height. Five QTLs for flowering time were mapped, all corresponding to major QTLs for number of nodes. Three additional QTLs for number of nodes were mapped. Besides flowering time, the QTLs for number of nodes drove phenotypic variation for plant height and number of nodes below and above the top ear, but not for internode length. A number of apparently Mendelian-inherited phenotypes were also observed. Conclusions While the inheritance of flowering time was dominated by the well-known QTL Vgt1, a number of other important flowering time QTLs were identified and, thanks to the type of plant material here utilized, immediately isogenized and made available for fine mapping. At each flowering time QTL, early flowering correlated with fewer vegetative phytomeres, indicating the latter as a key developmental strategy to adapt the maize crop from the original tropical environment to the northern border of the temperate zone (southern Canada, where Gaspé Flint was originally cultivated. Because of

  14. Intraspecific differentiation of Colletotrichum gloeosporioides sensu lato based on in silico multilocus PCR-RFLP fingerprinting.

    Science.gov (United States)

    Ramdeen, Stephen; Rampersad, Sephra N

    2013-02-01

    Colletotrichum gloeosporioides sensu lato is one of the most common and widely distributed plant pathogens in the world. Understanding fungal biodiversity is hinged on accurate identification and delimitation at the inter- and intraspecific levels. Sequences of the ITS1-5.8S-ITS2 region (ITS), β-tubulin (TUB), actin (ACT), and glyceraldehyde-3-phosphate dehydrogenase (GPDH) genes of 30 C. gloeosporioides sensu lato isolates, collected from anthracnose infected papaya fruits grown in the main production areas in Trinidad, were analyzed by in silico PCR-RFLP analysis with the aim of identifying which gene region(s) had the highest level of intraspecific polymorphism. Restriction site polymorphisms generated from 13 restriction enzymes enabled the identification of specific enzymes that were successful at intraspecific discrimination of the C. gloeosporioides isolates. Genetic distance values were reflective of the level of polymorphisms obtained for the four different gene regions. In both cases (calculated genetic distance and percentage of polymorphic loci from RFLP profiles), ACT and ITS gene regions had the highest level of restriction site polymorphisms and genetic diversity, GPDH and TUB had the lowest. Cluster analysis based on PCR-RFLP genetic distance data revealed sub-specific placement of the isolates which appeared to be gene-dependent. The implications of these findings are discussed relative to biodiversity monitoring and the need for multilocus, polyphasic investigations which must take into account the possibility of exaggerated estimates of genetic diversity.

  15. Intraspecific Variation in Armillaria Species from Shrubs and Trees in Northwestern Spain

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    O. Aguín

    2004-08-01

    Full Text Available Until recently, the identification of Armillaria species relied upon morphological characteristics and mating tests, but now molecular techniques based on polymorphisms in the IGS region of the fungal rDNA are more commonly used, since these are more rapid and reliable. Differences found in RFLP patterns identifying Armillaria species have suggested the existence of intraspecific variation. In this work, 185 Armillaria isolates from different plant species (including fruit trees, broadleaf and coniferous trees, ornamental shrubs, kiwifruit and grapevine affected by white root rot were analyzed by RFLP-PCR, in order to study intraspecific variation in Armillaria and the relationship with the plant host. Armillaria mellea was found in the majority of samples (71%, and was the most frequent Armillaria species in symptomatic ornamental shrubs, kiwifruit, grapevine, fruit trees and broadleaf trees. In conifers however white root rot was generally caused by Armillaria ostoyae. Armillaria gallica was identified, although with low incidence, in ornamental, coniferous, broadleaf and fruit hosts. Intraspecies variation was recorded only in A. mellea, for which RFLP patterns mel 1 and mel 2 were found. Most plants infected with A. mellea showed the mel 2 pattern. Further research is needed to study whether Armillaria RFLP patterns are specific to certain plant hosts, and whether intraspecific variation is related to differences in pathogenicity.

  16. Experimental test of intraspecific competition mechanisms among tadpoles of Leptodactylus ocellatus (Anura: Leptodactylidae).

    Science.gov (United States)

    Laufer, Gabriel; Maneyro, Raúl

    2008-03-01

    Intraspecific competition is predicted to strongly influence species abundance and dynamics through two main mechanisms: consumption and interference of resources. Tadpoles were used in experiments in which we tried to elucidate the relative importance of each mechanism. Our goal was to apply this experimental procedure to Leptodactylus ocellatus, a common South American anuran, a species whose larvae exhibit aggregative behavior and receive parental care. Previous work suggests that tadpole schools should present lower levels of intraspecific competition. Tadpoles from a single nest were reared in the laboratory in three densities (1, 2, and 4 individuals/container) and three food levels (1, 2, and 4 ration multiples) in a randomized three-block design for a factorial analysis of variance, up to day eight. Contrary to previous work with other species, our results show both the absence of interference competition effects, and that larval growth depends only on per capita food availability. The differences between species in intraspecific competition mechanisms are probably related to strong differences in ecology and life history. Leptodactylus ocellatus tadpoles could be directing interference competition away from their kin, reducing schooling costs. Further studies (including kinship as a factor) would give more information about these larvae, allowing a better understanding of the evolutionary and ecological mechanisms behind the biological patterns observed in Leptodactylus species.

  17. Effects of intraspecific competition on the life cycle of the stonefly, Nemurella pictetii (Plecoptera: Nemouridae).

    Science.gov (United States)

    Lieske, Reimo; Zwick, Peter

    2008-04-16

    Considerable variation of life cycle duration in given insect species has been frequently recorded. Splitting of populations into cohorts with different life cycle lengths may occur, sometimes even between siblings from the same batch. Larval populations of the stonefly Nemurella pictetii in central Europe regularly split into a very fast developing and a normal univoltine cohort, leading to partial multivoltinism. The causes for such variation remain unknown but presumably act on the larval stage in which most of the life cycle is spent. We therefore studied possible effects of intraspecific competition on growth and development of larvae in the laboratory. Intraspecific competition had important influence on growth and development of the larvae. High larval densities led to reduced growth and retarded development through interference, not through exploitative competition. All specimens were negatively affected by frequent encounters and the resulting disturbance. There were no dominant individuals able to grow and develop faster than the rest, at the expense of the others. Differences in life cycle length of Nemurella pictetii may result from different larval densities in different microhabitats and resultant different degrees of interference competition. Although competition alone probably does not cause splitting of populations into cohorts with different life cycle duration differences in size and development caused by other factors are certainly enhanced by intraspecific competition.

  18. Intraspecific Competition and Inbreeding Depression: Increased Competitive Effort by Inbred Males Is Costly to Outbred Opponents.

    Science.gov (United States)

    Richardson, Jon; Smiseth, Per T

    2017-05-01

    A recent theoretical model suggests that intraspecific competition is an important determinant of the severity of inbreeding depression. The reason for this is that intraspecific competition is density dependent, leading to a stronger negative effect on inbred individuals if they are weaker competitors than outbred ones. In support of this prediction, previous empirical work shows that inbred individuals are weaker competitors than outbred ones and that intraspecific competition often exacerbates inbreeding depression. Here, we report an experiment on the burying beetle Nicrophorus vespilloides, in which we recorded the outcome of competition over a small vertebrate carcass between an inbred or outbred male resident caring for a brood and a size-matched inbred or outbred male intruder. We found that inbred males were more successful as intruders in taking over a carcass from a male resident and were injured more frequently as either residents or intruders. Furthermore, inbred males gained less mass during the breeding attempt and had a shorter adult life span than outbred males. Finally, successful resident males reared a substantially smaller brood comprised of lighter larvae when the intruder was inbred than when it was outbred. Our results shows that inbred males increased their competitive effort, thus contradicting previous work suggesting that inbred males are weaker competitors. Furthermore, our results shows that inbred intruders impose a greater cost to resident males, suggesting that outbred individuals can suffer fitness costs as a result of competition with inbred ones.

  19. Intraspecific variation in sperm length is negatively related to sperm competition in passerine birds.

    Science.gov (United States)

    Kleven, Oddmund; Laskemoen, Terje; Fossøy, Frode; Robertson, Raleigh J; Lifjeld, Jan T

    2008-02-01

    Spermatozoa are among the most diversified cells in the animal kingdom, but the underlying evolutionary forces affecting intraspecific variation in sperm morphology are poorly understood. It has been hypothesized that sperm competition is a potent selection pressure on sperm variation within species. Here, we examine intraspecific variation in total sperm length of 22 wild passerine bird species (21 genera, 11 families) in relation to the risk of sperm competition, as expressed by the frequency of extrapair paternity and relative testis size. We demonstrate, by using phylogenetic comparative methods, that between-male variation in sperm length within species is closely and negatively linked to the risk of sperm competition. This relationship was even stronger when only considering species in which data on sperm length and extrapair paternity originated from the same populations. Intramale variation in sperm length within species was also negatively, although nonsignificantly, related to sperm competition risk. Our findings suggest that postcopulatory sexual selection is a powerful evolutionary force reducing the intraspecific phenotypic variation in sperm-size traits, potentially driving the diversification of sperm morphology across populations and species.

  20. Effects of clonal fragmentation on intraspecific competition of a stoloniferous floating plant.

    Science.gov (United States)

    Wang, P; Xu, Y-S; Dong, B-C; Xue, W; Yu, F-H

    2014-11-01

    Disturbance is common and can fragment clones of plants. Clonal fragmentation may affect the density and growth of ramets so that it could alter intraspecific competition. To test this hypothesis, we grew one (low density), five (medium density) or nine (high density) parent ramets of the floating invasive plant Pistia stratiotes in buckets, and newly produced offspring ramets were either severed (with fragmentation) or remained connected to parent ramets (no fragmentation). Increasing density reduced biomass of the whole clone (i.e. parent ramet plus its offspring ramets), showing intense intraspecific competition. Fragmentation decreased biomass of offspring ramets, but increased biomass of parent ramets and the whole clone, suggesting significant resource translocation from parent to offspring ramets when clones were not fragmented. There was no interaction effect of density x fragmentation on biomass of the whole clone, and fragmentation did not affect competition intensity index. We conclude that clonal fragmentation does not alter intraspecific competition between clones of P. stratiotes, but increases biomass production of the whole clone. Thus, fragmentation may contribute to its interspecific competitive ability and invasiveness, and intentional fragmentation should not be recommended as a measure to stop the rapid growth of this invasive species. © 2014 German Botanical Society and The Royal Botanical Society of the Netherlands.

  1. The role of intraspecific variation in the ecological and evolutionary success of diatoms in changing environments.

    Science.gov (United States)

    Godhe, Anna; Rynearson, Tatiana

    2017-09-05

    Intraspecific variation in diatoms has been shown to play a key role in species' responses to several important environmental factors such as light, salinity, temperature and nutrients. Furthermore, modelling efforts indicate that this variation within species extends bloom periods, and likely provides sufficient variability in competitive interactions between species under hydrographically variable conditions. The intraspecific variation most likely corresponds to optimal fitness in temporary microhabitats and may help to explain the paradox of the plankton. Here, we examine the implications of intraspecific variation for the ecology and success of diatoms in general and emphasize the potential implications for our understanding of carbon metabolism in these important organisms. Additionally, data from palaeoecological studies have the potential for evaluating genetic variation through past climate changes, going thousands of years back in time. We suggest pathways for future research including the adoption of multiple strains of individual species into studies of diatom carbon metabolism, to refine our understanding of the variation within and between species, and the inclusion of experimental evolution as a tool for understanding potential evolutionary responses of diatom carbon metabolism to climate change.This article is part of the themed issue 'The peculiar carbon metabolism in diatoms'. © 2017 The Author(s).

  2. Intraspecific competition between co-infecting parasite strains enhances host survival in African trypanosomes.

    Science.gov (United States)

    Balmer, Oliver; Stearns, Stephen Curtis; Schötzau, Andreas; Brun, Reto

    2009-12-01

    It is becoming increasingly clear that under natural conditions parasitic infections commonly consist of co-infections with multiple conspecific strains. Multiple-strain infections lead to intraspecific interactions and may have important ecological and evolutionary effects on both hosts and parasites. However, experimental evidence on intraspecific competition or facilitation in infections has been scarce because of the technical challenges of distinguishing and tracking individual co-infecting strains. To overcome this limitation, we engineered transgenic strains of the protozoan parasite Trypanosoma brucei, the causal agent of human African sleeping sickness. Different strains were transfected with fluorescence genes of different colors to make them visually distinguishable in order to investigate the effects of multiple-strain infections on parasite population dynamics and host fitness. We infected mice either with each strain alone or with mixes of two strains. Our results show a strong mutual competitive suppression of co-infecting T. brucei strains very early in infection. This mutual suppression changes within-host parasite dynamics and alleviates the effects of infection on the host. The strength of suppression depends on the density of the co-infecting strain, and differences in life-history traits between the strains determine the consequences of strain-strain competition for the host. Unexpectedly, co-infection with a less virulent strain significantly enhances host survival (+15%). Analysis of the strain dynamics reveals that this is due to the suppression of the density of the more virulent strain (-33%), whose degree of impact ultimately determines the physical condition of the host. The competitive suppression is likely caused by allelopathic interference or by apparent competition mediated by strain-specific immune responses. These findings highlight the importance of intraspecific variation for parasite-parasite and parasite-host interactions. To

  3. Genomic resources for multiple species in the Drosophila ananassae species group.

    Science.gov (United States)

    Signor, Sarah; Seher, Thaddeus; Kopp, Artyom

    2013-01-01

    The development of genomic resources in non-model taxa is essential for understanding the genetic basis of biological diversity. Although the genomes of many Drosophila species have been sequenced, most of the phenotypic diversity in this genus remains to be explored. To facilitate the genetic analysis of interspecific and intraspecific variation, we have generated new genomic resources for seven species and subspecies in the D. ananassae species subgroup. We have generated large amounts of transcriptome sequence data for D. ercepeae, D. merina, D. bipectinata, D. malerkotliana malerkotliana, D. m. pallens, D. pseudoananassae pseudoananassae, and D. p. nigrens. de novo assembly resulted in contigs covering more than half of the predicted transcriptome and matching an average of 59% of annotated genes in the complete genome of D. ananassae. Most contigs, corresponding to an average of 49% of D. ananassae genes, contain sequence polymorphisms that can be used as genetic markers. Subsets of these markers were validated by genotyping the progeny of inter- and intraspecific crosses. The ananassae subgroup is an excellent model system for examining the molecular basis of speciation and phenotypic evolution. The new genomic resources will facilitate the genetic analysis of inter- and intraspecific differences in this lineage. Transcriptome sequencing provides a simple and cost-effective way to identify molecular markers at nearly single-gene density, and is equally applicable to any non-model taxa.

  4. Species-level phylogeographical history of Myricaria plants in the mountain ranges of western China and the origin of M. laxiflora in the Three Gorges mountain region.

    Science.gov (United States)

    Liu, Yifei; Wang, Yong; Huang, Hongwen

    2009-06-01

    Myricaria species in China occur mostly in the major high-altitude mountain areas in and around the Qinghai-Tibetan Plateau. The one major exception to this is M. laxiflora which is restricted to the Three Gorges mountain region. In this study, we investigate species-level phylogeographical patterns of Myricaria species in western China and the origin of M. laxiflora. The results show that most chloroplast haplotypes are species-specific, except for one haplotype which is shared by three widespread species. Higher haplotype diversity within the Qinghai-Tibetan Plateau region supports the hypothesis that the Himalayas are the centre of origin for Myricaria. The phylogeny of Myricaria was geographically structured, and an estimated Bayesian chronology suggested the main divergence events occurred during the Late Pliocene and Early Pleistocene (approximately 1.46-2.30 million years ago). The overall phylogeographical pattern was characterized by vicariance events and regional demographical expansion, reflecting a major influence of geological and climatic events on the evolution of Myricaria species. Our data suggest that M. laxiflora has an ancient origin, but has experienced recent population expansion through the Three Gorges Valley. The origin of M. laxiflora was estimated to be during the Early Pleistocene but its demographical expansion was more recent at about 0.015 million years ago. This highlights the unique phylogeographical history of the Three Gorges mountain region, and the deep imprint of the watercourse connections of the Yangtze River Valley on the phylogeographical structure of the species in this region.

  5. Y-Chromosome variation in hominids: intraspecific variation is limited to the polygamous chimpanzee.

    Directory of Open Access Journals (Sweden)

    Gabriele Greve

    Full Text Available BACKGROUND: We have previously demonstrated that the Y-specific ampliconic fertility genes DAZ (deleted in azoospermia and CDY (chromodomain protein Y varied with respect to copy number and position among chimpanzees (Pan troglodytes. In comparison, seven Y-chromosomal lineages of the bonobo (Pan paniscus, the chimpanzee's closest living relative, showed no variation. We extend our earlier comparative investigation to include an analysis of the intraspecific variation of these genes in gorillas (Gorilla gorilla and orangutans (Pongo pygmaeus, and examine the resulting patterns in the light of the species' markedly different social and mating behaviors. METHODOLOGY/PRINCIPAL FINDINGS: Fluorescence in situ hybridization analysis (FISH of DAZ and CDY in 12 Y-chromosomal lineages of western lowland gorilla (G. gorilla gorilla and a single lineage of the eastern lowland gorilla (G. beringei graueri showed no variation among lineages. Similar findings were noted for the 10 Y-chromosomal lineages examined in the Bornean orangutan (Pongo pygmaeus, and 11 Y-chromosomal lineages of the Sumatran orangutan (P. abelii. We validated the contrasting DAZ and CDY patterns using quantitative real-time polymerase chain reaction (qPCR in chimpanzee and bonobo. CONCLUSION/SIGNIFICANCE: High intraspecific variation in copy number and position of the DAZ and CDY genes is seen only in the chimpanzee. We hypothesize that this is best explained by sperm competition that results in the variant DAZ and CDY haplotypes detected in this species. In contrast, bonobos, gorillas and orangutans-species that are not subject to sperm competition-showed no intraspecific variation in DAZ and CDY suggesting that monoandry in gorillas, and preferential female mate choice in bonobos and orangutans, probably permitted the fixation of a single Y variant in each taxon. These data support the notion that the evolutionary history of a primate Y chromosome is not simply encrypted in its DNA

  6. Assessing the Importance of Intraspecific Variability in Dung Beetle Functional Traits.

    Directory of Open Access Journals (Sweden)

    Hannah M Griffiths

    Full Text Available Functional diversity indices are used to facilitate a mechanistic understanding of many theoretical and applied questions in current ecological research. The use of mean trait values in functional indices assumes that traits are robust, in that greater variability exists between than within species. While the assertion of robust traits has been explored in plants, there exists little information on the source and extent of variability in the functional traits of higher trophic level organisms. Here we investigated variability in two functionally relevant dung beetle traits, measured from individuals collected from three primary forest sites containing distinct beetle communities: body mass and back leg length. In doing so we too addressed the following questions: (i what is the contribution of intra vs. interspecific differences in trait values; (ii what sample size is needed to provide representative species mean trait values; and (iii what impact does omission of intraspecific trait information have on the calculation of functional diversity (FD indices from naturally assembled communities? At the population level, interspecific differences explained the majority of variability in measured traits (between 94% and 96%. In accordance with this, the error associated with calculating FD without inclusion of intraspecific variability was low, less than 20% in all cases. This suggests that complete sampling to capture intraspecific variance in traits is not necessary even when investigating the FD of small and/or naturally formed communities. To gain an accurate estimation of species mean trait values we encourage the measurement of 30-60 individuals and, where possible, these should be taken from specimens collected from the site of study.

  7. Assessing the Importance of Intraspecific Variability in Dung Beetle Functional Traits.

    Science.gov (United States)

    Griffiths, Hannah M; Louzada, Julio; Bardgett, Richard D; Barlow, Jos

    2016-01-01

    Functional diversity indices are used to facilitate a mechanistic understanding of many theoretical and applied questions in current ecological research. The use of mean trait values in functional indices assumes that traits are robust, in that greater variability exists between than within species. While the assertion of robust traits has been explored in plants, there exists little information on the source and extent of variability in the functional traits of higher trophic level organisms. Here we investigated variability in two functionally relevant dung beetle traits, measured from individuals collected from three primary forest sites containing distinct beetle communities: body mass and back leg length. In doing so we too addressed the following questions: (i) what is the contribution of intra vs. interspecific differences in trait values; (ii) what sample size is needed to provide representative species mean trait values; and (iii) what impact does omission of intraspecific trait information have on the calculation of functional diversity (FD) indices from naturally assembled communities? At the population level, interspecific differences explained the majority of variability in measured traits (between 94% and 96%). In accordance with this, the error associated with calculating FD without inclusion of intraspecific variability was low, less than 20% in all cases. This suggests that complete sampling to capture intraspecific variance in traits is not necessary even when investigating the FD of small and/or naturally formed communities. To gain an accurate estimation of species mean trait values we encourage the measurement of 30-60 individuals and, where possible, these should be taken from specimens collected from the site of study.

  8. Warming effects on consumption and intraspecific interference competition depend on predator metabolism.

    Science.gov (United States)

    Lang, Birgit; Rall, Björn C; Brose, Ulrich

    2012-05-01

    1. Model analyses show that the stability of population dynamics and food web persistence increase with the strength of interference competition. Despite this critical importance for community stability, little is known about how external factors such as the environmental temperature affect intraspecific interference competition. 2. We aimed to fill this void by studying the functional responses of two ground beetle species of different body size, Pterostichus melanarius and Poecilus versicolor. These functional response experiments were replicated across four predator densities and two temperatures to address the impact of temperature on intraspecific interference competition. 3. We generally expected that warming should increase the speed of movement, encounter rates and in consequence interference among predator individuals. In our experiment, this expectation was supported by the results obtained for the larger predator, P. melanarius, whereas the opposite pattern characterized the interference behaviour of the smaller predator P. versicolor. 4. These results suggest potentially nontrivial implications for the effects of environmental temperature on intraspecific interference competition, for which we propose an explanation based on the different sensitivity to warming of metabolic rates of both species. As expected, increasing temperature led to stronger interference competition of the larger species, P. melanarius, which exhibited a weaker increase in metabolic rate with increasing temperature. The stronger increase in the metabolic rate of the smaller predator, P. versicolor, had to be compensated by increasing searching activity for prey, which did not leave time for increasing interference. 5. Together, these results suggest that any generalization how interference competition responds to warming should also take the species' metabolic response to temperature increases into account. © 2011 The Authors. Journal of Animal Ecology © 2011

  9. Long-term evolution of polygenic traits under frequency-dependent intraspecific competition.

    Science.gov (United States)

    Schneider, Kristan A

    2007-05-01

    We analytically investigate the long-term evolution of a continuously varying quantitative character in a diploid population that is determined additively by a finite number of loci. The trait is under a mixture of frequency-dependent disruptive selection induced by intraspecific competition and frequency-independent stabilizing selection. Moreover, the trait is restricted to a finite range by constraints on the particular loci. Our investigations are based on explicit analytical results (provided by Bürger [2005. A multilocus analysis of intraspecific competition and stabilizing selection on a quantitative trait. J. Math. Biol. 50, 355-396]; Schneider [2006. A multilocus-multiallele analysis of frequency-dependent selection induced by intraspecific competition. J. Math. Biol. 52, 483-523]) on the short-term dynamics under the assumption of linkage equilibrium. We show that the population always reaches a long-term equilibrium (LTE), i.e., an equilibrium that is resistant against perturbations of mutations of sufficiently small effect. In general, several LTEs can coexist. They can be calculated explicitly, and we provide necessary and sufficient conditions for their existence. In the case that more than one LTE exists, we exemplify numerically that the evolutionary outcome depends crucially on the initial genetic architecture, on the joint distribution of mutational effects across loci, and on the particular realization of the mutation process. Therefore, long-term evolution cannot be predicted from the ecology alone. We further show that a partial order exists for the LTEs. The set of LTEs has a 'largest' element, an LTE which is reached during long-term evolution if the effects of the occurring mutant alleles are sufficiently large.

  10. Larval intraspecific competition for food in the European grapevine moth Lobesia botrana.

    Science.gov (United States)

    Thiéry, D; Monceau, K; Moreau, J

    2014-08-01

    Effective pest management with lower amounts of pesticides relies on accurate prediction of insect pest growth rates. Knowledge of the factors governing this trait and the resulting fitness of individuals is thus necessary to refine predictions and make suitable decisions in crop protection. The European grapevine moth, Lobesia botrana, the major pest of grapes in Europe, is responsible for huge economic losses. Larvae very rarely leave the grape bunch on which they were oviposited and thus cannot avoid intraspecific competition. In this study, we determined the impact of intraspecific competition during the larval stage on development and adult fitness in this species. This was tested by rearing different numbers of larvae on an artificial diet and measuring developmental and reproductive life history traits. We found that intraspecific competition during larval development has a slight impact on the fitness of L. botrana. The principal finding of this work is that larval density has little effect on the life history traits of survivors. Thus, the timing of eclosion, duration of subsequent oviposition, fecundity appears to be more uniform in L. botrana than in other species. The main effect of larval crowding was a strong increase of larval mortality at high densities whereas the probability of emergence, sex ratio, pupal mass, fecundity and longevity of mated females were not affected by larval crowding. Owing to increased larval mortality at high larval densities, we hypothesized that mortality of larvae at high densities provided better access to food for the survivors with the result that more food was available per capita and there were no effect on fitness of survivors. From our results, larval crowding alters the reproductive capacity of this pest less than expected but this single factor should now be tested in interaction with limited resources in the wild.

  11. Sampling intraspecific variability in leaf functional traits: Practical suggestions to maximize collected information.

    Science.gov (United States)

    Petruzzellis, Francesco; Palandrani, Chiara; Savi, Tadeja; Alberti, Roberto; Nardini, Andrea; Bacaro, Giovanni

    2017-12-01

    The choice of the best sampling strategy to capture mean values of functional traits for a species/population, while maintaining information about traits' variability and minimizing the sampling size and effort, is an open issue in functional trait ecology. Intraspecific variability (ITV) of functional traits strongly influences sampling size and effort. However, while adequate information is available about intraspecific variability between individuals (ITV BI ) and among populations (ITV POP ), relatively few studies have analyzed intraspecific variability within individuals (ITV WI ). Here, we provide an analysis of ITV WI of two foliar traits, namely specific leaf area (SLA) and osmotic potential (π), in a population of Quercus ilex L. We assessed the baseline ITV WI level of variation between the two traits and provided the minimum and optimal sampling size in order to take into account ITV WI , comparing sampling optimization outputs with those previously proposed in the literature. Different factors accounted for different amount of variance of the two traits. SLA variance was mostly spread within individuals (43.4% of the total variance), while π variance was mainly spread between individuals (43.2%). Strategies that did not account for all the canopy strata produced mean values not representative of the sampled population. The minimum size to adequately capture the studied functional traits corresponded to 5 leaves taken randomly from 5 individuals, while the most accurate and feasible sampling size was 4 leaves taken randomly from 10 individuals. We demonstrate that the spatial structure of the canopy could significantly affect traits variability. Moreover, different strategies for different traits could be implemented during sampling surveys. We partially confirm sampling sizes previously proposed in the recent literature and encourage future analysis involving different traits.

  12. Multi-clone infections and the impact of intraspecific competition on trematode colonies with a division of labour.

    Science.gov (United States)

    Lloyd, Melanie M; Poulin, Robert

    2014-02-01

    A division of labour occurs in colonies of the trematode Philophthalmus sp. within their first intermediate hosts. Two castes exist: one which reproduces and one which does not reproduce. It has been hypothesized that the benefit of the non-reproductive caste is in competitive interactions. Evidence for this from past experiments with Philophthalmus sp. colonies has been contradictory: the non-reproductive caste appears to benefit the colony in some way but not necessarily by combating interspecific competitors. The aims of this study were to consider intraspecific competition as a possible cause of the division of labour in Philophthalmus sp. colonies. Results show that mixed genotype infections occur in Philophthalmus sp. infected hosts and thus intraspecific competition is likely. Furthermore, the total number of individuals per colony is reduced in mixed genotype infections, indicating that intraspecific competition reduces colony fitness. However, the results do not indicate that the division of labour in Philophthalmus sp. plays a role in competitive interactions as the ratio of small, non-reproductive to large, reproductive individuals is unaffected by the presence of intraspecific competition. This is the first study to identify and quantify intraspecific competition in Philophthalmus sp., and to assess its selective role in this species' division of labour.

  13. Rhizosphere priming effects on soil carbon and nitrogen dynamics among tree species with and without intraspecific competition.

    Science.gov (United States)

    Yin, Liming; Dijkstra, Feike A; Wang, Peng; Zhu, Biao; Cheng, Weixin

    2018-03-07

    Rhizosphere priming effects (RPEs) play a central role in modifying soil organic matter mineralization. However, effects of tree species and intraspecific competition on RPEs are poorly understood. We investigated RPEs of three tree species (larch, ash and Chinese fir) and the impact of intraspecific competition of these species on the RPE by growing them at two planting densities for 140 d. We determined the RPE on soil organic carbon (C) decomposition, gross and net nitrogen (N) mineralization and net plant N acquisition. Differences in the RPE among species were associated with differences in plant biomass. Gross N mineralization and net plant N acquisition increased, but net N mineralization decreased, as the RPE on soil organic C decomposition increased. Intraspecific competition reduced the RPE on soil organic C decomposition, gross and net N mineralization, and net plant N acquisition, especially for ash and Chinese fir. Microbial N mining may explain the overall positive RPEs across species, whereas intensified plant-microbe competition for N may have reduced the RPE with intraspecific competition. Overall, the species-specific effects of tree species play an important role in modulating the magnitude and mechanisms of RPEs and the intraspecific competition on soil C and N dynamics. © 2018 The Authors New Phytologist © 2018 New Phytologist Trust.

  14. Buffer zones of territories of gray wolves as regions of intraspecific strife

    Science.gov (United States)

    Mech, L.D.

    1994-01-01

    The locations of 22 territorial gray wolves (Canis lupus) killed by conspecifics in northeastern Minnesota were analyzed in a study involving radio-telemetry from 1968 through 1992. Twenty-three percent of the wolves were killed precisely on the borders of their estimated territories; 41%, within 1.0 km (16% of the radius of their mean-estimated territory) inside or outside the estimated edge; 91%, within 3.2 km inside or outside (50% of the radius of their mean-estimated territory) of the estimated edge. This appears to be the first report of intraspecific mortality of mammals along territorial boundaries.

  15. Phylogeographic Characterization of Tick-Borne Encephalitis Virus from Patients, Rodents and Ticks in Slovenia

    Science.gov (United States)

    Fajs, Luka; Durmiši, Emina; Knap, Nataša; Strle, Franc; Avšič-Županc, Tatjana

    2012-01-01

    Tick-borne encephalitis virus (TBEV) is the most important arboviral agent causing infections of the central nervous system in central Europe. Previous studies have shown that TBEV exhibits pronounced genetic variability, which is often correlated to the geographical origin of TBEV. Genetic variability of TBEV has previously been studied predominantly in rodents and ticks, while information about the variability in patients is scarce. In order to understand the molecular relationships of TBEV between natural hosts, vectors and humans, as well as correlation between phylogenetic and geographical clustering, sequences of TBEV E and NS5 protein genes, were obtained by direct sequencing of RT-PCR products from TBE-confirmed patients as well as from rodents and ticks collected from TBE-endemic regions in Slovenia. A total of 27 partial E protein gene sequences representing 15 human, 4 rodent and 8 tick samples and 30 partial NS5 protein gene sequences representing 17 human, 5 rodent and 8 tick samples were obtained. The complete genome sequence of TBEV strain Ljubljana I was simultaneously obtained. Phylogenetic analysis of the E and NS5 protein gene sequences revealed a high degree of TBEV variability in patients, ticks and rodents. Furthermore, an evident correlation between geographical and phylogenetic clustering was shown that was independent of the TBEV host. Moreover, we show the presence of a possible recombination event in the TBEV genome obtained from a patient sample, which was supported with multiple recombination event detection methods. This is the first study that simultaneously analyzed the genetic relationships of directly sequenced TBEV samples from patients, ticks and rodents and provides the largest set of patient-derived TBEV sequences up to date. In addition, we have confirmed the geographical clustering of TBEV sequences in Slovenia and have provided evidence of a possible recombination event in the TBEV genome, obtained from a patient. PMID

  16. Phylogeographic characterization of tick-borne encephalitis virus from patients, rodents and ticks in Slovenia.

    Directory of Open Access Journals (Sweden)

    Luka Fajs

    Full Text Available Tick-borne encephalitis virus (TBEV is the most important arboviral agent causing infections of the central nervous system in central Europe. Previous studies have shown that TBEV exhibits pronounced genetic variability, which is often correlated to the geographical origin of TBEV. Genetic variability of TBEV has previously been studied predominantly in rodents and ticks, while information about the variability in patients is scarce. In order to understand the molecular relationships of TBEV between natural hosts, vectors and humans, as well as correlation between phylogenetic and geographical clustering, sequences of TBEV E and NS5 protein genes, were obtained by direct sequencing of RT-PCR products from TBE-confirmed patients as well as from rodents and ticks collected from TBE-endemic regions in Slovenia. A total of 27 partial E protein gene sequences representing 15 human, 4 rodent and 8 tick samples and 30 partial NS5 protein gene sequences representing 17 human, 5 rodent and 8 tick samples were obtained. The complete genome sequence of TBEV strain Ljubljana I was simultaneously obtained. Phylogenetic analysis of the E and NS5 protein gene sequences revealed a high degree of TBEV variability in patients, ticks and rodents. Furthermore, an evident correlation between geographical and phylogenetic clustering was shown that was independent of the TBEV host. Moreover, we show the presence of a possible recombination event in the TBEV genome obtained from a patient sample, which was supported with multiple recombination event detection methods. This is the first study that simultaneously analyzed the genetic relationships of directly sequenced TBEV samples from patients, ticks and rodents and provides the largest set of patient-derived TBEV sequences up to date. In addition, we have confirmed the geographical clustering of TBEV sequences in Slovenia and have provided evidence of a possible recombination event in the TBEV genome, obtained from a

  17. The use and limits of ITS data in the analysis of intraspecific variation in Passiflora L. (Passifloraceae

    Directory of Open Access Journals (Sweden)

    Geraldo Mäder

    2010-01-01

    Full Text Available The discovery and characterization of informative intraspecific genetic markers is fundamental for evolutionary and conservation genetics studies. Here, we used nuclear ribosomal ITS sequences to access intraspecific genetic diversity in 23 species of the genus Passiflora L. Some degree of variation was detected in 21 of these. The Passiflora and Decaloba (DC. Rchb. subgenera showed significant differences in the sizes of the two ITS regions and in GC content, which can be related to reproductive characteristics of species in these subgenera. Furthermore, clear geographical patterns in the spatial distribution of sequence types were identified in six species. The results indicate that ITS may be a useful tool for the evaluation of intraspecific genetic variation in Passiflora.

  18. The use and limits of ITS data in the analysis of intraspecific variation in Passiflora L. (Passifloraceae).

    Science.gov (United States)

    Mäder, Geraldo; Zamberlan, Priscilla M; Fagundes, Nelson J R; Magnus, Tielli; Salzano, Francisco M; Bonatto, Sandro L; Freitas, Loreta B

    2010-01-01

    The discovery and characterization of informative intraspecific genetic markers is fundamental for evolutionary and conservation genetics studies. Here, we used nuclear ribosomal ITS sequences to access intraspecific genetic diversity in 23 species of the genus Passiflora L. Some degree of variation was detected in 21 of these. The Passiflora and Decaloba (DC.) Rchb. subgenera showed significant differences in the sizes of the two ITS regions and in GC content, which can be related to reproductive characteristics of species in these subgenera. Furthermore, clear geographical patterns in the spatial distribution of sequence types were identified in six species. The results indicate that ITS may be a useful tool for the evaluation of intraspecific genetic variation in Passiflora.

  19. Which species will successfully track climate change? The influence of intraspecific competition and density dependent dispersal on range shifting dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Best, A.S.; Johst, K.; Muenkemueller, T.; Travis, J.M.J.

    2007-09-15

    Understanding the ability of species to shift their geographic range is of considerable importance given the current period of rapid climate change. Furthermore, a greater understanding of the spatial population dynamics underlying range shifting is required to complement the advances made in climate niche modelling. A simulation model is developed which incorporates three key features that have been largely overlooked in studies of range shifting dynamics: the form of intraspecific competition, density dependent dispersal and the transient dynamics of habitat patches. The results show that the exact shape of the response depends critically on both local and patch dynamics. Species whose intraspecific competition is contest based are more vulnerable than those whose competition is scramble based. Contesters are especially sensitive when combined with density dependent dispersal. Species living in patches whose carrying capacity grows slowly are also susceptible to rapid shifts of environmental conditions. A complementary analytic approach further highlights the importance of intraspecific competition. (au)

  20. The Complete Chloroplast Genome of Catha edulis: A Comparative Analysis of Genome Features with Related Species

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    Cuihua Gu

    2018-02-01

    Full Text Available Qat (Catha edulis, Celastraceae is a woody evergreen species with great economic and cultural importance. It is cultivated for its stimulant alkaloids cathine and cathinone in East Africa and southwest Arabia. However, genome information, especially DNA sequence resources, for C. edulis are limited, hindering studies regarding interspecific and intraspecific relationships. Herein, the complete chloroplast (cp genome of Catha edulis is reported. This genome is 157,960 bp in length with 37% GC content and is structurally arranged into two 26,577 bp inverted repeats and two single-copy areas. The size of the small single-copy and the large single-copy regions were 18,491 bp and 86,315 bp, respectively. The C. edulis cp genome consists of 129 coding genes including 37 transfer RNA (tRNA genes, 8 ribosomal RNA (rRNA genes, and 84 protein coding genes. For those genes, 112 are single copy genes and 17 genes are duplicated in two inverted regions with seven tRNAs, four rRNAs, and six protein coding genes. The phylogenetic relationships resolved from the cp genome of qat and 32 other species confirms the monophyly of Celastraceae. The cp genomes of C. edulis, Euonymus japonicus and seven Celastraceae species lack the rps16 intron, which indicates an intron loss took place among an ancestor of this family. The cp genome of C. edulis provides a highly valuable genetic resource for further phylogenomic research, barcoding and cp transformation in Celastraceae.

  1. Intraspecific morphological and genetic variation of common species predicts ranges of threatened ones

    Science.gov (United States)

    Fuller, Trevon L.; Thomassen, Henri A.; Peralvo, Manuel; Buermann, Wolfgang; Milá, Borja; Kieswetter, Charles M.; Jarrín-V, Pablo; Devitt, Susan E. Cameron; Mason, Eliza; Schweizer, Rena M.; Schlunegger, Jasmin; Chan, Janice; Wang, Ophelia; Schneider, Christopher J.; Pollinger, John P.; Saatchi, Sassan; Graham, Catherine H.; Wayne, Robert K.; Smith, Thomas B.

    2013-01-01

    Predicting where threatened species occur is useful for making informed conservation decisions. However, because they are usually rare, surveying threatened species is often expensive and time intensive. Here, we show how regions where common species exhibit high genetic and morphological divergence among populations can be used to predict the occurrence of species of conservation concern. Intraspecific variation of common species of birds, bats and frogs from Ecuador were found to be a significantly better predictor for the occurrence of threatened species than suites of environmental variables or the occurrence of amphibians and birds. Fully 93 per cent of the threatened species analysed had their range adequately represented by the geographical distribution of the morphological and genetic variation found in seven common species. Both higher numbers of threatened species and greater genetic and morphological variation of common species occurred along elevation gradients. Higher levels of intraspecific divergence may be the result of disruptive selection and/or introgression along gradients. We suggest that collecting data on genetic and morphological variation in common species can be a cost effective tool for conservation planning, and that future biodiversity inventories include surveying genetic and morphological data of common species whenever feasible. PMID:23595273

  2. Intraspecific variation in Trichogramma bruni Nagaraja, 1983 (Hymenoptera: Trichogrammatidae) associated with different hosts.

    Science.gov (United States)

    Querino, R B; Zucchi, R A

    2002-11-01

    Trichogramma bruni is an insufficiently studied South American species whose limits are still not well defined. Thus, the objective of the present study was to characterize T. bruni taxonomically and to determine the association between morphological variations as well as host and habitat, based on morphological and biological studies. Specimens from the Escola Superior de Agricultura "Luiz de Queiroz" (ESALQ) collection, and from the University of California Riverside (UCR) and specimens collected from the vegetation of forest parks with native areas planted with eucalyptus in Piracicaba and Itatinga, State of São Paulo, were also analyzed. The holotype deposited at Univeridade Federal de Minas Gerais (UFMG) collection was also examined. The variability in the genital capsule of T. bruni observed both among individuals of the same progeny and among specimens from different hosts is remarkable and is mainly related to the dorsal lamina. Therefore, an association of diagnostic characters rather than the dorsal lamina alone should be used for the identification of T. bruni and intraspecific variations should be considered. The intraspecific variation observed for T. bruni is a factor that should be considered for its identification, since the influence of the environment (habitat + host) and the variation among individuals itself is responsible for the plasticity observed in the genital capsule. Heliconius erato phyllis, Hamadryas feronia, Erosina hyberniata and Mechanitis lysiminia are new hosts of T. bruni.

  3. Recent observations of intraspecific predation and cannibalism among polar bears in the southern Beaufort Sea

    Science.gov (United States)

    Amstrup, Steven C.; Stirling, I.; Smith, T.S.; Perham, C.; Thiemann, G.W.

    2006-01-01

    Intraspecific killing has been reported among polar bears (Ursus maritimus), brown bears (U. arctos), and black bears (U. americanus). Although cannibalism is one motivation for such killings, the ecological factors mediating such events are poorly understood. Between 24 January and 10 April 2004, we confirmed three instances of intraspecific predation and cannibalism in the Beaufort Sea. One of these, the first of this type ever reported for polar bears, was a parturient female killed at her maternal den. The predating bear was hunting in a known maternal denning area and apparently discovered the den by scent. A second predation event involved an adult female and cub recently emerged from their den, and the third involved a yearling male. During 24 years of research on polar bears in the southern Beaufort Sea region of northern Alaska and 34 years in northwestern Canada, we have not seen other incidents of polar bears stalking, killing, and eating other polar bears. We hypothesize that nutritional stresses related to the longer ice-free seasons that have occurred in the Beaufort Sea in recent years may have led to the cannibalism incidents we observed in 2004. ?? Springer-Verlag 2006.

  4. Rare insights into intraspecific brood parasitism and apparent quasi–parasitism in black–capped chickadees

    Directory of Open Access Journals (Sweden)

    Otter, K. A.

    2011-06-01

    Full Text Available Genetic analysis of passerine birds often finds evidence of extra–pair copulations within species, but genetic evidence of intraspecific brood parasitism (IBP and quasi–parasitism (Q–P are relatively rare. Further, it is even rarer for genetic patterns that might indicate quasi–parasitism (resident male sires offspring through extra–pair copulations, and allows the female to lay these within the male’s nest to be coupled with observational evidence of this behavior. In this paper, we report behavioral observations surrounding the nest of black–capped chickadee, one of the few species in which both IBP and Q–P have been detected through a genetic analysis. These were later confirmed to have young genetically mismatched with both attending parents, as well as mismatched with the attending female but sired by the attending male. The behavioral patterns associated with this nest are contrasted with the two previously reported cases of IPB/Q–P in this species, and suggest that rare ‘detection’ of quasi–parasitism may be explained by converging patterns of extra–pair behavior and the rarer strategy of intraspecific brood parasitism.

  5. Cultivar mixtures: a meta-analysis of the effect of intraspecific diversity on crop yield.

    Science.gov (United States)

    Reiss, Emily R; Drinkwater, Laurie E

    2018-01-01

    Extensive research has shown that greater plant community diversity leads to higher levels of productivity and other ecosystem services, and such increased diversity has been suggested as a way to improve yield and agricultural sustainability. Increasing intraspecific diversity with cultivar mixtures is one way to increase diversity in agricultural systems. We examined the relationship between intraspecific diversity and yield in cultivar mixtures using a meta-analysis of 91 studies and >3,600 observations. Additionally, we investigated how environmental and management factors might influence this relationship, and if the yield stability of cultivar mixtures differed from that of monocultures. We found that the yield increased by 2.2% overall in cultivar mixtures relative to their monoculture components. Mixtures with more cultivars and those with more functional trait diversity showed higher relative yields. Under biotic stressors, such as disease pressure, and abiotic stressors, such as low levels of soil organic matter and nutrient availability, this diversity effect was stronger, resulting in higher relative yields. Finally, cultivar mixtures generally showed higher yield stability compared to monocultures, especially in response to annual weather variability at a site over time. This practice of mixing cultivars can be integrated into intensified cropping systems where species monocultures dominate, as well as in smallholder cropping systems where low-cost improvements are in demand. Overall, these results suggest that cultivar mixtures are a viable strategy to increase diversity in agroecosystems, promoting increased yield and yield stability, with minimal environmental impact. © 2017 by the Ecological Society of America.

  6. Concordance between stabilizing sexual selection, intraspecific variation, and interspecific divergence inPhymata.

    Science.gov (United States)

    Punzalan, David; Rowe, Locke

    2016-11-01

    Empirical studies show that lineages typically exhibit long periods of evolutionary stasis and that relative levels of within-species trait covariance often correlate with the extent of between-species trait divergence. These observations have been interpreted by some as evidence of genetic constraints persisting for long periods of time. However, an alternative explanation is that both intra- and interspecific variation are shaped by the features of the adaptive landscape (e.g., stabilizing selection). Employing a genus of insects that are diverse with respect to a suite of secondary sex traits, we related data describing nonlinear phenotypic (sexual) selection to intraspecific trait covariances and macroevolutionary divergence. We found support for two key predictions (1) that intraspecific trait covariation would be aligned with stabilizing selection and (2) that there would be restricted macroevolutionary divergence in the direction of stabilizing selection. The observed alignment of all three matrices offers a point of caution in interpreting standing variability as metrics of evolutionary constraint. Our results also illustrate the power of sexual selection for determining variation observed at both short and long timescales and account for the apparently slow evolution of some secondary sex characters in this lineage.

  7. Intraspecific reproductive character displacement in a polymorphic poison dart frog, Dendrobates pumilio.

    Science.gov (United States)

    Richards-Zawacki, Corinne L; Cummings, Molly E

    2011-01-01

    Divergence in male mating signals and associated female preferences is often an important step in the process of speciation. Reproductive character displacement, the pattern of greater divergence of male signals and/or female preference in sympatry than in allopatry, has been observed in a variety of taxa with different degrees of postzygotic isolation. A number of selective processes, including reinforcement, have been proposed to cause such a pattern. Cases in which reproductive character displacement occurs among intraspecific variants are especially informative for understanding how selection acting within a species can lead to the evolution of reproductive barriers and speciation. This study tested the hypothesis that female strawberry poison dart frogs (Dendrobates pumilio) in polymorphic populations of the Bocas del Toro archipelago of Panama show stronger mating discrimination than do females from monomorphic populations, exhibiting an intraspecific pattern of reproductive character displacement. Our results contribute important insights into understanding selection's role in generating the striking diversity of Bocas del Toro's D. pumilio and provide a snapshot of what could be the early stages of reproductive isolation and speciation. © 2010 The Author(s). Evolution© 2010 The Society for the Study of Evolution.

  8. Intraspecific relationship within the genus convolvulus l. inferred by rbcl gene using different phylogenetic approaches

    International Nuclear Information System (INIS)

    Kausar, S.; Qamarunnisa, S.

    2016-01-01

    A molecular systematics analysis was conducted using sequence data of chloroplast rbcL gene for the genus Convolvulus L., by distance and character based phylogenetic methods. Fifteen representative members from genus Convolvulus L., were included as in group whereas two members from a sister family Solanaceae were taken as out group to root the tree. Intraspecific relationships within Convolvulus were inferred by distance matrix, maximum parsimony and bayesian analysis. Transition/transversion ratio was also calculated and it was revealed that in the investigated Convolvulus species, transitional changes were more prevalent in rbcL gene. The nature of rbcL gene in the present study was observed to be conserved, as it does not show major variations between examined species. Distance matrix represented the minimal genetic variations between some species (C. glomeratus and C. pyrrhotrichus), thus exhibiting them as close relatives. The result of parsimonious and bayesian analysis revealed almost similar clades however maximum parsimony based tree was unable to establish relationship between some Convolvulus species. The bayesian inference method was found to be the method of choice for establishing intraspecific associations between Convolvulus species using rbcL data as it clearly defined the connections supported by posterior probability values. (author)

  9. Intraspecific Variation in Female Sex Pheromone of the Codling Moth Cydia pomonella.

    Science.gov (United States)

    Duménil, Claire; Judd, Gary J R; Bosch, Dolors; Baldessari, Mario; Gemeno, César; Groot, Astrid T

    2014-09-26

    The codling moth, Cydia pomonella L. (Lepidoptera, Tortricidae), is a major pest of apple, pear and walnut orchards worldwide. This pest is often controlled using the biologically friendly control method known as pheromone-based mating disruption. Mating disruption likely exerts selection on the sexual communication system of codling moth, as male and female moths will persist in their attempt to meet and mate. Surprisingly little is known on the intraspecific variation of sexual communication in this species. We started an investigation to determine the level of individual variation in the female sex pheromone composition of this moth and whether variation among different populations might be correlated with use of mating disruption against those populations. By extracting pheromone glands of individual females from a laboratory population in Canada and from populations from apple orchards in Spain and Italy, we found significant between- and within-population variation. Comparing females that had been exposed to mating disruption, or not, revealed a significant difference in sex pheromone composition for two of the minor components. Overall, the intraspecific variation observed shows the potential for a shift in female sexual signal when selection pressure is high, as is the case with continuous use of mating disruption.

  10. Intraspecific Variation in Female Sex Pheromone of the Codling Moth Cydia pomonella

    Directory of Open Access Journals (Sweden)

    Claire Duménil

    2014-09-01

    Full Text Available The codling moth, Cydia pomonella L. (Lepidoptera, Tortricidae, is a major pest of apple, pear and walnut orchards worldwide. This pest is often controlled using the biologically friendly control method known as pheromone-based mating disruption. Mating disruption likely exerts selection on the sexual communication system of codling moth, as male and female moths will persist in their attempt to meet and mate. Surprisingly little is known on the intraspecific variation of sexual communication in this species. We started an investigation to determine the level of individual variation in the female sex pheromone composition of this moth and whether variation among different populations might be correlated with use of mating disruption against those populations. By extracting pheromone glands of individual females from a laboratory population in Canada and from populations from apple orchards in Spain and Italy, we found significant between- and within-population variation. Comparing females that had been exposed to mating disruption, or not, revealed a significant difference in sex pheromone composition for two of the minor components. Overall, the intraspecific variation observed shows the potential for a shift in female sexual signal when selection pressure is high, as is the case with continuous use of mating disruption.

  11. Ecological opportunities and intraspecific competition alter trophic niche specialization in an opportunistic stream predator.

    Science.gov (United States)

    Evangelista, Charlotte; Boiche, Anatole; Lecerf, Antoine; Cucherousset, Julien

    2014-09-01

    Many generalist populations are composed of specialized individuals that use a narrow part of the population's niche. Ecological theories predict that individual specialization and population trophic niche are determined by biotic interactions and resource diversity emerging from environmental variations (i.e. ecological opportunities). However, due to the paucity of empirical and experimental demonstrations, the genuine importance of each of these drivers in determining trophic niche attributes is not fully appreciated. The present study aimed at determining the population level and individual responses of brown trout (Salmo trutta) to variations in ecological opportunities (terrestrial prey inputs) and autochthonous prey communities among 10 stream reaches along a riparian condition gradient using individual longitudinal monitoring and stable isotope analyses. Our results suggested that trophic niche diversity varied along the environmental gradient, while individual trophic specialization was indirectly driven by ecological opportunities through strengthened intraspecific competition. Individual diet was repeatable over the study period, and the growth rate of juvenile brown trout increased with their specialization for aquatic predatory invertebrates. Our findings highlight the dual influences of intraspecific competition and ecological opportunities on individual trophic specialization and population trophic niche. © 2014 The Authors. Journal of Animal Ecology © 2014 British Ecological Society.

  12. Evolution of dominance under frequency-dependent intraspecific competition in an assortatively mating population.

    Science.gov (United States)

    Peischl, Stephan; Schneider, Kristan A

    2010-02-01

    We study the evolution of higher levels of dominance as a response to negative frequency-dependent selection. In contrast to previous studies, we focus on the effect of assortative mating on the evolution of dominance under frequency-dependent intraspecific competition. We analyze a two-locus two-allele model, in which the primary locus has a major effect on a quantitative trait that is under a mixture of frequency-independent stabilizing selection, density-dependent selection, and frequency-dependent selection caused by intraspecific competition for a continuum of resources. The second (modifier) locus determines the degree of dominance at the trait level. Additionally, the population mates assortatively with respect to similarities in the ecological trait. Our analysis shows that the parameter region in which dominance can be established decreases if small levels of assortment are introduced. In addition, the degree of dominance that can be established also decreases. In contrast, if assortment is intermediate, sexual selection for extreme types can be established, which leads to evolution of higher levels of dominance than under random mating. For modifiers with large effects, intermediate levels of assortative mating are most favorable for the evolution of dominance. For large modifiers, the speed of fixation can even be higher for intermediate levels of assortative mating than for random mating.

  13. Effect of intraspecific competition and substrate type on terpene emissions from some Mediterranean plant species.

    Science.gov (United States)

    Ormeño, Elena; Bousquet-Mélou, Anne; Mévy, Jean-Philippe; Greff, Stéphane; Robles, Christine; Bonin, Gilles; Fernandez, Catherine

    2007-02-01

    Competition is an important factor that has been extensively reported in the Mediterranean area. There is evidence that leaf terpene accumulation may vary between plants growing on calcareous and siliceous soils. In the present study, leaf terpene emissions from potted seedlings of Pinus halepensis, Cistus albidus, and Quercus coccifera, growing under natural environmental conditions on calcareous and siliceous substrates, were studied by using a bag enclosure method. In both substrates, seedlings were potted alone and in intraspecific competition, to examine the effect of substrate type and that of intraspecific competition on terpene emissions. The results showed that competition favored: (i) overall monoterpene and sesquiterpene emissions from Q. coccifera; (ii) overall monoterpene emissions from P. halepensis; (iii) overall sesquiterpene emissions from C. albidus. Substrate type affected terpene emissions to a limited extent and in a species-specific way. Whereas for Q. coccifera, the overall monoterpene emissions and that of Allo-aromadendrene were favored on siliceous substrate, no significant changes were found in emissions from P. halepensis. Only the release of AR-curcumene from C. albidus was higher on siliceous substrate. We also found high variability in terpene emission composition from the study species, particularly for P. halepensis and Q. coccifera. These two species released both monoterpenes and sesquiterpenes, instead of monoterpenes only, as shown in previous studies.

  14. Conflicting selection in the course of adaptive diversification: the interplay between mutualism and intraspecific competition.

    Science.gov (United States)

    Raimundo, Rafael L G; Gibert, Jean P; Hembry, David H; Guimarães, Paulo R

    2014-03-01

    Adaptive speciation can occur when a population undergoes assortative mating and disruptive selection caused by frequency-dependent intraspecific competition. However, other interactions, such as mutualisms based on trait matching, may generate conflicting selective pressures that constrain species diversification. We used individual-based simulations to explore how different types of mutualism affect adaptive diversification. A magic trait was assumed to simultaneously mediate mate choice, intraspecific competition, and mutualisms. In scenarios of intimate, specialized mutualisms, individuals interact with one or few individual mutualistic partners, and diversification is constrained only if the mutualism is obligate. In other scenarios, increasing numbers of different partners per individual limit diversification by generating stabilizing selection. Stabilizing selection emerges from the greater likelihood of trait mismatches for rare, extreme phenotypes than for common intermediate phenotypes. Constraints on diversification imposed by increased numbers of partners decrease if the trait matching degree has smaller positive effects on fitness. These results hold after the relaxation of various assumptions. When trait matching matters, mutualism-generated stabilizing selection would thus often constrain diversification in obligate mutualisms, such as ant-myrmecophyte associations, and in low-intimacy mutualisms, including plant-seed disperser systems. Hence, different processes, such as trait convergence favoring the incorporation of nonrelated species, are needed to explain the higher richness of low-intimacy assemblages--shown here to be up to 1 order of magnitude richer than high-intimacy systems.

  15. Multiple infestation by seed predators: the effect of loculate fruits on intraspecific insect larval competition

    Science.gov (United States)

    Serrano, José M.; Delgado, Juan A.; López, Francisco; Acosta, Francisco J.; Fungairiño, Sara G.

    2001-06-01

    Many morphological features of fruits are important factors affecting predispersal seed predation by insects. This paper analyses the predispersal seed predation process of a major predator (a Noctuidae lepidopteran larvae) in loculate fruits of a bushy perennial plant, Cistus ladanifer. The main aim of the study is to assess the potential effect of internal valvae (which partition groups of seeds) in the intraspecific competition between larvae in multiple-infested fruits. Our results show that larvae do not reject already infested fruits, but they avoid the proximity of other larvae within the fruit, keeping an average minimum distance of one locule. In multiple-infested fruits, larval mortality increases and the proportion of seeds consumed by each larvae decreases. In those situations in which valvae keep apart larvae within a fruit, these only suffer the cost of exploitation competition with a low acquisition of resources. However, when all valvae between them are pierced by the larvae, competition switches to an interference component and larval mortality increases markedly. The existence of valvae within a fruit allows larvae to diminish the cost of intraspecific competition, obtaining high life expectancies (70%), even in triple-infested fruits.

  16. Natural variation in dauer pheromone production and sensing supports intraspecific competition in nematodes.

    Science.gov (United States)

    Bose, Neelanjan; Meyer, Jan M; Yim, Joshua J; Mayer, Melanie G; Markov, Gabriel V; Ogawa, Akira; Schroeder, Frank C; Sommer, Ralf J

    2014-07-07

    Dauer formation, a major nematode survival strategy, represents a model for small-molecule regulation of metazoan development [1-10]. Free-living nematodes excrete dauer-inducing pheromones that have been assumed to target conspecifics of the same genotype [9, 11]. However, recent studies in Pristionchus pacificus revealed that the dauer pheromone of some strains affects conspecifics of other genotypes more strongly than individuals of the same genotype [12]. To elucidate the mechanistic basis for this intriguing cross-preference, we compared six P. pacificus wild isolates to determine the chemical composition of their dauer-inducing metabolomes and responses to individual pheromone components. We found that these isolates produce dauer pheromone blends of different composition and respond differently to individual pheromone components. Strikingly, there is no correlation between production of and dauer response to a specific compound in individual strains. Specifically, pheromone components that are abundantly produced by one genotype induce dauer formation in other genotypes, but not necessarily in the abundant producer. Furthermore, some genotypes respond to pheromone components they do not produce themselves. These results support a model of intraspecific competition in nematode dauer formation. Indeed, we observed intraspecific competition among sympatric strains in a novel experimental assay, suggesting a new role of small molecules in nematode ecology. Copyright © 2014 Elsevier Ltd. All rights reserved.

  17. Experimental Evidence for an Eco-Evolutionary Coupling between Local Adaptation and Intraspecific Competition.

    Science.gov (United States)

    Siepielski, Adam M; Nemirov, Alex; Cattivera, Matthew; Nickerson, Avery

    2016-04-01

    Determining how adaptive evolution can be coupled to ecological processes is key for developing a more integrative understanding of the demographic factors that regulate populations. Intraspecific competition is an especially important ecological process because it generates negative density dependence in demographic rates. Although ecological factors are most often investigated to determine the strength of density dependence, evolutionary processes such as local adaptation could also feed back to shape variation in the strength of density dependence among populations. Using an experimental approach with damselflies, a predaceous aquatic insect, we find evidence that both density-dependent intraspecific competition and local adaptation can reduce per capita growth rates. In some cases, the effects of local adaptation on reducing per capita growth rates exceeded the ecological competitive effects of a doubling of density. However, we also found that these ecological and evolutionary properties of populations are coupled, and we offer two interpretations of the causes underlying this pattern: (1) the strength of density-dependent competition depends on the extent of local adaptation, or (2) the extent of local adaptation is shaped by the strength of density-dependent competition. Regardless of the underlying causal pathway, these results show how eco-evolutionary dynamics can affect a key demographic process regulating populations.

  18. Intraspecific adaptive radiation: Competition, ecological opportunity, and phenotypic diversification within species.

    Science.gov (United States)

    Levis, Nicholas A; Martin, Ryan A; O'Donnell, Kerry A; Pfennig, David W

    2017-10-01

    Intraspecific variation in resource-use traits can have profound ecological and evolutionary implications. Among the most striking examples are resource polymorphisms, where alternative morphs that utilize different resources evolve within a population. An underappreciated aspect of their evolution is that the same conditions that favor resource polymorphism-competition and ecological opportunity-might foster additional rounds of diversification within already existing morphs. We examined these issues in spadefoot toad tadpoles that develop into either a generalist "omnivore" or a specialist "carnivore" morph. Specifically, we assessed the morphological diversity of tadpoles from natural ponds and experimentally induced carnivores reared on alternative diets. We also surveyed natural ponds to determine if the strength of intramorph competition and the diversity and abundance of dietary resources (measures of ecological opportunity) influenced the diversity of within-morph variation. We found that five omnivore and four carnivore types were present in natural ponds; alternative diets led to shape differences, some of which mirrored variation in the wild; and both competition and ecological opportunity were associated with enhanced morphological diversity in natural ponds. Such fine-scale intraspecific variation might represent an underappreciated form of biodiversity and might constitute a crucible of evolutionary innovation and diversification. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

  19. Intraspecific competition facilitates the evolution of tolerance to insect damage in the perennial plant Solanum carolinense.

    Science.gov (United States)

    McNutt, David W; Halpern, Stacey L; Barrows, Kahaili; Underwood, Nora

    2012-12-01

    Tolerance to herbivory (the degree to which plants maintain fitness after damage) is a key component of plant defense, so understanding how natural selection and evolutionary constraints act on tolerance traits is important to general theories of plant-herbivore interactions. These factors may be affected by plant competition, which often interacts with damage to influence trait expression and fitness. However, few studies have manipulated competitor density to examine the evolutionary effects of competition on tolerance. In this study, we tested whether intraspecific competition affects four aspects of the evolution of tolerance to herbivory in the perennial plant Solanum carolinense: phenotypic expression, expression of genetic variation, the adaptive value of tolerance, and costs of tolerance. We manipulated insect damage and intraspecific competition for clonal lines of S. carolinense in a greenhouse experiment, and measured tolerance in terms of sexual and asexual fitness components. Compared to plants growing at low density, plants growing at high density had greater expression of and genetic variation in tolerance, and experienced greater fitness benefits from tolerance when damaged. Tolerance was not costly for plants growing at either density, and only plants growing at low density benefited from tolerance when undamaged, perhaps due to greater intrinsic growth rates of more tolerant genotypes. These results suggest that competition is likely to facilitate the evolution of tolerance in S. carolinense, and perhaps in other plants that regularly experience competition, while spatio-temporal variation in density may maintain genetic variation in tolerance.

  20. Intra-specific pelage color variation in a South American small rodent species

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    M. L. Sandoval Salinas

    Full Text Available Abstract Intra-specific color variation is often underestimated by researchers, and among mammals, intra-specific differences in coloration are poorly documented for most species. The main goal of this study was to apply an objective color measurement methodology to the study of a specific problem: the detection, if any, of patterns of changes in the fur color of specimens of Akodon budini in relation to biological (i.e., sex and environmental (i.e., season variables. We hypothesize that coat color will be more homogeneous in males than in females and that coat color will be darker in winter than in summer, the latter being orange. We measured the pelage color on five points over the dorsal surface of 26 A. budini museum specimens using a spectroradiometer and a diffuse illumination cabin. We used Principal Component Analysis to describe the association between the color variables, sex and season, and each of the observations. We then used general linear models of Analysis of Variance to examine relationships between color data, season, and sex. The results clearly confirm the hypothesis related to seasonal coat color change but do not directly confirm the hypothesis related to changes in coat color in relation to sex, and we show the complexity of the studied pattern. In conclusion, undoubtedly, the studied variables should accordingly be considered when studying the coloration of specimens for characterization, identification and discrimination of different taxonomic units based on color.

  1. Intra-specific pelage color variation in a South American small rodent species.

    Science.gov (United States)

    Sandoval Salinas, M L; Barquez, R M; Colombo, E M; Sandoval, J D

    2017-03-01

    Intra-specific color variation is often underestimated by researchers, and among mammals, intra-specific differences in coloration are poorly documented for most species. The main goal of this study was to apply an objective color measurement methodology to the study of a specific problem: the detection, if any, of patterns of changes in the fur color of specimens of Akodon budini in relation to biological (i.e., sex) and environmental (i.e., season) variables. We hypothesize that coat color will be more homogeneous in males than in females and that coat color will be darker in winter than in summer, the latter being orange. We measured the pelage color on five points over the dorsal surface of 26 A. budini museum specimens using a spectroradiometer and a diffuse illumination cabin. We used Principal Component Analysis to describe the association between the color variables, sex and season, and each of the observations. We then used general linear models of Analysis of Variance to examine relationships between color data, season, and sex. The results clearly confirm the hypothesis related to seasonal coat color change but do not directly confirm the hypothesis related to changes in coat color in relation to sex, and we show the complexity of the studied pattern. In conclusion, undoubtedly, the studied variables should accordingly be considered when studying the coloration of specimens for characterization, identification and discrimination of different taxonomic units based on color.

  2. Intraspecific variation in alkaline phosphatase activity in Phaeodactylum tricornutum (Bacillariophyceae, Bohlin

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    Domênica Teixeira de Lima

    2016-01-01

    Full Text Available ABSTRACT To describe potential intraspecific variation in phosphorus incorporation in two strains of Phaeodactylum tricornutum (Bohlin, Ub3 and Ub7, alkaline phosphatase (AP activity was evaluated via enzyme-labeled fluorescence assay. Analysis using the probe ELF-97(r provides individual evaluation, and therefore can determine the nutritional status of inorganic phosphorus in phytoplanktonic cells. Bioassays compared the control treatment to both phosphate-enriched and phosphate-depleted treatments by varying only the phosphate concentration in the media. The P. tricornutum strains exhibited differences in their development when incubated in the phosphate-enriched media. The development of the Ub7 strain differed by exhibiting "luxury uptake" and utilization of organic phosphorus, and the alkaline phosphatase analysis indicated limitations of this clone under such conditions. The Ub7 strain showed higher AP activity, when compared to Ub3, in the P-enriched condition. P. tricornutum presented increases in AP activity and low variation in Surface/Volume ratio, by increasing biovolume and its maximum linear dimension, as strategies for phosphate incorporation. Our results highlight intraspecific differences in alkaline phosphatase activity, and hence differences in the incorporation of organic phosphorus, as the tested species regulated enzymatic activity under different external phosphate concentrations.

  3. Light induced intraspecific variability in response to thermal stress in the hard coral Stylophora pistillata

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    Arjen Tilstra

    2017-10-01

    Full Text Available Recent research suggests that prior exposure of several months to elevated irradiance induces enhanced thermal tolerance in scleractinian corals. While this tolerance has been reported at the species level, individual coral colonies may react differently due to individual variability in thermal tolerance. As thermal anomalies are predicted to become common in the upcoming future, intraspecific variation may be key to the survival of coral populations. In order to study light-history based thermal stress responses on individual colonies, we developed a preliminary microcosm experiment where three randomly chosen, aquacultured colonies of the model coral Stylophora pistillata were exposed to two irradiance treatments (200 and 400 μmol photons m−2 s−1 for 31 days, followed by artificially induced heat stress (∼33.4 °C. We found different responses to occur at both the intraspecific and the intracolonial levels, as indicated by either equal, less severe, delayed, and/or even non-necrotic responses of corals previously exposed to the irradiance of 400 compared to 200 μmol photons m−2 s−1. In addition, all individual colonies revealed light-enhanced calcification. Finally, elevated irradiance resulted in a lower chlorophyll a concentration in one colony compared to the control treatment, and the same colony displayed more rapid bleaching compared to the other ones. Taken together, this study highlights the potential importance of intra-individual variability in physiological responses of scleractinian corals and provides recommendations for improving methodological designs for future studies.

  4. Intraspecific Crossability in Andrographis paniculata Nees: A Barrier against Breeding of the Species

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    Alireza Valdiani

    2012-01-01

    Full Text Available The ambiguity of crossability in Andrographis paniculata (AP was pointed out in the present research. Accordingly, the effects of different style length and crossing time on intraspecific crossability of seven AP accessions in 21 possible combinations were investigated. The best results came out between 08:00 to 11:00 h for manual out-crossing of AP, while the time from 12:00 to 18:00 h showed a decreasing trend. Moreover, 12 mm style length was found as the most proper phenological stage in terms of stigmatic receptivity to perform out-crossing in this plant. All in all, AP behaved unlikely in each combination, and a significant difference was observed in crossability of AP accessions (<0.01. The lowest and highest crossability rate was found in hybrids 21 (11261NS × 11344K and 27 (11322PA × 11350T with 0.25% and 13.33%, respectively. Furthermore, a significant negative relationship between style length and crossibility (2=0.762∗∗ was recorded in this research. As a final conclusion, crossing time and proper style length can improve the intraspecific crossability in the species, considerably. Despite all the mentioned contrivances, we still believe that a genetic incongruity should be involved as an additional obstacle in crossability of those combinations that failed or responded deficiently to outcrossing.

  5. Specialist-generalist model of body temperature regulation can be applied at the intraspecific level.

    Science.gov (United States)

    Przybylska, Anna S; Boratyński, Jan S; Wojciechowski, Michał S; Jefimow, Małgorzata

    2017-07-01

    According to theoretical predictions, endothermic homeotherms can be classified as either thermal specialists or thermal generalists. In high cost environments, thermal specialists are supposed to be more prone to using facultative heterothermy than generalists. We tested this hypothesis at the intraspecific level using male laboratory mice (C57BL/cmdb) fasted under different thermal conditions (20 and 10°C) and for different time periods (12-48 h). We predicted that variability of body temperature ( T b ) and time spent with T b below normothermy would increase with the increase of environmental demands (duration of fasting and cold). To verify the above prediction, we measured T b and energy expenditure of fasted mice. We did not record torpor bouts but we found that variations in T b and time spent in hypothermia increased with environmental demands. In response to fasting, mice also decreased their energy expenditure. Moreover, animals that showed more precise thermoregulation when fed had more variable T b when fasted. We postulate that the prediction of the thermoregulatory generalist-specialist trade-off can be applied at the intraspecific level, offering a valid tool for identifying mechanistic explanations of the differences in animal responses to variations in energy supply. © 2017. Published by The Company of Biologists Ltd.

  6. How recruitment, intraspecific interactions, and predation control species borders in a tidal estuary.

    Science.gov (United States)

    Leonard, George H; Ewanchuk, Patrick J; Bertness, Mark D

    1999-03-01

    We examined the relative contribution of recruitment, intraspecific species interactions, and predation in controlling the upper intertidal border of the northern acorn barnacle, Semibalanusbalanoides, in a tidal estuary in Maine. We hypothesized that the contracted border at sites that experienced low tidal currents was due to flow-mediated recruitment that resulted in reduced survival due to the absence of neighbor buffering of thermal stress (i.e., positive intraspecific interactions). We tested this hypothesis by manipulating the density of recently settled barnacles and their thermal environment in a field experiment. Counter to our original hypothesis, barnacles with neighbors suffered severe mortality at low-flow sites. When density-dependent predation by the green crab (Carcinusmaenus) was experimentally eliminated, however, we did detect evidence for positive interactions at the low-flow sites but not at the high-flow sites. In spite of the close proximity of the sites, maximum daily rock temperatures at the low-flow sites were slightly, but consistently, greater than those at high-flow sites. Our findings suggest that the upper intertidal border of S. balanoides in the Damariscotta River is limited at low-flow sites by a combination of reduced recruitment, elevated mortality from thermal stress and enhanced predation by green crabs. More generally, our findings highlight how physical stress and predation interact to alter the nature of density-dependent species interactions in natural assemblages.

  7. Solid-phase microextraction-based cuticular hydrocarbon profiling for intraspecific delimitation in Acyrthosiphon pisum.

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    Nan Chen

    Full Text Available Insect cuticular hydrocarbons (CHCs play critical roles in reducing water loss and chemical communication. Species-specific CHC profiles have been used increasingly as an excellent character for species classification. However, considerably less is known about their potential for population delimitation within species. The aims of this study were to develop a solid-phase microextraction (SPME-based CHC collection method and to investigate whether CHC profiles could serve as potential chemotaxonomic tools for intraspecific delimitation in Acyrthosiphon pisum. Optimization of fibers for SPME sampling revealed that 7 μm polydimethylsiloxane (PDMS demonstrated the most efficient adsorption of CHCs among five different tested fibers. SPME sampling showed good reproducibility with repeated collections of CHCs from a single aphid. Validation of SPME was performed by comparing CHC profiles with those from conventional hexane extractions. The two methods showed no qualitative differences in CHCs, although SPME appeared to extract relatively fewer short-chained CHCs. While CHC profiles of a given population differed among developmental stages, wing dimorphism types, and host plants, wingless adult aphids showed very low variance in relative proportions of individual CHC components. Reproducibility of CHC profiles was explored further to classify wingless adult morphs of A. pisum from five different geographic regions that showed no variation in mitochondrial COI gene sequences. Our results demonstrate that CHC profiles are useful in intraspecific delimitation in the field of insect chemotaxonomy.

  8. Solid-phase microextraction-based cuticular hydrocarbon profiling for intraspecific delimitation in Acyrthosiphon pisum

    Science.gov (United States)

    Chen, Nan; Bai, Yu; Fan, Yong-Liang

    2017-01-01

    Insect cuticular hydrocarbons (CHCs) play critical roles in reducing water loss and chemical communication. Species-specific CHC profiles have been used increasingly as an excellent character for species classification. However, considerably less is known about their potential for population delimitation within species. The aims of this study were to develop a solid-phase microextraction (SPME)-based CHC collection method and to investigate whether CHC profiles could serve as potential chemotaxonomic tools for intraspecific delimitation in Acyrthosiphon pisum. Optimization of fibers for SPME sampling revealed that 7 μm polydimethylsiloxane (PDMS) demonstrated the most efficient adsorption of CHCs among five different tested fibers. SPME sampling showed good reproducibility with repeated collections of CHCs from a single aphid. Validation of SPME was performed by comparing CHC profiles with those from conventional hexane extractions. The two methods showed no qualitative differences in CHCs, although SPME appeared to extract relatively fewer short-chained CHCs. While CHC profiles of a given population differed among developmental stages, wing dimorphism types, and host plants, wingless adult aphids showed very low variance in relative proportions of individual CHC components. Reproducibility of CHC profiles was explored further to classify wingless adult morphs of A. pisum from five different geographic regions that showed no variation in mitochondrial COI gene sequences. Our results demonstrate that CHC profiles are useful in intraspecific delimitation in the field of insect chemotaxonomy. PMID:28859151

  9. The evolutionary and phylogeographic history of woolly mammoths: a comprehensive mitogenomic analysis

    Science.gov (United States)

    Chang, Dan; Knapp, Michael; Enk, Jacob; Lippold, Sebastian; Kircher, Martin; Lister, Adrian; MacPhee, Ross D. E.; Widga, Christopher; Czechowski, Paul; Sommer, Robert; Hodges, Emily; Stümpel, Nikolaus; Barnes, Ian; Dalén, Love; Derevianko, Anatoly; Germonpré, Mietje; Hillebrand-Voiculescu, Alexandra; Constantin, Silviu; Kuznetsova, Tatyana; Mol, Dick; Rathgeber, Thomas; Rosendahl, Wilfried; Tikhonov, Alexey N.; Willerslev, Eske; Hannon, Greg; Lalueza-Fox, Carles; Joger, Ulrich; Poinar, Hendrik; Hofreiter, Michael; Shapiro, Beth

    2017-01-01

    Near the end of the Pleistocene epoch, populations of the woolly mammoth (Mammuthus primigenius) were distributed across parts of three continents, from western Europe and northern Asia through Beringia to the Atlantic seaboard of North America. Nonetheless, questions about the connectivity and temporal continuity of mammoth populations and species remain unanswered. We use a combination of targeted enrichment and high-throughput sequencing to assemble and interpret a data set of 143 mammoth mitochondrial genomes, sampled from fossils recovered from across their Holarctic range. Our dataset includes 54 previously unpublished mitochondrial genomes and significantly increases the coverage of the Eurasian range of the species. The resulting global phylogeny confirms that the Late Pleistocene mammoth population comprised three distinct mitochondrial lineages that began to diverge ~1.0–2.0 million years ago (Ma). We also find that mammoth mitochondrial lineages were strongly geographically partitioned throughout the Pleistocene. In combination, our genetic results and the pattern of morphological variation in time and space suggest that male-mediated gene flow, rather than large-scale dispersals, was important in the Pleistocene evolutionary history of mammoths. PMID:28327635

  10. Consequences of intra-specific metabolic diversity in plants for soil organisms : a baseline approach for evaluating ecological effects of genetic modifications

    NARCIS (Netherlands)

    Kabouw, P.

    2012-01-01

    Plant intra-specific variation, i.e. variation within a plant species, is known to affect organisms that are directly associated to plants. These effects may be due to for example differences in nutritional quality or defensive metabolites. Plant intra-specific variation can also affect

  11. Genotyping of Mycobacterium tuberculosis clinical isolates in two cities of Turkey: Description of a new family of genotypes that is phylogeographically specific for Asia Minor

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    Durmaz Riza

    2005-07-01

    Full Text Available Abstract Background Population-based bacterial genetics using repeated DNA loci is an efficient approach to study the biodiversity and phylogeographical structure of human pathogens, such as Mycobacterium tuberculosis, the agent of tuberculosis. Indeed large genetic diversity databases are available for this pathogen and are regularly updated. No population-based polymorphism data were yet available for M. tuberculosis in Turkey, at the crossroads of Eurasia. Results A total of 245 DNAs from Mycobacterium tuberculosis clinical isolates from tuberculosis patients residing in Turkey (Malatya n = 147 or Ankara n = 98 were genotyped by spoligotyping, a high-throughput genotyping method based on the polymorphism of the Direct Repeat locus. Thirty-three spoligotyping-defined clusters including 206 patients and 39 unique patterns were found. The ST41 cluster, as designated according to the international SpolDB3 database project, represented one fourth and when gathered to three genotypes, ST53, ST50 and ST284, one half of all the isolates. Out of 34 clinical isolates harboring ST41 which were further genotyped by IS6110 and by MIRU-VNTR typing, a typical 2-copy IS6110-RFLP pattern and a "215125113322" MIRU-VNTR pattern were observed among 21 clinical isolates. Further search in various databases confirms the likely Turkish-phylogeographical specificity of this clonal complex. Conclusion We described a new phylogeographically-specific clone of M. tuberculosis, designated LAM7-TUR. Further investigations to assess its frequency within all regions of Turkey and its phylogeographical origin and phylogenetic position within the global M. tuberculosis phylogenetic tree will shed new light on its endemicity in Asia Minor.

  12. Niche separation in Varecia variegata rubra and Eulemur fulvus albifrons: II. Intraspecific patterns.

    Science.gov (United States)

    Vasey, Natalie

    2002-06-01

    Based on a year-long field study in northeastern Madagascar, I summarize annual patterns of niche use (food patch size, diet, forest height, and forest site) in two sympatric lemurs, Varecia variegata rubra and Eulemur fulvus albifrons. Furthermore, I examine intraspecific patterns of niche use according to sex, season, and reproductive stage in these two lemurs that differ in terms of energetic investment in reproduction. Lemurs as a group provide a special opportunity to test hypotheses concerning sex differences in niche use. Due to their body size monomorphism and seasonal, synchronous pattern of breeding, it is possible to directly evaluate whether sex differences in diet reflect high energetic investment in reproduction by females. Results confirm the hypothesis that intraspecific variation in niche use (e.g., sex differences, seasonal differences) would be more pronounced in V. v. rubra than in E. f. albifrons, due in large measure to the former's relatively high energetic investment in reproduction: 1a) Dietary sex differences in V. v. rubra are most pronounced during costly reproductive stages and involve acquisition of low-fiber, high-protein plant foods. Females of both species consume more seasonally available low-fiber protein (young leaves, flowers) relative to conspecific males during the hot dry season, but only in V. v. rubra females is this pattern also evident during gestation and lactation. 1b) The diets of female V. v. rubra and female E. f. albifrons are more similar to each other than are the diets of conspecific males and females in the case of V. v. rubra. This is not uniformly the case for female E. f. albifrons. This finding confirms a hypothesis put forward in Vasey ([2000] Am J Phys Anthropol 112:411-431) that energetic requirements of reproductive females drive niche separation more than do the energetic requirements of males. 1c) Both species synchronize most or all of lactation with seasonal food abundance and diversity. E. f

  13. Intraspecific non-sexual interactions of Grammostola schulzei (Araneae: Theraphosidae under laboratory conditions

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    Nelson E Ferretti

    2011-09-01

    Full Text Available Intraspecific interactions of araneomorph spiders have received considerable attention, but there are few detailed studies on intraspecific interactions of mygalomorph spiders. Moreover, a thorough understanding of theraphosid biology and ecology is necessary from a conservation standpoint because natural populations may be threatened by habitat disturbances and captures for pet commerce. We described the behavior of conspecific individuals of Grammostola schulzei during non-sexual interactions, under laboratory conditions. Pairs of individuals involving adult males, adult females and juveniles were confronted and observed in resident and intruder conditions, totalizing 115 trials. When confronted two adult females, they retreated or grappled, and performed gaping display with bite attempts, usually resulted in severe injury of the intruder spiders. When confronted females with large juveniles, we frequently observed cannibalism on juveniles. Juveniles exposed to females or to other juveniles retreated or made leg tapping with forelegs and palpal drumming, which are common displays of courting adult males. Adult males courted and clasped some juveniles, but juveniles avoided or reject clasping. The behaviors observed during intraspecific interactions could play an important role determining spatial distribution and could lead to behavioral adaptations of territoriality. Rev. Biol. Trop. 59 (3: 1173-1182. Epub 2011 September 01.Hay pocos estudios detallados sobre las interacciones intraespecíficas de arañas migalomorfas. Por lo tanto, se describe el comportamiento de individuos conspecíficos de Grammostola schulzei durante interacciones nosexuales en condiciones de laboratorio. Se confrontaron y observaron pares de individuos involucrando machos adultos, hembras adultas y juveniles en condiciones de locatarios y visitantes, totalizando 115 encuentros. Cuando dos hembras adultas se enfrentaron, retrocedieron o lucharon adoptando elevaciones

  14. Causes and Consequences of Intraspecific Variation in Nesting Behaviors: Insights from Blue Tits and Great Tits

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    Mark C. Mainwaring

    2017-05-01

    Full Text Available Nest building is an important and yet under-studied stage of the reproductive cycle in many taxa, including birds, and whilst we have a decent understanding of interspecific variation in avian nesting behaviors, our understanding of intraspecific variation in nesting behaviors is much less developed. This is largely because an insufficient number of studies have been performed on any one species to draw robust conclusions. Fortunately, though, the amount of research on the nesting behaviors of nestbox-breeding blue tits (Cyanistes caeruleus and great tits (Parus major has increased dramatically in recent years and their nesting behaviors are now sufficiently well-studied to offer useful insights into intraspecific variation in avian nesting behaviors. Studies show that individuals of both species select nest sites based on the presence and/or absence of conspecifics and heterospecifics and whilst neighbors were assumed to adversely affect focal individuals by competing for resources, they are now considered beneficial as they provide information about habitat quality and contribute to anti-predator defenses. Nest-building females accurately gauge local weather conditions and respond to predictable variation in environmental conditions by building nests with variable amounts of cup lining material to create suitable nest microclimates for nestlings. Meanwhile, both species vary the amount of aromatic plant materials in their nests in relation to the abundance of nest-dwelling parasites and pathogens and as aromatic plant materials also play a role in sexual selection then nest materials can have multiple functions. The height of nests is negatively correlated with the local risk of predation but whilst predator avoidance favors lower nests, sexual selection favors taller nests. In fact, higher quality females build taller nests that contain more green plant material which in turn influences the amount of care provided by males. This suggests

  15. Density-dependent intraspecific aggression regulates survival in northern Yellowstone wolves (Canis lupus).

    Science.gov (United States)

    Cubaynes, Sarah; MacNulty, Daniel R; Stahler, Daniel R; Quimby, Kira A; Smith, Douglas W; Coulson, Tim

    2014-11-01

    Understanding the population dynamics of top-predators is essential to assess their impact on ecosystems and to guide their management. Key to this understanding is identifying the mechanisms regulating vital rates. Determining the influence of density on survival is necessary to understand the extent to which human-caused mortality is compensatory or additive. In wolves (Canis lupus), empirical evidence for density-dependent survival is lacking. Dispersal is considered the principal way in which wolves adjust their numbers to prey supply or compensate for human exploitation. However, studies to date have primarily focused on exploited wolf populations, in which density-dependent mechanisms are likely weak due to artificially low wolf densities. Using 13 years of data on 280 collared wolves in Yellowstone National Park, we assessed the effect of wolf density, prey abundance and population structure, as well as winter severity, on age-specific survival in two areas (prey-rich vs. prey-poor) of the national park. We further analysed cause-specific mortality and explored the factors driving intraspecific aggression in the prey-rich northern area of the park. Overall, survival rates decreased during the study. In northern Yellowstone, density dependence regulated adult survival through an increase in intraspecific aggression, independent of prey availability. In the interior of the park, adult survival was less variable and density-independent, despite reduced prey availability. There was no effect of prey population structure in northern Yellowstone, or of winter severity in either area. Survival was similar among yearlings and adults, but lower for adults older than 6 years. Our results indicate that density-dependent intraspecific aggression is a major driver of adult wolf survival in northern Yellowstone, suggesting intrinsic density-dependent mechanisms have the potential to regulate wolf populations at high ungulate densities. When low prey availability or high

  16. Intraspecific competition affects population size and resource allocation in an ant dispersing by colony fission.

    Science.gov (United States)

    Boulay, Raphaël; Galarza, Juan A; Chéron, Blandine; Hefetz, Abraham; Lenoir, Alain; van Oudenhove, Louise; Cerdá, Xim

    2010-11-01

    Intraspecific competition is a pervasive phenomenon with important ecological and evolutionary consequences, yet its effect in natural populations remains controversial. Although numerous studies suggest that in many cases populations across all organisms are limited by density-dependent processes, this conclusion often relies on correlative data. Here, using an experimental approach, we examined the effect of intraspecific competition on population regulation of the ant Aphaenogaster senilis. In this species females are philopatric while males disperse by flying over relatively long distances. All colonies were removed from 15 experimental plots, except for one focal colony in each plot, while 15 other plots remained unmanipulated. After the first reproductive season, nest density in the experimental plots returned to a level nonsignificantly different from that in the control plots, which was not expected if the populations were indeed regulated by density-independent phenomena. In both the control plots and the experimental plots colonies remained overdispersed throughout the experiment, suggesting colony mutual exclusion. Nests outside the plots rapidly extended their foraging span, but we did not detect any significant inward migration into the experimental plots. Experimental reduction in density did not significantly affect the focal colonies' biomass, measured just before the first reproductive season. However, the ratio of males to workers-pupae biomasses was smaller in experimental plots, suggesting that colonies there had redirected part of the resources normally allocated to male production to the production instead of new workers. Microsatellite analysis indicated that, after the reproductive season, many colonies in the experimental plots were headed by a young queen that was the mother of the brood but not of the old workers, indicating that reduction in colony density stimulated fission of the remaining colonies. Finally, at the end of the

  17. A Novel Approach to Helicobacter pylori Pan-Genome Analysis for Identification of Genomic Islands.

    Directory of Open Access Journals (Sweden)

    Ikuo Uchiyama

    Full Text Available Genomes of a given bacterial species can show great variation in gene content and thus systematic analysis of the entire gene repertoire, termed the pan-genome, is important for understanding bacterial intra-species diversity, population genetics, and evolution. Here, we analyzed the pan-genome from 30 completely sequenced strains of the human gastric pathogen Helicobacter pylori belonging to various phylogeographic groups, focusing on 991 accessory (not fully conserved orthologous groups (OGs. We developed a method to evaluate the mobility of genes within a genome, using the gene order in the syntenically conserved regions as a reference, and classified the 991 accessory OGs into five classes: Core, Stable, Intermediate, Mobile, and Unique. Phylogenetic networks based on the gene content of Core and Stable classes are highly congruent with that created from the concatenated alignment of fully conserved core genes, in contrast to those of Intermediate and Mobile classes, which show quite different topologies. By clustering the accessory OGs on the basis of phylogenetic pattern similarity and chromosomal proximity, we identified 60 co-occurring gene clusters (CGCs. In addition to known genomic islands, including cag pathogenicity island, bacteriophages, and integrating conjugative elements, we identified some novel ones. One island encodes TerY-phosphorylation triad, which includes the eukaryote-type protein kinase/phosphatase gene pair, and components of type VII secretion system. Another one contains a reverse-transcriptase homolog, which may be involved in the defense against phage infection through altruistic suicide. Many of the CGCs contained restriction-modification (RM genes. Different RM systems sometimes occupied the same (orthologous locus in the strains. We anticipate that our method will facilitate pan-genome studies in general and help identify novel genomic islands in various bacterial species.

  18. Intraspecific variation in mitochondrial genome sequence, structure, and gene content in Silene vulgaris, an angiosperm with pervasive cytoplasmic male sterility

    Czech Academy of Sciences Publication Activity Database

    Sloan, D.B.; Müller, Karel; McCauley, D.; Taylor, D.R.; Štorchová, Helena

    2012-01-01

    Roč. 196, č. 4 (2012), s. 1228-1239 ISSN 0028-646X R&D Projects: GA ČR GA521/09/0261; GA MŠk(CZ) LC06004; GA MŠk ME09035 Institutional research plan: CEZ:AV0Z50380511 Keywords : cytoplasmic male sterility (CMS) * gynodioecy * intracellular gene transfer Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 6.736, year: 2012

  19. The effect of medium composition on ovary-slice culture and ovule culture in intraspecific Tulipa gesneriana crosses

    NARCIS (Netherlands)

    Creij, van M.G.M.; Kerckhoffs, D.M.F.J.; Bruijn, de S.M.; Tuyl, van J.M.; Vreugdenhil, D.

    2000-01-01

    The effect of several media components on the germination percentage of ovules in intraspecific T. gesneriana L. crosses was studied by using two embryo rescue techniques, viz. ovary-slice culture followed by ovule culture and direct ovule culture. The addition of 9% sucrose to medium for

  20. Are negative intra-specific interactions important for recruitment dynamics? A case study of Atlantic fish stocks.

    Czech Academy of Sciences Publication Activity Database

    Ricard, Daniel; Zimmermann, F.; Heino, M.

    2016-01-01

    Roč. 547, April (2016), s. 211-217 ISSN 0171-8630 R&D Projects: GA MŠk(CZ) EE2.3.30.0032 Institutional support: RVO:60077344 Keywords : cannibalism * intra-specific competition * recruitment * population dynamics * Atlantic Ocean Subject RIV: EH - Ecology , Behaviour Impact factor: 2.292, year: 2016

  1. Molecular evidence for extra-pair paternity and intraspecific brood parasitism in the Black-headed Gull

    Czech Academy of Sciences Publication Activity Database

    Ležalová-Piálková, Radka

    2011-01-01

    Roč. 152, č. 2 (2011), s. 291-295 ISSN 0021-8375 Institutional research plan: CEZ:AV0Z60930519 Keywords : Black-headed Gull * genetic mating system * extra-pair paternity * intraspecific brood parasitism Subject RIV: EG - Zoology Impact factor: 1.636, year: 2011

  2. The importance of intraspecific variation in tree responses to elevated [CO2]: breeding and management of future forests

    Science.gov (United States)

    One strategy for managing forests to sustain or increase productivity under global climate change is to initiate breeding programs which maximize responses to elevated [CO2] within species. The basis for any breeding program is intraspecific variation in the traits of interest, and for forests, grow...

  3. Intraspecific morphological and genetic variability in the European freshwater snail Radix labiata (Rossmaessler, 1835) (Gastropoda: Basommatophora: Lymnaeidae)

    NARCIS (Netherlands)

    Schniebs, K.; Glöer, P.; Vinarski, M.V.; Hundsdoerfer, A.K.

    2013-01-01

    Radix labiata is a widely distributed Palaearctic freshwater snail. This work aims to improve the knowledge of the intraspecific variability in the most important characters used for its determination. To find out which characters are really suitable to distinguish this species from other similar

  4. Comparative genomics of wild type yeast strains unveils important genome diversity

    Directory of Open Access Journals (Sweden)

    Pereira Patrícia M

    2008-11-01

    Full Text Available Abstract Background Genome variability generates phenotypic heterogeneity and is of relevance for adaptation to environmental change, but the extent of such variability in natural populations is still poorly understood. For example, selected Saccharomyces cerevisiae strains are variable at the ploidy level, have gene amplifications, changes in chromosome copy number, and gross chromosomal rearrangements. This suggests that genome plasticity provides important genetic diversity upon which natural selection mechanisms can operate. Results In this study, we have used wild-type S. cerevisiae (yeast strains to investigate genome variation in natural and artificial environments. We have used comparative genome hybridization on array (aCGH to characterize the genome variability of 16 yeast strains, of laboratory and commercial origin, isolated from vineyards and wine cellars, and from opportunistic human infections. Interestingly, sub-telomeric instability was associated with the clinical phenotype, while Ty element insertion regions determined genomic differences of natural wine fermentation strains. Copy number depletion of ASP3 and YRF1 genes was found in all wild-type strains. Other gene families involved in transmembrane transport, sugar and alcohol metabolism or drug resistance had copy number changes, which also distinguished wine from clinical isolates. Conclusion We have isolated and genotyped more than 1000 yeast strains from natural environments and carried out an aCGH analysis of 16 strains representative of distinct genotype clusters. Important genomic variability was identified between these strains, in particular in sub-telomeric regions and in Ty-element insertion sites, suggesting that this type of genome variability is the main source of genetic diversity in natural populations of yeast. The data highlights the usefulness of yeast as a model system to unravel intraspecific natural genome diversity and to elucidate how natural

  5. Comparative genomics of wild type yeast strains unveils important genome diversity.

    Science.gov (United States)

    Carreto, Laura; Eiriz, Maria F; Gomes, Ana C; Pereira, Patrícia M; Schuller, Dorit; Santos, Manuel A S

    2008-11-04

    Genome variability generates phenotypic heterogeneity and is of relevance for adaptation to environmental change, but the extent of such variability in natural populations is still poorly understood. For example, selected Saccharomyces cerevisiae strains are variable at the ploidy level, have gene amplifications, changes in chromosome copy number, and gross chromosomal rearrangements. This suggests that genome plasticity provides important genetic diversity upon which natural selection mechanisms can operate. In this study, we have used wild-type S. cerevisiae (yeast) strains to investigate genome variation in natural and artificial environments. We have used comparative genome hybridization on array (aCGH) to characterize the genome variability of 16 yeast strains, of laboratory and commercial origin, isolated from vineyards and wine cellars, and from opportunistic human infections. Interestingly, sub-telomeric instability was associated with the clinical phenotype, while Ty element insertion regions determined genomic differences of natural wine fermentation strains. Copy number depletion of ASP3 and YRF1 genes was found in all wild-type strains. Other gene families involved in transmembrane transport, sugar and alcohol metabolism or drug resistance had copy number changes, which also distinguished wine from clinical isolates. We have isolated and genotyped more than 1000 yeast strains from natural environments and carried out an aCGH analysis of 16 strains representative of distinct genotype clusters. Important genomic variability was identified between these strains, in particular in sub-telomeric regions and in Ty-element insertion sites, suggesting that this type of genome variability is the main source of genetic diversity in natural populations of yeast. The data highlights the usefulness of yeast as a model system to unravel intraspecific natural genome diversity and to elucidate how natural selection shapes the yeast genome.

  6. Intra-specific diversity of Serratia marcescens in Anopheles mosquito midgut defines Plasmodium transmission capacity

    Science.gov (United States)

    Bando, Hironori; Okado, Kiyoshi; Guelbeogo, Wamdaogo M.; Badolo, Athanase; Aonuma, Hiroka; Nelson, Bryce; Fukumoto, Shinya; Xuan, Xuenan; Sagnon, N'Fale; Kanuka, Hirotaka

    2013-01-01

    A critical stage in malaria transmission occurs in the Anopheles mosquito midgut, when the malaria parasite, Plasmodium, ingested with blood, first makes contact with the gut epithelial surface. To understand the response mechanisms within the midgut environment, including those influenced by resident microbiota against Plasmodium, we focus on a midgut bacteria species' intra-specific variation that confers diversity to the mosquito's competency for malaria transmission. Serratia marcescens isolated from either laboratory-reared mosquitoes or wild populations in Burkina Faso shows great phenotypic variation in its cellular and structural features. Importantly, this variation is directly correlated with its ability to inhibit Plasmodium development within the mosquito midgut. Furthermore, this anti-Plasmodium function conferred by Serratia marcescens requires increased expression of the flagellum biosynthetic pathway that is modulated by the motility master regulatory operon, flhDC. These findings point to new strategies for controlling malaria through genetic manipulation of midgut bacteria within the mosquito. PMID:23571408

  7. Intraspecific genetic diversity of Oenococcus oeni as derived from DNA fingerprinting and sequence analyses.

    Science.gov (United States)

    Zavaleta, A I; Martínez-Murcia, A J; Rodríguez-Valera, F

    1997-04-01

    The intraspecific genetic diversity of Oenococcus oeni, the key organism in the malolactic fermentation of wine, has been evaluated by random amplified polymorphic DNA (RAPD), ribotyping, small-plasmid content, and sequencing of RAPD markers with widespread distribution among the strains. Collection strains representing the diversity of this species have been studied together with some new isolates, many of which were obtained from wines produced by spontaneous malolactic fermentation. The RAPD profiles were strain specific and discerned two main groups of strains coincident with clusters obtained by macrorestriction typing in a previous work. Ribotyping and the conservation of RAPD markers indicates that O. oeni is a relatively homogeneous species. Furthermore, identical DNA sequences of some RAPD markers among strains representative of the most divergent RAPD clusters indicates that O. oeni is indeed a phylogenetically tight group, probably corresponding to a single clone, or clonal line of descent, specialized to grow in the wine environment and universally spread.

  8. Role of intraspecific competition in the coexistence of mobile populations in spatially extended ecosystems

    Science.gov (United States)

    Yang, Rui; Wang, Wen-Xu; Lai, Ying-Cheng; Grebogi, Celso

    2010-06-01

    Evolutionary-game based models of nonhierarchical, cyclically competing populations have become paradigmatic for addressing the fundamental problem of species coexistence in spatially extended ecosystems. We study the role of intraspecific competition in the coexistence and find that the competition can strongly promote the coexistence for high individual mobility in the sense that stable coexistence can arise in parameter regime where extinction would occur without the competition. The critical value of the competition rate beyond which the coexistence is induced is found to be independent of the mobility. We derive a theoretical model based on nonlinear partial differential equations to predict the critical competition rate and the boundaries between the coexistence and extinction regions in a relevant parameter space. We also investigate pattern formation and well-mixed spatiotemporal population dynamics to gain further insights into our findings.

  9. Strain specific differences in intraspecific competition in Aedes albopictus (Diptera: Culicidae).

    Science.gov (United States)

    Kesavaraju, Banugopan; Afify, Ali; Gaugler, Randy

    2012-09-01

    Malathion is an organophosphate insecticide that is used for the control of adult mosquitoes and agricultural pests. Recent studies have shown that malathion affects competition among mosquitoes in the larval stage. Individuals from laboratory colonies are often used in experiments but it is not known whether there is a difference between laboratory and field strains in their response to competition and malathion. Intraspecific larval competition in the presence of malathion (0.11 mg/liter) was compared between laboratory and field strains of Aedes albopictus (Skuse), a native of Asia that has established in the United States. There was no difference in the responses of the two strains to the presence of malathion. The fitness (finite growth rate) of the field strain decreased at the highest larval density tested but there was no difference in fitness across densities for the laboratory strain. This finding suggests that laboratory rearing could reduce sensitivity to crowding.

  10. Paternal, maternal, and biparental inheritance of the chloroplast genome in Passiflora (Passifloraceae): implications for phylogenetic studies.

    Science.gov (United States)

    Hansen, A Katie; Escobar, Linda K; Gilbert, Lawrence E; Jansen, Robert K

    2007-01-01

    Patterns of inheritance of the chloroplast genome in Passiflora were analyzed by examining the progeny from both interspecific and intraspecific crosses. Artificial crosses of field-collected material were performed in greenhouses at The University of Texas at Austin. DNA from fresh leaf material was analyzed by Southern blot techniques to identify the donor of the chloroplast genome. Initially, single progeny were analyzed for 11 crosses; two intraspecific crosses demonstrated maternal inheritance, whereas the nine interspecific crosses had paternal inheritance. Subsequently, the donor of the chloroplast genome was determined for multiple progeny in seven crosses. Passiflora oerstedii × P. retipetala showed strict paternal inheritance in all of 17 progeny. A series of five crosses and backcrosses between P. oerstedii and P. menispermifolia demonstrated strictly paternal inheritance. Finally, when 15 progeny were analyzed for the P. costaricensis × P. costaricensis cross, 12 of the 15 showed maternal inheritance, whereas the remaining three were biparental. Interestingly, all interspecific crosses had primarily paternal inheritance, whereas all intraspecific crosses had primarily maternal inheritance. The implications of heteroplasmy on phylogenetic analyses of chloroplast DNA are discussed.

  11. Intraspecific variation in vertical habitat use by tiger sharks (Galeocerdo cuvier) in the western North Atlantic

    Science.gov (United States)

    Vaudo, Jeremy J; Wetherbee, Bradley M; Harvey, Guy; Nemeth, Richard S; Aming, Choy; Burnie, Neil; Howey-Jordan, Lucy A; Shivji, Mahmood S

    2014-01-01

    Tiger sharks (Galeocerdo cuvier) are a wide ranging, potentially keystone predator species that display a variety of horizontal movement patterns, making use of coastal and pelagic waters. Far less, however, is known about their vertical movements and use of the water column. We used pop-up satellite archival tags with two data sampling rates (high rate and standard rate tags) to investigate the vertical habitat use and diving behavior of tiger sharks tagged on the Puerto Rico–Virgin Islands platform and off Bermuda between 2008 and 2009. Useable data were received from nine of 14 sharks tagged, tracked over a total of 529 days. Sharks spent the majority of their time making yo-yo dives within the upper 50 m of the water column and considerable time within the upper 5 m of the water column. As a result, sharks typically occupied a narrow daily temperature range (∼2°C). Dives to greater than 200 m were common, and all sharks made dives to at least 250 m, with one shark reaching a depth of 828 m. Despite some similarities among individuals, a great deal of intraspecific variability in vertical habit use was observed. Four distinct depth distributions that were not related to tagging location, horizontal movements, sex, or size were detected. In addition, similar depth distributions did not necessitate similar dive patterns among sharks. Recognition of intraspecific variability in habitat use of top predators can be crucial for effective management of these species and for understanding their influence on ecosystem dynamics. PMID:24963376

  12. Intraspecific Variation in and Environment-Dependent Resource Allocation to Embryonic Development Time in Common Terns.

    Science.gov (United States)

    Vedder, Oscar; Kürten, Nathalie; Bouwhuis, Sandra

    Embryonic development time is thought to impact life histories through trade-offs against life-history traits later in life, yet the inference is based on interspecific comparative analyses only. It is largely unclear whether intraspecific variation in embryonic development time that is not caused by environmental differences occurs, which would be required to detect life-history trade-offs. Here we performed a classical common-garden experiment by incubating fresh eggs of free-living common terns (Sterna hirundo) in a controlled incubation environment at two different temperatures. Hatching success was high but was slightly lower at the lower temperature. While correcting for effects of year, incubation temperature, and laying order, we found significant variation in the incubation time embryos required until hatching and in their heart rate. Embryonic heart rate was significantly positively correlated within clutches, and a similar tendency was found for incubation time, suggesting that intrinsic differences in embryonic development rate between offspring of different parents exist. Incubation time and embryonic heart rate were strongly correlated: embryos with faster heart rates required shorter incubation time. However, after correction for heart rate, embryos still required more time for development at the lower incubation temperature. This suggests that processes other than development require a greater share of resources in a suboptimal environment and that relative resource allocation to development is, therefore, environment dependent. We conclude that there is opportunity to detect intraspecific life-history trade-offs with embryonic development time and that the resolution of trade-offs may differ between embryonic environments.

  13. Epigenetic variation predicts regional and local intraspecific functional diversity in a perennial herb.

    Science.gov (United States)

    Medrano, Mónica; Herrera, Carlos M; Bazaga, Pilar

    2014-10-01

    The ecological significance of epigenetic variation has been generally inferred from studies on model plants under artificial conditions, but the importance of epigenetic differences between individuals as a source of intraspecific diversity in natural plant populations remains essentially unknown. This study investigates the relationship between epigenetic variation and functional plant diversity by conducting epigenetic (methylation-sensitive amplified fragment length polymorphisms, MSAP) and genetic (amplified fragment length polymorphisms, AFLP) marker-trait association analyses for 20 whole-plant, leaf and regenerative functional traits in a large sample of wild-growing plants of the perennial herb Helleborus foetidus from ten sampling sites in south-eastern Spain. Plants differed widely in functional characteristics, and exhibited greater epigenetic than genetic diversity, as shown by per cent polymorphism of MSAP fragments (92%) or markers (69%) greatly exceeding that for AFLP ones (41%). After controlling for genetic structuring and possible cryptic relatedness, every functional trait considered exhibited a significant association with at least one AFLP or MSAP marker. A total of 27 MSAP (13.0% of total) and 12 AFLP (4.4%) markers were involved in significant associations, which explained on average 8.2% and 8.0% of trait variance, respectively. Individual MSAP markers were more likely to be associated with functional traits than AFLP markers. Between-site differences in multivariate functional diversity were directly related to variation in multilocus epigenetic diversity after multilocus genetic diversity was statistically accounted for. Results suggest that epigenetic variation can be an important source of intraspecific functional diversity in H. foetidus, possibly endowing this species with the capacity to exploit a broad range of ecological conditions despite its modest genetic diversity. © 2014 John Wiley & Sons Ltd.

  14. Network analysis reveals contrasting effects of intraspecific competition on individual vs. population diets.

    Science.gov (United States)

    Araújo, Márcio S; Guimarães, Paulo R; Svanbäck, Richard; Pinheiro, Aluisio; Guimarães, Paulo; Dos Reis, Sérgio F; Bolnick, Daniel I

    2008-07-01

    Optimal foraging theory predicts that individuals should become more opportunistic when intraspecific competition is high and preferred resources are scarce. This density-dependent diet shift should result in increased diet breadth for individuals as they add previously unused prey to their repertoire. As a result, the niche breadth of the population as a whole should increase. In a recent study, R. Svanbäck and D. I. Bolnick confirmed that intraspecific competition led to increased population diet breadth in threespine stickleback (Gasterosteus aculeatus). However, individual diet breadth did not expand as resource levels declined. Here, we present a new method based on complex network theory that moves beyond a simple measure of diet breadth, and we use the method to reexamine the stickleback experiment. This method reveals that the population as a whole added new types of prey as stickleback density was increased. However, whereas foraging theory predicts that niche expansion is achieved by individuals accepting new prey in addition to previously preferred prey, we found that a subset of individuals ceased to use their previously preferred prey, even though other members of their population continued to specialize on the original prey types. As a result, populations were subdivided into groups of ecologically similar individuals, with diet variation among groups reflecting phenotype-dependent changes in foraging behavior as prey density declined. These results are consistent with foraging theory if we assume that quantitative trait variation among consumers affects prey preferences, and if cognitive constraints prevent individuals from continuing to use their formerly preferred prey while adding new prey.

  15. The Orphan Gene dauerless Regulates Dauer Development and Intraspecific Competition in Nematodes by Copy Number Variation.

    Science.gov (United States)

    Mayer, Melanie G; Rödelsperger, Christian; Witte, Hanh; Riebesell, Metta; Sommer, Ralf J

    2015-06-01

    Many nematodes form dauer larvae when exposed to unfavorable conditions, representing an example of phenotypic plasticity and a major survival and dispersal strategy. In Caenorhabditis elegans, the regulation of dauer induction is a model for pheromone, insulin, and steroid-hormone signaling. Recent studies in Pristionchus pacificus revealed substantial natural variation in various aspects of dauer development, i.e. pheromone production and sensing and dauer longevity and fitness. One intriguing example is a strain from Ohio, having extremely long-lived dauers associated with very high fitness and often forming the most dauers in response to other strains' pheromones, including the reference strain from California. While such examples have been suggested to represent intraspecific competition among strains, the molecular mechanisms underlying these dauer-associated patterns are currently unknown. We generated recombinant-inbred-lines between the Californian and Ohioan strains and used quantitative-trait-loci analysis to investigate the molecular mechanism determining natural variation in dauer development. Surprisingly, we discovered that the orphan gene dauerless controls dauer formation by copy number variation. The Ohioan strain has one dauerless copy causing high dauer formation, whereas the Californian strain has two copies, resulting in strongly reduced dauer formation. Transgenic animals expressing multiple copies do not form dauers. dauerless is exclusively expressed in CAN neurons, and both CAN ablation and dauerless mutations increase dauer formation. Strikingly, dauerless underwent several duplications and acts in parallel or downstream of steroid-hormone signaling but upstream of the nuclear-hormone-receptor daf-12. We identified the novel or fast-evolving gene dauerless as inhibitor of dauer development. Our findings reveal the importance of gene duplications and copy number variations for orphan gene function and suggest daf-12 as major target for

  16. Effects of soil nutrient heterogeneity on intraspecific competition in the invasive, clonal plant Alternanthera philoxeroides.

    Science.gov (United States)

    Zhou, Jian; Dong, Bi-Cheng; Alpert, Peter; Li, Hong-Li; Zhang, Ming-Xiang; Lei, Guang-Chun; Yu, Fei-Hai

    2012-03-01

    Fine-scale, spatial heterogeneity in soil nutrient availability can increase the growth of individual plants, the productivity of plant communities and interspecific competition. If this is due to the ability of plants to concentrate their roots where nutrient levels are high, then nutrient heterogeneity should have little effect on intraspecific competition, especially when there are no genotypic differences between individuals in root plasticity. We tested this hypothesis in a widespread, clonal species in which individual plants are known to respond to nutrient heterogeneity. Plants derived from a single clone of Alternanthera philoxeroides were grown in the greenhouse at low or high density (four or 16 plants per 27·5 × 27·5-cm container) with homogeneous or heterogeneous availability of soil nutrients, keeping total nutrient availability per container constant. After 9 weeks, measurements of size, dry mass and morphology were taken. Plants grew more in the heterogeneous than in the homogeneous treatment, showing that heterogeneity promoted performance; they grew less in the high- than in the low-density treatment, showing that plants competed. There was no interactive effect of nutrient heterogeneity and plant density, supporting the hypothesis that heterogeneity does not affect intraspecific competition in the absence of genotypic differences in plasticity. Treatments did not affect morphological characteristics such as specific leaf area or root/shoot ratio. Results indicate that fine-scale, spatial heterogeneity in the availability of soil nutrients does not increase competition when plants are genetically identical, consistent with the suggestion that effects of heterogeneity on competition depend upon differences in plasticity between individuals. Heterogeneity is only likely to increase the spread of monoclonal, invasive populations such as that of A. philoxeroides in China.

  17. Inter- and intra-specific competition of duckweed under multiple heavy metal contaminated water.

    Science.gov (United States)

    Zhao, Zhao; Shi, Huijuan; Kang, Xianjiang; Liu, Cunqi; Chen, Lingci; Liang, Xiaofei; Jin, Lei

    2017-11-01

    The influences of intra- and inter-species competition on ecosystems are poorly understood. Lemna aequinoctialis and Spirodela polyrhiza were used to assess the effects of exposure to different concentrations of multiple heavy metals (copper-cadmium-zinc), when the plants were grown in mixed- or mono-culture. Parameters assessed included relative growth rate (RGR), content of chlorophyll, glutathione (GSH), malondialdehyde (MDA), as well as the activity of catalase (CAT), superoxide dismutase (SOD) and peroxidase (POD). Inter-specific competition was affected by metal concentration, with results indicating that inter-specific competition significantly affected duckweed growth and metal uptake in different heavy metal exposure conditions. Inter-specific competition increased growth rate of duckweed under high metal concentrations, although when compared with intra-specific competition, it caused no obvious differences under low metal concentrations. The growth of L. aequinoctialis was further increased in mixed culture when exposed to high metal concentrations, with inter-specific competition increasing the content of cadmium and zinc, while decreasing copper content of L. aequinoctialis compared with under intra-specific conditions. Conversely, inter-specific competition increased the content of copper and cadmium of S. polyrhiza, without causing obvious differences in zinc accumulation under high ambient concentrations. Under high metal conditions, inter-specific competition increased antioxidant enzyme activities in duckweed species, increasing resistance to heavy metals. Results show that inter-specific competition makes duckweed develop mechanisms to increase fitness and survival, such as enhancement of antioxidant enzyme activities, rather than limiting metal uptake when exposed to high concentrations of multiple metals. Copyright © 2017 Elsevier B.V. All rights reserved.

  18. Ancient DNA analyses reveal contrasting phylogeographic patterns amongst kiwi (Apteryx spp. and a recently extinct lineage of spotted kiwi.

    Directory of Open Access Journals (Sweden)

    Lara D Shepherd

    Full Text Available The little spotted kiwi (Apteryx owenii is a flightless ratite formerly found throughout New Zealand but now greatly reduced in distribution. Previous phylogeographic studies of the related brown kiwi (A. mantelli, A. rowi and A. australis, with which little spotted kiwi was once sympatric, revealed extremely high levels of genetic structuring, with mitochondrial DNA haplotypes often restricted to populations. We surveyed genetic variation throughout the present and pre-human range of little spotted kiwi by obtaining mitochondrial DNA sequences from contemporary and ancient samples. Little spotted kiwi and great spotted kiwi (A. haastii formed a monophyletic clade sister to brown kiwi. Ancient samples of little spotted kiwi from the northern North Island, where it is now extinct, formed a lineage that was distinct from remaining little spotted kiwi and great spotted kiwi lineages, potentially indicating unrecognized taxonomic diversity. Overall, little spotted kiwi exhibited much lower levels of genetic diversity and structuring than brown kiwi, particularly through the South Island. Our results also indicate that little spotted kiwi (or at least hybrids involving this species survived on the South Island mainland until more recently than previously thought.

  19. Phylogeographical Analysis on Squalidus argentatus Recapitulates Historical Landscapes and Drainage Evolution on the Island of Taiwan and Mainland China

    Directory of Open Access Journals (Sweden)

    Hung-Du Lin

    2012-01-01

    Full Text Available Phylogeographical analyses on Squalidus argentatus samples from thirteen localities within mainland China and Taiwan were conducted for biogeographic studies, as their dispersal strictly depends on geological evolution of the landmasses. A total of 95 haplotypes were genotyped for mtDNA cyt b gene in 160 specimens from nine river systems. Relatively high levels of haplotype diversity (h = 0.984 and low levels of nucleotide diversity (π = 0.020 were detected in S. argentatus. Two major phylogenetic haplotype groups, A and B, were revealed via phylogenetic analysis. The degree of intergroup divergence (3.96% indicates that these groups diverged about 4.55 myr (million years ago. Haplotype network and population analyses indicated significant genetic structure (FST = 0.775, largely concordant with the geographical location of the populations. According to SAMOVA analysis, we divided these populations into four units: Yangtze-Pearl, Qiantang-Minjiang, Jiulong-Beijiang and Taiwan groups. Mismatch distribution analysis, neutrality tests and Bayesian skyline plots indicated a significant population expansion for lineage A and B, approximately dated 0.35 and 0.04 myr ago, respectively. We found strong geographical organization of the haplotype clades across different geographic scales that can be explained by episodes of dispersal and population expansion followed by population fragmentation and restricted gene flow.

  20. Phylogeographic analysis elucidates the influence of the ice ages on the disjunct distribution of relict dragonflies in Asia.

    Directory of Open Access Journals (Sweden)

    Sebastian Büsse

    Full Text Available Unusual biogeographic patterns of closely related groups reflect events in the past, and molecular analyses can help to elucidate these events. While ample research on the origin of disjunct distributions of different organism groups in the Western Paleartic has been conducted, such studies are rare for Eastern Palearctic organisms. In this paper we present a phylogeographic analysis of the disjunct distribution pattern of the extant species of the strongly cool-adapted Epiophlebia dragonflies from Asia. We investigated sequences of the usually more conserved 18 S rDNA and 28 S rDNA genes and the more variable sequences of ITS1, ITS2 and CO2 of all three currently recognised Epiophlebia species and of a sample of other odonatan species. In all genes investigated the degrees of similarity between species of Epiophlebia are very high and resemble those otherwise found between different populations of the same species in Odonata. This indicates that substantial gene transfer between these populations occurred in the comparatively recent past. Our analyses imply a wide distribution of the ancestor of extant Epiophlebia in Southeast Asia during the last ice age, when suitable habitats were more common. During the following warming phase, its range contracted, resulting in the current disjunct distribution. Given the strong sensitivity of these species to climatic parameters, the current trend to increasing global temperatures will further reduce acceptable habitats and seriously threaten the existences of these last representatives of an ancient group of Odonata.

  1. Phylogeographical patterns of a generalist acorn weevil: insight into the biogeographical history of broadleaved deciduous and evergreen forests

    Directory of Open Access Journals (Sweden)

    Kato Makoto

    2009-05-01

    Full Text Available Abstract Background Climatic changes during glacial periods have had a major influence on the recent evolutionary history of living organisms, even in temperate forests on islands, where the land was not covered with ice sheets. We investigated the phylogeographical patterns of the weevil Curculio sikkimensis (Curculionidae, a generalist seed predator of Fagaceae plants living in both deciduous oak and evergreen forests of Japan. Its genetic structure was compared to that of another host-specific seed predator, C. hilgendorfi, inhabiting only evergreen forests. Results We examined 921 bp of mitochondrial DNA for 115 individuals collected from 33 populations of C. sikkimensis from 11 plant species of three genera, Quercus, Lithocarpus, and Castanopsis. An analysis of molecular variance revealed that a large proportion (almost 50%, P Conclusion Our results suggest that geology and historical environment have contributed to shaping the present genetic structure of C. sikkimensis. The geographical patterns of genetic differentiation in the Chugoku-Shikoku region observed in the two types of Fagaceae-associated Curculio in this study have also been observed in several plant species growing in warm and cool temperate zones of Japan. The occurrence of this common pattern suggests that deciduous oak and evergreen forests of Japan survived together, or adjacent to each other, in small refugia during glacial ages, in the southwestern and northeastern parts of the main islands, although these two types of forests are presently distributed in cool and warm temperate zones of Japan, respectively.

  2. Comparison of phylogeographic structure and population history of two Phrynocephalus species in the Tarim Basin and adjacent areas.

    Science.gov (United States)

    Zhang, Qian; Xia, Lin; He, Jingbo; Wu, Yonghua; Fu, Jinzhong; Yang, Qisen

    2010-12-01

    An aridification of the Tarim Basin and adjacent areas since middle Pleistocene has produced significant genetic structuring of the local fauna. We examined the phylogeographic patterns, population structure and history of Phrynocephalus axillaris and Phrynocephalus forsythii using a mitochondrial fragment ND4-tRNA(LEU). Phylogenetic hypotheses were constructed using maximum parsimony and Bayesian inference, and the divergence times of major lineages were estimated by BEAST. Population structure and history were inferred by nested clade analysis, neutrality tests, mismatch distribution, and isolation by distance analysis. The two species might have experienced different evolutionary history throughout their current distribution. For P. forsythii, a vicariant event, as a consequence of geological isolation and desert expansion, might have produced the significant divergence between the Tarim and the Yanqi populations. For P. axillaris, populations of the Yanqi, Turpan and Hami Basins might have been established through dispersal during demographic expansion. Climatic fluctuations caused alternate expansion and shrinkage of rivers and oases several times, which likely led to habitat fragmentation for both species. Interaction between vicariance, dispersal and habitat fragmentation produced the current distribution and genetic diversity. The observed difference between the two species may be due partially to their different reproductive modes (ovoviviparous vs. oviparous). Copyright © 2010 Elsevier Inc. All rights reserved.

  3. Cancer genomics

    DEFF Research Database (Denmark)

    Norrild, Bodil; Guldberg, Per; Ralfkiær, Elisabeth Methner

    2007-01-01

    Almost all cells in the human body contain a complete copy of the genome with an estimated number of 25,000 genes. The sequences of these genes make up about three percent of the genome and comprise the inherited set of genetic information. The genome also contains information that determines when...

  4. Cancer genomics

    DEFF Research Database (Denmark)

    Norrild, Bodil; Guldberg, Per; Ralfkiær, Elisabeth Methner

    2007-01-01

    Almost all cells in the human body contain a complete copy of the genome with an estimated number of 25,000 genes. The sequences of these genes make up about three percent of the genome and comprise the inherited set of genetic information. The genome also contains information that determines whe...

  5. Cytogenetics and genome evolution in the subfamily Triatominae (Hemiptera, Reduviidae).

    Science.gov (United States)

    Panzera, F; Pérez, R; Panzera, Y; Ferrandis, I; Ferreiro, M J; Calleros, L

    2010-01-01

    The subfamily Triatominae (Hemiptera, Reduviidae), vectors of Chagas disease, includes over 140 species. Karyotypic information is currently available for 80 of these species. This paper summarizes the chromosomal variability of the subfamily and how it may reveal aspects of genome evolution in this group. The Triatominae present a highly conserved chromosome number. All species, except 3, present 20 autosomes. The differences in chromosome number are mainly caused by variation in the number of sex chromosomes, due to the existence of 3 sex systems in males (XY, X(1)X(2)Y and X(1)X(2)X(3)Y). However, inter- and intraspecific differences in the position, quantity and meiotic behavior of constitutive heterochromatin, in the total genome size, and in the location of ribosomal 45S rRNA clusters, have revealed considerable cytogenetic variability within the subfamily. This cytogenetic diversity offers the opportunity to perform cytotaxonomic and phylogenetic studies, as well as structural, evolutionary, and functional analyses of the genome. The imminent availability of the complete genome of Rhodnius prolixus also opens new perspectives for understanding the evolution and genome expression of triatomines. The application of fluorescence in situ hybridization for the mapping of genes and sequences, as well as comparative analyses of genome homology by comparative genomic hybridization will be useful tools for understanding the genomic changes in relation to evolutionary processes such as speciation and adaptation to different environments. Copyright 2010 S. Karger AG, Basel.

  6. Tracing the Spread of Clostridium difficile Ribotype 027 in Germany Based on Bacterial Genome Sequences.

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    Matthias Steglich

    Full Text Available We applied whole-genome sequencing to reconstruct the spatial and temporal dynamics underpinning the expansion of Clostridium difficile ribotype 027 in Germany. Based on re-sequencing of genomes from 57 clinical C. difficile isolates, which had been collected from hospitalized patients at 36 locations throughout Germany between 1990 and 2012, we demonstrate that C. difficile genomes have accumulated sequence variation sufficiently fast to document the pathogen's spread at a regional scale. We detected both previously described lineages of fluoroquinolone-resistant C. difficile ribotype 027, FQR1 and FQR2. Using Bayesian phylogeographic analyses, we show that fluoroquinolone-resistant C. difficile 027 was imported into Germany at least four times, that it had been widely disseminated across multiple federal states even before the first outbreak was noted in 2007, and that it has continued to spread since.

  7. Tracing the Spread of Clostridium difficile Ribotype 027 in Germany Based on Bacterial Genome Sequences.

    Science.gov (United States)

    Steglich, Matthias; Nitsche, Andreas; von Müller, Lutz; Herrmann, Mathias; Kohl, Thomas A; Niemann, Stefan; Nübel, Ulrich

    2015-01-01

    We applied whole-genome sequencing to reconstruct the spatial and temporal dynamics underpinning the expansion of Clostridium difficile ribotype 027 in Germany. Based on re-sequencing of genomes from 57 clinical C. difficile isolates, which had been collected from hospitalized patients at 36 locations throughout Germany between 1990 and 2012, we demonstrate that C. difficile genomes have accumulated sequence variation sufficiently fast to document the pathogen's spread at a regional scale. We detected both previously described lineages of fluoroquinolone-resistant C. difficile ribotype 027, FQR1 and FQR2. Using Bayesian phylogeographic analyses, we show that fluoroquinolone-resistant C. difficile 027 was imported into Germany at least four times, that it had been widely disseminated across multiple federal states even before the first outbreak was noted in 2007, and that it has continued to spread since.

  8. Niche construction within riparian corridors. Part II: The unexplored role of positive intraspecific interactions in Salicaceae species

    Science.gov (United States)

    Corenblit, Dov; Garófano-Gómez, Virginia; González, Eduardo; Hortobágyi, Borbála; Julien, Frédéric; Lambs, Luc; Otto, Thierry; Roussel, Erwan; Steiger, Johannes; Tabacchi, Eric; Till-Bottraud, Irène

    2018-03-01

    Within riparian corridors, Salicaceae trees and shrubs affect hydrogeomorphic processes and lead to the formation of wooded fluvial landforms. These trees form dense stands and enhance plant anchorage, as grouped plants are less prone to be uprooted than free-standing individuals. This also enhances their role as ecosystem engineers through the trapping of sediment, organic matter, and nutrients. The landform formation caused by these wooded biogeomorphic landforms probably represents a positive niche construction, which ultimately leads, through facilitative processes, to an improved capacity of the individual trees to survive, exploit resources, and reach sexual maturity in the interval between destructive floods. The facilitative effects of riparian vegetation are well established; however, the nature and intensity of biotic interactions among trees of the same species forming dense woody stands and constructing the niche remain unclear. Our hypothesis is that the niche construction process also comprises more direct intraspecific interactions, such as cooperation or altruism. Our aim in this paper is to propose an original theoretical framework for positive intraspecific interactions among riparian Salicaceae species operating from establishment to sexual maturity. Within this framework, we speculate that (i) positive intraspecific interactions among trees are maximized in dynamic river reaches; (ii) during establishment, intraspecific facilitation (or helping) occurs among trees and this leads to the maintenance of a dense stand that improves survival and growth because saplings protect each other from shear stress and scour; (iii) in addition to the improved capacity to trap mineral and organic matter, individuals that constitute the dense stand can cooperate to mutually support a mycorrhizal network that will connect plants, soil, and groundwater and influence nutrient transfer, cycling, and storage within the shared constructed niche; (iv) during post

  9. Phylogeographic Structure in Penguin Ticks across an Ocean Basin Indicates Allopatric Divergence and Rare Trans-Oceanic Dispersal.

    Science.gov (United States)

    Moon, Katherine L; Banks, Sam C; Fraser, Ceridwen I

    2015-01-01

    The association of ticks (Acarina) and seabirds provides an intriguing system for assessing the influence of long-distance dispersal on the evolution of parasitic species. Recent research has focused on host-parasite evolutionary relationships and dispersal capacity of ticks parasitising flighted seabirds. Evolutionary research on the ticks of non-flighted seabirds is, in contrast, scarce. We conducted the first phylogeographic investigation of a hard tick species (Ixodes eudyptidis) that parasitises the Little Blue Penguin (Eudyptula minor). Using one nuclear (28S) and two mitochondrial (COI and 16S) markers, we assessed genetic diversity among several populations in Australia and a single population on the South Island of New Zealand. Our results reveal two deeply divergent lineages, possibly representing different species: one comprising all New Zealand samples and some from Australia, and the other representing all other samples from Australian sites. No significant population differentiation was observed among any Australian sites from within each major clade, even those separated by hundreds of kilometres of coastline. In contrast, the New Zealand population was significantly different to all samples from Australia. Our phylogenetic results suggest that the New Zealand and Australian populations are effectively isolated from each other; although rare long-distance dispersal events must occur, these are insufficient to maintain trans-Tasman gene flow. Despite the evidence for limited dispersal of penguin ticks between Australia and New Zealand, we found no evidence to suggest that ticks are unable to disperse shorter distances at sea with their hosts, with no pattern of population differentiation found among Australian sites. Our results suggest that terrestrial seabird parasites may be quite capable of short-distance movements, but only sporadic longer-distance (trans-oceanic) dispersal.

  10. Gene flow and genetic drift contribute to high genetic diversity with low phylogeographical structure in European hoopoes (Upupa epops).

    Science.gov (United States)

    Wang, Erjia; Van Wijk, Rien E; Braun, Markus Santhosh; Wink, Michael

    2017-08-01

    The Hoopoe (Upupa epops epops) breeds widely in Eurasia and most populations migrate to Africa during the boreal winter. To date, data regarding its phylogeography in Europe are missing. In this study, we investigated the phylogeography and population genetics of Hoopoes by means of mitochondrial DNA (mtDNA) sequencing as well as microsatellite genotyping. Our analyses revealed 32 haplotypes in the cytochrome c oxidase subunit I (COI) (269 individuals) and 50 haplotypes in cytochrome b (cyt b) (233 individuals). Analyses of mtDNA clearly demonstrated that the bulk of variance (98.23%) could be attributed to inner-population variance. Thus, the low frequency single nucleotide substitutions resulted in "star-like" haplotype networks without define geographical structure. Hoopoes clearly experienced a bottleneck followed by sudden expansion, as was also apparent from tests on the unimodal mismatch, Bayesian skyline plot, significant negative neutrality tests as well as bottleneck signals. These tests pointed to strong demographic fluctuations in the hoopoe populations. GENELAND, DAPC and STRUCTURE analyses of microsatellites along with their corresponding Fst values suggested that current genetic restriction separates birds from Armenia from the remaining populations. Except for hoopoes from Armenia, all the European populations exhibited an admixed phylogeographic pattern. We conclude that this genetic panmixia might be a consequence of a combination of historical events (e.g. repeated colonizations and retreatments from northern habitats during the Pleistocene and a sudden postglacial expansion) and current processes (e.g. long-distance migration, immigration or population recruitments). Copyright © 2017 Elsevier Inc. All rights reserved.

  11. Phylogeographic analyses of submesophotic snappers Etelis coruscans and Etelis "marshi" (family Lutjanidae reveal concordant genetic structure across the Hawaiian Archipelago.

    Directory of Open Access Journals (Sweden)

    Kimberly R Andrews

    Full Text Available The Hawaiian Archipelago has become a natural laboratory for understanding genetic connectivity in marine organisms as a result of the large number of population genetics studies that have been conducted across this island chain for a wide taxonomic range of organisms. However, population genetic studies have been conducted for only two species occurring in the mesophotic or submesophotic zones (30+m in this archipelago. To gain a greater understanding of genetic connectivity in these deepwater habitats, we investigated the genetic structure of two submesophotic fish species (occurring ∼200-360 m in this archipelago. We surveyed 16 locations across the archipelago for submesophotic snappers Etelis coruscans (N = 787 and E. "marshi" (formerly E. carbunculus; N = 770 with 436-490 bp of mtDNA cytochrome b and 10-11 microsatellite loci. Phylogeographic analyses reveal no geographic structuring of mtDNA lineages and recent coalescence times that are typical of shallow reef fauna. Population genetic analyses reveal no overall structure across most of the archipelago, a pattern also typical of dispersive shallow fishes. However some sites in the mid-archipelago (Raita Bank to French Frigate Shoals had significant population differentiation. This pattern of no structure between ends of the Hawaiian range, and significant structure in the middle, was previously observed in a submesophotic snapper (Pristipomoides filamentosus and a submesophotic grouper (Hyporthodus quernus. Three of these four species also have elevated genetic diversity in the mid-archipelago. Biophysical larval dispersal models from previous studies indicate that this elevated diversity may result from larval supplement from Johnston Atoll, ∼800 km southwest of Hawaii. In this case the boundaries of stocks for fishery management cannot be defined simply in terms of geography, and fishery management in Hawaii may need to incorporate external larval supply into management

  12. Phylogeographic structure, cryptic speciation and demographic history of the sharpbelly (Hemiculter leucisculus), a freshwater habitat generalist from southern China.

    Science.gov (United States)

    Chen, Weitao; Zhong, Zaixuan; Dai, Wei; Fan, Qi; He, Shunping

    2017-09-12

    Species with broad distributions frequently divide into multiple genetic forms and may therefore be viewed as "cryptic species". Here, we used the mitochondrial cytochrome b (Cytb) and 12 nuclear DNA loci to investigate phylogeographic structures of the sharpbelly (Hemiculter leucisculus) in rivers in southern China and explored how the geological and climatic factors have shaped the genetic diversity and evolutionary history of this species. Our mitochondrial phylogenetic analysis identified three major lineages (lineages A, B, and C). Lineages B and C showed a relatively narrower geographic distribution, whereas lineage A was widely distributed in numerous drainages. Divergence dates suggested that H. leucisculus populations diverged between 1.61-2.38 Ma. Bayesian species delimitation analysis using 12 nuclear DNA loci indicated the three lineages probably represented three valid taxa. Isolation-with-migration (IM) analysis found substantial gene flow has occurred among the three lineages. Demographic analyses showed that lineages B and C have experienced rapid demographic expansion at 0.03 Ma and 0.08 Ma, respectively. Hemiculter leucisculus populations in drainages in southern China comprise three mtDNA lineages, and each of which may represent a separate species. Intense uplift of the Qinghai-Tibetan Plateau, evolution of Asian monsoons, changes in paleo-drainages, and poor dispersal ability may have driven the divergence of the three putative species. However, gene flow occurs among the three lineages. Climatic fluctuations have a prominent impact on the populations from the lineages B and C, but exerted little influence on the lineage A.

  13. Phylogeographical footprint of colonial history in the global dispersal of human immunodeficiency virus type 2 group A.

    Science.gov (United States)

    Faria, Nuno R; Hodges-Mameletzis, Ioannis; Silva, Joana C; Rodés, Berta; Erasmus, Smit; Paolucci, Stefania; Ruelle, Jean; Pieniazek, Danuta; Taveira, Nuno; Treviño, Ana; Gonçalves, Maria F; Jallow, Sabelle; Xu, Li; Camacho, Ricardo J; Soriano, Vincent; Goubau, Patrick; de Sousa, João D; Vandamme, Anne-Mieke; Suchard, Marc A; Lemey, Philippe

    2012-04-01

    Human immunodeficiency virus type 2 (HIV-2) emerged in West Africa and has spread further to countries that share socio-historical ties with this region. However, viral origins and dispersal patterns at a global scale remain poorly understood. Here, we adopt a Bayesian phylogeographic approach to investigate the spatial dynamics of HIV-2 group A (HIV-2A) using a collection of 320 partial pol and 248 partial env sequences sampled throughout 19 countries worldwide. We extend phylogenetic diffusion models that simultaneously draw information from multiple loci to estimate location states throughout distinct phylogenies and explicitly attempt to incorporate human migratory fluxes. Our study highlights that Guinea-Bissau, together with Côte d'Ivoire and Senegal, have acted as the main viral sources in the early stages of the epidemic. We show that convenience sampling can obfuscate the estimation of the spatial root of HIV-2A. We explicitly attempt to circumvent this by incorporating rate priors that reflect the ratio of human flow from and to West Africa. We recover four main routes of HIV-2A dispersal that are laid out along colonial ties: Guinea-Bissau and Cape Verde to Portugal, Côte d'Ivoire and Senegal to France. Within Europe, we find strong support for epidemiological linkage from Portugal to Luxembourg and to the UK. We demonstrate that probabilistic models can uncover global patterns of HIV-2A dispersal providing sampling bias is taken into account and we provide a scenario for the international spread of this virus.

  14. Intraspecific variation in thermal acclimation of photosynthesis across a range of temperatures in a perennial crop.

    Science.gov (United States)

    Zaka, Serge; Frak, Ela; Julier, Bernadette; Gastal, François; Louarn, Gaëtan

    2016-01-01

    Interest in the thermal acclimation of photosynthesis has been stimulated by the increasing relevance of climate change. However, little is known about intra-specific variations in thermal acclimation and its potential for breeding. In this article, we examined the difference in thermal acclimation between alfalfa (Medicago sativa) cultivars originating from contrasting origins, and sought to analyze the mechanisms in play. A series of experiments was carried out at seven growth temperatures between 5 and 35 °C using four cultivars from temperate and Mediterranean origin. Leaf traits, the photosynthetic rate at 25 °C (A400 (25)), the photosynthetic rate at optimal temperature (A400 (opt)), the thermal optimum of photosynthesis (Topt), and the photosynthetic parameters from the Farqhuar model were determined. Irrespective of cultivar origin, a clear shift in the temperature responses of photosynthesis was observed as a function of growth temperature, affecting thermal optimum of photosynthesis, photosynthetic rate at optimal temperature and photosynthetic rate at 25 °C. For both cultivars, Topt values increased linearly in leaves grown between 5 and 35 °C. Relative homeostasis of A400 (25) and A400 (opt) was found between 10 °C and 30 °C growth temperatures, but sharp declines were recorded at 5 and 35 °C. This homeostasis was achieved in part through modifications to leaf nitrogen content, which increased at extreme temperatures. Significant changes were also recorded regarding nitrogen partitioning in the photosynthetic apparatus and in the temperature dependence of photosynthetic parameters. The cultivars differed only in terms of the temperature response of photosynthetic parameters, with Mediterranean genotypes displaying a greater sensitivity of the maximum rate of Rubisco carboxylation to elevated temperatures. It was concluded that intra-specific variations in the temperature acclimation of photosynthesis exist among alfalfa cultivars

  15. INTRASPECIFIC PHYLOGEOGRAPHY OF NORTH AMERICAN HIGHLAND FISHES: A TEST OF THE PLEISTOCENE VICARIANCE HYPOTHESIS.

    Science.gov (United States)

    Strange, Rex Meade; Burr, Brooks M

    1997-06-01

    The highland fish fauna of eastern North America consists of Appalachian and Ozark centers of endemism separated by the intervening Glacial Till Plains. Clades within these areas are more closely related phylogenetically to each other than to clades occurring in the intervening formerly glaciated region, suggesting that the Pleistocene glaciations fragmented a widespread highland region and its associated fauna. Alternatively, it is possible that these faunal assemblages predate the glaciations or that recent dispersals may have been more important than vicariance in determining faunal compositions. We examined the relationships among mitochondrial DNA (mtDNA) haplotypes within five clades of highland fishes, each with a distribution suggestive of a Pleistocene vicariance event. Darters of the subgenera Litocara and Odontopholis have distributions and mtDNA relationships that are consistent with the Pleistocene integration and burial of the Teays-Mahomet valley, a major drainage of the early Pleistocene. The distribution and mtDNA relationships among subspecies of Erimystax dissimilis are not consistent with Pleistocene vicariance, but relationships among Appalachian haplotypes are consistent with the late Pleistocene integration of the modern Ohio River system. Both Cottus carolinae and the Fundulus catenatus species group have representatives in the Mobile basin consistent with pre-Pleistocene divergences. Three haplotype clusters were found in C. carolinae, corresponding to the Appalachian, Ozark, and upper Kanawha River populations. However, Appalachian and Ozark F. catenatus populations are paraphyletic with respect to each other. This, coupled with a relatively low degree of sequence divergence, suggests that no long-term barriers to gene flow exist for C. carolinae and F. catenatus. These three distinct phylogeographic patterns indicate that Pleistocene vicariance is not the only explanation for the Appalachian-Ozark distribution of highland fish communities

  16. Large intraspecific genetic variation within the Saffron-Crocus group (Crocus L., Series Crocus; Iridaceae)

    DEFF Research Database (Denmark)

    Larsen, Bjarne; Orabi, Jihad; Pedersen, Carsten

    2015-01-01

    generally were grouped with C. sativus samples. Pollination and maintenance of genetic variation are discussed. The large intraspecific variation found within the three specifically studied species reflects dynamic population structures with potential to meet future ecological fluctuations. It emphasises...

  17. Effects of Intraspecific Competition and Host-Parasitoid Developmental Timing on Foraging Behaviour of a Parasitoid Wasp.

    Science.gov (United States)

    Couchoux, Christelle; van Nouhuys, Saskya

    2014-01-01

    In a context where hosts are distributed in patches and susceptible to parasitism for a limited time, female parasitoids foraging for hosts might experience intraspecific competition. We investigated the effects of host and parasitoid developmental stage and intraspecific competition among foraging females on host-searching behaviour in the parasitoid wasp Hyposoter horticola. We found that H. horticola females have a pre-reproductive adult stage during which their eggs are not mature yet and they forage very little for hosts. The wasps foraged for hosts more once they were mature. Behavioural experiments showed that wasps' foraging activity also increased as host eggs aged and became susceptible to parasitism, and as competition among foraging wasps increased.

  18. Genomic epidemiology of the haitian cholera outbreak: a single introduction followed by rapid, extensive, and continued spread characterized the onset of the epidemic

    DEFF Research Database (Denmark)

    Eppinger, Mark; Pearson, Talima; Koenig, Sara S. K.

    2014-01-01

    In this genomic epidemiology study, we have applied high-resolution whole-genome-based sequence typing methodologies on a comprehensive set of genome sequences that have become available in the aftermath of the Haitian cholera epidemic. These sequence resources enabled us to reassess the degree...... of genomic heterogeneity within the Vibrio cholerae O1 serotype and to refine boundaries and evolutionary relationships. The established phylogenomic framework showed how outbreak isolates fit into the global phylogeographic patterns compared to a comprehensive globally and temporally diverse strain...... collection and provides strong molecular evidence that points to a nonindigenous source of the 2010 Haitian cholera outbreak and refines epidemiological standards used in outbreak investigations for outbreak inclusion/exclusion following the concept of genomic epidemiology. The generated phylogenomic data...

  19. Phylogeographic structure of cotton pest Adelphocoris suturalis (Hemiptera: Miridae): strong subdivision in China inferred from mtDNA and rDNA ITS markers

    OpenAIRE

    Zhang, Lijuan; Li, Hu; Li, Shujuan; Zhang, Aibing; Kou, Fei; Xun, Huaizhu; Wang, Pei; Wang, Ying; Song, Fan; Cui, Jianxin; Cui, Jinjie; Gouge, Dawn H.; Cai, Wanzhi

    2015-01-01

    Phylogeographic patterns of some extant plant and vertebrate species have been well studied; however, they are poorly understood in the majority of insects. The study documents analysis of mitochondrial (COI, CYTB and ND5) and nuclear (5.8S rDNA, ITS2 and 28S rDNA) data from 419 individuals of Adelphocoris suturalis, which is one of the main cotton pests found in the 31 locations in China and Japan involved in the study. Results show that the species is highly differentiated between populatio...

  20. Genomic epidemiology of the Haitian cholera outbreak: a single introduction followed by rapid, extensive, and continued spread characterized the onset of the epidemic.

    Science.gov (United States)

    Eppinger, Mark; Pearson, Talima; Koenig, Sara S K; Pearson, Ofori; Hicks, Nathan; Agrawal, Sonia; Sanjar, Fatemeh; Galens, Kevin; Daugherty, Sean; Crabtree, Jonathan; Hendriksen, Rene S; Price, Lance B; Upadhyay, Bishnu P; Shakya, Geeta; Fraser, Claire M; Ravel, Jacques; Keim, Paul S

    2014-11-04

    For centuries, cholera has been one of the most feared diseases. The causative agent Vibrio cholerae is a waterborne Gram-negative enteric pathogen eliciting a severe watery diarrheal disease. In October 2010, the seventh pandemic reached Haiti, a country that had not experienced cholera for more than a century. By using whole-genome sequence typing and mapping strategies of 116 serotype O1 strains from global sources, including 44 Haitian genomes, we present a detailed reconstructed evolutionary history of the seventh pandemic with a focus on the Haitian outbreak. We catalogued subtle genomic alterations at the nucleotide level in the genome core and architectural rearrangements from whole-genome map comparisons. Isolates closely related to the Haitian isolates caused several recent outbreaks in southern Asia. This study provides evidence for a single-source introduction of cholera from Nepal into Haiti followed by rapid, extensive, and continued clonal expansion. The phylogeographic patterns in both southern Asia and Haiti argue for the rapid dissemination of V. cholerae across the landscape necessitating real-time surveillance efforts to complement the whole-genome epidemiological analysis. As eradication efforts move forward, phylogeographic knowledge will be important for identifying persistent sources and monitoring success at regional levels. The results of molecular and epidemiological analyses of this outbreak suggest that an indigenous Haitian source of V. cholerae is unlikely and that an indigenous source has not contributed to the genomic evolution of this clade. In this genomic epidemiology study, we have applied high-resolution whole-genome-based sequence typing methodologies on a comprehensive set of genome sequences that have become available in the aftermath of the Haitian cholera epidemic. These sequence resources enabled us to reassess the degree of genomic heterogeneity within the Vibrio cholerae O1 serotype and to refine boundaries and

  1. Food choice effects on herbivory: Intra-specific seagrass palatability and inter-specific macrophyte palatability in seagrass communities

    Science.gov (United States)

    Jiménez-Ramos, Rocío; Brun, Fernando G.; Egea, Luis G.; Vergara, Juan J.

    2018-05-01

    Interactions between the palatability and abundance of different food sources may influence herbivory patterns in seagrass-dominated communities. In addition, intra-specific differences in nutrient and structural quality of leaves may also alter seagrass palatability and generate different rates of consumption within these communities. We offered two temperate seagrasses species, (Cymodocea nodosa and Zostera noltei) from two different locations to look at intraspecific differences, and two other macrophytes, both of which occur at the same location as seagrasses but represent the extremes of palatability, to a generalist herbivore Paracentrotus lividus (purple sea urchin). Using feeding assays, we compared the consumption rates in individual (single plant species) and combined diets at different food availabilities. Intra-specific differences between seagrass species growing at different locations (inner and outer bay) were indeed found to significantly modify the consumption rate for one species. Structural traits such as carbon content were linked to the low consumption found in Cymodocea nodosa from the inner bay location. In addition, we found that the co-occurrence of different macrophyte species can result in preferential consumption of the more palatable macrophyte with high nutritional content and low structural defence over seagrasses, especially when P. lividus has an abundant food supply. Overall, our findings suggest that intra- and inter-specific differences in seagrass traits and the relative abundance of other macrophytes may explain the variability in patterns of herbivory found within seagrass communities.

  2. Species interactions and chemical stress: combined effects of intraspecific and interspecific interactions and pyrene on Daphnia magna population dynamics.

    Science.gov (United States)

    Viaene, Karel P J; De Laender, Frederik; Rico, Andreu; Van den Brink, Paul J; Di Guardo, Antonio; Morselli, Melissa; Janssen, Colin R

    2015-08-01

    Species interactions are often suggested as an important factor when assessing the effects of chemicals on higher levels of biological organization. Nevertheless, the contribution of intraspecific and interspecific interactions to chemical effects on populations is often overlooked. In the present study, Daphnia magna populations were initiated with different levels of intraspecific competition, interspecific competition, and predation and exposed to pyrene pulses. Generalized linear models were used to test which of these factors significantly explained population size and structure at different time points. Pyrene had a negative effect on total population densities, with effects being more pronounced on smaller D. magna individuals. Among all species interactions tested, predation had the largest negative effect on population densities. Predation and high initial intraspecific competition were shown to interact antagonistically with pyrene exposure. This was attributed to differences in population structure before pyrene exposure and pyrene-induced reductions in predation pressure by Chaoborus sp. larvae. The present study provides empirical evidence that species interactions within and between populations can alter the response of aquatic populations to chemical exposure. Therefore, such interactions are important factors to be considered in ecological risk assessments. © 2015 SETAC.

  3. Intraspecific competition reveals conditional fitness effects of single gene polymorphism at the Arabidopsis root growth regulator BRX.

    Science.gov (United States)

    Shindo, Chikako; Bernasconi, Giorgina; Hardtke, Christian S

    2008-01-01

    Intraspecific genetic variation for morphological traits is observed in many organisms. In Arabidopsis thaliana, alleles responsible for intraspecific morphological variation are increasingly being identified. However, the fitness consequences remain unclear in most cases. Here, the fitness effects of alleles of the BRX gene are investigated. A brx loss-of-function allele, which was found in a natural accession, results in a highly branched but poorly elongated root system. Comparison between the control accession Sav-0 and an introgression of brx into this background (brxS) indicated that, surprisingly, brx loss of function did not negatively affect fitness in pure stands. However, in mixed, well-watered stands brxS performance and reproductive output decreased significantly, as the proportion of Sav-0 neighbors increased. Additional comparisons between brxS and a brxS line that was complemented by a BRX transgene confirmed a direct effect of the loss-of-function allele on plant performance, as indicated by restored competitive ability of the transgenic genotype. Further, because plant height was very similar across genotypes and because the experimental setup largely excluded shading effects, the impaired competitiveness of the brx loss-of-function genotype likely reflects below-ground competition. In summary, these data reveal conditional fitness effects of a single gene polymorphism in response to intraspecific competition in Arabidopsis.

  4. Biomechanical implications of intraspecific shape variation in chimpanzee crania: moving towards an integration of geometric morphometrics and finite element analysis

    Science.gov (United States)

    Smith, Amanda L.; Benazzi, Stefano; Ledogar, Justin A.; Tamvada, Kelli; Smith, Leslie C. Pryor; Weber, Gerhard W.; Spencer, Mark A.; Dechow, Paul C.; Grosse, Ian R.; Ross, Callum F.; Richmond, Brian G.; Wright, Barth W.; Wang, Qian; Byron, Craig; Slice, Dennis E.; Strait, David S.

    2014-01-01

    In a broad range of evolutionary studies, an understanding of intraspecific variation is needed in order to contextualize and interpret the meaning of variation between species. However, mechanical analyses of primate crania using experimental or modeling methods typically encounter logistical constraints that force them to rely on data gathered from only one or a few individuals. This results in a lack of knowledge concerning the mechanical significance of intraspecific shape variation that limits our ability to infer the significance of interspecific differences. This study uses geometric morphometric methods (GM) and finite element analysis (FEA) to examine the biomechanical implications of shape variation in chimpanzee crania, thereby providing a comparative context in which to interpret shape-related mechanical variation between hominin species. Six finite element models (FEMs) of chimpanzee crania were constructed from CT scans following shape-space Principal Component Analysis (PCA) of a matrix of 709 Procrustes coordinates (digitized onto 21 specimens) to identify the individuals at the extremes of the first three principal components. The FEMs were assigned the material properties of bone and were loaded and constrained to simulate maximal bites on the P3 and M2. Resulting strains indicate that intraspecific cranial variation in morphology is associated with quantitatively high levels of variation in strain magnitudes, but qualitatively little variation in the distribution of strain concentrations. Thus, interspecific comparisons should include considerations of the spatial patterning of strains rather than focus only their magnitude. PMID:25529239

  5. Does intraspecific behavioural variation of pollinator species influence pollination? A quantitative study with hummingbirds and a Neotropical shrub.

    Science.gov (United States)

    Maruyama, P K; Justino, D G; Oliveira, P E

    2016-11-01

    Floral visitors differ in their efficacy as pollinators, and the impact of different pollinator species on pollen flow and plant reproduction has been frequently evaluated. In contrast, the impact of intraspecific behavioural changes on their efficacy as pollinators has seldom been quantified. We studied a self-incompatible shrub Palicourea rigida (Rubiaceae) and its hummingbird pollinators, which adjust their behaviour according to floral resource availability. Fluorescence microscopy was used to access pollen tube growth and incompatibility reaction in pistils after a single visit of territorial or intruder hummingbirds in two populations. To characterise the plant populations and possible differences in resource availability between areas we used a three-term quadrat variance method to detect clusters of floral resources. Within-species variation in foraging behaviour, but not species identity, affected pollinator efficacy. Effectively, hummingbirds intruding into territories deposited more compatible pollen grains on P. rigida stigmas than territory holders in both study areas. Additionally, territory holders deposited more incompatible than compatible pollen grains. Our results imply that intraspecific foraging behaviour variation has consequences for pollination success. Quantifying such variation and addressing the implications of intraspecific variability contribute to a better understanding of the dynamics and consequences of plant-pollinator interactions. © 2016 German Botanical Society and The Royal Botanical Society of the Netherlands.

  6. Intraspecific variation in feeding strategies of Galapagos sea lions: A case of trophic specialization

    Science.gov (United States)

    Villegas-Amtmann, Stella; Costa, Daniel

    2017-01-01

    The trophic behavior of marine predators varies according to the level of competition to which they are exposed. In general, populations that inhabit lower productivity systems face a strong intraspecific competition, which contributes to the development of different foraging strategies to maximize nutritional efficiency. Given the high trophic flexibility of Zalophus wollebaeki, this species is considered appropriate for the analysis of such behavior. Furthermore, this trophic flexibility has allowed them to persist in a seemingly marginal ecosystem. In this study, we used a comparative analysis of variables (diet and dive behavior) related to Z. wollebaeki trophic niche plasticity to better understand their foraging ecology, using techniques such scat analysis, satellite telemetry and complementarily an isotopic analysis. Scat analysis revealed intra-population variation in their diet, represented by prey from different environments (epipelagic and benthic). These results are supported by the animals’ locations at sea and diving profiles. Global Positioning System (GPS) and time-depth recorder (TDR) records showed the existence of two groups, with differing feeding areas and diving behavior. Also the δ15N values showed differences in the trophic level at which the species fed. These results constitute a relevant finding in the evolutionary behavior of the species, showing that Z. wollebaeki has developed a high degree of foraging flexibility, thus increasing its survival rate in an ecosystem that is highly demanding in terms of resource availability. PMID:29059188

  7. Intraspecific variation in feeding strategies of Galapagos sea lions: A case of trophic specialization.

    Directory of Open Access Journals (Sweden)

    Diego Páez-Rosas

    Full Text Available The trophic behavior of marine predators varies according to the level of competition to which they are exposed. In general, populations that inhabit lower productivity systems face a strong intraspecific competition, which contributes to the development of different foraging strategies to maximize nutritional efficiency. Given the high trophic flexibility of Zalophus wollebaeki, this species is considered appropriate for the analysis of such behavior. Furthermore, this trophic flexibility has allowed them to persist in a seemingly marginal ecosystem. In this study, we used a comparative analysis of variables (diet and dive behavior related to Z. wollebaeki trophic niche plasticity to better understand their foraging ecology, using techniques such scat analysis, satellite telemetry and complementarily an isotopic analysis. Scat analysis revealed intra-population variation in their diet, represented by prey from different environments (epipelagic and benthic. These results are supported by the animals' locations at sea and diving profiles. Global Positioning System (GPS and time-depth recorder (TDR records showed the existence of two groups, with differing feeding areas and diving behavior. Also the δ15N values showed differences in the trophic level at which the species fed. These results constitute a relevant finding in the evolutionary behavior of the species, showing that Z. wollebaeki has developed a high degree of foraging flexibility, thus increasing its survival rate in an ecosystem that is highly demanding in terms of resource availability.

  8. The composition of cell walls from grape skin in Vitis vinifera intraspecific hybrids.

    Science.gov (United States)

    Apolinar-Valiente, Rafael; Gómez-Plaza, Encarna; Terrier, Nancy; Doco, Thierry; Ros-García, José María

    2017-09-01

    Monastrell is a red grape cultivar adapted to the dry environmental conditions of Murcia, SE Spain. Its berries seem to be characterized by a rigid cell wall structure, which could make difficult the winemaking process. Cabernet Sauvignon cultivar is used to complement Monastrell wines in this region owing to its high phenolic content with high extractability. This study explores the skin cell wall composition of grapes from plants resulting from intraspecific crosses of Vitis vinifera cultivars Monastrell × Cabernet Sauvignon. Moreover, the morphology of the cell wall material (CWM) from some representative samples was visualized by transmission optical microscopy. The total sugar content of CWM from nine out of ten genotypes of the progeny was lower than that from Monastrell. Seven out of ten genotypes showed lower phenolic content than Cabernet Sauvignon. The CWM from nine out of ten hybrids presented lower protein content than that from Monastrell. This study confirms that skin cell walls from Monastrell × Cabernet Sauvignon hybrid grapes presented major differences in composition compared with their parents. These data could help in the development of new cultivars adapted to the dry conditions of SE Spain and with a cell wall composition favouring extractability. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

  9. Intraspecific variation in feeding strategies of Galapagos sea lions: A case of trophic specialization.

    Science.gov (United States)

    Páez-Rosas, Diego; Villegas-Amtmann, Stella; Costa, Daniel

    2017-01-01

    The trophic behavior of marine predators varies according to the level of competition to which they are exposed. In general, populations that inhabit lower productivity systems face a strong intraspecific competition, which contributes to the development of different foraging strategies to maximize nutritional efficiency. Given the high trophic flexibility of Zalophus wollebaeki, this species is considered appropriate for the analysis of such behavior. Furthermore, this trophic flexibility has allowed them to persist in a seemingly marginal ecosystem. In this study, we used a comparative analysis of variables (diet and dive behavior) related to Z. wollebaeki trophic niche plasticity to better understand their foraging ecology, using techniques such scat analysis, satellite telemetry and complementarily an isotopic analysis. Scat analysis revealed intra-population variation in their diet, represented by prey from different environments (epipelagic and benthic). These results are supported by the animals' locations at sea and diving profiles. Global Positioning System (GPS) and time-depth recorder (TDR) records showed the existence of two groups, with differing feeding areas and diving behavior. Also the δ15N values showed differences in the trophic level at which the species fed. These results constitute a relevant finding in the evolutionary behavior of the species, showing that Z. wollebaeki has developed a high degree of foraging flexibility, thus increasing its survival rate in an ecosystem that is highly demanding in terms of resource availability.

  10. Foliar Substrate Affects Cuticular Hydrocarbon Profiles and Intraspecific Aggression in the Leafcutter Ant Atta sexdens

    Directory of Open Access Journals (Sweden)

    Lohan Valadares

    2015-02-01

    Full Text Available Cuticular hydrocarbons (CHCs are traditionally considered to be one of the most important chemical cues used in the nestmate recognition process of social hymenopterans. However, it has been suggested that in the leafcutter ant genus Atta, it is not the CHCs, but the alarm pheromone that is involved in the nestmate recognition process. In this study we used a laboratory population of Atta sexdens to explore the association between their CHC profile variation and intraspecific aggression. In the first part of the experiment, four colonies were divided into two groups with distinct diets to stimulate differentiation of their CHC profiles. In the second part of the experiment, all colonies received the same diet to examine resemblance of chemical profiles. At the end of each part of the experiment we extracted the CHCs from workers. The results demonstrated that colonies that shared the same food resource had similar cuticular hydrocarbon profiles. Furthermore, colonies were significantly more aggressive towards conspecifics that used a different foliar substrate and consequently had greater differences in their cuticular chemical composition. This study suggests that the CHC profiles of A. sexdens can be affected by the foliar substrates used, and that the CHCs are used in the nestmate recognition process of this species.

  11. Intraspecific allometry of standard metabolic rate in green iguanas, Iguana iguana.

    Science.gov (United States)

    Maxwell, Lara K; Jacobson, Elliott R; McNab, Brian K

    2003-10-01

    To study the allometric relationship between standard metabolic rate and body mass (mass range 16-3627 g) in green iguanas, Iguana iguana (n=32), we measured rates of oxygen consumption (V(O(2))) at 30 degrees C during scotophase. The relationship could be described as: V(O(2))(ml h(-1))=0.478W(0.734). The resulting mass exponent was similar to the 3/4 power commonly used in interspecific curves (P>0.05), but differed from a proposed intraspecific value of 2/3 (Piguanas did not differ (P>0.05). The mass adjusted V(O(2)) was higher than predicted from generalized squamate curves. The mean mass exponent of intra-individual allometric equations of iguanas (n=7) at varying masses during ontogeny did not differ from that of the pooled equation, indicating that scaling of V(O(2)) is similar for both between and within individuals. Thermal acclimation, compensatory changes in V(O(2)) with prolonged exposure to a constant temperature, was not observed in juvenile iguanas (n=11) between 1 and 5 weeks of acclimation at 30 degrees C.

  12. Size does matter - Intraspecific variation of feeding mechanics in the crested newt Triturus dobrogicus (Kiritzescu, 1903)

    Science.gov (United States)

    Kucera, Florian; Beisser, Christian J.; Lemell, Patrick

    2018-03-01

    Many studies have yet been conducted on suction feeding in aquatic salamander species. Within the Salamandridae, the crested newt Triturus dobrogicus (Kiritzescu, 1903), occurring from the Austrian Danube floodplains to the Danube Delta, was not subject of investigations so far. The present study examines the kinematics of aquatic suction feeding in this species by means of high-speed videography. Recordings of five individuals of different size and sex while feeding on bloodworms were conducted, in order to identify potential discrepancies among individuals and sizes. Five coordinate points were digitized from recordings of prey capture and twelve time- and velocity-determined variables were evaluated. All specimens follow a typical inertial suction feeding process, where rapid hyoid depression expands the buccal cavity. Generated negative pressure within the buccal cavity causes influx of water along with the prey item into the mouth. Results demonstrate higher distance values and angles for gape in individuals with smaller size. In addition, hyoid depression is maximized in smaller individuals. While Triturus dobrogicus resembles a typical inertial suction feeder in its functional morphology, intraspecific differences could be found regarding the correlation of different feeding patterns and body size.

  13. Larval size in acanthocephalan parasites: Influence of intraspecific competition and effects on intermediate host behavioural changes

    Directory of Open Access Journals (Sweden)

    Dianne Lucile

    2012-08-01

    Full Text Available Abstract Background Parasites often face a trade-off between exploitation of host resources and transmission probabilities to the next host. In helminths, larval growth, a major component of adult parasite fitness, is linked to exploitation of intermediate host resources and is influenced by the presence of co-infecting conspecifics. In manipulative parasites, larval growth strategy could also interact with their ability to alter intermediate host phenotype and influence parasite transmission. Methods We used experimental infections of Gammarus pulex by Pomphorhynchus laevis (Acanthocephala, to investigate larval size effects on host behavioural manipulation among different parasite sibships and various degrees of intra-host competition. Results Intra-host competition reduced mean P. laevis cystacanth size, but the largest cystacanth within a host always reached the same size. Therefore, all co-infecting parasites did not equally suffer from intraspecific competition. Under no intra-host competition (1 parasite per host, larval size was positively correlated with host phototaxis. At higher infection intensities, this relationship disappeared, possibly because of strong competition for host resources, and thus larval growth, and limited manipulative abilities of co-infecting larval acanthocephalans. Conclusions Our study indicates that behavioural manipulation is a condition-dependant phenomenon that needs the integration of parasite-related variables to be fully understood.

  14. Intraspecific variation in 137Cs activity concentration in sporocarps of Suillus variegatus in seven Swedish populations

    International Nuclear Information System (INIS)

    Dahlberg, Anders; Nikolova, Ivanka; Johanson, K.-J.

    1997-01-01

    Following the Chernobyl accident in 1986, sporocarps of Suillus variegatus in Sweden showed a large amount of individual variation in concentration of 137 Cs activity. Our aim was to determine the degrees to which this variability in sporocarp 137 Cs levels could be explained by differences between (i) local populations, (ii) fungal genets and (iii) locations within genets. Five populations in a 100-yr-old Scots pine forest, located within a 1 km 2 area, and two populations in Scots pine/Norway spruce forest, located 40 km north-west of Uppsala, were investigated. In total, 154 sporocarps were analysed to determine their 137 Cs content. Of these, the genetic affiliations of 86 were successfully characterized using somatic incompatibility reactions. Twenty-six genets were found which, on average, consisted of 6.5 sporocarps. The genets averaged 7.5 m in size, measured as the length between the most distant sporocarps. The mean sporocarp 137 Cs level was 67.1 ± 2.8 kBq kgsup(-1) D.W. (range between 13.6 and 182). According to analyses of variance, within-population variation accounted for 60% of the total variation in 137 Cs levels, while 40% was ascribed to variation among populations. Within a population, 137 Cs levels did not generally differ significantly between genets. Plausible reasons for intraspecific variation in radiocaesium content in sporocarps are discussed. (author)

  15. Intraspecific variation in the diet of the Mexican garter snake Thamnophis eques

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    Javier Manjarrez

    2017-11-01

    Full Text Available The Mexican Garter Snake (Thamnophis eques is a terrestrial-aquatic generalist that feeds on both aquatic and terrestrial prey. We describe size-related variation and sexual variation in the diet of T. eques through analysis of 262 samples of identifiable stomach contents in snakes from 23 locations on the Mexican Plateau. The snake T. eques we studied consumed mostly fish, followed in lesser amounts by leeches, earthworms, frogs, and tadpoles. Correspondence analysis suggested that the frequency of consumption of various prey items differed between the categories of age but not between sex of snakes, and the general pattern was a reduction of prey item diversity with size of snake. Snake length was correlated positively with mass of ingested prey. Large snakes consumed large prey and continued to consume smaller prey. In general, no differences were found between the prey taxa of male and female snakes, although males ate two times more tadpoles than females. Males and females did not differ in the mass of leeches, earthworms, fishes, frogs and tadpoles that they ate, and males and females that ate each prey taxon were similar in length. We discuss proximate and functional determinants of diet and suggest that the observed intraspecific variation in T. eques could be explored by temporal variation in prey availability, proportions of snake size classes and possible sexual dimorphism in head traits and prey dimensions to assess the role of intersexual resource competition.

  16. Does intraspecific competition facilitate age separation in timing of southward migration in waders?

    Science.gov (United States)

    Minias, Piotr; Kaczmarek, Krzysztof; Włodarczyk, Radosław; Janiszewski, Tomasz

    2014-07-01

    In many Palaearctic wader species there is a clear separation in the timing of adult and juvenile southward migration. This phenomenon is traditionally explained by the selection on adults to depart early from breeding grounds and necessity of juveniles to prepare longer for migration. In this study we hypothesize that late departure from natal grounds may also be adaptive for juveniles, as it allows them to avoid intensified interference competition at stopover sites with adult, usually more dominant conspecifics. To test this hypothesis we analysed long-term data on stopover behaviour of juvenile wood sandpipers (Tringa glareola) staying at a central Polish stopover site under varying levels of competition from adult birds. The results clearly indicated that juveniles were highly disadvantaged by the simultaneous presence of adults at the same staging site, as under intense competition from older conspecifics they refuelled more slowly and attained lower fat reserves. It was also found that juveniles which were forced to compete with adults left the site quickly and possibly searched for more favourable staging places. All these imply that delayed departure from natal grounds may be adaptive for juvenile waders, allowing them to mismatch the timing of their first migration with the peak of adult passage and, thus, reduce the negative consequences of intraspecific competition during migration.

  17. Intraspecific variations in responses to ocean acidification in two branching coral species.

    Science.gov (United States)

    Sekizawa, Ayami; Uechi, Hikaru; Iguchi, Akira; Nakamura, Takashi; Kumagai, Naoki H; Suzuki, Atsushi; Sakai, Kazuhiko; Nojiri, Yukihiro

    2017-09-15

    Ocean acidification is widely recognised to have a negative impact on marine calcifying organisms by reducing calcifications, but controversy remains over whether such organisms could cope with ocean acidification within a range of phenotypic plasticity and/or adapt to future acidifying ocean. We performed a laboratory rearing experiment using clonal fragments of the common branching corals Montipora digitata and Porites cylindrica under control and acidified seawater (lower pH) conditions (approximately 400 and 900μatm pCO 2 , respectively) and evaluated the intraspecific variations in their responses to ocean acidification. Intra- and interspecific variations in calcification and photosynthetic efficiency were evident according to both pCO 2 conditions and colony, indicating that responses to acidification may be individually variable at the colony level. Our results suggest that some corals may cope with ocean acidification within their present genotypic composition by adaptation through phenotypic plasticity, while others may be placed under selective pressures resulting in population alteration. Copyright © 2017 Elsevier Ltd. All rights reserved.

  18. PERFORMANCE AND HETEROTIC ESTIMATION OF GROWTH IN INTRASPECIFIC CROSSING OF GIANT GOURAMY

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    Didik Ariyanto

    2011-06-01

    Full Text Available Intraspecific crossing of giant gouramy was done to get better hybrid population. This study was conducted to evaluate the hybrid vigour or heterotic value of the hybrids line, especially for growth rate character. Besides that, we want to know the effect of hybridization on performance of phenotypic variability. Two days post hatching age larvae of four populations i.e. Bastar and Blue-saphire strain, F-1 hybrid and F-1 hybrid reciprocal, were used in this experiment. All fish were reared in aquaria for 30 days period in indoor hatchery. The fish were fed with live food such as Moina and Daphnia for the first ten days, followed by Tubifex for the second ten days and finally, commercial feed were given until the end of the study. The collected data were total length, standard length, and body weight of each population. The results showed that the phenotypic variability of the hybrid population was higher than that of inbred population. Hybrid population from female of Bastar and male of Blue-saphire has better growth than both of its parents. Heterotic values of total length, standard length, and body weight of the hybrid population was 9.5%, 2.9%, and 15.6% respectively. Maternal effect was detected in hybrid population.

  19. Antagonistic properties of two recombinant strains of Streptomyces melanosporofaciens obtained by intraspecific protoplast fusion.

    Science.gov (United States)

    Agbessi, S; Beauséjour, J; Déry, C; Beaulieu, C

    2003-08-01

    Intraspecific protoplast fusion was used to produce stable prototrophic recombinants of Streptomyces melanosporofaciens EF-76, a biocontrol agent of plant disease producing geldanamycin. Two recombinant strains (FP-54 and FP-60) that differed with regard to their antagonistic properties against Bacillus cereus ATCC 14579, Streptomyces scabies EF-35 and Phytophthora fragariae var. rubi 390 were characterized. FP-60 lost the ability to inhibit the in vitro growth of these microbial strains while FP-54 exhibited higher antagonistic activities against them. FP-60 was deficient in geldanamycin biosynthesis whereas FP-54 was shown to produce, in addition to geldanamycin, at least two other antimicrobial compounds that were absent in the culture supernatants of strain EF-76. Like the wild-type strain EF-76, strain FP-54 reduced common scab symptoms on potato tuber but no significant difference was observed between the disease index attributed to tubers treated with strain EF-76 or with strain FP-54. Strain FP-60 showed no protective effect against common scab. The disease index of tubers treated with this recombinant was worse than the index associated with potato tubers from control treatments.

  20. Intraspecific sperm competition genes enforce post-mating species barriers in Drosophila.

    Science.gov (United States)

    Castillo, Dean M; Moyle, Leonie C

    2014-12-22

    Sexual selection and sexual conflict are considered important drivers of speciation, based on both theoretical models and empirical correlations between sexually selected traits and diversification. However, whether reproductive isolation between species evolves directly as a consequence of intrapopulation sexual dynamics remains empirically unresolved, in part because knowledge of the genetic mechanisms (if any) connecting these processes is limited. Here, we provide evidence of a direct mechanistic link between intraspecies sexual selection and reproductive isolation. We examined genes with known roles in intraspecific sperm competition (ISC) in D. melanogaster and assayed their impact on conspecific sperm precedence (CSP). We found that two such genes (Acp36DE and CG9997) contribute to both offensive sperm competition and CSP; null/knockdown lines both had lower competitive ability against D. melanogaster conspecifics and were no longer able to displace heterospecific D. simulans sperm in competitive matings. In comparison, Sex Peptide (Acp70A)-another locus essential for ISC-does not contribute to CSP. These data indicate that two loci important for sperm competitive interactions have an additional role in similar interactions that enforce post-mating reproductive isolation between species, and show that sexual selection and sexual isolation can act on the same molecular targets in a gene-specific manner. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

  1. Effects of intraspecific larval competition on adult longevity in the mosquitoes Aedes aegypti and Aedes albopictus.

    Science.gov (United States)

    Reiskind, M H; Lounibos, L P

    2009-03-01

    Larval competition is common in container-breeding mosquitoes. The impact of competition on larval growth has been thoroughly examined and findings that larval competition can lead to density-dependent effects on adult body size have been documented. The effects of larval competition on adult longevity have been less well explored. The effects of intraspecific larval densities on the longevity of adults maintained under relatively harsh environmental conditions were tested in the laboratory by measuring the longevity of adult Aedes aegypti (L.) and Aedes albopictus (Skuse) (Diptera: Culicidae) that had been reared under a range of larval densities and subsequently maintained in high- or low-humidity regimes (85% or 35% relative humidity [RH], respectively) as adults. We found significant negative effects of competition on adult longevity in Ae. aegypti, but not in Ae. albopictus. Multivariate analysis of variance suggested that the negative effect of the larval environment on the longevity of Ae. aegypti adults was most strongly associated with increased development time and decreased wing length as adults. Understanding how larval competition affects adult longevity under a range of environmental conditions is important in establishing the relationship between models of mosquito population regulation and epidemiological models of vector-borne disease transmission.

  2. Consequences of the Allee effect and intraspecific competition on population persistence under adverse environmental conditions.

    Science.gov (United States)

    Petrovskii, Sergei; Blackshaw, Rod; Li, Bai-Lian

    2008-02-01

    The impact of intraspecific interactions on ecological stability and population persistence in terms of steady state(s) existence is considered theoretically based on a general competition model. We compare persistence of a structured population consisting of a few interacting (competitive) subpopulations, or groups, to persistence of the corresponding unstructured population. For a general case, we show that if the intra-group competition is stronger than the inter-group competition, then the structured population is less prone to extinction, i.e. it can persist in a parameter range where the unstructured population goes extinct. For a more specific case of a population with hierarchical competition, we show that relative viability of structured and unstructured populations depend on the type of density dependence in the population growth. Namely, while in the case of logistic growth, structured and unstructured populations exhibit equivalent persistence; in the case of Allee dynamics, the persistence of a hierarchically structured population is shown to be higher. We then apply these results to the case of behaviourally structured populations and demonstrate that an extreme form of individual aggression can be beneficial at the population level and enhance population persistence.

  3. Environmental stochasticity and intraspecific competition influence the population dynamics of Culex quinquefasciatus (Diptera: Culicidae).

    Science.gov (United States)

    Koval, William T; Vazquez-Prokopec, Gonzalo M

    2018-02-27

    Members of the Culex pipiens complex (Cx. pipiens quinquefasciatus in Southern USA) play a critical role in the spillover of urban arboviruses such as West Nile virus or St. Louis encephalitis virus. Field studies have shown strong correlation between the periodicity of rainfall events and larval proliferation. However, mechanistic determinants driving this relationship are poorly understood. We hypothesize that rainfall events decrease strain from intraspecific competition through the associated reduction of immature density and the introduction of detritus. To address our hypothesis, we used laboratory competition experiments to inform a deterministic matrix projection model consisting of an age-structured larval matrix coupled with a stage-structured adult mosquito matrix. Rain events were simulated in a competition-based metabolic age model and compared to a null model including environmental variability. Variable rain delays in two-event simulations showed optimal proliferation occurring with rain delays between 16 and 21 days when including density-dependent effects. These results are comparable to the pattern observed in natural populations, indicating that Cx. quinquefasciatus proliferation rates can be modeled mechanistically as a density-dependent system. The empirical understanding of density-dependence as it relates to environmental stochasticity provides a theoretical platform for the study of larval dynamics and the impact of larval control in this medically relevant disease vector.

  4. Intraspecific competition drives increased resource use diversity within a natural population.

    Science.gov (United States)

    Svanbäck, Richard; Bolnick, Daniel I

    2007-03-22

    Resource competition is thought to play a major role in driving evolutionary diversification. For instance, in ecological character displacement, coexisting species evolve to use different resources, reducing the effects of interspecific competition. It is thought that a similar diversifying effect might occur in response to competition among members of a single species. Individuals may mitigate the effects of intraspecific competition by switching to use alternative resources not used by conspecific competitors. This diversification is the driving force in some models of sympatric speciation, but has not been demonstrated in natural populations. Here, we present experimental evidence confirming that competition drives ecological diversification within natural populations. We manipulated population density of three-spine sticklebacks (Gasterosteus aculeatus) in enclosures in a natural lake. Increased population density led to reduced prey availability, causing individuals to add alternative prey types to their diet. Since phenotypically different individuals added different alternative prey, diet variation among individuals increased relative to low-density control enclosures. Competition also increased the diet-morphology correlations, so that the frequency-dependent interactions were stronger in high competition. These results not only confirm that resource competition promotes niche variation within populations, but also show that this increased diversity can arise via behavioural plasticity alone, without the evolutionary changes commonly assumed by theory.

  5. Larval size in acanthocephalan parasites: influence of intraspecific competition and effects on intermediate host behavioural changes.

    Science.gov (United States)

    Dianne, Lucile; Bollache, Loïc; Lagrue, Clément; Franceschi, Nathalie; Rigaud, Thierry

    2012-08-09

    Parasites often face a trade-off between exploitation of host resources and transmission probabilities to the next host. In helminths, larval growth, a major component of adult parasite fitness, is linked to exploitation of intermediate host resources and is influenced by the presence of co-infecting conspecifics. In manipulative parasites, larval growth strategy could also interact with their ability to alter intermediate host phenotype and influence parasite transmission. We used experimental infections of Gammarus pulex by Pomphorhynchus laevis (Acanthocephala), to investigate larval size effects on host behavioural manipulation among different parasite sibships and various degrees of intra-host competition. Intra-host competition reduced mean P. laevis cystacanth size, but the largest cystacanth within a host always reached the same size. Therefore, all co-infecting parasites did not equally suffer from intraspecific competition. Under no intra-host competition (1 parasite per host), larval size was positively correlated with host phototaxis. At higher infection intensities, this relationship disappeared, possibly because of strong competition for host resources, and thus larval growth, and limited manipulative abilities of co-infecting larval acanthocephalans. Our study indicates that behavioural manipulation is a condition-dependant phenomenon that needs the integration of parasite-related variables to be fully understood.

  6. Everybody loses: intraspecific competition induces tragedy of the commons in Allenby's gerbils.

    Science.gov (United States)

    Berger-Tal, Oded; Embar, Keren; Kotler, Burt P; Saltz, David

    2015-01-01

    Interference competition may lead to a tragedy of the commons in which individuals driven by self-interest reduce the fitness of the entire group. We investigated this hypothesis in Allenby's gerbils, Gerbillus andersoni allenbyi, by comparing foraging behaviors of single vs. pairs of gerbils. We recorded strong interference competition within the foraging pairs. Competition reduced the amount of time the gerbils spent foraging, as well as foraging efficiency since part of the foragers' attention was directed toward detecting competitors (apparent predation risk). Single gerbils harvested significantly more food than the combined efforts of two gerbils foraging together. Competition reduced the success of both individuals within a pair by more than 50%, making this a case of the tragedy of the commons where each individual's investment in competition reduces the success of all individuals within the group, including its own. Despite their great costs, competitive behaviors will be selected for as long as one individual achieves higher fitness than the other. In nature, interspecific interactions, such as predation risk, may act to reduce and regulate the deleterious effects of intraspecific competition.

  7. Variation in Streptococcus pneumoniae susceptibility to human antimicrobial peptides may mediate intraspecific competition.

    Science.gov (United States)

    Habets, Michelle G J L; Rozen, Daniel E; Brockhurst, Michael A

    2012-09-22

    Streptococcus pneumoniae is a facultative pathogen inhabiting the nasopharynx of humans where it is exposed to a range of antimicrobial peptides (AMPs) of the innate immune response. It is possible therefore that the susceptibility of strains to AMPs plays a role in determining their ability to colonize, and furthermore, that AMPs could mediate competitive interactions between co-colonizing genotypes. However, little is known about patterns of natural variation in AMP susceptibility of S. pneumoniae, and it is unclear whether the susceptibilities of an isolate to multiple human AMPs are correlated. We tested this by characterizing the susceptibility of 31 S. pneumoniae natural isolates to human neutrophil peptide (HNP-1) (α-defensin) and LL-37 (cathelicidin). We observed significant variation in susceptibility between isolates to both AMPs, and in the majority of isolates, susceptibilities to HNP-1 and LL-37 were uncorrelated. Clinical isolates were more susceptible to AMPs than were carriage isolates. The polysaccharide capsule of S. pneumoniae is thought to protect cells against AMPs. However, serotype alone could not explain the observed variation in susceptibility suggesting that genetic background plays an equally important role. We tested directly whether AMPs could mediate competition between isolates using competition experiments in the presence and absence of AMPs. These experiments demonstrated that AMPs could indeed reverse the outcome of competition between selected isolates. AMP-mediated competition could therefore contribute to the maintenance of intraspecific genetic diversity in S. pneumoniae.

  8. Can we control the invasive cane toad using chemicals that have evolved under intraspecific competition?

    Science.gov (United States)

    Clarke, Gregory S; Crossland, Michael R; Shine, Richard

    2016-03-01

    Many invasive species experience intense intraspecific competition, because they are abundant in anthropogenically disturbed habitats where few native species persist. Species-specific competitive mechanisms that evolve in this context may offer novel, highly targeted means to control invasive taxa. We conducted laboratory experiments to evaluate the feasibility of this method of control, based on waterborne cues that are produced by tadpoles of the cane toad (Rhinella marina) to suppress the development of conspecific embryos. Our trials examined the nature and species-specificity of the effect, the robustness of the cue to freezing and storage, and the amounts required to suppress toad embryos. Our results were encouraging. The cue appears to be chemical rather than a biological organism, and may well be species-specific; the four species of native anurans that we tested were not influenced by toad larval cues. The cue retains its effectiveness after being frozen, but not after being dried, or after 7 d in water. It is effective at very low concentrations (the amount produced by three tadpoles within 750 L of water). Overall, the cane toad's suppressor pheromone may offer an effective new way to control invasive toads.

  9. Host and symbiont intraspecific variability: The case of Paramecium calkinsi and "Candidatus Trichorickettsia mobilis".

    Science.gov (United States)

    Sabaneyeva, E; Castelli, M; Szokoli, F; Benken, K; Lebedeva, N; Salvetti, A; Schweikert, M; Fokin, S; Petroni, G

    2018-02-01

    Newly isolated strains of the ciliate Paramecium calkinsi and their cytoplasmic bacterial endosymbionts were characterized by a multidisciplinary approach, including live observation, ultrastructural investigation, and molecular analysis. Despite morphological resemblance, the characterized P. calkinsi strains showed a significant molecular divergence compared to conspecifics, possibly hinting for a cryptic speciation. The endosymbionts were clearly found to be affiliated to the species "Candidatus Trichorickettsia mobilis" (Rickettsiales, Rickettsiaceae), currently encompassing only bacteria retrieved in an obligate intracellular association with other ciliates. However, a relatively high degree of intraspecific divergence was observed as well, thus it was possible to split "Candidatus Trichorickettsia" into three subspecies, one of which represented so far only by the newly characterized endosymbionts of P. calkinsi. Other features distinguished the members of each different subspecies. In particular, the endosymbionts of P. calkinsi resided in the cytoplasm and possessed numerous peritrichous flagella, although no motility was evidenced, whereas their conspecifics in other hosts were either cytoplasmic and devoid of flagella, or macronuclear, displaying flagellar-driven motility. Moreover, contrarily to previously analyzed "Candidatus Trichorickettsia" hosts, infected P. calkinsi cells frequently became amicronucleate and demonstrated abnormal cell division, eventually leading to decline of the laboratory culture. Copyright © 2017 Elsevier GmbH. All rights reserved.

  10. Inter- and intra-specific responses to elevated ozone and chamber climate in northern birches

    International Nuclear Information System (INIS)

    Manninen, S.; Huttunen, S.; Vanhatalo, M.; Pakonen, T.; Haemaelaeinen, A.

    2009-01-01

    We studied the responses of micropropagated, northern provenances of downy, mountain and silver birches to elevated ozone (O 3 ) and changing climate using open-top chambers (OTCs). Contrary to our hypothesis, northern birches were sensitive to O 3 , i.e. O 3 levels of 31-36 ppb reduced the leaf and root biomasses by -10%, whereas wood biomass was affected to a lesser extent. The warmer and drier OTC climate enhanced growth in general, though there were differences among the species and clones, e.g. in bud burst and biomass production. Inter- and intra-specific responses to O 3 and changing climate relate to traits such as allocation patterns between the above- and belowground parts (i.e. root/shoot ratio), which further relate to nutrient and water economy. Our experiments may have mimicked future conditions quite well, but only long-term field studies can yield the information needed to forecast responses at both tree and ecosystem levels. - Northern birches are responsive to ambient ozone levels.

  11. Inter- and intra-specific responses to elevated ozone and chamber climate in northern birches.

    Science.gov (United States)

    Manninen, S; Huttunen, S; Vanhatalo, M; Pakonen, T; Hämäläinen, A

    2009-05-01

    We studied the responses of micropropagated, northern provenances of downy, mountain and silver birches to elevated ozone (O(3)) and changing climate using open-top chambers (OTCs). Contrary to our hypothesis, northern birches were sensitive to O(3), i.e. O(3) levels of 31-36 ppb reduced the leaf and root biomasses by -10%, whereas wood biomass was affected to a lesser extent. The warmer and drier OTC climate enhanced growth in general, though there were differences among the species and clones, e.g. in bud burst and biomass production. Inter- and intra-specific responses to O(3) and changing climate relate to traits such as allocation patterns between the above- and belowground parts (i.e. root/shoot ratio), which further relate to nutrient and water economy. Our experiments may have mimicked future conditions quite well, but only long-term field studies can yield the information needed to forecast responses at both tree and ecosystem levels.

  12. Intraspecific variation in erythrocyte sizes among populations of Hypsiboas cordobas (Anura: Hylidae

    Directory of Open Access Journals (Sweden)

    Mariana Baraquet

    2013-12-01

    Full Text Available We studied the morphology and size of erythrocytes of H. cordobae, and analysed the geographic variation of this character along the distribution of the species, in relation to the latitudinal and altitudinal distances. Erythrocyte shape of the H. cordobae is ellipsoidal and the nuclei are also ellipsoidal and centrally oriented. Erythrocyte and nuclear size showed significant differences among populations, with the highest mean size corresponding to the population of Achiras (low altitude site and the lowest mean size to Los Linderos (high altitude site. There was no significant relationship between the latitude of each population and the both erythrocyte and nuclear size. The altitudinal variation in erythrocyte cell size may be attributable to the surface available for gas exchange; a small erythrocyte offers a possibility of greater rate of exchange than a larger one. Our results are consistent with studies of other amphibians, where intraspecific comparisons of populations at different altitudes show that individuals at higher altitudes are characterized by smaller erythrocytes.

  13. Intra-specific downsizing of frugivores affects seed germination of fleshy-fruited plant species

    Science.gov (United States)

    Pérez-Méndez, Néstor; Rodríguez, Airam; Nogales, Manuel

    2018-01-01

    The loss of largest-bodied individuals within species of frugivorous animals is one of the major consequences of defaunation. The gradual disappearance of large-bodied frugivores is expected to entail a parallel deterioration in seed dispersal functionality if the remaining smaller-sized individuals are not so effective as seed dispersers. While the multiple impacts of the extinction of large bodied species have been relatively well studied, the impact of intraspecific downsizing (i.e. the extinction of large individuals within species) on seed dispersal has rarely been evaluated. Here we experimentally assessed the impact of body-size reduction in the frugivorous lizard Gallotia galloti (Lacertidae), an endemic species of the Canary Islands, on the seed germination patterns of two fleshy-fruited plant species (Rubia fruticosa and Withania aristata). Seed germination curves and the proportions of germinated seeds were compared for both plant species after being defecated by large-sized individuals and small-sized individuals. The data show that seeds of W. aristata defecated by larger-sized lizards germinated faster and in a higher percentage than those defecated by small-sized lizards, while no differences were found for R. fruticosa seeds. Our results suggest that disappearance of the largest individuals of frugivorous species may impair recruitment of some plant species by worsening seed germination. They also warn us of a potential cryptic loss of seed dispersal functionality on defaunated ecosystems, even when frugivorous species remain abundant.

  14. On the distribution and intraspecific taxonomy of Scrophularia olympica Boiss. (Scrophulariaceae

    Directory of Open Access Journals (Sweden)

    M. B. Sheludyakova

    2015-10-01

    Full Text Available The article deals with the distribution and intraspecific systematics of Scrophularia olympica Boiss., one of taxonomically problematic species of figworts. The special attention is given to the record of thisspecies from the Crimea from where it had been reported based on the single herbarium specimen collected “infra Baidara” by F. J. Ruprecht in 1861. This collection was previously regarded as made near the village of Orlinoye (former Baydary in the vicinity of Sevastopol. Actually, the locality “infra Baidara” should be referred to the river Baydara in Georgia, and S. olympica should be excludedboth from the floras of the Crimea and Europe as a whole. Six varieties are recognized within the species; a key to their identification is proposed. Lectotypes of S. olympica var. integrifolia Freyn et Sint., S. olympica var. macrophylla Freyn et Sint., S. olympica var. pinnatifida Trautv. ex Grossh. and S. olympica var. platyloma Grossh. are designated. A new name, S. olympica var. bordzilowskii Sheludyakova, nom. nov. ≡ S. olympica var. integrifoliaBordz., non Freyn et Sint., is proposed.

  15. Comparative Genomics

    Indian Academy of Sciences (India)

    An important hallmark of biological research is the aspect of 'comparisons'. As the complete genome sequences of numerous organisms have become available, the emphasis in biology has shifted to comparisons at the genome level. Indeed, the last few years have witnessed an exponential rise in the number of ...

  16. Comparative Genomics

    Indian Academy of Sciences (India)

    structions of the tree of life, drug discovery programs, func- tion predictions of hypothetical proteins and genes, regula- tory motifs and other non-coding DNA motifs, and genome ... expertise in assembling sequences. Beginning with the complete genome sequence of the bacterial pathogen Haemophilus influenzae that was ...

  17. Mitogenomes from The 1000 Genome Project reveal new Near Eastern features in present-day Tuscans.

    Directory of Open Access Journals (Sweden)

    Alberto Gómez-Carballa

    Full Text Available Genetic analyses have recently been carried out on present-day Tuscans (Central Italy in order to investigate their presumable recent Near East ancestry in connection with the long-standing debate on the origins of the Etruscan civilization. We retrieved mitogenomes and genome-wide SNP data from 110 Tuscans analyzed within the context of The 1000 Genome Project. For phylogeographic and evolutionary analysis we made use of a large worldwide database of entire mitogenomes (>26,000 and partial control region sequences (>180,000.Different analyses reveal the presence of typical Near East haplotypes in Tuscans representing isolated members of various mtDNA phylogenetic branches. As a whole, the Near East component in Tuscan mitogenomes can be estimated at about 8%; a proportion that is comparable to previous estimates but significantly lower than admixture estimates obtained from autosomal SNP data (21%. Phylogeographic and evolutionary inter-population comparisons indicate that the main signal of Near Eastern Tuscan mitogenomes comes from Iran.Mitogenomes of recent Near East origin in present-day Tuscans do not show local or regional variation. This points to a demographic scenario that is compatible with a recent arrival of Near Easterners to this region in Italy with no founder events or bottlenecks.

  18. Integrating phylogeographic patterns of microsatellite and mtDNA divergence to infer the evolutionary history of chamois (genus Rupicapra).

    Science.gov (United States)

    Rodríguez, Fernando; Pérez, Trinidad; Hammer, Sabine E; Albornoz, Jesús; Domínguez, Ana

    2010-07-22

    ornata as an extremely low diversity. The phylogeographic patterns for mtDNA and microsatellites suggest an evolutionary history with limited range contractions and expansions during the Quaternary period and reflect a major effect of the Alpine barrier on west-east differentiation. The contrasting phylogenies for mtDNA and microsatellites indicate events of hybridization among highly divergent lineages in the central area of distribution. Our study points to the importance of reticulate evolution, with periods of isolation and reduction of population size followed by expansions and hybridizations, in the diversification at the level of close species or subspecies.

  19. Integrating phylogeographic patterns of microsatellite and mtDNA divergence to infer the evolutionary history of chamois (genus Rupicapra

    Directory of Open Access Journals (Sweden)

    Albornoz Jesús

    2010-07-01

    Full Text Available Abstract Background The chamois, distributed over most of the medium to high altitude mountain ranges of southern Eurasia, provides an excellent model for exploring the effects of historical and evolutionary events on diversification. Populations have been grouped into two species, Rupicapra pyrenaica from southwestern Europe and R. rupicapra from eastern Europe. However, a previous study of cytochrome b revealed that the two proposed species were non-monophyletic. The reconstruction of phylogenetic relationships between animal species often depends on the markers studied. To further elucidate the evolutionary history of chamois, we extended earlier studies by analysing DNA sequences of four mitochondrial regions (ND1, 12S, tRNApro and Control Region and microsatellites (20 loci to include all subspecies and cover its entire distribution range. Results We found discordant microsatellite (μsat and mitochondrial (mt DNA phylogenies. Mitochondrial phylogenies form three clades, West, Central and East (mtW, mtC and mtE, at variance with taxonomic classification. Our divergence age estimates indicate an initial separation into branches mtW-mtC and mtE 1.7 million years ago (mya, in the late Pliocene-early Pleistocene, quickly followed by the split of clades mtW and mtC. Clade mtW contains haplotypes from the Iberian peninsula and the western Alps, Clade mtC includes haplotypes from the Apennines and the Massif of Chartreuse and Clade mtE comprises populations to the east of the Alps. Divergence among populations within these three major clades is recent (ornata as an extremely low diversity. Conclusions The phylogeographic patterns for mtDNA and microsatellites suggest an evolutionary history with limited range contractions and expansions during the Quaternary period and reflect a major effect of the Alpine barrier on west-east differentiation. The contrasting phylogenies for mtDNA and microsatellites indicate events of hybridization among highly

  20. MLVA Based Classification of Mycobacterium tuberculosis Complex Lineages for a Robust Phylogeographic Snapshot of Its Worldwide Molecular Diversity

    Science.gov (United States)

    Hill, Véronique; Zozio, Thierry; Sadikalay, Syndia; Viegas, Sofia; Streit, Elisabeth; Kallenius, Gunilla; Rastogi, Nalin

    2012-01-01

    Multiple-locus variable-number tandem repeat analysis (MLVA) is useful to establish transmission routes and sources of infections for various microorganisms including Mycobacterium tuberculosis complex (MTC). The recently released SITVITWEB database contains 12-loci Mycobacterial Interspersed Repetitive Units – Variable Number of Tandem DNA Repeats (MIRU-VNTR) profiles and spoligotype patterns for thousands of MTC strains; it uses MIRU International Types (MIT) and Spoligotype International Types (SIT) to designate clustered patterns worldwide. Considering existing doubts on the ability of spoligotyping alone to reveal exact phylogenetic relationships between MTC strains, we developed a MLVA based classification for MTC genotypic lineages. We studied 6 different subsets of MTC isolates encompassing 7793 strains worldwide. Minimum spanning trees (MST) were constructed to identify major lineages, and the most common representative located as a central node was taken as the prototype defining different phylogenetic groups. A total of 7 major lineages with their respective prototypes were identified: Indo-Oceanic/MIT57, East Asian and African Indian/MIT17, Euro American/MIT116, West African-I/MIT934, West African-II/MIT664, M. bovis/MIT49, M.canettii/MIT60. Further MST subdivision identified an additional 34 sublineage MIT prototypes. The phylogenetic relationships among the 37 newly defined MIRU-VNTR lineages were inferred using a classification algorithm based on a bayesian approach. This information was used to construct an updated phylogenetic and phylogeographic snapshot of worldwide MTC diversity studied both at the regional, sub-regional, and country level according to the United Nations specifications. We also looked for IS6110 insertional events that are known to modify the results of the spoligotyping in specific circumstances, and showed that a fair portion of convergence leading to the currently observed bias in phylogenetic classification of strains may

  1. Species distribution and introgressive hybridization of two Avicennia species from the Western Hemisphere unveiled by phylogeographic patterns.

    Science.gov (United States)

    Mori, Gustavo M; Zucchi, Maria I; Sampaio, Iracilda; Souza, Anete P

    2015-04-10

    Mangrove plants grow in the intertidal zone in tropical and subtropical regions worldwide. The global latitudinal distribution of the mangrove is mainly influenced by climatic and oceanographic features. Because of current climate changes, poleward range expansions have been reported for the major biogeographic regions of mangrove forests in the Western and Eastern Hemispheres. There is evidence that mangrove forests also responded similarly after the last glaciation by expanding their ranges. In this context, the use of genetic tools is an informative approach for understanding how historical processes and factors impact the distribution of mangrove species. We investigated the phylogeographic patterns of two Avicennia species, A. germinans and A. schaueriana, from the Western Hemisphere using nuclear and chloroplast DNA markers. Our results indicate that, although Avicennia bicolor, A. germinans and A. schaueriana are independent lineages, hybridization between A. schaueriana and A. germinans is a relevant evolutionary process. Our findings also reinforce the role of long-distance dispersal in widespread mangrove species such as A. germinans, for which we observed signs of transatlantic dispersal, a process that has, most likely, contributed to the breadth of the distribution of A. germinans. However, along the southern coast of South America, A. schaueriana is the only representative of the genus. The distribution patterns of A. germinans and A. schaueriana are explained by their different responses to past climate changes and by the unequal historical effectiveness of relative gene flow by propagules and pollen. We observed that A. bicolor, A. germinans and A. schaueriana are three evolutionary lineages that present historical and ongoing hybridization on the American continent. We also inferred a new evidence of transatlantic dispersal for A. germinans, which may have contributed to its widespread distribution. Despite the generally wider distribution of A

  2. Genome-scale multilocus microsatellite typing of Trypanosoma cruzi discrete typing unit I reveals phylogeographic structure and specific genotypes linked to human infection.

    Directory of Open Access Journals (Sweden)

    Martin S Llewellyn

    2009-05-01

    Full Text Available Trypanosoma cruzi is the most important parasitic infection in Latin America and is also genetically highly diverse, with at least six discrete typing units (DTUs reported: Tc I, IIa, IIb, IIc, IId, and IIe. However, the current six-genotype classification is likely to be a poor reflection of the total genetic diversity present in this undeniably ancient parasite. To determine whether epidemiologically important information is "hidden" at the sub-DTU level, we developed a 48-marker panel of polymorphic microsatellite loci to investigate population structure among 135 samples from across the geographic distribution of TcI. This DTU is the major cause of resurgent human disease in northern South America but also occurs in silvatic triatomine vectors and mammalian reservoir hosts throughout the continent. Based on a total dataset of 12,329 alleles, we demonstrate that silvatic TcI populations are extraordinarily genetically diverse, show spatial structuring on a continental scale, and have undergone recent biogeographic expansion into the southern United States of America. Conversely, the majority of human strains sampled are restricted to two distinct groups characterised by a considerable reduction in genetic diversity with respect to isolates from silvatic sources. In Venezuela, most human isolates showed little identity with known local silvatic strains, despite frequent invasion of the domestic setting by infected adult vectors. Multilocus linkage indices indicate predominantly clonal parasite propagation among all populations. However, excess homozygosity among silvatic strains and raised heterozygosity among domestic populations suggest that some level of genetic recombination cannot be ruled out. The epidemiological significance of these findings is discussed.

  3. Cardiovascular genomics.

    Science.gov (United States)

    Wung, Shu-Fen; Hickey, Kathleen T; Taylor, Jacquelyn Y; Gallek, Matthew J

    2013-03-01

    This article provides an update on cardiovascular genomics using three clinically relevant exemplars, including myocardial infarction (MI) and coronary artery disease (CAD), stroke, and sudden cardiac death (SCD). ORGANIZATIONAL CONSTRUCT: Recent advances in cardiovascular genomic research, testing, and clinical implications are presented. Genomic nurse experts reviewed and summarized recent salient literature to provide updates on three selected cardiovascular genomic conditions. Research is ongoing to discover comprehensive genetic markers contributing to many common forms of cardiovascular disease (CVD), including MI and stroke. However, genomic technologies are increasingly being used clinically, particularly in patients with long QT syndrome (LQTS) or hypertrophic cardiomyopathy (HCM) who are at risk for SCD. Currently, there are no clinically recommended genetic tests for many common forms of CVD even though direct-to-consumer genetic tests are being marketed to healthcare providers and the general public. On the other hand, genetic testing for patients with certain single gene conditions, including channelopathies (e.g., LQTS) and cardiomyopathies (e.g., HCM), is recommended clinically. Nurses play a pivotal role in cardiogenetics and are actively engaged in direct clinical care of patients and families with a wide variety of heritable conditions. It is important for nurses to understand current development of cardiovascular genomics and be prepared to translate the new genomic knowledge into practice. © 2013 Sigma Theta Tau International.

  4. Cryptic invasion of Northern Leopard Frogs (Rana pipiens) across phylogeographic boundaries and a dilemma for conservation of a declining amphibian

    Science.gov (United States)

    O'Donnell, Ryan P.; Drost, Charles A.; Mock, Karen E.

    2017-01-01

    Anthropogenic introduction of species is a major contributor to loss of biodiversity. Translocations within the range of a species are less frequently recognized, but have the potential for negative effects as well. Genetic mixing may lead to loss of local adaptations or further decline through outbreeding depression. These cryptic invasions may be quite difficult to recognize, but genetic tools can be used to recognize and monitor such intraspecific introductions. Conversely, translocations within species can be an important conservation tool to reduce inbreeding depression and replace lost genetic diversity. Thus, cryptic invasions can be either an aid or a hindrance to conservation efforts. We tested for the presence of non-native genotypes and assessed the extent and nature of introgression in populations of Northern Leopard Frog (Rana pipiens) in the southwestern US, where populations have declined to a few remnant populations. The most abundant and diverse complex of populations in the region contained a mitochondrial haplotype that was not native to the western US, probably resulting from the introduction of released pets, laboratory animals, or release during fish stocking. These non-native haplotypes were well integrated into a large complex of ponds and lakes, contributing to high genetic diversity in this area. Logistically, the geographic extent of non-native genetic influence within this population precludes eliminating or controlling the non-native component of this population. We recommend assessing the progress and fate of the introgression over time—along with population fitness parameters—to determine whether this introduction is beneficial or detrimental to population persistence. Meanwhile, translocations from nearby locations with similar environmental conditions have the best prospects for avoiding problems with outbreeding depression in other declining populations and will also most effectively preserve regional genetic diversity.

  5. Deep phylogeographic structuring of populations of the trapdoor spider Moggridgea tingle (Migidae) from southwestern Australia: evidence for long-term refugia within refugia.

    Science.gov (United States)

    Cooper, Steven J B; Harvey, Mark S; Saint, Kathleen M; Main, Barbara Y

    2011-08-01

    Southwestern Australia has been recognized as a biodiversity hot spot of global significance, and it is particularly well known for its considerable diversity of flowering plant species. Questions of interest are how this region became so diverse and whether its fauna show similar diverse patterns of speciation. Here, we carried out a phylogeographic study of trapdoor spiders (Migidae: Moggridgea), a presumed Gondwanan lineage found in wet forest localities across southwestern Australia. Phylogenetic, molecular clock and population genetic analyses of mitochondrial (mtDNA) COI gene and ITS rRNA (internal transcribed spacer) data revealed considerable phylogeographic structuring of Moggridgea populations, with evidence for long-term (>3 million years) isolation of at least nine populations in different geographic locations, including upland regions of the Stirling and Porongurup Ranges. High levels of mtDNA divergence and no evidence of recent mitochondrial gene flow among valley populations of the Stirling Range suggest that individual valleys have acted as refugia for the spiders throughout the Pleistocene. Our findings support the hypothesis that climate change, particularly the aridification of Australia after the late Miocene, and the topography of the landscape, which allowed persistence of moist habitats, have been major drivers of speciation in southwestern Australia. © 2011 Blackwell Publishing Ltd.

  6. The phylogeographic structure of Hydrilla verticillata (Hydrocharitaceae) in China and its implications for the biogeographic history of this worldwide-distributed submerged macrophyte.

    Science.gov (United States)

    Zhu, Jinning; Yu, Dan; Xu, Xinwei

    2015-05-24

    Aquatic vascular plants are a distinctive group, differing from terrestrial plants in their growth forms and habitats. Among the various aquatic plant life forms, the evolutionary processes of freshwater submerged species are most likely distinct due to their exclusive occurrence in the discrete and patchy aquatic habitats. Using the chloroplast trnL-F region sequence data, we investigated the phylogeographic structure of a submerged macrophyte, Hydrilla verticillata, the single species in the genus Hydrilla, throughout China, in addition to combined sample data from other countries to reveal the colonisation and diversification processes of this species throughout the world. We sequenced 681 individuals from 123 sampling locations throughout China and identified a significant phylogeographic structure (NST > GST, p China indicates that China is most likely the centre of Hydrilla genetic diversity. The worldwide distribution of Hydrilla is due to recent vicariance and dispersal events that occurred in different clades during the Pleistocene. Our findings also provide useful information for the management of invasive Hydrilla in North America.

  7. Zoogeography of the San Andreas Fault system: Great Pacific Fracture Zones correspond with spatially concordant phylogeographic boundaries in western North America.

    Science.gov (United States)

    Gottscho, Andrew D

    2016-02-01

    The purpose of this article is to provide an ultimate tectonic explanation for several well-studied zoogeographic boundaries along the west coast of North America, specifically, along the boundary of the North American and Pacific plates (the San Andreas Fault system). By reviewing 177 references from the plate tectonics and zoogeography literature, I demonstrate that four Great Pacific Fracture Zones (GPFZs) in the Pacific plate correspond with distributional limits and spatially concordant phylogeographic breaks for a wide variety of marine and terrestrial animals, including invertebrates, fish, amphibians, reptiles, birds, and mammals. These boundaries are: (1) Cape Mendocino and the North Coast Divide, (2) Point Conception and the Transverse Ranges, (3) Punta Eugenia and the Vizcaíno Desert, and (4) Cabo Corrientes and the Sierra Transvolcanica. However, discussion of the GPFZs is mostly absent from the zoogeography and phylogeography literature likely due to a disconnect between biologists and geologists. I argue that the four zoogeographic boundaries reviewed here ultimately originated via the same geological process (triple junction evolution). Finally, I suggest how a comparative phylogeographic approach can be used to test the hypothesis presented here. © 2014 Cambridge Philosophical Society.

  8. Extracting transmission networks from phylogeographic data for epidemic and endemic diseases: Ebola virus in Sierra Leone, 2009 H1N1 pandemic influenza and polio in Nigeria.

    Science.gov (United States)

    Famulare, Michael; Hu, Hao

    2015-03-01

    Phylogeography improves our understanding of spatial epidemiology. However, application to practical problems requires choices among computational tools to balance statistical rigor, computational complexity, sensitivity to sampling strategy and interpretability. We introduce a fast, heuristic algorithm to reconstruct partially-observed transmission networks (POTN) that combines features of phylogenetic and transmission tree approaches. We compare the transmission network generated by POTN with existing algorithms (BEAST and SeqTrack), and discuss the benefits and challenges of phylogeographic analysis on examples of epidemic and endemic diseases: Ebola virus, H1N1 pandemic influenza and polio. For the 2014 Sierra Leone Ebola virus outbreak and the 2009 H1N1 outbreak, all three methods provide similarly plausible transmission histories but differ in detail. For polio in northern Nigeria, we discuss performance trade-offs between the POTN and discrete phylogeography in BEAST and conclude that spatial history reconstruction is limited by under-sampling. POTN is complementary to available tools on densely-sampled data, fails gracefully on under-sampled data and is scalable to accommodate larger datasets. We provide further evidence for the utility of phylogeography for understanding transmission networks of rapidly evolving epidemics. We propose simple heuristic criteria to identify how sampling rates and disease dynamics interact to determine fundamental limitations of phylogeographic inference. © The Author 2015. Published by Oxford University Press on behalf of Royal Society of Tropical Medicine and Hygiene.

  9. The complete chloroplast genome sequence of Dodonaea viscosa: comparative and phylogenetic analyses.

    Science.gov (United States)

    Saina, Josphat K; Gichira, Andrew W; Li, Zhi-Zhong; Hu, Guang-Wan; Wang, Qing-Feng; Liao, Kuo

    2018-02-01

    The plant chloroplast (cp) genome is a highly conserved structure which is beneficial for evolution and systematic research. Currently, numerous complete cp genome sequences have been reported due to high throughput sequencing technology. However, there is no complete chloroplast genome of genus Dodonaea that has been reported before. To better understand the molecular basis of Dodonaea viscosa chloroplast, we used Illumina sequencing technology to sequence its complete genome. The whole length of the cp genome is 159,375 base pairs (bp), with a pair of inverted repeats (IRs) of 27,099 bp separated by a large single copy (LSC) 87,204 bp, and small single copy (SSC) 17,972 bp. The annotation analysis revealed a total of 115 unique genes of which 81 were protein coding, 30 tRNA, and four ribosomal RNA genes. Comparative genome analysis with other closely related Sapindaceae members showed conserved gene order in the inverted and single copy regions. Phylogenetic analysis clustered D. viscosa with other species of Sapindaceae with strong bootstrap support. Finally, a total of 249 SSRs were detected. Moreover, a comparison of the synonymous (Ks) and nonsynonymous (Ka) substitution rates in D. viscosa showed very low values. The availability of cp genome reported here provides a valuable genetic resource for comprehensive further studies in genetic variation, taxonomy and phylogenetic evolution of Sapindaceae family. In addition, SSR markers detected will be used in further phylogeographic and population structure studies of the species in this genus.

  10. Bioaccumulation of photoprotective compounds in copepods: environmental triggers and sources of intra-specific variability

    Science.gov (United States)

    Zagarese, H. E.; García, P.; Diéguez, M. D.; Ferraro, M. A.

    2012-12-01

    Ultraviolet radiation (UVR) and temperature are two globally important abiotic factors affecting freshwater ecosystems. Planktonic organisms have developed a battery of counteracting mechanisms to minimize the risk of being damaged by UVR, which respond to three basic principles: avoid, protect, repair. Copepods are among the most successful zooplankton groups. They are highly adaptable animals, capable of displaying flexible behaviors, physiologies, and life strategies. In particular, they are well equipped to cope with harmful UVR. Their arsenal includes vertical migration, accumulation of photoprotective compounds, and photorepair. The preference for a particular strategy is affected by a plethora of environmental (extrinsic) parameters, such as the existence of a depth refuge, the risk of visual predation, and temperature. Temperature modifies the environment (e.g. the lake thermal structure), and animal metabolism (e.g., swimming speed, bioaccumulation of photoprotective compounds). In addition, the relative weight of UVR-coping strategies is also influenced by the organism (intrinsic) characteristics (e.g., inter- and intra-specific variability). The UV absorbing compounds, mycosporine-like amino acids (MAAs), are widely distributed among freshwater copepods. Animals are unable to synthesize MAAs, and therefore depend on external sources for accumulating these compounds. Although copepods may acquire MAAs from their food, for the few centropagic species investigated so far, the main source of MAAs are microbial (most likely prokaryotic) organisms living in close association with the copepods. Boeckella gracilipes is a common centropagic copepod in Patagonian lakes. We suspected that its occurrence in different types of lakes, hydrologically unconnected, but within close geographical proximity, could have resulted in different microbial-copepod associations (i.e., different MAAs sources) that could translate into intra-specific differences in the accumulation

  11. Growth, inter- and intraspecific variation, palaeobiogeography, taphonomy and systematics of the Cenozoic ghost shrimp Glypturus

    Science.gov (United States)

    Klompmaker, Adiël A.; Hyžný, Matúš; Portell, Roger W.; Kowalewski, Michał

    2015-01-01

    Studies in systematic palaeontology are greatly aided when numerous, well-preserved specimens are available so that quantitative methods can be used to substantiate qualitative observations. This is often not the case for fossil decapod crustaceans due to their relatively low preservation potential. Here, we examined primarily two large collections of the well-preserved ghost shrimp Glypturus from the Holo-Pleistocene of Panama and the late Miocene of Florida. Using descriptive, bivariate, multivariate and geometric morphometric methods, two new species are described based on appendage material: Glypturus panamacanalensis sp. nov. and G. sikesi sp. nov. New characters are identified, and size-related and intraspecific variation are assessed for these taxa and modern G. acanthochirus. Taxonomic placement of single specimens from other localities was confirmed by multivariate methods. Furthermore, Glypturus is revised, especially with regard to Western Atlantic species that inhabited both carbonate and siliciclastic environments. Callianassa anguillensis, C. latidigata, and Neocallichirus? quisquellanus are referred to as Glypturus sp. until more material is available to determine the validity of these species. Diversity within Glypturus may thus be underestimated, thereby also impacting the assessment of phylogenetic relationships. Minor propodi appear under-represented relative to major propodi, suggesting a taphonomic bias. Single specimens of interest include a specimen of G. panamacanalensis sp. nov. exhibiting a peculiar swelling in the fixed finger and another showing damage on the propodal upper margin, suggesting failed predation or antagonistic behaviour. Glypturus is first found in the Oligocene in the Western Atlantic and may have expanded its palaeobiogeographical range since the Miocene. The genus was still present on the Pacific side of the Isthmus of Panama in the Holo-Pleistocene, but is only known from the Western Atlantic today, suggesting a

  12. Use of RAPD and AFLP markers to identify inter- and intraspecific hybrids of Mentha.

    Science.gov (United States)

    Shasany, A K; Darokar, M P; Dhawan, S; Gupta, A K; Gupta, S; Shukla, A K; Patra, N K; Khanuja, S P S

    2005-01-01

    Three controlled crosses were carried out involving Mentha arvensis and Mentha spicata [M. spicata CIMAP/C30 x M. spicata CIMAP/C33 (cv. Neera); M. arvensis CIMAP/C18 x CIMAP/C17 (cv. Kalka); and M. arvensis CIMAP/C17 x M. spicata CIMAP/C33]. The parents were subjected to random amplified polymorphic DNA (RAPD) analysis with 80 primers, and polymorphic primers were tested for detecting coinherited RAPD profiles among the progeny of these crosses. Of 50 seedlings tested from each intraspecific cross, all demonstrated dominant profiles with the selected RAPD primers except the detected hybrid from respective crosses. Coinherited markers could be detected with the primers OPJ 01, MAP 06, OPT 08, and OPO 20 for M. arvensis; OPJ 05, OPJ 14, OPO 19, and OPT 09 for M. spicata; and OPJ 07, OPJ 10, OPJ 11, OPJ 14, and OPO 02 for the cross M. arvensis x M. spicata. In our amplified fragment length polymorphism (AFLP) analysis, 40 coinherited marker fragments were identified for the cross involving M. arvensis, 32 for the cross involving M. spicata, and 41 for the interspecific cross between M. arvensis and M. spicata. In all crosses, similarity values between the parents were less than those between the parents and the hybrids. Although RAPD markers are generally considered dominant, it is possible to identify a few codominant markers that behave like restriction fragment length polymorphism (RFLP) markers. This molecular marker system may be helpful in rapidly screening out hybrids in crops where cross-pollination is a problem.

  13. Intraspecific gestural laterality in chimpanzees and gorillas and the impact of social propensities.

    Science.gov (United States)

    Prieur, Jacques; Pika, Simone; Barbu, Stéphanie; Blois-Heulin, Catherine

    2017-09-01

    A relevant approach to address the mechanisms underlying the emergence of the right-handedness/left-hemisphere language specialization of humans is to investigate both proximal and distal causes of language lateralization through the study of non-human primates' gestural laterality. We carried out the first systematic, quantitative comparison of within-subjects' and between-species' laterality by focusing on the laterality of intraspecific gestures of chimpanzees (Pan troglodytes) and gorillas (Gorilla gorilla) living in six different captive groups. We addressed the following two questions: (1) Do chimpanzees and gorillas exhibit stable direction of laterality when producing different types of gestures at the individual level? If yes, is it related to the strength of laterality? (2) Is there a species difference in gestural laterality at the population level? If yes, which factors could explain this difference? During 1356 observation hours, we recorded 42335 cases of dyadic gesture use in the six groups totalling 39 chimpanzees and 35 gorillas. Results showed that both species could exhibit either stability or flexibility in their direction of gestural laterality. These results suggest that both stability and flexibility may have differently modulated the strength of laterality depending on the species social structure and dynamics. Furthermore, a multifactorial analysis indicates that these particular social components may have specifically impacted gestural laterality through the influence of gesture sensory modality and the position of the recipient in the signaller's visual field during interaction. Our findings provide further support to the social theory of laterality origins proposing that social pressures may have shaped laterality through natural selection. Copyright © 2017 Elsevier B.V. All rights reserved.

  14. Intraspecific variation in cellular and biochemical heat response strategies of Mediterranean Xeropicta derbentina [Pulmonata, Hygromiidae].

    Science.gov (United States)

    Troschinski, Sandra; Di Lellis, Maddalena A; Sereda, Sergej; Hauffe, Torsten; Wilke, Thomas; Triebskorn, Rita; Köhler, Heinz-R

    2014-01-01

    Dry and hot environments challenge the survival of terrestrial snails. To minimize overheating and desiccation, physiological and biochemical adaptations are of high importance for these animals. In the present study, seven populations of the Mediterranean land snail species Xeropicta derbentina were sampled from their natural habitat in order to investigate the intraspecific variation of cellular and biochemical mechanisms, which are assigned to contribute to heat resistance. Furthermore, we tested whether genetic parameters are correlated with these physiological heat stress response patterns. Specimens of each population were individually exposed to elevated temperatures (25 to 52°C) for 8 h in the laboratory. After exposure, the health condition of the snails' hepatopancreas was examined by means of qualitative description and semi-quantitative assessment of histopathological effects. In addition, the heat-shock protein 70 level (Hsp70) was determined. Generally, calcium cells of the hepatopancreas were more heat resistant than digestive cells - this phenomenon was associated with elevated Hsp70 levels at 40°C.We observed considerable variation in the snails' heat response strategy: Individuals from three populations invested much energy in producing a highly elevated Hsp70 level, whereas three other populations invested energy in moderate stress protein levels - both strategies were in association with cellular functionality. Furthermore, one population kept cellular condition stable despite a low Hsp70 level until 40°C exposure, whereas prominent cellular reactions were observed above this thermal limit. Genetic diversity (mitochondrial cytochrome c oxidase subunit I gene) within populations was low. Nevertheless, when using genetic indices as explanatory variables in a multivariate regression tree (MRT) analysis, population structure explained mean differences in cellular and biochemical heat stress responses, especially in the group exposed to 40°C. Our

  15. Molecular assessment of trematode co-infection and intraspecific competition in molluscan intermediate hosts.

    Science.gov (United States)

    Thiele, Elizabeth A; Minchella, Dennis J

    2013-01-01

    In natural populations of the human parasite Schistosoma mansoni, parasite distribution among snail intermediate hosts is generally overdispersed, such that a small proportion of hosts harbor the majority of parasite genotypes. Within these few infected snails, researchers have found that it can be common for hosts to harbor multiple parasite genotypes, creating circumstances in which co-infecting parasites are faced with potential competition over limited host resources. Much theoretical modeling has focused on parasite competition, especially regarding the influence of co-infection on parasite exploitation strategy evolution. However, particularly in the case of intra-molluscan intermediate stages, empirical investigations of parasite-parasite competition have often hinged on the untested assumption that co-exposure produces co-infection. That is, infected hosts exposed to multiple strains have been assumed to harbor multiple strains, regardless of the true nature of the infection outcome. Here we describe a real-time quantitative PCR method to distinguish the conditions of multiple- versus single-strain infection, as well as quantify the relative larval output of co-infecting strains. We applied the method to an empirical investigation of intraspecific parasite competition between S. mansoni strains within the intermediate snail host Biomphalaria glabrata, assessing co-exposure's effects on parasite infectivity and productivity and the concomitant effects on host fitness. Overall, there was no effect of parasite co-infection on snail life history traits relative to single-strain infection. Parasite infectivity significantly increased as a result of increasing overall miracidial dose, rather than co-exposure, though strain-specific productivity was significantly reduced in co-infections in manner consistent with resource competition. Moreover, we show that less than half of infected, co-exposed hosts had patent co-infections and demonstrate the utility of this

  16. Intraspecific variation in cellular and biochemical heat response strategies of Mediterranean Xeropicta derbentina [Pulmonata, Hygromiidae].

    Directory of Open Access Journals (Sweden)

    Sandra Troschinski

    Full Text Available Dry and hot environments challenge the survival of terrestrial snails. To minimize overheating and desiccation, physiological and biochemical adaptations are of high importance for these animals. In the present study, seven populations of the Mediterranean land snail species Xeropicta derbentina were sampled from their natural habitat in order to investigate the intraspecific variation of cellular and biochemical mechanisms, which are assigned to contribute to heat resistance. Furthermore, we tested whether genetic parameters are correlated with these physiological heat stress response patterns. Specimens of each population were individually exposed to elevated temperatures (25 to 52°C for 8 h in the laboratory. After exposure, the health condition of the snails' hepatopancreas was examined by means of qualitative description and semi-quantitative assessment of histopathological effects. In addition, the heat-shock protein 70 level (Hsp70 was determined. Generally, calcium cells of the hepatopancreas were more heat resistant than digestive cells - this phenomenon was associated with elevated Hsp70 levels at 40°C.We observed considerable variation in the snails' heat response strategy: Individuals from three populations invested much energy in producing a highly elevated Hsp70 level, whereas three other populations invested energy in moderate stress protein levels - both strategies were in association with cellular functionality. Furthermore, one population kept cellular condition stable despite a low Hsp70 level until 40°C exposure, whereas prominent cellular reactions were observed above this thermal limit. Genetic diversity (mitochondrial cytochrome c oxidase subunit I gene within populations was low. Nevertheless, when using genetic indices as explanatory variables in a multivariate regression tree (MRT analysis, population structure explained mean differences in cellular and biochemical heat stress responses, especially in the group

  17. Multiple dimensions of intraspecific diversity affect biomass of eelgrass and its associated community.

    Science.gov (United States)

    Abbott, Jessica M; Grosberg, Richard K; Williams, Susan L; Stachowicz, John J

    2017-12-01

    Genetic diversity within key species can play an important role in the functioning of entire communities. However, the extent to which different dimensions of diversity (e.g., the number of genotypes vs. the extent of genetic differentiation among those genotypes) best predicts functioning is unknown and may yield clues into the different mechanisms underlying diversity effects. We explicitly test the relative influence of genotypic richness and genetic relatedness on eelgrass productivity, biomass, and the diversity of associated invertebrate grazers in a factorial field experiment using the seagrass species, Zostera marina (eelgrass). Genotypic richness had the strongest effect on eelgrass biomass accumulation, such that plots with more genotypes at the end of the experiment attained a higher biomass. Genotypic diversity (richness + evenness) was a stronger predictor of biomass than richness alone, and both genotype richness and diversity were positively correlated with trait diversity. The relatedness of genotypes in a plot reduced eelgrass biomass independently of richness. Plots containing eelgrass with greater trait diversity also had a higher abundance of invertebrate grazers, while the diversity and relatedness of eelgrass genotypes had little effect on invertebrate abundance or richness. Our work extends previous findings by explicitly relating genotypic diversity to trait diversity, thus mechanistically connecting genotypic diversity to plot-level yields. We also show that other dimensions of diversity, namely relatedness, influence eelgrass performance independent of trait differentiation. Ultimately, richness and relatedness captured fundamentally different components of intraspecific variation and should be treated as complementary rather than competing dimensions of biodiversity affecting ecosystem functioning. © 2017 by the Ecological Society of America.

  18. Metabolites and hormones are involved in the intraspecific variability of drought hardening in radiata pine.

    Science.gov (United States)

    De Diego, N; Saiz-Fernández, I; Rodríguez, J L; Pérez-Alfocea, P; Sampedro, M C; Barrio, R J; Lacuesta, M; Moncaleán, P

    2015-09-01

    Studies of metabolic and physiological bases of plant tolerance and hardening against drought are essential to improve genetic breeding programs, especially in productive species such as Pinus radiata. The exposure to different drought cycles is a highly effective tool that improves plant conditioning, but limited information is available about the mechanisms that modulate this process. To clarify this issue, six P. radiata breeds with well-known differences in drought tolerance were analyzed after two consecutive drought cycles. Survival rate, concentration of several metabolites such as free soluble amino acids and polyamines, and main plant hormones varied between them after drought hardening, while relative growth ratio and water potential at both predawn and dawn did not. Hardening induced a strong increase in total soluble amino acids in all breeds, accumulating mainly those implicated in the glutamate metabolism (GM), especially L-proline, in the most tolerant breeds. Other amino acids from GM such as γ-aminobutyric acid (GABA) and L-arginine (Arg) were also strongly increased. GABA pathway could improve the response against drought, whereas Arg acts as precursor for the synthesis of spermidine. This polyamine showed a positive relationship with the survival capacity, probably due to its role as antioxidant under stress conditions. Finally, drought hardening also induced changes in phytohormone content, showing each breed a different profile. Although all of them accumulated indole-3-acetic acid and jasmonic acid and reduced zeatin content in needles, significant differences were observed regarding abscisic acid, salicylic acid and mainly zeatin riboside. These results confirm that hardening is not only species-dependent but also an intraspecific processes controlled through metabolite changes. Copyright © 2015 Elsevier GmbH. All rights reserved.

  19. Redescription of Atractus albuquerquei (Serpentes: Colubridae: Dipsadinae, with comments on geographical distribution and intraspecific variation

    Directory of Open Access Journals (Sweden)

    Hussam Zaher

    2005-01-01

    Full Text Available Atractus albuquerquei Cunha and Nascimento, 1983 was previously known from a holotype from eastern Pará, and 15 specimens from Rondônia and Acre, all in Brazil. We report on 23 additional specimens from the Brazilian states of Rondônia, Goiás, Mato Grosso, and Mato Grosso do Sul. These specimens extend the known range of A. albuquerquei substantially, and beyond the southern limits of the Amazon basin. The holotype of A. albuquerquei is redescribed and intraspecific variation in external morphology, hemipenes, and colour is documented. Sexual dimorphism exists in total length, and number of ventral (significantly greater in females and subcaudal scales (greater in males. There is a significant correlation between number of subcaudal scales and longitude (decreasing from East to West for both males and females.Atractus albuquerquei Cunha & Nascimento, 1983 era conhecida apenas do holótipo procedente do leste do estado do Pará e de 15 espécimes dos estados de Rondônia e Acre, no Brasil. Registramos aqui 23 espécimes adicionais provenientes dos estados de Rondônia, Goiás, Mato Grosso e Mato Grosso do Sul. Estes exemplares ampliam a área de distribuição conhecida de A. albuquerquei, para além do limite sul da bacia amazônica. O holótipo de A. albuquerquei é redescrito e a variação intraespecífica da morfologia externa, dos hemipenis e da coloração dos exemplares estudados é analizada. Foi detectado dimorfismo sexual no comprimento total do corpo bem como no número de ventrais (maior nas fêmeas e de subcaudais (maior nos machos. Foi notada uma correlação significativa entre o número de escamas subcaudais e a longitude (que diminuem de leste para oeste em ambos os sexos.

  20. Genomic Imprinting

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 5; Issue 9. Genomic Imprinting - Some Interesting Implications for the Evolution of Social Behaviour. Raghavendra Gadagkar. General Article Volume 5 Issue 9 September 2000 pp 58-68 ...

  1. What can comparative genomics tell us about species concepts in the genus Aspergillus?

    Energy Technology Data Exchange (ETDEWEB)

    Rokas, Antonis; payne, gary; Federova, Natalie D.; Baker, Scott E.; Machida, Masa; yu, Jiujiang; georgianna, D. R.; Dean, Ralph A.; Bhatnagar, Deepak; Cleveland, T. E.; Wortman, Jennifer R.; Maiti, R.; Joardar, V.; Amedeo, Paolo; Denning, David W.; Nierman, William C.

    2007-12-15

    Understanding the nature of species" boundaries is a fundamental question in evolutionary biology. The availability of genomes from several species of the genus Aspergillus allows us for the first time to examine the demarcation of fungal species at the whole-genome level. Here, we examine four case studies, two of which involve intraspecific comparisons, whereas the other two deal with interspecific genomic comparisons between closely related species. These four comparisons reveal significant variation in the nature of species boundaries across Aspergillus. For example, comparisons between A. fumigatus and Neosartorya fischeri (the teleomorph of A. fischerianus) and between A. oryzae and A. flavus suggest that measures of sequence similarity and species-specific genes are significantly higher for the A. fumigatus - N. fischeri pair. Importantly, the values obtained from the comparison between A. oryzae and A. flavus are remarkably similar to those obtained from an intra-specific comparison of A. fumigatus strains, giving support to the proposal that A. oryzae represents a distinct ecotype of A. flavus and not a distinct species. We argue that genomic data can aid Aspergillus taxonomy by serving as a source of novel and unprecedented amounts of comparative data, as a resource for the development of additional diagnostic tools, and finally as a knowledge database about the biological differences between strains and species.

  2. Intraspecific aflatoxin inhibition in Aspergillus flavus is thigmoregulated, independent of vegetative compatibility group and is strain dependent.

    Directory of Open Access Journals (Sweden)

    Changwei Huang

    Full Text Available Biological control of preharvest aflatoxin contamination by atoxigenic stains of Aspergillus flavus has been demonstrated in several crops. The assumption is that some form of competition suppresses the fungus's ability to infect or produce aflatoxin when challenged. Intraspecific aflatoxin inhibition was demonstrated by others. This work investigates the mechanistic basis of that phenomenon. A toxigenic and atoxigenic isolate of A. flavus which exhibited intraspecific aflatoxin inhibition when grown together in suspended disc culture were not inhibited when grown in a filter insert-plate well system separated by a .4 or 3 µm membrane. Toxigenic and atoxigenic conidial mixtures (50∶50 placed on both sides of these filters restored inhibition. There was ∼50% inhibition when a 12 µm pore size filter was used. Conidial and mycelial diameters were in the 3.5-7.0 µm range and could pass through the 12 µm filter. Larger pore sizes in the initially separated system restored aflatoxin inhibition. This suggests isolates must come into physical contact with one another. This negates a role for nutrient competition or for soluble diffusible signals or antibiotics in aflatoxin inhibition. The toxigenic isolate was maximally sensitive to inhibition during the first 24 hrs of growth while the atoxigenic isolate was always inhibition competent. The atoxigenic isolate when grown with a green fluorescent protein (GFP toxigenic isolate failed to inhibit aflatoxin indicating that there is specificity in the touch inhibiton. Several atoxigenic isolates were found which inhibited the GFP isolate. These results suggest that an unknown signaling pathway is initiated in the toxigenic isolate by physical interaction with an appropriate atoxigenic isolate in the first 24 hrs which prevents or down-regulates normal expression of aflatoxin after 3-5 days growth. We suspect thigmo-downregulation of aflatoxin synthesis is the mechanistic basis of intraspecific

  3. Effects of Spatial Patch Arrangement and Scale of Covarying Resources on Growth and Intraspecific Competition of a Clonal Plant.

    Science.gov (United States)

    Wang, Yong-Jian; Shi, Xue-Ping; Meng, Xue-Feng; Wu, Xiao-Jing; Luo, Fang-Li; Yu, Fei-Hai

    2016-01-01

    Spatial heterogeneity in two co-variable resources such as light and water availability is common and can affect the growth of clonal plants. Several studies have tested effects of spatial heterogeneity in the supply of a single resource on competitive interactions of plants, but none has examined those of heterogeneous distribution of two co-variable resources. In a greenhouse experiment, we grew one (without intraspecific competition) or nine isolated ramets (with competition) of a rhizomatous herb Iris japonica under a homogeneous environment and four heterogeneous environments differing in patch arrangement (reciprocal and parallel patchiness of light and soil water) and patch scale (large and small patches of light and water). Intraspecific competition significantly decreased the growth of I. japonica, but at the whole container level there were no significant interaction effects of competition by spatial heterogeneity or significant effect of heterogeneity on competitive intensity. Irrespective of competition, the growth of I. japonica in the high and the low water patches did not differ significantly in the homogeneous treatments, but it was significantly larger in the high than in the low water patches in the heterogeneous treatments with large patches. For the heterogeneous treatments with small patches, the growth of I. japonica was significantly larger in the high than in the low water patches in the presence of competition, but such an effect was not significant in the absence of competition. Furthermore, patch arrangement and patch scale significantly affected competitive intensity at the patch level. Therefore, spatial heterogeneity in light and water supply can alter intraspecific competition at the patch level and such effects depend on patch arrangement and patch scale.

  4. Effects of host plant and larval density on intraspecific competition in larvae of the emerald ash borer (Coleoptera: Buprestidae).

    Science.gov (United States)

    Duan, Jian J; Larson, Kristi; Watt, Tim; Gould, Juli; Lelito, Jonathan P

    2013-12-01

    Competition for food, mates, and space among different individuals of the same insect species can affect density-dependent regulation of insect abundance or population dynamics. The emerald ash borer, Agrilus planipennis Fairmaire (Coleoptera: Buprestidae), is a serious invasive pest of North American ash (Fraxinus spp.) trees, with its larvae feeding in serpentine galleries between the interface of sapwood and phloem tissues of ash trees. Using artificial infestation of freshly cut logs of green ash (Fraxinus pennsylvanica Marshall) and tropical ash (Fraxinus uhdei [Wenzig] Lingelsh) with a series of egg densities, we evaluated the mechanism and outcome of intraspecific competition in larvae of A. planipennis in relation to larval density and host plant species. Results from our study showed that as the egg densities on each log (1.5-6.5 cm in diameter and 22-25 cm in length) increased from 200 to 1,600 eggs per square meter of surface area, larval survivorship declined from ≍68 to 10% for the green ash logs, and 86 to 55% for tropical ash logs. Accordingly, larval mortality resulting from cannibalism, starvation, or both, significantly increased as egg density increased, and the biomass of surviving larvae significantly decreased on both ash species. When larval density was adjusted to the same level, however, larval mortality from intraspecific competition was significantly higher and mean biomasses of surviving larvae was significantly lower in green ash than in tropical ash. The role of intraspecific competition of A. planipennis larvae in density-dependent regulation of its natural population dynamics is discussed.

  5. Assessing intraspecific variation in effective dispersal along an altitudinal gradient: a test in two Mediterranean high-mountain plants.

    Directory of Open Access Journals (Sweden)

    Carlos Lara-Romero

    Full Text Available Plant recruitment depends among other factors on environmental conditions and their variation at different spatial scales. Characterizing dispersal in contrasting environments may thus be necessary to understand natural intraspecific variation in the processes underlying recruitment. Silene ciliata and Armeria caespitosa are two representative species of cryophilic pastures above the tree line in Mediterranean high mountains. No explicit estimations of dispersal kernels have been made so far for these or other high-mountain plants. Such data could help to predict their dispersal and recruitment patterns in a context of changing environments under ongoing global warming.We used an inverse modelling approach to analyse effective seed dispersal patterns in five populations of both Silene ciliata and Armeria caespitosa along an altitudinal gradient in Sierra de Guadarrama (Madrid, Spain. We considered four commonly employed two-dimensional seedling dispersal kernels exponential-power, 2Dt, WALD and log-normal.No single kernel function provided the best fit across all populations, although estimated mean dispersal distances were short (<1 m in all cases. S. ciliata did not exhibit significant among-population variation in mean dispersal distance, whereas significant differences in mean dispersal distance were found in A. caespitosa. Both S. ciliata and A. caespitosa exhibited among-population variation in the fecundity parameter and lacked significant variation in kernel shape.This study illustrates the complexity of intraspecific variation in the processes underlying recruitment, showing that effective dispersal kernels can remain relatively invariant across populations within particular species, even if there are strong variations in demographic structure and/or physical environment among populations, while the invariant dispersal assumption may not hold for other species in the same environment. Our results call for a case-by-case analysis in a

  6. Demographic History and Reproductive Output Correlates with Intraspecific Genetic Variation in Seven Species of Indo-Pacific Mangrove Crabs.

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    Sara Fratini

    Full Text Available The spatial distribution and the amount of intraspecific genetic variation of marine organisms are strongly influenced by many biotic and abiotic factors. Comparing biological and genetic data characterizing species living in the same habitat can help to elucidate the processes driving these variation patterns. Here, we present a comparative multispecies population genetic study on seven mangrove crabs co-occurring in the West Indian Ocean characterized by planktotrophic larvae with similar pelagic larval duration. Our main aim was to investigate whether a suite of biological, behavioural and ecological traits could affect genetic diversities of the study species in combination with historical demographic parameters. As possible current explanatory factors, we used the intertidal micro-habitat colonised by adult populations, various parameters of individual and population fecundity, and the timing of larval release. As the genetic marker, we used partial sequences of cytochrome oxidase subunit I gene. Genetic and ecological data were collected by the authors and/or gathered from primary literature. Permutational multiple regression models and ANOVA tests showed that species density and their reproductive output in combination with historical demographic parameters could explain the intraspecific genetic variation indexes across the seven species. In particular, species producing consistently less eggs per spawning event showed higher values of haplotype diversity. Moreover, Tajima's D parameters well explained the recorded values for haplotype diversity and average γst. We concluded that current intraspecific gene diversities in crabs inhabiting mangrove forests were affected by population fecundity as well as past demographic history. The results were also discussed in terms of management and conservation of fauna in the Western Indian Ocean mangroves.

  7. Genomic profiling of plastid DNA variation in the Mediterranean olive tree.

    Science.gov (United States)

    Besnard, Guillaume; Hernández, Pilar; Khadari, Bouchaib; Dorado, Gabriel; Savolainen, Vincent

    2011-05-10

    Characterisation of plastid genome (or cpDNA) polymorphisms is commonly used for phylogeographic, population genetic and forensic analyses in plants, but detecting cpDNA variation is sometimes challenging, limiting the applications of such an approach. In the present study, we screened cpDNA polymorphism in the olive tree (Olea europaea L.) by sequencing the complete plastid genome of trees with a distinct cpDNA lineage. Our objective was to develop new markers for a rapid genomic profiling (by Multiplex PCRs) of cpDNA haplotypes in the Mediterranean olive tree. Eight complete cpDNA genomes of Olea were sequenced de novo. The nucleotide divergence between olive cpDNA lineages was low and not exceeding 0.07%. Based on these sequences, markers were developed for studying two single nucleotide substitutions and length polymorphism of 62 regions (with variable microsatellite motifs or other indels). They were then used to genotype the cpDNA variation in cultivated and wild Mediterranean olive trees (315 individuals). Forty polymorphic loci were detected on this sample, allowing the distinction of 22 haplotypes belonging to the three Mediterranean cpDNA lineages known as E1, E2 and E3. The discriminating power of cpDNA variation was particularly low for the cultivated olive tree with one predominating haplotype, but more diversity was detected in wild populations. We propose a method for a rapid characterisation of the Mediterranean olive germplasm. The low variation in the cultivated olive tree indicated that the utility of cpDNA variation for forensic analyses is limited to rare haplotypes. In contrast, the high cpDNA variation in wild populations demonstrated that our markers may be useful for phylogeographic and populations genetic studies in O. europaea.

  8. Genomic profiling of plastid DNA variation in the Mediterranean olive tree

    Science.gov (United States)

    2011-01-01

    Background Characterisation of plastid genome (or cpDNA) polymorphisms is commonly used for phylogeographic, population genetic and forensic analyses in plants, but detecting cpDNA variation is sometimes challenging, limiting the applications of such an approach. In the present study, we screened cpDNA polymorphism in the olive tree (Olea europaea L.) by sequencing the complete plastid genome of trees with a distinct cpDNA lineage. Our objective was to develop new markers for a rapid genomic profiling (by Multiplex PCRs) of cpDNA haplotypes in the Mediterranean olive tree. Results Eight complete cpDNA genomes of Olea were sequenced de novo. The nucleotide divergence between olive cpDNA lineages was low and not exceeding 0.07%. Based on these sequences, markers were developed for studying two single nucleotide substitutions and length polymorphism of 62 regions (with variable microsatellite motifs or other indels). They were then used to genotype the cpDNA variation in cultivated and wild Mediterranean olive trees (315 individuals). Forty polymorphic loci were detected on this sample, allowing the distinction of 22 haplotypes belonging to the three Mediterranean cpDNA lineages known as E1, E2 and E3. The discriminating power of cpDNA variation was particularly low for the cultivated olive tree with one predominating haplotype, but more diversity was detected in wild populations. Conclusions We propose a method for a rapid characterisation of the Mediterranean olive germplasm. The low variation in the cultivated olive tree indicated that the utility of cpDNA variation for forensic analyses is limited to rare haplotypes. In contrast, the high cpDNA variation in wild populations demonstrated that our markers may be useful for phylogeographic and populations genetic studies in O. europaea. PMID:21569271

  9. Unveiling current Guanaco distribution in chile based upon niche structure of phylogeographic lineages: Andean puna to subpolar forests.

    Directory of Open Access Journals (Sweden)

    Benito A González

    provides a scientific tool to further develop large scale plans for habitat conservation and preservation of intraspecific genetic variability for this far ranging South American camelid, which inhabits a diversity of ecoregion types from Andean puna to subpolar forests.

  10. Trait-Based Community Assembly along an Elevational Gradient in Subalpine Forests: Quantifying the Roles of Environmental Factors in Inter- and Intraspecific Variability.

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    Ya-Huang Luo

    Full Text Available Understanding how communities respond to environmental variation is a central goal in ecology. Plant communities respond to environmental gradients via intraspecific and/or interspecific variation in plant functional traits. However, the relative contribution of these two responses to environmental factors remains poorly tested. We measured six functional traits (height, leaf thickness, specific leaf area (SLA, leaf carbon concentration (LCC, leaf nitrogen concentration (LNC and leaf phosphorus concentration (LPC for 55 tree species occurring at five elevations across a 1200 m elevational gradient of subalpine forests in Yulong Mountain, Southwest China. We examined the relative contribution of interspecific and intraspecific traits variability based on community weighted mean trait values and functional diversity, and tested how different components of trait variation respond to different environmental axes (climate and soil variables. Species turnover explained the largest amount of variation in leaf morphological traits (leaf thickness and SLA across the elevational gradient. However, intraspecific variability explained a large amount of variation (49.3%-76.3% in three other traits (height, LNC and LPC despite high levels of species turnover. The detection of limiting similarity in community assembly was improved when accounting for both intraspecific and interspecific variability. Different components of trait variation respond to different environmental axes, especially soil water content and climatic variables. Our results indicate that intraspecific variation is critical for understanding community assembly and evaluating community response to environmental change.

  11. Trait-Based Community Assembly along an Elevational Gradient in Subalpine Forests: Quantifying the Roles of Environmental Factors in Inter- and Intraspecific Variability.

    Science.gov (United States)

    Luo, Ya-Huang; Liu, Jie; Tan, Shao-Lin; Cadotte, Marc William; Wang, Yue-Hua; Xu, Kun; Li, De-Zhu; Gao, Lian-Ming

    2016-01-01

    Understanding how communities respond to environmental variation is a central goal in ecology. Plant communities respond to environmental gradients via intraspecific and/or interspecific variation in plant functional traits. However, the relative contribution of these two responses to environmental factors remains poorly tested. We measured six functional traits (height, leaf thickness, specific leaf area (SLA), leaf carbon concentration (LCC), leaf nitrogen concentration (LNC) and leaf phosphorus concentration (LPC)) for 55 tree species occurring at five elevations across a 1200 m elevational gradient of subalpine forests in Yulong Mountain, Southwest China. We examined the relative contribution of interspecific and intraspecific traits variability based on community weighted mean trait values and functional diversity, and tested how different components of trait variation respond to different environmental axes (climate and soil variables). Species turnover explained the largest amount of variation in leaf morphological traits (leaf thickness and SLA) across the elevational gradient. However, intraspecific variability explained a large amount of variation (49.3%-76.3%) in three other traits (height, LNC and LPC) despite high levels of species turnover. The detection of limiting similarity in community assembly was improved when accounting for both intraspecific and interspecific variability. Different components of trait variation respond to different environmental axes, especially soil water content and climatic variables. Our results indicate that intraspecific variation is critical for understanding community assembly and evaluating community response to environmental change.

  12. On the intraspecific variation in morphometry and shape of sagittal otoliths of common sardine, Strangomera bentincki, off central-southern Chile

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    Sandra Curin-Osorio

    2012-11-01

    Full Text Available Size and shape of fish otoliths are species-specific, but some species also display intraspecific variations. The common sardine, Strangomera bentincki, is a small pelagic fish inhabiting a seasonal upwelling ecosystem off central-southern Chile, having two discrete spawning sites along its latitudinal distribution. Otoliths of specimens were collected from commercial catches in Talcahuano and Corral, representing the central and south spawning zones. On the basis of otolith images, size-based shape descriptors were used to detect ontogenetic variation, and morphometric variables (length, breadth, area, perimeter and weight were used to detect geographical differences in size and shape of otoliths. Outline analysis was studied on the basis of elliptic Fourier descriptors through multivariate statistical procedures. Size-based shape descriptors showed that otolith shape starts to be stable for fish larger than 12 cm total length, which keep an elliptical form. Morphometric variables for fish larger than 12 cm revealed intraspecific variation between central and south zones, which were associated with otolith weight and breadth. Outline analysis did not reveal significant spatial differences, but extreme intraspecific variation was due to the antirostrum, excisure, and posterior part of otoliths. Intraspecific variation in otolith size could be linked to differences in each spawning habitat and related to geographical origin, whose differences are not clearly identified. It is concluded that intraspecific variability in morphometric variables of sardine otoliths revealed geographic differences in size that are not attributable to allometric effects, and that otolith shape was similar between specimens from different geographic origin.

  13. Parapatric genetic divergence among deep evolutionary lineages in the Mediterranean green crab, Carcinus aestuarii (Brachyura, Portunoidea, Carcinidae), accounts for a sharp phylogeographic break in the Eastern Mediterranean.

    Science.gov (United States)

    Deli, Temim; Kalkan, Evrim; Karhan, Selahattin Ünsal; Uzunova, Sonya; Keikhosravi, Alireza; Bilgin, Raşit; Schubart, Christoph D

    2018-04-11

    Recently, population genetic studies of Mediterranean marine species highlighted patterns of genetic divergence and phylogeographic breaks, due to the interplay between impacts of Pleistocene climate shifts and contemporary hydrographical barriers. These factors markedly shaped the distribution of marine organisms and their genetic makeup. The present study is part of an ongoing effort to understand the phylogeography and evolutionary history of the highly dispersive Mediterranean green crab, Carcinus aestuarii (Nardo, 1847), across the Mediterranean Sea. Recently, marked divergence between two highly separated haplogroups (genetic types I and II) of C. aestuarii was discerned across the Siculo-Tunisian Strait, suggesting an Early Pleistocene vicariant event. In order to better identify phylogeographic patterns in this species, a total of 263 individuals from 22 Mediterranean locations were analysed by comparing a 587 basepair region of the mitochondrial gene Cox1 (cytochrome oxidase subunit 1). The examined dataset is composed of both newly generated sequences (76) and previously investigated ones (187). Our results unveiled the occurrence of a highly divergent haplogroup (genetic type III) in the most north-eastern part of the Mediterranean Sea. Divergence between the most distinct type III and the common ancestor of both types I and II corresponds to the Early Pleistocene and coincides with the historical episode of separation between types I and II. Our results also revealed strong genetic divergence among adjacent regions (separating the Aegean and Marmara seas from the remaining distribution zone) and confirmed a sharp phylogeographic break across the Eastern Mediterranean. The recorded parapatric genetic divergence, with the potential existence of a contact zone between both groups in the Ionian Sea and notable differences in the demographic history, suggest the likely impact of paleoclimatic events, as well as past and contemporary oceanographic processes

  14. [Nutrition genomics].

    Science.gov (United States)

    Sedová, L; Seda, O

    2004-01-01

    The importance of nutrition for human health and its influence on the onset and course of many diseases are nowadays considered as proven. Only the recent development of molecular biology and biochemical methods allows the elucidation of the molecular mechanisms of diet constituent actions and their subsequent effect on homeostatic mechanisms in health and disease states. The availability of the draft human genome sequence as well as the genome sequences of model organisms, combined with the functional and integrative genomics approaches of systems biology, bring about the possibility to identify alleles and haplotypes responsible for specific reaction to the dietary challenge in susceptible individuals. Such complex interactions are studied within the newly conceived field, the nutrition genomics (nutrigenomics). Using the tools of highly parallel analyses of transcriptome, proteome and metabolome, the nutrition genomics pursues its ultimate goal, i.e. the individualized diet, respecting not only quantitative and qualitative nutritional needs and the actual health status, but also the genetic predispositions of an individual. This approach should lead to prevention of the onset of such diseases as obesity, hypertension or type 2 diabetes, or enhance the efficiency of their therapy.

  15. Intra-specific variation in social organization of gorillas: implications for their social evolution.

    Science.gov (United States)

    Yamagiwa, Juichi; Kahekwa, John; Basabose, Augustin Kanyunyi

    2003-10-01

    We analysed intra-specific variation in the social organization of gorillas and ecological and social factors influencing them, based on recent data on diet, day journey length, home range size, group size and proportion of multi-male groups in three subspecies [western lowland gorillas (WLG); eastern lowland gorillas (ELG); mountain gorillas (MG)]. Median group size was similar across subspecies and across habitats, but the extraordinarily large group including >30 gorillas was only found in habitat with dense terrestrial herbaceous vegetation. Within-group competition may determine the upper limit of group size in frugivorous WLGs and ELGs in lowland habitats with scarce undergrowth. A frugivorous diet may be a causal factor of subgrouping in multi-male groups of WLGs and ELGs, while a folivorous diet may prevent subgrouping in multi-male groups of MGs. Social factors, rather than ecological factors, may play an important role in the formation of multi-male groups and their cohesiveness in MGs. High gregariousness of female gorillas and their prolonged association with a protector male are explained by their vulnerability to both infanticide (MGs) and predators (ELGs). Comparison of long-term changes in group composition and individual movements between ELGs in Kahuzi and MGs in the Virungas suggest that the occurrence of infanticide may promote kin-male association within a group. Threat of infanticide may stimulate MG females to transfer into multi-male groups to seek reliable protection and maturing MG males to stay in their natal groups after maturity. By contrast, the absence of infanticide may facilitate ELG females to associate with infants and other females at transfer and ELG males to establish large groups in a short period by taking females from their natal groups, by luring females from neighbouring groups, or by takeover of a widow group after the death of its leading male. These conditions may prevent ELG and WLG maturing males from remaining to

  16. First evidence of genetic intraspecific variability and occurrence of Entamoeba gingivalis in HIV(+)/AIDS.

    Science.gov (United States)

    Cembranelli, Sibeli B S; Souto, Fernanda O; Ferreira-Paim, Kennio; Richinho, Túlio T; Nunes, Poliana L; Nascentes, Gabriel A N; Ferreira, Thatiana B; Correia, Dalmo; Lages-Silva, Eliane

    2013-01-01

    Entamoeba gingivalis is considered an oral commensal but demonstrates a pathogenic potential associated with periodontal disease in immunocompromised individuals. Therefore, this study evaluated the occurrence, opportunistic conditions, and intraspecific genetic variability of E. gingivalis in HIV(+)/AIDS patients. Entamoeba gingivalis was studied using fresh examination (FE), culture, and PCR from bacterial plaque samples collected from 82 HIV(+)/AIDS patients. Genetic characterization of the lower ribosomal subunit of region 18S (18S-SSU rRNA) was conducted in 9 positive samples using low-stringency single specific primer PCR (LSSP-PCR) and sequencing analysis. Entamoeba gingivalis was detected in 63.4% (52/82) of the samples. No association was detected between the presence of E. gingivalis and the CD4(+) lymphocyte count (≤200 cells/mm(3) (p = 0.912) or viral load (p = 0.429). The LSSP-PCR results helped group E. gingivalis populations into 2 polymorphic groups (68.3% similarity): group I, associated with 63.6% (7/11) of the samples, and group II, associated with 36.4% (4/11) of the samples, which shared 74% and 83.7% similarity and association with C and E isolates from HIV(-) individuals, respectively. Sequencing of 4 samples demonstrated 99% identity with the reference strain ATCC 30927 and also showed 2 divergent clusters, similar to those detected by LSSP-PCR. Opportunistic behavior of E. gingivalis was not detected, which may be related to the use of highly active antiretroviral therapy by all HIV(+)/AIDS patients. The high occurrence of E. gingivalis in these patients can be influenced by multifactorial components not directly related to the CD4(+) lymphocyte counts, such as cholesterol and the oral microbiota host, which could mask the potential opportunistic ability of E. gingivalis. The identification of the 18S SSU-rRNA polymorphism by LSSP-PCR and sequencing analysis provides the first evidence of genetic variability in E. gingivalis

  17. Navigating the Interface Between Landscape Genetics and Landscape Genomics

    Directory of Open Access Journals (Sweden)

    Andrew Storfer

    2018-03-01

    ' phylogeographic history. To this end, we summarize recent simulation studies that test the power and accuracy of genome scan methods under a variety of demographic scenarios and sampling designs. We conclude with a discussion of additional considerations for future method development, and a summary of methods that show promise for landscape genomics studies but are not yet widely used.

  18. Navigating the Interface Between Landscape Genetics and Landscape Genomics.

    Science.gov (United States)

    Storfer, Andrew; Patton, Austin; Fraik, Alexandra K

    2018-01-01

    As next-generation sequencing data become increasingly available for non-model organisms, a shift has occurred in the focus of studies of the geographic distribution of genetic variation. Whereas landscape genetics studies primarily focus on testing the effects of landscape variables on gene flow and genetic population structure, landscape genomics studies focus on detecting candidate genes under selection that indicate possible local adaptation. Navigating the transition between landscape genomics and landscape genetics can be challenging. The number of molecular markers analyzed has shifted from what used to be a few dozen loci to thousands of loci and even full genomes. Although genome scale data can be separated into sets of neutral loci for analyses of gene flow and population structure and putative loci under selection for inference of local adaptation, there are inherent differences in the questions that are addressed in the two study frameworks. We discuss these differences and their implications for study design, marker choice and downstream analysis methods. Similar to the rapid proliferation of analysis methods in the early development of landscape genetics, new analytical methods for detection of selection in landscape genomics studies are burgeoning. We focus on genome scan methods for detection of selection, and in particular, outlier differentiation methods and genetic-environment association tests because they are the most widely used. Use of genome scan methods requires an understanding of the potential mismatches between the biology of a species and assumptions inherent in analytical methods used, which can lead to high false positive rates of detected loci under selection. Key to choosing appropriate genome scan methods is an understanding of the underlying demographic structure of study populations, and such data can be obtained using neutral loci from the generated genome-wide data or prior knowledge of a species' phylogeographic history. To

  19. Marine genomics

    DEFF Research Database (Denmark)

    Oliveira Ribeiro, Ângela Maria; Foote, Andrew David; Kupczok, Anne

    2017-01-01

    evolutionary biology of non-model organisms to species of commercial relevance for fishing, aquaculture and biomedicine. Instead of providing an exhaustive list of available genomic data, we rather set to present contextualized examples that best represent the current status of the field of marine genomics.......Marine ecosystems occupy 71% of the surface of our planet, yet we know little about their diversity. Although the inventory of species is continually increasing, as registered by the Census of Marine Life program, only about 10% of the estimated two million marine species are known. This lag......-throughput sequencing approaches have been helping to improve our knowledge of marine biodiversity, from the rich microbial biota that forms the base of the tree of life to a wealth of plant and animal species. In this review, we present an overview of the applications of genomics to the study of marine life, from...

  20. Listeria Genomics

    Science.gov (United States)

    Cabanes, Didier; Sousa, Sandra; Cossart, Pascale

    The opportunistic intracellular foodborne pathogen Listeria monocytogenes has become a paradigm for the study of host-pathogen interactions and bacterial adaptation to mammalian hosts. Analysis of L. monocytogenes infection has provided considerable insight into how bacteria invade cells, move intracellularly, and disseminate in tissues, as well as tools to address fundamental processes in cell biology. Moreover, the vast amount of knowledge that has been gathered through in-depth comparative genomic analyses and in vivo studies makes L. monocytogenes one of the most well-studied bacterial pathogens. This chapter provides an overview of progress in the exploration of genomic, transcriptomic, and proteomic data in Listeria spp. to understand genome evolution and diversity, as well as physiological aspects of metabolism used by bacteria when growing in diverse environments, in particular in infected hosts.

  1. Cephalopod genomics

    DEFF Research Database (Denmark)

    Albertin, Caroline B.; Bonnaud, Laure; Brown, C. Titus

    2012-01-01

    The Cephalopod Sequencing Consortium (CephSeq Consortium) was established at a NESCent Catalysis Group Meeting, ``Paths to Cephalopod Genomics-Strategies, Choices, Organization,'' held in Durham, North Carolina, USA on May 24-27, 2012. Twenty-eight participants representing nine countries (Austri...... in this white paper......., Australia, China, Denmark, France, Italy, Japan, Spain and the USA) met to address the pressing need for genome sequencing of cephalopod mollusks. This group, drawn from cephalopod biologists, neuroscientists, developmental and evolutionary biologists, materials scientists, bioinformaticians and researchers...

  2. Phylogeographical structure of the neotropical forest tree Hymenaea courbaril (Leguminosae: Caesalpinioideae) and its relationship with the Vicariant Hymenaea stigonocarpa from Cerrado.

    Science.gov (United States)

    Ramos, Ana Carolina Simões; De Lemos-Filho, José Pires; Lovato, Maria Bernadete

    2009-01-01

    The phylogeography of Hymenaea courbaril var. stilbocarpa from Atlantic Forest and riverine forests of the Cerrado biome in central and southeastern Brazil was investigated. The data were compared with those of its congeneric Hymenaea stigonocarpa, a typical tree from savanna. In the Cerrado, H. courbaril var. stilbocarpa is found in sites contiguous with those of H. stigonocarpa, and they share common life-history attributes. The psbC/trnS3 region of the chloroplast DNA was sequenced in 149 individuals of H. courbaril var. stilbocarpa. High genetic variation was found in this species, with the identification of 18 haplotypes, similarly to what was found in H. stigonocarpa with 23 haplotypes in the same geographic region. Populations of H. courbaril var. stilbocarpa could be structured in 3 phylogeographic groups. Spatial analysis of molecular variation indicated that 46.4% of the genetic variation was due to differences among these groups. Three haplotypes were shared by H. courbaril var. stilbocarpa and H. stigonocarpa, and only 10.5% of the total genetic variation could be attributed to between-species difference. We surmise that during the glacial times, H. courbaril var. stilbocarpa populations must have gone extinct in most parts of the southern of its present-day occurrence area. After climate amelioration, these areas were probably recolonized from northern and eastern. The relatively similar phylogeographic structure of vicariant Hymenaea species suggests that they were subjected to the same impacts during the Quaternary climatic fluctuations. The sharing of haplotypes and the genetic similarity between the 2 Hymenaea species suggest the existence of ancestral polymorphism and/or hybridization.

  3. Intraspecific variation in aerobic metabolic rate of fish: relations with organ size and enzyme activity in brown trout.

    Science.gov (United States)

    Norin, Tommy; Malte, Hans

    2012-01-01

    Highly active animals require a high aerobic capacity (i.e., a high maximum metabolic rate [MMR]) to sustain such activity, and it has been speculated that a greater capacity for aerobic performance is reflected in larger organs, which serve as energy processors but are also expensive to maintain and which increase the minimal cost of living (i.e., the basal or standard metabolic rate [SMR]). In this study, we assessed the extent of intraspecific variation in metabolic rate within a group of brown trout (Salmo trutta L.) and tested whether the observed variation in residual (body-mass-corrected) SMR, MMR, and absolute aerobic scope could be explained by variations in the residual size (mass) of metabolically active internal organs. Residual SMR was found to correlate positively with residual MMR, indicating a link between these two metabolic parameters, but no relationship between organ mass and metabolic rate was found for liver, heart, spleen, intestine, or stomach. Instead, activity in the liver of two aerobic mitochondrial enzymes, cytochrome c oxidase and, to a lesser extent, citrate synthase, was found to correlate with whole-animal metabolic rate, indicating that causes for intraspecific variation in the metabolic rate of fish can be found at a lower organizational level than organ size.

  4. Evaluating the Intraspecific Interactions of Indian Rosewood (Dalbergia sissoo Roxb. Trees in Indian Rosewood Reserveof Khuzestan Province

    Directory of Open Access Journals (Sweden)

    Y. Erfanifard

    2016-05-01

    Full Text Available Positive and negative (facilitative and competitive interactions of plants are important issues in autecology and can be evaluated by the spatial pattern analysis in plant ecosystems. This study investigates the intraspecific interactions of Indian rosewood (Dalbergia sissoo Roxb. trees in Indian rosewood Reserve of Khuzestan province. Three 150 m × 200 m plots were selected and the spatial locations of all Indian rosewoods (239 trees were specified. Structurally different summary statistics (nearest neighbour distribution function D(r, K2-index K2(r, pair correlation function g(r, and O-ring O(r were also implemented to analyze the spatial pattern of the trees. The distribution of Indian rosewood trees significantly followed inhomogeneous Poisson process (α=0.05. The results of D(r and K2(r showed that the maximum distance to nearest tree was 12 m and density was decreased to this scale. The results of g(r and O(r also revealed the significant aggregation of Indian rosewood trees at scales of 1.5 to 4 m (α=0.05. In general, it was concluded that Indian rosewood trees had positive intraspecific interactions in Indian rosewood Reserve of Khuzestan province and their aggregation showed their facilitative effects on one another.

  5. Intraspecific Variability in Seed Quality of Native Tree Species in Mountain Forests in Southern Ecuador: Implications for Forest Restoration

    Directory of Open Access Journals (Sweden)

    Ximena Palomeque

    2017-06-01

    Full Text Available One of the most important aspects in efficient plant production for restoration purposes is seed quality and its variability. The main goal of this study was to evaluate seed parameters according to the rules of “International Seed Testing Association” among different mother trees or individuals of seven native tree species (Cedrela montana, Morella pubescens, Inga acreana, Tabebuia chrysantha, Ocotea heterochroma, Oreocallis grandiflora and Myrcianthes rhopaloides in two mountain forests in the Southern of Ecuador. These species were selected based on the ecological, socioeconomic importance, and their high potential for restoration. From a total of 35 mother trees for all species, seeds were collected in their fructification periods, and in the laboratory the following seed parameters were analyzed: purity, seed weight, moisture content, and germination; in addition, the coefficient of velocity of germination was determined as well. The results showed an intraspecific similarity in each species for the majority of seed parameters. However, the seed weight showed a high intraspecific variability for all species. The germination parameter showed differences among individuals for C. montana, T. chrysantha, O. heterochroma and M. rophaloides. In regard to the coefficient of velocity of germination, individual of species such as O. grandiflora and I. acreana showed a high coefficient in contrast to the individuals of O. heterochroma and M. pubescens. The information generated in this study could be a first step in the formulation of guidelines for the mass plant production for restoration purposes.

  6. The extended phenotypes of marine symbioses: ecological and evolutionary consequences of intraspecific genetic diversity in coral-algal associations

    Directory of Open Access Journals (Sweden)

    John Everett Parkinson

    2014-08-01

    Full Text Available Reef-building corals owe much of their success to a symbiosis with dinoflagellate microalgae in the genus Symbiodinium. In this association, the performance of each organism is tied to that of its partner, and together the partners form a holobiont that can be subject to selection. Climate change affects coral reefs, which are declining globally as a result. Yet the extent to which coral holobionts will be able to acclimate or evolve to handle climate change and other stressors remains unclear. Selection acts on individuals and evidence from terrestrial systems demonstrates that intraspecific genetic diversity plays a significant role in symbiosis ecology and evolution. However, we have a limited understanding of the effects of such diversity in corals. As molecular methods have advanced, so too has our recognition of the taxonomic and functional diversity of holobiont partners. Resolving the major components of the holobiont to the level of the individual will help us assess the importance of intraspecific diversity and partner interactions in coral-algal symbioses. Here, we hypothesize that unique combinations of coral and algal individuals yield functional diversity that affects not only the ecology and evolution of the coral holobiont, but associated communities as well. Our synthesis is derived from reviewing existing evidence and presenting novel data. By incorporating the effects of holobiont extended phenotypes into predictive models, we may refine our understanding of the evolutionary trajectory of corals and reef communities responding to climate change.

  7. The extended phenotypes of marine symbioses: ecological and evolutionary consequences of intraspecific genetic diversity in coral-algal associations.

    Science.gov (United States)

    Parkinson, John E; Baums, Iliana B

    2014-01-01

    Reef-building corals owe much of their success to a symbiosis with dinoflagellate microalgae in the genus Symbiodinium. In this association, the performance of each organism is tied to that of its partner, and together the partners form a holobiont that can be subject to selection. Climate change affects coral reefs, which are declining globally as a result. Yet the extent to which coral holobionts will be able to acclimate or evolve to handle climate change and other stressors remains unclear. Selection acts on individuals and evidence from terrestrial systems demonstrates that intraspecific genetic diversity plays a significant role in symbiosis ecology and evolution. However, we have a limited understanding of the effects of such diversity in corals. As molecular methods have advanced, so too has our recognition of the taxonomic and functional diversity of holobiont partners. Resolving the major components of the holobiont to the level of the individual will help us assess the importance of intraspecific diversity and partner interactions in coral-algal symbioses. Here, we hypothesize that unique combinations of coral and algal individuals yield functional diversity that affects not only the ecology and evolution of the coral holobiont, but associated communities as well. Our synthesis is derived from reviewing existing evidence and presenting novel data. By incorporating the effects of holobiont extended phenotypes into predictive models, we may refine our understanding of the evolutionary trajectory of corals and reef communities responding to climate change.

  8. Application of high resolution melting assay (HRM) to study temperature-dependent intraspecific competition in a pathogenic bacterium.

    Science.gov (United States)

    Ashrafi, Roghaieh; Bruneaux, Matthieu; Sundberg, Lotta-Riina; Pulkkinen, Katja; Ketola, Tarmo

    2017-04-20

    Studies on species' responses to climate change have focused largely on the direct effect of abiotic factors and in particular temperature, neglecting the effects of biotic interactions in determining the outcome of climate change projections. Many microbes rely on strong interference competition; hence the fitness of many pathogenic bacteria could be a function of both their growth properties and intraspecific competition. However, due to technical challenges in distinguishing and tracking individual strains, experimental evidence on intraspecific competition has been limited so far. Here, we developed a robust application of the high-resolution melting (HRM) assay to study head-to-head competition between mixed genotype co-cultures of a waterborne bacterial pathogen of fish, Flavobacterium columnare, at two different temperatures. We found that competition outcome in liquid cultures seemed to be well predicted by growth yield of isolated strains, but was mostly inconsistent with interference competition results measured in inhibition tests on solid agar, especially as no growth inhibition between strain pairs was detected at the higher temperature. These results suggest that, for a given temperature, the factors driving competition outcome differ between liquid and solid environments.

  9. Consumer interaction strength may limit the diversifying effect of intraspecific competition: a test in alewife (Alosa pseudoharengus).

    Science.gov (United States)

    Jones, Andrew W; Post, David M

    2013-06-01

    Intraspecific competition is considered a principal driver of dietary variation, but empirical studies provide mixed support for this mechanism. Here we link comparative and experimental work testing the effects of competition and resource availability on the dietary variation of the alewife (Alosa pseudoharengus). The alewife, a consumer with extreme effects on its resources, was specifically utilized to additionally test the idea that strong interactions between a consumer and its resources can diminish the diversifying effect of competition. First, we compared the short- and long-term diet measures of wild populations across a wide range of densities. Second, in a pair of large-scale field mesocosm experiments, we explored the influence of competition and interaction strength on alewife dietary variation. Results from a whole-lake comparison and field experiments indicated that increasing competition was negatively correlated with population dietary variation. Further, altering the strength of the interaction between the alewife and its prey via prey supplementation eliminated this negative relationship. Collectively, our results suggest that competitive interactions may not drive dietary diversification in the alewife and, potentially, in other highly effective consumers. Our results also indicate that further consideration of the strength of species interactions (and the consumer traits that underlie them) would improve our understanding of the link between intraspecific competition and variation.

  10. Intraspecific competition between ectomycorrhizal Pisolithus microcarpus isolates impacts plant and fungal performance under elevated CO2 and temperature.

    Science.gov (United States)

    Hortal, S; Powell, J R; Plett, J M; Simonin, A; Anderson, I C

    2016-08-01

    Root systems are simultaneously colonized by multiple individuals of mycorrhizal fungi. Intraspecific competitive interactions between fungal isolates are likely to affect both fungal and plant performance and be influenced by abiotic factors. Here, we assessed the impact of intraspecific competition between three Pisolithus microcarpus isolates on the establishment of, and benefit derived from, symbioses with Eucalyptus grandis seedlings. We investigated the outcomes of competition under ambient and elevated temperature and CO2 concentration ([CO2]) in a factorial design. We observed a reduction in mycelium growth, mycorrhiza formation and seedling mass when two P. microcarpus isolates were co-inoculated on a single E. grandis seedling. Isolates invested more in mycelium than in mycorrhizas in the presence of a competitor. All isolates responded negatively to elevated [CO2] and positively to elevated temperature, which led to no changes on the outcomes of the interactions with changing conditions. However, the presence of a competitor hindered the positive response of P. microcarpus isolates to warming, which resulted in larger negative effects of competition under elevated temperature than under ambient conditions. Our study highlights the need to consider how competition affects individual fungal responses as well as plant performance when trying to predict the impacts of climate change. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  11. Intraspecific variation among clones of a naïve rare grass affects competition with a nonnative, invasive forb.

    Science.gov (United States)

    Gibson, David J; Dewey, Justin; Goossens, Hélène; Dodd, Misty M

    2014-01-01

    Intraspecific variation can have a major impact on plant community composition yet there is little information available on the extent that such variation by an already established species affects interspecific interactions of an invading species. The current research examined the competitiveness of clones of a globally rare but locally common native grass, Calamagrostis porteri ssp. insperata to invasion by Alliaria petiolata, a non-native invasive species. A greenhouse experiment was conducted twice over consecutive years in which 15 clones from three populations of Calamagrostis were paired with rosettes of Alliaria in pots containing native forest soil previously uninvaded by Alliaria. Both species showed a negative response to the presence of the other species, although Alliaria more so than Calamagrostis. Moreover, the effect of Calamagrostis depended upon population, and, to a lesser extent, the individual clone paired with Alliaria. Competitive effects were stronger in the first experiment compared with when the experiment was repeated in the second year. The influence of Calamagrostis clones on the outcome of the experiment varied among populations and among clones, but also between years. Clones from one of the three populations were more influential than clones from the other two populations. Only one of 15 clones, both from the same population, was influential in both experiments. This research supports a growing literature indicating that intraspecific variability among clones of a dominant species can affect interspecific interactions and that such variability in a native species can affect performance of an invading species.

  12. Analysis of transferability of microsatellite primers (SSR) in wild Passiflora species and intraspecific genetic diversity in Passiflora alata.

    Science.gov (United States)

    Silva, M A A; Souza, M M; Silva, G S; Melo, C A F; Corrêa, R X; Araújo, I S; Conceição, L D H C S

    2014-08-07

    The genus Passiflora L. is the most representative of Passifloraceae, with over 500 known species, among which 150-200 originated from Brazil. In addition to the great commercial importance of this genus for the fruit market, many of the species have exotic flowers with a huge diversity of colors and can thereby be exploited as ornamental plants. This study was aimed at investigating the transferability of microsatellite primers in wild Passiflora species (P. cacao, P. cincinnata, P. glandulosa, P. gibertii, and P. mucronata) and characterizing 29 P. alata accessions using microsatellite primers that were previously developed in a library enriched with microsatellites from P. edulis f. flavicarpa for P. alata. The interspecies cross-amplification rate varied, and P. cacao exhibited the highest rate of amplification, suggesting a greater degree of proximity to P. edulis. The study of intraspecific accessions in P. alata found genetic similarity, with values ranging from 0.47 to 1.00 and an average similarity of 0.74. Hence, this study revealed the intraspecific genetic variability of P. alata in the Universidade Estadual de Santa Cruz's Active Germplasm Bank and will lead to the adoption of mating strategies between accessions; thus making their use more suitable for breeding purposes.

  13. Genome Imprinting

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 5; Issue 9. Genome Imprinting - The Silencing of ... General Article Volume 5 Issue 9 September 2000 pp 49-57 ... M T Tanuja1. Drosophila Stock Centre, Department of Studies in Zoology, University of Mysore Manasagangotri Mysore 570 006, India.

  14. Genome Imprinting

    Indian Academy of Sciences (India)

    ring pathological condition cystic fibrosis is due to inheritance of both copies of chromosome 7 from the mother. Similarly,. Prader-Willi syndrome in humans is due to the inheritance of both copies of chromosome 15 from the mother. Human Triploids. The triploid (Le. 3 copies of the haploid genome are present instead of the ...

  15. genome editing

    Indian Academy of Sciences (India)

    2016-02-11

    Feb 11, 2016 ... What history tells us. XL. The success story of the expression 'genome editing'. MICHEL MORANGE. Centre Cavaillès, République des Savoirs: Lettres, Sciences, Philosophie USR 3608, Ecole. Normale Supérieure, 29 Rue d'Ulm, 75230, Paris Cedex 05, France. (Fax, 33-144-323941; Email, ...

  16. Ancient genomics

    DEFF Research Database (Denmark)

    Der Sarkissian, Clio; Allentoft, Morten Erik; Avila Arcos, Maria del Carmen

    2015-01-01

    The past decade has witnessed a revolution in ancient DNA (aDNA) research. Although the field's focus was previously limited to mitochondrial DNA and a few nuclear markers, whole genome sequences from the deep past can now be retrieved. This breakthrough is tightly connected to the massive sequen...

  17. Comparative Genomics

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 11; Issue 8. Comparative Genomics - A Powerful New Tool in Biology. Anand K Bachhawat. General Article Volume 11 Issue 8 August 2006 pp 22-40. Fulltext. Click here to view fulltext PDF. Permanent link:

  18. Molecular characterization of a naturally occurring intraspecific recombinant begomovirus with close relatives widespread in southern Arabia

    KAUST Repository

    Al-Saleh, Mohammed A

    2014-06-02

    Background: Tomato leaf curl Sudan virus (ToLCSDV) is a single-stranded DNA begomovirus of tomato that causes downward leaf curl, yellowing, and stunting. Leaf curl disease results in significant yield reduction in tomato crops in the Nile Basin. ToLCSDV symptoms resemble those caused by Tomato yellow leaf curl virus, a distinct and widespread begomovirus originating in the Middle East. In this study, tomato samples exhibiting leaf curl symptoms were collected from Gezira, Sudan. The associated viral genome was molecularly characterized, analyzed phylogenetically, and an infectious clone for one isolate was constructed. Findings. The complete genomes for five newly discovered variants of ToLCSDV, ranging in size from 2765 to 2767-bp, were cloned and sequenced, and subjected to pairwise and phylogenetic analyses. Pairwise analysis indicated that the five Gezira isolates shared 97-100% nucleotide identity with each other. Further, these variants of ToLCSDV shared their highest nucleotide identity at 96-98%, 91-95%, 91-92%, and 91-92% with the Shambat, Gezira, Oman and Yemen strains of ToLCSDV, respectively. Based on the high maximum nucleotide identities shared between these ToLCSDV variants from Gezira and other previously recognized members of this taxonomic group, they are considered isolates of the Shambat strain of ToLCSDV. Analysis of the complete genome sequence for these new variants revealed that they were naturally occurring recombinants between two previously reported strains of ToLCSDV. Finally, a dimeric clone constructed from one representative ToLCSV genome from Gezira was shown to be infectious following inoculation to tomato and N. benthamiana plants. Conclusion: Five new, naturally occurring recombinant begomovirus variants (>96% shared nt identity) were identified in tomato plants from Gezira in Sudan, and shown to be isolates of the Shambat strain of ToLCSDV. The cloned viral genome was infectious in N. benthamiana and tomato plants, and symptoms

  19. Analysis of plastid DNA-like sequences within the nuclear genomes of higher plants.

    Science.gov (United States)

    Ayliffe, M A; Scott, N S; Timmis, J N

    1998-06-01

    A wide-ranging examination of plastid (pt)DNA sequence homologies within higher plant nuclear genomes (promiscuous DNA) was undertaken. Digestion with methylation-sensitive restriction enzymes and Southern analysis was used to distinguish plastid and nuclear DNA in order to assess the extent of variability of promiscuous sequences within and between plant species. Some species, such as Gossypium hirsutum (cotton), Nicotiana tabacum (tobacco), and Chenopodium quinoa, showed homogenity of these sequences, while intraspecific sequence variation was observed among different cultivars of Pisum sativum (pea), Hordeum vulgare (barley), and Triticum aestivum (wheat). Hypervariability of plastid sequence homologies was identified in the nuclear genomes of Spinacea oleracea (spinach) and Beta vulgaris (beet), in which individual plants were shown to possess a unique spectrum of nuclear sequences with ptDNA homology. This hypervariability apparently extended to somatic variation in B. vulgaris. No sequences with ptDNA homology were identified by this method in the nuclear genome of Arabidopsis thaliana.

  20. Life-cycle modification in open oceans accounts for genome variability in a cosmopolitan phytoplankton

    Science.gov (United States)

    von Dassow, Peter; John, Uwe; Ogata, Hiroyuki; Probert, Ian; Bendif, El Mahdi; Kegel, Jessica U; Audic, Stéphane; Wincker, Patrick; Da Silva, Corinne; Claverie, Jean-Michel; Doney, Scott; Glover, David M; Flores, Daniella Mella; Herrera, Yeritza; Lescot, Magali; Garet-Delmas, Marie-José; de Vargas, Colomban

    2015-01-01

    Emiliania huxleyi is the most abundant calcifying plankton in modern oceans with substantial intraspecific genome variability and a biphasic life cycle involving sexual alternation between calcified 2N and flagellated 1N cells. We show that high genome content variability in Emiliania relates to erosion of 1N-specific genes and loss of the ability to form flagellated cells. Analysis of 185 E. huxleyi strains isolated from world oceans suggests that loss of flagella occurred independently in lineages inhabiting oligotrophic open oceans over short evolutionary timescales. This environmentally linked physiogenomic change suggests life cycling is not advantageous in very large/diluted populations experiencing low biotic pressure and low ecological variability. Gene loss did not appear to reflect pressure for genome streamlining in oligotrophic oceans as previously observed in picoplankton. Life-cycle modifications might be common in plankton and cause major functional variability to be hidden from traditional taxonomic or molecular markers. PMID:25461969

  1. Personal genomics services: whose genomes?

    Science.gov (United States)

    Gurwitz, David; Bregman-Eschet, Yael

    2009-07-01

    New companies offering personal whole-genome information services over the internet are dynamic and highly visible players in the personal genomics field. For fees currently ranging from US$399 to US$2500 and a vial of saliva, individuals can now purchase online access to their individual genetic information regarding susceptibility to a range of chronic diseases and phenotypic traits based on a genome-wide SNP scan. Most of the companies offering such services are based in the United States, but their clients may come from nearly anywhere in the world. Although the scientific validity, clinical utility and potential future implications of such services are being hotly debated, several ethical and regulatory questions related to direct-to-consumer (DTC) marketing strategies of genetic tests have not yet received sufficient attention. For example, how can we minimize the risk of unauthorized third parties from submitting other people's DNA for testing? Another pressing question concerns the ownership of (genotypic and phenotypic) information, as well as the unclear legal status of customers regarding their own personal information. Current legislation in the US and Europe falls short of providing clear answers to these questions. Until the regulation of personal genomics services catches up with the technology, we call upon commercial providers to self-regulate and coordinate their activities to minimize potential risks to individual privacy. We also point out some specific steps, along the trustee model, that providers of DTC personal genomics services as well as regulators and policy makers could consider for addressing some of the concerns raised below.

  2. Rapid Increase in Genome Size as a Consequence of Transposable Element Hyperactivity in Wood-White (Leptidea) Butterflies

    Science.gov (United States)

    Talla, Venkat; Suh, Alexander; Kalsoom, Faheema; Dincă, Vlad; Vila, Roger; Friberg, Magne; Wiklund, Christer

    2017-01-01

    Abstract Characterizing and quantifying genome size variation among organisms and understanding if genome size evolves as a consequence of adaptive or stochastic processes have been long-standing goals in evolutionary biology. Here, we investigate genome size variation and association with transposable elements (TEs) across lepidopteran lineages using a novel genome assembly of the common wood-white (Leptidea sinapis) and population re-sequencing data from both L. sinapis and the closely related L. reali and L. juvernica together with 12 previously available lepidopteran genome assemblies. A phylogenetic analysis confirms established relationships among species, but identifies previously unknown intraspecific structure within Leptidea lineages. The genome assembly of L. sinapis is one of the largest of any lepidopteran taxon so far (643 Mb) and genome size is correlated with abundance of TEs, both in Lepidoptera in general and within Leptidea where L. juvernica from Kazakhstan has considerably larger genome size than any other Leptidea population. Specific TE subclasses have been active in different Lepidoptera lineages with a pronounced expansion of predominantly LINEs, DNA elements, and unclassified TEs in the Leptidea lineage after the split from other Pieridae. The rate of genome expansion in Leptidea in general has been in the range of four Mb/Million year (My), with an increase in a particular L. juvernica population to 72 Mb/My. The considerable differences in accumulation rates of specific TE classes in different lineages indicate that TE activity plays a major role in genome size evolution in butterflies and moths. PMID:28981642

  3. A high-density genetic recombination map of sequence-tagged sites for sorghum, as a framework for comparative structural and evolutionary genomics of tropical grains and grasses.

    Science.gov (United States)

    Bowers, John E; Abbey, Colette; Anderson, Sharon; Chang, Charlene; Draye, Xavier; Hoppe, Alison H; Jessup, Russell; Lemke, Cornelia; Lennington, Jennifer; Li, Zhikang; Lin, Yann-Rong; Liu, Sin-Chieh; Luo, Lijun; Marler, Barry S; Ming, Reiguang; Mitchell, Sharon E; Qiang, Dou; Reischmann, Kim; Schulze, Stefan R; Skinner, D Neil; Wang, Yue-Wen; Kresovich, Stephen; Schertz, Keith F; Paterson, Andrew H

    2003-09-01

    We report a genetic recombination map for Sorghum of 2512 loci spaced at average 0.4 cM ( approximately 300 kb) intervals based on 2050 RFLP probes, including 865 heterologous probes that foster comparative genomics of Saccharum (sugarcane), Zea (maize), Oryza (rice), Pennisetum (millet, buffelgrass), the Triticeae (wheat, barley, oat, rye), and Arabidopsis. Mapped loci identify 61.5% of the recombination events in this progeny set and reveal strong positive crossover interference acting across intervals of intraspecific allelic richness. While cDNA and genomic clones are similarly distributed across the genome, SSR-containing clones show different abundance patterns. Rapidly evolving hypomethylated DNA may contribute to intraspecific genomic differentiation. Nonrandom distribution patterns of multiple loci detected by 357 probes suggest ancient chromosomal duplication followed by extensive rearrangement and gene loss. Exemplifying the value of these data for comparative genomics, we support and extend prior findings regarding maize-sorghum synteny-in particular, 45% of comparative loci fall outside the inferred colinear/syntenic regions, suggesting that many small rearrangements have occurred since maize-sorghum divergence. These genetically anchored sequence-tagged sites will foster many structural, functional and evolutionary genomic studies in major food, feed, and biomass crops.

  4. Nutritional genomics.

    Science.gov (United States)

    Ordovas, Jose M; Corella, Dolores

    2004-01-01

    Nutritional genomics has tremendous potential to change the future of dietary guidelines and personal recommendations. Nutrigenetics will provide the basis for personalized dietary recommendations based on the individual's genetic make up. This approach has been used for decades for certain monogenic diseases; however, the challenge is to implement a similar concept for common multifactorial disorders and to develop tools to detect genetic predisposition and to prevent common disorders decades before their manifestation. The preliminary results involving gene-diet interactions for cardiovascular diseases and cancer are promising, but mostly inconclusive. Success in this area will require the integration of different disciplines and investigators working on large population studies designed to adequately investigate gene-environment interactions. Despite the current difficulties, preliminary evidence strongly suggests that the concept should work and that we will be able to harness the information contained in our genomes to achieve successful aging using behavioral changes; nutrition will be the cornerstone of this endeavor.

  5. Inter-and intraspecific variation in fern mating systems after long-distance colonization: the importance of selfing

    Directory of Open Access Journals (Sweden)

    de Groot G Arjen

    2012-01-01

    Full Text Available Abstract Background Previous studies on the reproductive biology of ferns showed that mating strategies vary among species, and that polyploid species often show higher capacity for self-fertilization than diploid species. However, the amount of intraspecific variation in mating strategy and selfing capacity has only been assessed for a few species. Yet, such variation may have important consequences during colonization, as the establishment of any selfing genotypes may be favoured after long-distance dispersal (an idea known as Baker's law. Results We examined intra-and interspecific variation in potential for self-fertilization among four rare fern species, of which two were diploids and two were tetraploids: Asplenium scolopendrium (2n, Asplenium trichomanes subsp. quadrivalens (4n, Polystichum setiferum (2n and Polystichum aculeatum (4n. Sporophyte production was tested at different levels of inbreeding, by culturing gametophytes in isolation, as well as in paired cultures with a genetically different gametophyte. We tested gametophytes derived from various genetically different sporophytes from populations in a recently planted forest colonized through long-distance dispersal (Kuinderbos, the Netherlands, as well as from older, less disjunct populations. Sporophyte production in isolation was high for Kuinderbos genotypes of all four species. Selfing capacity did not differ significantly between diploids and polyploids, nor between species in general. Rather selfing capacity differed between genotypes within species. Intraspecific variation in mating system was found in all four species. In two species one genotype from the Kuinderbos showed enhanced sporophyte production in paired cultures. For the other species, including a renowned out crosser, selfing capacity was consistently high. Conclusions Our results for four different species suggest that intraspecific variation in mating system may be common, at least among temperate calcicole

  6. Towards the Genomic Basis of Local Adaptation in Landraces

    Directory of Open Access Journals (Sweden)

    Giandomenico Corrado

    2017-11-01

    Full Text Available Landraces are key elements of agricultural biodiversity that have long been considered a source of useful traits. Their importance goes beyond subsistence agriculture and the essential need to preserve genetic diversity, because landraces are farmer-developed populations that are often adapted to environmental conditions of significance to tackle environmental concerns. It is therefore increasingly important to identify adaptive traits in crop landraces and understand their molecular basis. This knowledge is potentially useful for promoting more sustainable agricultural techniques, reducing the environmental impact of high-input cropping systems, and diminishing the vulnerability of agriculture to global climate change. In this review, we present an overview of the opportunities and limitations offered by landraces’ genomics. We discuss how rapid advances in DNA sequencing techniques, plant phenotyping, and recombinant DNA-based biotechnology encourage both the identification and the validation of the genomic signature of local adaptation in crop landraces. The integration of ‘omics’ sciences, molecular population genetics, and field studies can provide information inaccessible with earlier technological tools. Although empirical knowledge on the genetic and genomic basis of local adaptation is still fragmented, it is predicted that genomic scans for adaptation will unlock an intraspecific molecular diversity that may be different from that of modern varieties.

  7. Visualization for genomics: the Microbial Genome Viewer.

    NARCIS (Netherlands)

    Kerkhoven, R.; Enckevort, F.H.J. van; Boekhorst, J.; Molenaar, D; Siezen, R.J.

    2004-01-01

    SUMMARY: A Web-based visualization tool, the Microbial Genome Viewer, is presented that allows the user to combine complex genomic data in a highly interactive way. This Web tool enables the interactive generation of chromosome wheels and linear genome maps from genome annotation data stored in a

  8. Untangling interacting mechanisms of see variation with elevation: insights from the comparison of interspecific and intraspecific studies on eastern Tibetan angiosperm species

    NARCIS (Netherlands)

    Qi, Wei; Bu, Haiyan; Cornelissen, J.H.C.; Zhang, Chunhui; Guo, Shuqing; Wang, Juhong; Zhou, Xianhui; Li, Wenjin; Du, Guozhen

    2015-01-01

    With increasing elevation, seed mass is expected to be either larger for its advantage during seedling establishment in stressful high-elevation environments (“stress-tolerance” mechanism) or smaller due to energy constraints. Based on the combination of inter- and intra-specific analyses on 4,023

  9. Macroscale intraspecific variation and environmental heterogeneity: analysis of cold and warm zone abundance, mortality, and regeneration distributions of four eastern US tree species

    Science.gov (United States)

    Anantha M. Prasad

    2015-01-01

    I test for macroscale intraspecific variation of abundance, mortality, and regeneration of four eastern US tree species (Tsuga canadensis, Betula lenta, Liriodendron tulipifera, and Quercus prinus) by splitting them into three climatic zones based on plant hardiness zones (PHZs). The primary goals of the analysis are to assess the...

  10. Use of flow cytometry, fluorescence microscopy, and PCR-based techniques to assess intraspecific and interspecific matings of Armillaria species

    Science.gov (United States)

    Mee-Sook Kim; Ned B. Klopfenstein; Geral I. McDonald; Kathiravetpillai Arumuganathan

    2001-01-01

    For assessments of intraspecific mating using flow cytometry and fluorescence microscopy, two compatible basidiospore-derived isolates were selected from each of four parental basidiomata of North American Biological Species (NABS) X. The nuclear status in NABS X varied with basidiospore-derived isolates. Nuclei within basidiospore-derived isolates existed as haploids...

  11. Intraspecific variation between the ITS sequences of Toxocara canis, Toxocara cati and Toxascaris leonina from different host species in south-western Poland.

    Science.gov (United States)

    Fogt-Wyrwas, R; Mizgajska-Wiktor, H; Pacoń, J; Jarosz, W

    2013-12-01

    Some parasitic nematodes can inhabit different definitive hosts, which raises the question of the intraspecific variability of the nematode genotype affecting their preferences to choose particular species as hosts. Additionally, the issue of a possible intraspecific DNA microheterogeneity in specimens from different parts of the world seems to be interesting, especially from the evolutionary point of view. The problem was analysed in three related species - Toxocara canis, Toxocara cati and Toxascaris leonina - specimens originating from Central Europe (Poland). Using specific primers for species identification, internal transcribed spacer (ITS)-1 and ITS-2 regions were amplified and then sequenced. The sequences obtained were compared with sequences previously described for specimens originating from other geographical locations. No differences in nucleotide sequences were established in T. canis isolated from two different hosts (dogs and foxes). A comparison of ITS sequences of T. canis from Poland with sequences deposited in GenBank showed that the scope of intraspecific variability of the species did not exceed 0.4%, while in T. cati the differences did not exceed 2%. Significant differences were found in T. leonina, where ITS-1 differed by 3% and ITS-2 by as much as 7.4% in specimens collected from foxes in Poland and dogs in Australia. Such scope of differences in the nucleotide sequence seems to exceed the intraspecific variation of the species.

  12. Intraspecific competition and mating between fungal strains of the anther smut Microbotryum violaceum from the host plants Silene latifolia and S-dioica

    NARCIS (Netherlands)

    Van Putten, WF; Biere, A; Van Damme, JMM

    We studied intraspecific competition and assortative mating between strains of the anther smut fungus Microbotryum violaceum from two of its host species, Silene latifolia and S. dioica. Specifically. we investigated whether strains from allopatric host populations have higher competitive ability on

  13. Intraspecific competition and mating between fungal strains of the anther smut Microbotryum violaceum from the host plants Silene latifolia and S-dioica.

    NARCIS (Netherlands)

    Van Putten, W.F.; Biere, A.; Van Damme, J.M.M.

    2003-01-01

    We studied intraspecific competition and assortative mating between strains of the anther smut fungus Microbotryum violaceum from two of its host species, Silene latifolia and S. dioica. Specifically, we investigated whether strains from allopatric host populations have higher competitive ability on

  14. The good, the bad, and the ugly: the influence of skull reconstructions and intraspecific variability in studies of cranial morphometrics in theropods and Basal saurischians.

    Directory of Open Access Journals (Sweden)

    Christian Foth

    Full Text Available Several studies investigating macroevolutionary skull shape variation in fossil reptiles were published recently, often using skull reconstructions taken from the scientific literature. However, this approach could be potentially problematic, because skull reconstructions might differ notably due to incompleteness and/or deformation of the material. Furthermore, the influence of intraspecific variation has usually not been explored in these studies. Both points could influence the results of morphometric analyses by affecting the relative position of species to each other within the morphospace. The aim of the current study is to investigate the variation in morphometric data between skull reconstructions based on the same specimen, and to compare the results to shape variation occurring in skull reconstructions based on different specimens of the same species (intraspecific variation and skulls of closely related species (intraspecific variation. Based on the current results, shape variation of different skull reconstructions based on the same specimen seems to have generally little influence on the results of a geometric morphometric analysis, although it cannot be excluded that some erroneous reconstructions of poorly preserved specimens might cause problems occasionally. In contrast, for different specimens of the same species the variation is generally higher than between different reconstructions based on the same specimen. For closely related species, at least with similar ecological preferences in respect to the dietary spectrum, the degree of interspecific variation can overlap with that of intraspecific variation, most probably due to similar biomechanical constraints.

  15. Intraspecific DNA methylation polymorphism in the non-edible oilseed plant castor bean

    Directory of Open Access Journals (Sweden)

    Shan He

    2017-10-01

    Full Text Available Investigation of the relationships of phenotypic and epigenetic variations might be a good way to dissect the genetic or molecular basis of phenotypic variation and plasticity in plants. Castor bean (Ricinus communis L., an important non-edible oilseed crop, is a mono-species genus plant in the family Euphorbiaceae. Since it displays rich phenotypic variations with low genetic diversity, castor bean is a good model to investigate the molecular basis of phenotypic and epigenetic variations. Cytosine DNA methylation represents a major molecular mechanism of epigenetic occurrence. In this study, epigenetic diversity of sixty landrace accessions collected worldwide was investigated using the methylation-sensitive amplification polymorphism (MSAP technique. Results showed that the epigenetic diversity (based on the polymorphism of DNA methylated loci exhibited a medium variation (Ne = 1.395, He = 0.242, I = 0.366 at the population level though the variation was great, ranging from 3.80% to 34.31% among accessions. Both population structure analysis and the phylogenetic construction (using the neighbor-joining criteria revealed that the two main clades were identified, but they did not display a distinct geographic structure. After inspecting the location of polymorphic methylated loci on genome we identified that the polymorphic methylated loci occur widely in nuclear and organelle genomes. This study provides new data to understand phenotypic and epigenetic variations in castor bean.

  16. Density-dependent intraspecific competition in the larval stage of Aedes aegypti (Diptera: Culicidae): revisiting the current paradigm.

    Science.gov (United States)

    Legros, Mathieu; Lloyd, Alun L; Huang, Yunxin; Gould, Fred

    2009-05-01

    Density-dependent intraspecific competition has been considered an important determinant of the dynamics of larval stages of Aedes aegypti. A model was published in 1984 providing a mathematical description of this density dependence, based on field data, that has since been widely used. This description, however, is based on the strong assumption that all mortality is density-dependent. We re-examine the data without this premise and find a reduced importance of density dependence, as well as a different functional form. Based on these discrepancies, we emphasize that the characterization of density dependence in the larval stages of Ae. aegypti should be based on a more complete dataset, and we use artificially generated data to explore how such additional information could help developing a better description of this density dependence. We review other empirical studies on larval competition, discuss the need for further dedicated studies, and provide a few simple guidelines for the design of such studies.

  17. Experimental examination of intraspecific density-dependent competition during the breeding period in monarch butterflies (Danaus plexippus.

    Directory of Open Access Journals (Sweden)

    D T Tyler Flockhart

    Full Text Available A central goal of population ecology is to identify the factors that regulate population growth. Monarch butterflies (Danaus plexippus in eastern North America re-colonize the breeding range over several generations that result in population densities that vary across space and time during the breeding season. We used laboratory experiments to measure the strength of density-dependent intraspecific competition on egg laying rate and larval survival and then applied our results to density estimates of wild monarch populations to model the strength of density dependence during the breeding season. Egg laying rates did not change with density but larvae at high densities were smaller, had lower survival, and weighed less as adults compared to lower densities. Using mean larval densities from field surveys resulted in conservative estimates of density-dependent population reduction that varied between breeding regions and different phases of the breeding season. Our results suggest the highest levels of population reduction due to density-dependent intraspecific competition occur early in the breeding season in the southern portion of the breeding range. However, we also found that the strength of density dependence could be almost five times higher depending on how many life-stages were used as part of field estimates. Our study is the first to link experimental results of a density-dependent reduction in vital rates to observed monarch densities in the wild and show that the effects of density dependent competition in monarchs varies across space and time, providing valuable information for developing robust, year-round population models in this migratory organism.

  18. Intraspecific correlations of basal and maximal metabolic rates in birds and the aerobic capacity model for the evolution of endothermy.

    Science.gov (United States)

    Swanson, David L; Thomas, Nathan E; Liknes, Eric T; Cooper, Sheldon J

    2012-01-01

    The underlying assumption of the aerobic capacity model for the evolution of endothermy is that basal (BMR) and maximal aerobic metabolic rates are phenotypically linked. However, because BMR is largely a function of central organs whereas maximal metabolic output is largely a function of skeletal muscles, the mechanistic underpinnings for their linkage are not obvious. Interspecific studies in birds generally support a phenotypic correlation between BMR and maximal metabolic output. If the aerobic capacity model is valid, these phenotypic correlations should also extend to intraspecific comparisons. We measured BMR, M(sum) (maximum thermoregulatory metabolic rate) and MMR (maximum exercise metabolic rate in a hop-flutter chamber) in winter for dark-eyed juncos (Junco hyemalis), American goldfinches (Carduelis tristis; M(sum) and MMR only), and black-capped chickadees (Poecile atricapillus; BMR and M(sum) only) and examined correlations among these variables. We also measured BMR and M(sum) in individual house sparrows (Passer domesticus) in both summer, winter and spring. For both raw metabolic rates and residuals from allometric regressions, BMR was not significantly correlated with either M(sum) or MMR in juncos. Moreover, no significant correlation between M(sum) and MMR or their mass-independent residuals occurred for juncos or goldfinches. Raw BMR and M(sum) were significantly positively correlated for black-capped chickadees and house sparrows, but mass-independent residuals of BMR and M(sum) were not. These data suggest that central organ and exercise organ metabolic levels are not inextricably linked and that muscular capacities for exercise and shivering do not necessarily vary in tandem in individual birds. Why intraspecific and interspecific avian studies show differing results and the significance of these differences to the aerobic capacity model are unknown, and resolution of these questions will require additional studies of potential mechanistic

  19. Intraspecific correlations of basal and maximal metabolic rates in birds and the aerobic capacity model for the evolution of endothermy.

    Directory of Open Access Journals (Sweden)

    David L Swanson

    Full Text Available The underlying assumption of the aerobic capacity model for the evolution of endothermy is that basal (BMR and maximal aerobic metabolic rates are phenotypically linked. However, because BMR is largely a function of central organs whereas maximal metabolic output is largely a function of skeletal muscles, the mechanistic underpinnings for their linkage are not obvious. Interspecific studies in birds generally support a phenotypic correlation between BMR and maximal metabolic output. If the aerobic capacity model is valid, these phenotypic correlations should also extend to intraspecific comparisons. We measured BMR, M(sum (maximum thermoregulatory metabolic rate and MMR (maximum exercise metabolic rate in a hop-flutter chamber in winter for dark-eyed juncos (Junco hyemalis, American goldfinches (Carduelis tristis; M(sum and MMR only, and black-capped chickadees (Poecile atricapillus; BMR and M(sum only and examined correlations among these variables. We also measured BMR and M(sum in individual house sparrows (Passer domesticus in both summer, winter and spring. For both raw metabolic rates and residuals from allometric regressions, BMR was not significantly correlated with either M(sum or MMR in juncos. Moreover, no significant correlation between M(sum and MMR or their mass-independent residuals occurred for juncos or goldfinches. Raw BMR and M(sum were significantly positively correlated for black-capped chickadees and house sparrows, but mass-independent residuals of BMR and M(sum were not. These data suggest that central organ and exercise organ metabolic levels are not inextricably linked and that muscular capacities for exercise and shivering do not necessarily vary in tandem in individual birds. Why intraspecific and interspecific avian studies show differing results and the significance of these differences to the aerobic capacity model are unknown, and resolution of these questions will require additional studies of potential

  20. Experimental examination of intraspecific density-dependent competition during the breeding period in monarch butterflies (Danaus plexippus).

    Science.gov (United States)

    Flockhart, D T Tyler; Martin, Tara G; Norris, D Ryan

    2012-01-01

    A central goal of population ecology is to identify the factors that regulate population growth. Monarch butterflies (Danaus plexippus) in eastern North America re-colonize the breeding range over several generations that result in population densities that vary across space and time during the breeding season. We used laboratory experiments to measure the strength of density-dependent intraspecific competition on egg laying rate and larval survival and then applied our results to density estimates of wild monarch populations to model the strength of density dependence during the breeding season. Egg laying rates did not change with density but larvae at high densities were smaller, had lower survival, and weighed less as adults compared to lower densities. Using mean larval densities from field surveys resulted in conservative estimates of density-dependent population reduction that varied between breeding regions and different phases of the breeding season. Our results suggest the highest levels of population reduction due to density-dependent intraspecific competition occur early in the breeding season in the southern portion of the breeding range. However, we also found that the strength of density dependence could be almost five times higher depending on how many life-stages were used as part of field estimates. Our study is the first to link experimental results of a density-dependent reduction in vital rates to observed monarch densities in the wild and show that the effects of density dependent competition in monarchs varies across space and time, providing valuable information for developing robust, year-round population models in this migratory organism.

  1. The Venom of the Spine-Bellied Sea Snake (Hydrophis curtus): Proteome, Toxin Diversity and Intraspecific Variation.

    Science.gov (United States)

    Neale, Vanessa; Sotillo, Javier; Seymour, Jamie E; Wilson, David

    2017-12-12

    The spine-bellied sea snake ( Hydrophis curtus ) is known to cause human deaths, yet its venom composition has not yet been proteomically characterised. An indepth proteomic analysis was performed on H. curtus venom from two different seasons, January and June, corresponding to adults and subadults, respectively. Venoms from adult and subadult H. curtus individuals were compared using reversedphase high-performance liquid chromatography (RP-HPLC), matrix-assisted laser desorption ionisation-time of flight (MALDI-TOF) mass spectrometry and liquid chromatography electrospray ionisation mass spectrometry (LC-ESI-MS) to detect intraspecific variation, and the molecular weight data obtained with ESIMS were used to assess toxin diversity. RPHPLC and LCESIMS/MS were used to characterise the venom proteome and estimate the relative abundances of protein families present. The most abundant protein family in January and June venoms is phospholipase A₂ (PLA₂: January 66.7%; June 54.5%), followed by threefinger toxins (3FTx: January 30.4%; June 40.4%) and a minor component of cysteine-rich secretory proteins (CRISP: January 2.5%; June 5%). Trace amounts of snake venom metalloproteinases (SVMP), C-type lectins and housekeeping and regulatory proteins were also found. Although the complexity of the venom is low by number of families present, each family contained a more diverse set of isoforms than previously reported, a finding that may have implications for the development of next-generation sea snake antivenoms. Intraspecific variability was shown to be minor with one obvious exception of a 14,157-Da protein that was present in some January (adult) venoms, but not at all in June (subadult) venoms. There is also a greater abundance of short-chain neurotoxins in June (subadult) venom compared with January (adult) venom. These differences potentially indicate the presence of seasonal, ontogenetic or sexual variation in H. curtus venom.

  2. Centuries-old DNA from an extinct population of Aesculapian snake (Zamenis longissimus) offers new phylogeographic insight

    DEFF Research Database (Denmark)

    Allentoft, Morten; Redsted Rasmussen, Arne; Kristensen, Hans Viborg

    2018-01-01

    Abstract: The Aesculapian snake (Zamenis longissimus) is distributed in Central and Southern Europe, the Balkans, Anatolia, and Iran, but had a wider mid-Holocene distribution into Northern Europe. To investigate the genetic affinity of a Danish population that went extinct in historical times, we...... analysed three ethanol-preserved individuals dating back to 1810 using a silica-in-solution ancient DNA extraction method, combined with next-generation sequencing. Bioinformatic mapping of the reads against the published genome of a related colubrid snake revealed that two of the three specimens contained...... endogenous snake DNA (up to 8.6% of the reads), and this was evident for tooth, bone, and soft tissue samples. The DNA was highly degraded, observed by very short average sequence lengths (

  3. Trypanosoma cruzi IIc: phylogenetic and phylogeographic insights from sequence and microsatellite analysis and potential impact on emergent Chagas disease.

    Directory of Open Access Journals (Sweden)

    Martin S Llewellyn

    2009-09-01

    Full Text Available Trypanosoma cruzi, the etiological agent of Chagas disease, is highly genetically diverse. Numerous lines of evidence point to the existence of six stable genetic lineages or DTUs: TcI, TcIIa, TcIIb, TcIIc, TcIId, and TcIIe. Molecular dating suggests that T. cruzi is likely to have been an endemic infection of neotropical mammalian fauna for many millions of years. Here we have applied a panel of 49 polymorphic microsatellite markers developed from the online T. cruzi genome to document genetic diversity among 53 isolates belonging to TcIIc, a lineage so far recorded almost exclusively in silvatic transmission cycles but increasingly a potential source of human infection. These data are complemented by parallel analysis of sequence variation in a fragment of the glucose-6-phosphate isomerase gene. New isolates confirm that TcIIc is associated with terrestrial transmission cycles and armadillo reservoir hosts, and demonstrate that TcIIc is far more widespread than previously thought, with a distribution at least from Western Venezuela to the Argentine Chaco. We show that TcIIc is truly a discrete T. cruzi lineage, that it could have an ancient origin and that diversity occurs within the terrestrial niche independently of the host species. We also show that spatial structure among TcIIc isolates from its principal host, the armadillo Dasypus novemcinctus, is greater than that among TcI from Didelphis spp. opossums and link this observation to differences in ecology of their respective niches. Homozygosity in TcIIc populations and some linkage indices indicate the possibility of recombination but cannot yet be effectively discriminated from a high genome-wide frequency of gene conversion. Finally, we suggest that the derived TcIIc population genetic data have a vital role in determining the origin of the epidemiologically important hybrid lineages TcIId and TcIIe.

  4. Linking Changes to Intraspecific Trait Diversity to Community Functional Diversity and Biomass in Response to Snow and Nitrogen Addition Within an Inner Mongolian Grassland.

    Science.gov (United States)

    Mao, Wei; Felton, Andrew J; Zhang, Tonghui

    2017-01-01

    In recent years, both the intraspecific and interspecific functional diversity (FD) of plant communities have been studied with new approaches to improve an understanding about the mechanisms underlying plant species coexistence. Yet, little is known about how global change drivers will impact intraspecific FD and trait overlap among species, and in particular how this may scale to impacts on community level FD and ecosystem functioning. To address this uncertainty, we assessed the direct and indirect responses of specific leaf area (SLA) among both dominant annual and subordinate perennial species to the independent and interactive effects of nitrogen and snow addition within the Inner Mongnolian steppe. More specifically, we investigated the consequences for these responses on plant community FD, trait overlap and biomass. Nitrogen addition increased the biomass of the dominant annual species and as a result increased total community biomass. This occurred despite concurrent decreases in the biomass of subordinate perennial species. Nitrogen addition also increased intraspecific FD and trait overlap of both annual species and perennial species, and consequently increased the degree of trait overlap in SLA at the community level. However, snow addition did not significantly impact intraspecific FD and trait overlap of SLA for perennial species, but increased intraspecific FD and trait overlap of annual species, of which scaled to changes in community level FD. We found that the responses of the dominant annual species to nitrogen and snow additions were generally more sensitive than the subordinate perennial species within the inner Mongolian grassland communities of our study. As a consequence of this sensitivity, the responses of the dominant species largely drove impacts to community FD, trait overlap and community biomass. In total, our study demonstrates that the responses of dominant species in a community to environmental change may drive the initial

  5. Genome Sequencing

    DEFF Research Database (Denmark)

    Sato, Shusei; Andersen, Stig Uggerhøj

    2014-01-01

    The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based...... on transcriptional evidence. Analysis of repetitive sequences suggests that they are underrepresented in the reference assembly, reflecting an enrichment of gene-rich regions in the current assembly. Characterization of Lotus natural variation by resequencing of L. japonicus accessions and diploid Lotus species...... is currently ongoing, facilitated by the MG20 reference sequence...

  6. Genome-Wide Association Study on Male Genital Shape and Size in Drosophila melanogaster.

    Directory of Open Access Journals (Sweden)

    Baku Takahara

    Full Text Available Male genital morphology of animals with internal fertilization and promiscuous mating systems have been one of the most diverse and rapidly evolving morphological traits. The male genital morphology in general is known to have low phenotypic and genetic variations, but the genetic basis of the male genital variation remains unclear. Drosophila melanogaster and its closely related species are morphologically very similar, but the shapes of the posterior lobe, a cuticular projection on the male genital arch are distinct from each other, representing a model system for studying the genetic basis of male genital morphology. In this study, we used highly inbred whole genome sequenced strains of D. melanogaster to perform genome wide association analysis on posterior lobe morphology. We quantified the outline shape of posterior lobes with Fourier coefficients obtained from elliptic Fourier analysis and performed principal component analysis, and posterior lobe size. The first and second principal components (PC1 and PC2 explained approximately 88% of the total variation of the posterior lobe shape. We then examined the association between the principal component scores and posterior lobe size and 1902142 single nucleotide polymorphisms (SNPs. As a result, we obtained 15, 14 and 15 SNPs for PC1, PC2 and posterior lobe size with P-values smaller than 10(-5. Based on the location of the SNPs, 13, 13 and six protein coding genes were identified as potential candidates for PC1, PC2 and posterior lobe size, respectively. In addition to the previous findings showing that the intraspecific posterior shape variation are regulated by multiple QTL with strong effects, the present study suggests that the intraspecific variation may be under polygenic regulation with a number of loci with small effects. Further studies are required for investigating whether these candidate genes are responsible for the intraspecific posterior lobe shape variation.

  7. Phylogeographic analyses reveal Transpontic long distance dispersal in land snails belonging to the Caucasotachea atrolabiata complex (Gastropoda: Helicidae).

    Science.gov (United States)

    Neiber, Marco T; Sagorny, Christina; Sauer, Jan; Walther, Frank; Hausdorf, Bernhard

    2016-10-01

    The phylogeography and population structure of land snails belonging to the Caucasotachea atrolabiata complex in the Caucasus region was investigated to obtain a better understanding of diversification processes in this biodiversity hotspot. So far the complex has been classified into three species, C. atrolabiata from the north-western Caucasus, C. calligera from Transcaucasia and C. intercedens from the eastern Pontus Mountains. Phylogenetic (neighbor-net and neighbor-joining tree) as well as admixture analyses based on AFLP data showed that the complex consists of two population clusters corresponding to C. atrolabiata and C. calligera. The populations assigned to C. intercedens in fact represent hybrids consisting of different proportions of the genomes of C. atrolabiata and C. calligera. There is a broad transition zone between C. atrolabiata and C. calligera in the Pontic Mountains and a second transition zone in Abkhazia. Because of evidence for gene flow, it is suggested to classify the two aforementioned taxa as subspecies, namely C. a. atrolabiata and C. a. calligera. The presence of mitochondrial C. a. atrolabiata haplotypes in Turkey can only be explained by passive dispersal across the Black Sea. The distribution of C. a. atrolabiata and additional cases of land snails with disjunct Transpontic distribution patterns cannot be ascribed to a common cause but are results of long distance dispersal events at different times. Copyright © 2016 Elsevier Inc. All rights reserved.

  8. The platypus genome unraveled.

    Science.gov (United States)

    O'Brien, Stephen J

    2008-06-13

    The genome of the platypus has been sequenced, assembled, and annotated by an international genomics team. Like the animal itself the platypus genome contains an amalgam of mammal, reptile, and bird-like features.

  9. Phylogeographic structure of cotton pest Adelphocoris suturalis (Hemiptera: Miridae): strong subdivision in China inferred from mtDNA and rDNA ITS markers.

    Science.gov (United States)

    Zhang, Lijuan; Li, Hu; Li, Shujuan; Zhang, Aibing; Kou, Fei; Xun, Huaizhu; Wang, Pei; Wang, Ying; Song, Fan; Cui, Jianxin; Cui, Jinjie; Gouge, Dawn H; Cai, Wanzhi

    2015-09-21

    Phylogeographic patterns of some extant plant and vertebrate species have been well studied; however, they are poorly understood in the majority of insects. The study documents analysis of mitochondrial (COI, CYTB and ND5) and nuclear (5.8S rDNA, ITS2 and 28S rDNA) data from 419 individuals of Adelphocoris suturalis, which is one of the main cotton pests found in the 31 locations in China and Japan involved in the study. Results show that the species is highly differentiated between populations from central China and peripheral China regions. Analysis of molecular variance showed a high level of geographical differentiation at different hierarchical levels. Isolation-by-distance test showed no significant correlation between genetic distance and geographical distance among A. suturalis populations, which suggested gene flow is not restricted by distance. In seven peripheral populations, the high levels of genetic differentiation and the small Nem values implied that geographic barriers were more likely restrict gene flow. Neutrality tests and the Bayesian skyline plot suggested population expansion likely happened during the cooling transition between Last Interglacial and Last Glacial Maximum. All lines of evidence suggest that physical barriers, Pleistocene climatic oscillations and geographical heterogeneity have affected the population structure and distribution of this insect in China.

  10. Deep-Sea Phylogeographic Structure Shaped by Paleoenvironmental Changes and Ongoing Ocean Currents Around the Sea of Japan in a Crangonid Shrimp, Argis lar.

    Science.gov (United States)

    Fujita, Junta; Drumm, David T; Iguchi, Akira; Ueda, Yuji; Yamashita, Yuho; Ito, Masaki; Tominaga, Osamu; Kai, Yoshiaki; Ueno, Masahiro; Yamashita, Yoh

    2017-10-01

    The deep-sea crangonid shrimp, Argis lar, is a highly abundant species from the northern Pacific Ocean. We investigated its phylogeographic and demographic structure across the species' extensive range, using mitochondrial DNA sequence variation to evaluate the impact of deep-sea paleoenvironmental dynamics in the Sea of Japan on population histories. The haplotype network detected three distinct lineages with allopatric isolation, which roughly corresponded to the Sea of Japan (Lineage A), the northwestern Pacific off the Japanese Archipelago (Lineage B), and the Bering Sea/Gulf of Alaska (Lineage C). Lineage A showed relatively low haplotype and nucleotide diversity, a significantly negative value of Tajima's D, and a star-shaped network, suggesting that anoxic bottom-water in the Sea of Japan over the last glacial period may have brought about a reduction in the Sea of Japan population. Furthermore, unexpectedly, the distributions of Lineage A and B were closely related to the pathways of the two ocean currents, especially along the Sanriku Coast. This result indicated that A. lar could disperse across shallow straits through the ocean current, despite their deep-sea adult habitat. Bayesian inference of divergence time revealed that A. lar separated into three lineages approximately 1 million years before present (BP) in the Pleistocene, and then had been influenced by deep-sea paleoenvironmental change in the Sea of Japan during the last glacial period, followed by a more recent larval dispersal with the ocean current since ca. 6 kilo years BP.

  11. How do cold-sensitive species endure ice ages? Phylogeographic and paleodistribution models of postglacial range expansion of the mesothermic drought-tolerant conifer Austrocedrus chilensis.

    Science.gov (United States)

    Souto, Cintia P; Kitzberger, Thomas; Arbetman, Marina P; Premoli, Andrea C

    2015-11-01

    In view of global climate change, it is important to understand the responses of tree species to climate changes in the past. Combinations of phylogeographic analysis of genetic evidence, coupled with species distribution models (SDMs), are improving our understanding on this subject. We combined SDMs and microsatellite data from populations of the entire range of Austrocedrus chilensis, a dominant mesotherm (cold-sensitive) conifer of dryland forests of the southern Andes, to test the hypothesis of long-distance postglacial migration from northern and warmer refugia at the Last Glacial Maximum (LGM). The SDM indicated suitable conditions for Austrocedrus in northern Chile (western) at the LGM and largely unsuitable conditions in Argentina (eastern). Population genetic diversity and effective population sizes within populations decreased southward along the Andes, consistent with the hypothesis of long-distance dispersal from a northern refugium. Results support the hypothesis of one (or a few) warmer (low latitude) refugia in Chile for Austrocedrus. On balance, the evidence suggests that in contrast to cold-tolerant tree taxa with the capacity to fast-track postglacial warming thanks to local refugia, cold-sensitive species might have undergone long-distance range expansion, lagging behind progressive climate change throughout the Holocene. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

  12. The role of ecological factors in determining phylogeographic and population genetic structure of two sympatric island skinks (Plestiodon kishinouyei and P. stimpsonii).

    Science.gov (United States)

    Kurita, Kazuki; Toda, Mamoru

    2017-04-01

    We conducted comparative phylogeographic and population genetic analyses of Plestiodon kishinouyei and P. stimpsonii, two sympatric skinks endemic to islands in the southern Ryukyus, to explore different factors that have influenced population structure. Previous phylogenetic studies using partial mitochondrial DNA indicate similar divergence times from their respective closest relatives, suggesting that differences in population structure are driven by intrinsic attributes of either species rather than the common set of extrinsic factors that both presumably have been exposed to throughout their history. In this study, analysis of mtDNA sequences and microsatellite polymorphism demonstrate contrasting patterns of phylogeography and population structure: P. kishinouyei exhibits a lower genetic variability and lower genetic differentiation among islands than P. stimpsonii, consistent with recent population expansion. However, historical demographic analyses indicate that the relatively high genetic uniformity in P. kishinouyei is not attributable to recent expansion. We detected significant isolation-by-distance patterns among P. kishinouyei populations on the land bridge islands, but not among P. stimpsonii populations occurring on those same islands. Our results suggest that P. kishinouyei populations have maintained gene flows across islands until recently, probably via ephemeral Quaternary land bridges. The lower genetic variability in P. kishinouyei may also indicate smaller effective population sizes on average than that of P. stimpsonii. We interpret these differences as a consequence of ecological divergence between the two species, primarily in trophic level and habitat preference.

  13. Intraspecific ploidy variation: A hidden, minor player in plant-soil-mycorrhizal fungi interactions.

    Science.gov (United States)

    Sudová, Radka; Pánková, Hana; Rydlová, Jana; Münzbergová, Zuzana; Suda, Jan

    2014-01-01

    Genome duplication and arbuscular mycorrhizal (AM) symbiosis are ubiquitous in angiosperms. While the significance of each of these phenomena separately has been intensively studied, their interaction remains to be understood. Three diploid and three hexaploid populations of Aster amellus (Asteraceae) were characterized in terms of the soil conditions in situ and mycorrhizal root colonization. In a greenhouse experiment, the effects of ploidy level, substrate conditions, and AM fungi on plant performance were then separated by growing noninoculated plants or plants inoculated with AM fungi in substrates native to either the diploids or hexaploids. The diploids inhabited nutritionally richer sites but did not differ from hexaploid plants in the level of mycorrhizal root colonization in situ. In the experiment, hexaploids generally performed better than the diploids. This intercytotype growth difference was enhanced by soil fertility, with hexaploids benefiting more from nutritionally richer substrate than the diploids. AM inoculation was crucial for plant growth and phosphorus uptake. The interaction between ploidy level and AM inoculation significantly influenced only dry mass of roots, phosphorus concentrations in shoot biomass, and the length of the extraradical mycelium in the nonsterile substrates. Our results support the idea that polyploidy can affect the mycorrhizal growth response of host plants. Nevertheless, the effects of the interaction between ploidy and inoculation were weaker than the main effects of these factors.

  14. Genome cartography: charting the apicomplexan genome.

    Science.gov (United States)

    Kissinger, Jessica C; DeBarry, Jeremy

    2011-08-01

    Genes reside in particular genomic contexts that can be mapped at many levels. Historically, 'genetic maps' were used primarily to locate genes. Recent technological advances in the determination of genome sequences have made the analysis and comparison of whole genomes possible and increasingly tractable. What do we see if we shift our focus from gene content (the 'inventory' of genes contained within a genome) to the composition and organization of a genome? This review examines what has been learned about the evolution of the apicomplexan genome as well as the significance and impact of genomic location on our understanding of the eukaryotic genome and parasite biology. Copyright © 2011 Elsevier Ltd. All rights reserved.

  15. Herbarium genomics

    DEFF Research Database (Denmark)

    Bakker, Freek T.; Lei, Di; Yu, Jiaying

    2016-01-01

    Herbarium genomics is proving promising as next-generation sequencing approaches are well suited to deal with the usually fragmented nature of archival DNA. We show that routine assembly of partial plastome sequences from herbarium specimens is feasible, from total DNA extracts and with specimens...... Angiosperm families, 73 of which were from herbarium material with ages up to 146 years old. For 84 specimens, a sufficient number of paired-end reads were generated (in total 9.4 × 1012 nucleotides), yielding successful plastome assemblies for 74 specimens. Those derived from herbarium specimens have lower...... fractions of plastome-derived reads compared with those from fresh and silica-gel-dried specimens, but total herbarium assembly lengths are only slightly shorter. Specimens from wet-tropical conditions appear to have a higher number of contigs per assembly and lower N50 values. We find no significant...

  16. Species characteristics and intraspecific variation in growth and photosynthesis of Cryptomeria japonica under elevated O3 and CO2.

    Science.gov (United States)

    Hiraoka, Yuichiro; Iki, Taiichi; Nose, Mine; Tobita, Hiroyuki; Yazaki, Kenichi; Watanabe, Atsushi; Fujisawa, Yoshitake; Kitao, Mitsutoshi

    2017-06-01

    In order to predict the effects of future atmospheric conditions on forest productivity, it is necessary to clarify the physiological responses of major forest tree species to high concentrations of ozone (O3) and carbon dioxide (CO2). Furthermore, intraspecific variation of these responses should also be examined in order to predict productivity gains through tree improvements in the future. We investigated intraspecific variation in growth and photosynthesis of Cryptomeria japonica D. Don, a major silviculture species in Japan, in response to elevated concentrations of O3 (eO3) and CO2 (eCO2), separately and in combination. Cuttings of C. japonica were grown and exposed to two levels of O3 (ambient and twice-ambient levels) in combination with two levels of CO2 (ambient and 550 µmol mol-1 in the daytime) for two growing seasons in a free-air CO2 enrichment experiment. There was no obvious negative effect of eO3 on growth or photosynthetic traits of the C. japonica clones, but a positive effect was observed for annual height increments in the first growing season. Dry mass production and the photosynthetic rate increased under eCO2 conditions, while the maximum carboxylation rate decreased. Significant interaction effects of eO3 and eCO2 on growth and photosynthetic traits were not observed. Clonal effects on growth and photosynthetic traits were significant, but the interactions between clones and O3 and/or CO2 treatments were not. Spearman's rank correlation coefficients between growth traits under ambient conditions and for each treatment were significantly positive, implying that clonal ranking in growth abilities might not be affected by either eO3 or eCO2. The knowledge obtained from this study will be helpful for species selection in afforestation programs, to continue and to improve current programs involving this species, and to accurately predict the CO2 fixation capacity of Japanese forests. © The Author 2017. Published by Oxford University Press. All

  17. Flight Morphology, Compound Eye Structure and Dispersal in the Bog and the Cranberry Fritillary Butterflies: An Inter- and Intraspecific Comparison.

    Directory of Open Access Journals (Sweden)

    Camille Turlure

    Full Text Available Understanding dispersal is of prime importance in conservation and population biology. Individual traits related to motion and navigation during dispersal may differ: (1 among species differing in habitat distribution, which in turn, may lead to interspecific differences in the potential for and costs of dispersal, (2 among populations of a species that experiences different levels of habitat fragmentation; (3 among individuals differing in their dispersal strategy and (4 between the sexes due to sexual differences in behaviour and dispersal tendencies. In butterflies, the visual system plays a central role in dispersal, but exactly how the visual system is related to dispersal has received far less attention than flight morphology. We studied two butterfly species to explore the relationships between flight and eye morphology, and dispersal. We predicted interspecific, intraspecific and intersexual differences for both flight and eye morphology relative to i species-specific habitat distribution, ii variation in dispersal strategy within each species and iii behavioural differences between sexes. However, we did not investigate for potential population differences. We found: (1 sexual differences that presumably reflect different demands on both male and female visual and flight systems, (2 a higher wing loading (i.e. a proxy for flight performance, larger eyes and larger facet sizes in the frontal and lateral region of the eye (i.e. better navigation capacities in the species inhabiting naturally fragmented habitat compared to the species inhabiting rather continuous habitat, and (3 larger facets in the frontal region in dispersers compared to residents within a species. Hence, dispersers may have similar locomotory capacity but potentially better navigation capacity. Dispersal ecology and evolution have attracted much attention, but there are still significant gaps in our understanding of the mechanisms of dispersal. Unfortunately, for many

  18. Flight Morphology, Compound Eye Structure and Dispersal in the Bog and the Cranberry Fritillary Butterflies: An Inter- and Intraspecific Comparison.

    Science.gov (United States)

    Turlure, Camille; Schtickzelle, Nicolas; Van Dyck, Hans; Seymoure, Brett; Rutowski, Ronald

    2016-01-01

    Understanding dispersal is of prime importance in conservation and population biology. Individual traits related to motion and navigation during dispersal may differ: (1) among species differing in habitat distribution, which in turn, may lead to interspecific differences in the potential for and costs of dispersal, (2) among populations of a species that experiences different levels of habitat fragmentation; (3) among individuals differing in their dispersal strategy and (4) between the sexes due to sexual differences in behaviour and dispersal tendencies. In butterflies, the visual system plays a central role in dispersal, but exactly how the visual system is related to dispersal has received far less attention than flight morphology. We studied two butterfly species to explore the relationships between flight and eye morphology, and dispersal. We predicted interspecific, intraspecific and intersexual differences for both flight and eye morphology relative to i) species-specific habitat distribution, ii) variation in dispersal strategy within each species and iii) behavioural differences between sexes. However, we did not investigate for potential population differences. We found: (1) sexual differences that presumably reflect different demands on both male and female visual and flight systems, (2) a higher wing loading (i.e. a proxy for flight performance), larger eyes and larger facet sizes in the frontal and lateral region of the eye (i.e. better navigation capacities) in the species inhabiting naturally fragmented habitat compared to the species inhabiting rather continuous habitat, and (3) larger facets in the frontal region in dispersers compared to residents within a species. Hence, dispersers may have similar locomotory capacity but potentially better navigation capacity. Dispersal ecology and evolution have attracted much attention, but there are still significant gaps in our understanding of the mechanisms of dispersal. Unfortunately, for many species

  19. Plastid and mitochondrial genomes of Coccophora langsdorfii (Fucales, Phaeophyceae and the utility of molecular markers.

    Directory of Open Access Journals (Sweden)

    Louis Graf

    Full Text Available Coccophora langsdorfii (Turner Greville (Fucales is an intertidal brown alga that is endemic to Northeast Asia and increasingly endangered by habitat loss and climate change. We sequenced the complete circular plastid and mitochondrial genomes of C. langsdorfii. The circular plastid genome is 124,450 bp and contains 139 protein-coding, 28 tRNA and 6 rRNA genes. The circular mitochondrial genome is 35,660 bp and contains 38 protein-coding, 25 tRNA and 3 rRNA genes. The structure and gene content of the C. langsdorfii plastid genome is similar to those of other species in the Fucales. The plastid genomes of brown algae in other orders share similar gene content but exhibit large structural recombination. The large in-frame insert in the cox2 gene in the mitochondrial genome of C. langsdorfii is typical of other brown algae. We explored the effect of this insertion on the structure and function of the cox2 protein. We estimated the usefulness of 135 plastid genes and 35 mitochondrial genes for developing molecular markers. This study shows that 29 organellar genes will prove efficient for resolving brown algal phylogeny. In addition, we propose a new molecular marker suitable for the study of intraspecific genetic diversity that should be tested in a large survey of populations of C. langsdorfii.

  20. The genome of the recently domesticated crop plant sugar beet (Beta vulgaris).

    Science.gov (United States)

    Dohm, Juliane C; Minoche, André E; Holtgräwe, Daniela; Capella-Gutiérrez, Salvador; Zakrzewski, Falk; Tafer, Hakim; Rupp, Oliver; Sörensen, Thomas Rosleff; Stracke, Ralf; Reinhardt, Richard; Goesmann, Alexander; Kraft, Thomas; Schulz, Britta; Stadler, Peter F; Schmidt, Thomas; Gabaldón, Toni; Lehrach, Hans; Weisshaar, Bernd; Himmelbauer, Heinz

    2014-01-23

    Sugar beet (Beta vulgaris ssp. vulgaris) is an important crop of temperate climates which provides nearly 30% of the world's annual sugar production and is a source for bioethanol and animal feed. The species belongs to the order of Caryophylalles, is diploid with 2n = 18 chromosomes, has an estimated genome size of 714-758 megabases and shares an ancient genome triplication with other eudicot plants. Leafy beets have been cultivated since Roman times, but sugar beet is one of the most recently domesticated crops. It arose in the late eighteenth century when lines accumulating sugar in the storage root were selected from crosses made with chard and fodder beet. Here we present a reference genome sequence for sugar beet as the first non-rosid, non-asterid eudicot genome, advancing comparative genomics and phylogenetic reconstructions. The genome sequence comprises 567 megabases, of which 85% could be assigned to chromosomes. The assembly covers a large proportion of the repetitive sequence content that was estimated to be 63%. We predicted 27,421 protein-coding genes supported by transcript data and annotated them on the basis of sequence homology. Phylogenetic analyses provided evidence for the separation of Caryophyllales before the split of asterids and rosids, and revealed lineage-specific gene family expansions and losses. We sequenced spinach (Spinacia oleracea), another Caryophyllales species, and validated features that separate this clade from rosids and asterids. Intraspecific genomic variation was analysed based on the genome sequences of sea beet (Beta vulgaris ssp. maritima; progenitor of all beet crops) and four additional sugar beet accessions. We identified seven million variant positions in the reference genome, and also large regions of low variability, indicating artificial selection. The sugar beet genome sequence enables the identification of genes affecting agronomically relevant traits, supports molecular breeding and maximizes the plant

  1. The genome sequence of Trypanosoma brucei gambiense, causative agent of chronic human african trypanosomiasis.

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    Andrew P Jackson

    2010-04-01

    Full Text Available Trypanosoma brucei gambiense is the causative agent of chronic Human African Trypanosomiasis or sleeping sickness, a disease endemic across often poor and rural areas of Western and Central Africa. We have previously published the genome sequence of a T. b. brucei isolate, and have now employed a comparative genomics approach to understand the scale of genomic variation between T. b. gambiense and the reference genome. We sought to identify features that were uniquely associated with T. b. gambiense and its ability to infect humans.An improved high-quality draft genome sequence for the group 1 T. b. gambiense DAL 972 isolate was produced using a whole-genome shotgun strategy. Comparison with T. b. brucei showed that sequence identity averages 99.2% in coding regions, and gene order is largely collinear. However, variation associated with segmental duplications and tandem gene arrays suggests some reduction of functional repertoire in T. b. gambiense DAL 972. A comparison of the variant surface glycoproteins (VSG in T. b. brucei with all T. b. gambiense sequence reads showed that the essential structural repertoire of VSG domains is conserved across T. brucei.This study provides the first estimate of intraspecific genomic variation within T. brucei, and so has important consequences for future population genomics studies. We have shown that the T. b. gambiense genome corresponds closely with the reference, which should therefore be an effective scaffold for any T. brucei genome sequence data. As VSG repertoire is also well conserved, it may be feasible to describe the total diversity of variant antigens. While we describe several as yet uncharacterized gene families with predicted cell surface roles that were expanded in number in T. b. brucei, no T. b. gambiense-specific gene was identified outside of the subtelomeres that could explain the ability to infect humans.

  2. Genome size variation and incidence of polyploidy in Scrophulariaceae sensu lato from the Iberian Peninsula.

    Science.gov (United States)

    Castro, Mariana; Castro, Sílvia; Loureiro, João

    2012-01-01

    In the last decade, genomic studies using DNA markers have strongly influenced the current phylogeny of angiosperms. Genome size and ploidy level have contributed to this discussion, being considered important characters in biosystematics, ecology and population biology. Despite the recent increase in studies related to genome size evolution and polyploidy incidence, only a few are available for Scrophulariaceae. In this context, we assessed the value of genome size, mostly as a taxonomic marker, and the role of polyploidy as a process of genesis and maintenance of plant diversity in Scrophulariaceae sensu lato in the Iberian Peninsula. Large-scale analyses of genome size and ploidy-level variation across the Iberian Peninsula were performed using flow cytometry. One hundred and sixty-two populations of 59 distinct taxa were analysed. A bibliographic review on chromosome counts was also performed. From the 59 sampled taxa, 51 represent first estimates of genome size. The majority of the Scrophulariaceae species presented very small to small genome sizes (2C ≤ 7.0 pg). Furthermore, in most of the analysed genera it was possible to use this character to separate several taxa, independently if these genera were homoploid or heteroploid. Also, some genome-related phenomena were detected, such as intraspecific variation of genome size in some genera and the possible occurrence of dysploidy in Verbascum spp. With respect to polyploidy, despite a few new DNA ploidy levels having been detected in Veronica, no multiple cytotypes have been found in any taxa. This work contributed with important basic scientific knowledge on genome size and polyploid incidence in the Scrophulariaceae, providing important background information for subsequent studies, with several perspectives for future studies being opened.

  3. National Human Genome Research Institute

    Science.gov (United States)

    ... the Director Organization Reports & Publications Español The National Human Genome Research Institute conducts genetic and genomic research, funds ... genomic literacy among physicians. Funded by the National Human Genome Research Institute (NHGRI), The Universal Genomics Instructor Handbook ...

  4. Chromosome number and genome size variation in Colocasia (Araceae) from China.

    Science.gov (United States)

    Wang, Guang-Yan; Zhang, Xiao-Ming; Qian, Min; Hu, Xiang-Yang; Yang, Yong-Ping

    2017-11-01

    Chromosome number and genome size are important cytological characters that significantly influence various organismal traits. We investigated chromosome number and genome size variation in 73 accessions belonging to four Colocasia species from China. Five different chromosome counts (2n = 26, 28, 38, 42, and 56) were found, the largest one representing a new record in Colocasia. The basic chromosome numbers are x = 13, 14, and 19, corresponding to 2x, 3x, and 4x cytotypes. Yunnan Province, China is considered the center of Colocasia polyploid origin. The 2C values in our accessions ranged from 3.29 pg in C. gigantea to 12.51 pg in C. esculenta. All species exhibit inter- and intraspecific chromosomal variation. Differences in DNA content among the Colocasia species seem to have occurred by chromosomal gain under similar habitats. Polyploidization also obviously contributes to 2C value variation.

  5. Intra-specific variation of sperm length in the malaria vector Anopheles gambiae: males with shorter sperm have higher reproductive success

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    Voordouw Maarten J

    2008-10-01

    Full Text Available Abstract Background Intra-specific variation in sperm length influences male reproductive success in several species of insects. In males of the malaria vector Anopheles gambiae, sperm length is highly variable but the significance of this variation is unknown. Understanding what determines the reproductive success of male mosquitoes is critical for controlling malaria, and in particular for replacing natural populations with transgenic, malaria-resistant mosquitoes. Methods A laboratory population of A. gambiae males was tested for intra-specific variation in sperm length. A full-sib quantitative genetic design was used to test for a genetic component of sperm length in A. gambiae males and estimate its heritability. This study also tested for a relationship between sperm length and male reproductive success in A. gambiae. Male reproductive success was measured as the proportions of inseminated and ovipositing females. Results There was intra-specific variation of sperm length in A. gambiae. There was no significant genetic variation in sperm length and its heritability was low (h2 = 0.18 compared to other insects. Sperm length was correlated with male body size (measured as wing length. Males with short sperm had significantly higher reproductive success than males with long sperm and this was independent of body size. Conclusion This is the first study to demonstrate intra-specific variation in sperm length in A. gambiae and that males with short sperm have higher reproductive success. That sperm length influences female oviposition is important for any strategy considering the release of transgenic males.

  6. Intraspecific relationships among wood density, leaf structural traits and environment in four co-occurring species of Nothofagus in New Zealand.

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    Sarah J Richardson

    Full Text Available Plant functional traits capture important variation in plant strategy and function. Recent literature has revealed that within-species variation in traits is greater than previously supposed. However, we still have a poor understanding of how intraspecific variation is coordinated among different traits, and how it is driven by environment. We quantified intraspecific variation in wood density and five leaf traits underpinning the leaf economics spectrum (leaf dry matter content, leaf mass per unit area, size, thickness and density within and among four widespread Nothofagus tree species in southern New Zealand. We tested whether intraspecific relationships between wood density and leaf traits followed widely reported interspecific relationships, and whether variation in these traits was coordinated through shared responses to environmental factors. Sample sites varied widely in environmental variables, including soil fertility (25-900 mg kg(-1 total P, precipitation (668-4875 mm yr(-1, temperature (5.2-12.4 °C mean annual temperature and latitude (41-46 °S. Leaf traits were strongly correlated with one another within species, but not with wood density. There was some evidence for a positive relationship between wood density and leaf tissue density and dry matter content, but no evidence that leaf mass or leaf size were correlated with wood density; this highlights that leaf mass per unit area cannot be used as a surrogate for component leaf traits such as tissue density. Trait variation was predicted by environmental factors, but not consistently among different traits; e.g., only leaf thickness and leaf density responded to the same environmental cues as wood density. We conclude that although intraspecific variation in wood density and leaf traits is strongly driven by environmental factors, these responses are not strongly coordinated among functional traits even across co-occurring, closely-related plant species.

  7. Intraspecific invariability of the internal transcribed spacer region of rDNA of the truffle Terfezia terfezioides in Europe.

    Science.gov (United States)

    Kovács, G M; Rudnóy, S; Vágvölgyi, C; Lásztity, D; Rácz, I; Bratek, Z

    2001-01-01

    ITS regions (internal transcribed spacers--ITS1 and ITS2--with the 5.8S gene of the nuclear rDNA) of 25 fruit body samples of Terfezia terfezioides, originating from Hungary and Italy, were compared. The amplification and sequencing of the ITS region was successful with both the ITS1-ITS4 and ITS1F-ITS4 primer pairs. No differences of the restriction fragment length polymorphism profiles were detected among 19 samples collected in one place at the same time. The sequences of the ITS region of 9 samples collected in different localities were highly invariable, differing in only two bases. Thus the intraspecific homogeneity of the ITS region seems to be an important species-specific characteristic of T. terfezioides in contrast to other Terfezia species. As the samples of the species were collected from different and distant localities of Europe, the ITS sequence of T. terfezioides can be considered a very conservative, reliable molecular marker of the fungus.

  8. Intraspecific variation in {sup 137}Cs activity concentration in sporocarps of Suillus variegatus in seven Swedish populations

    Energy Technology Data Exchange (ETDEWEB)

    Dahlberg, Anders [Swedish Univ. of Agricultural Sciences, Forest Mycology and Pathology Dept., Uppsala (Sweden); Nikolova, Ivanka; Johanson, K.-J. [Swedish Univ. of Agricultural Sciences, Radioecology Dept., Uppsala (Sweden)

    1997-05-01

    Following the Chernobyl accident in 1986, sporocarps of Suillus variegatus in Sweden showed a large amount of individual variation in concentration of {sup 137}Cs activity. Our aim was to determine the degrees to which this variability in sporocarp {sup 137}Cs levels could be explained by differences between (i) local populations, (ii) fungal genets and (iii) locations within genets. Five populations in a 100-yr-old Scots pine forest, located within a 1 km{sup 2} area, and two populations in Scots pine/Norway spruce forest, located 40 km north-west of Uppsala, were investigated. In total, 154 sporocarps were analysed to determine their {sup 137}Cs content. Of these, the genetic affiliations of 86 were successfully characterized using somatic incompatibility reactions. Twenty-six genets were found which, on average, consisted of 6.5 sporocarps. The genets averaged 7.5 m in size, measured as the length between the most distant sporocarps. The mean sporocarp {sup 137}Cs level was 67.1 {+-} 2.8 kBq kgsup(-1) D.W. (range between 13.6 and 182). According to analyses of variance, within-population variation accounted for 60% of the total variation in {sup 137}Cs levels, while 40% was ascribed to variation among populations. Within a population, {sup 137}Cs levels did not generally differ significantly between genets. Plausible reasons for intraspecific variation in radiocaesium content in sporocarps are discussed. (author).

  9. Consequences of Intraspecific Competition and Environmental Variation for Selection in the Mustard Sinapsis arvensis: Contrasting Ecological and Evolutionary Perspectives.

    Science.gov (United States)

    Stanton, M L; Thiede, D A; Roy, B A

    2004-12-01

    Alternative models of plant life-history evolution differ in their views of how abiotic stress and competition interact to shape the evolution of plant life-history traits. To address this debate, which crosses traditional boundaries between community ecology and population biology, we grew wild turnip families from three selection histories in a field experiment in which we manipulated conspecific density and sun exposure. Hot spring conditions caused neutral shading to reduce drought stress, resulting in a greater mean and variance for lifetime fertility at low density and greater intensity of competition at high density. The variance in relative fitness among individuals or families was least in partial shade at low density. Prior selection under shade stress in the greenhouse reduced lifetime fitness in the less stressful partial-shade treatment under field conditions. Patterns of selection and predicted trait evolution were more similar between high and low densities than between the two light environments. Partial shade favored the proliferation of large leaves early in development, especially at high density. Selection in the stressful full-sun treatment favored reduced pathogen susceptibility at both densities and early flowering at low density. Because direct selection on traits changed principally in magnitude rather than in direction, genetic correlations for fitness were generally positive between light and density treatments. Greater intraspecific competition led to more rapid predicted trait evolution in the partial-shade environment but not in the stressful full-sun treatment.

  10. Biological control of indianmeal moth and rice weevil by parasitoids with reference to the intraspecific competition pattern.

    Science.gov (United States)

    Nam, Youngwoo; Ji, Jeongyeon; Na, Ja Hyun; Chun, Yong Shik; Ryoo, Mun Il

    2011-04-01

    Biological control of rice weevil, Sitophilus oryzae (L.), and Indianmeal moth, Plodia interpunctella (Hübner), by their parasitoids Anisopteromalus calandrae (Howard) and Bracon hebetor Say was examined while considering the intraspecific competition pattern of the pests. In both experimental and simulation studies, A. calandrae was shown to suppress the rice weevil population, a contest type competitor, regardless of the parasitoid/weevil ratios tested. In contrast, B. hebetor only significantly suppressed the Indianmeal moth, a scramble type competitor, when the parasitoid/moth ratio was >0.05. At ratios lower than 0.05, the role of B. hebetor was negligible, and the correlation coefficients between the number of moths that had emerged and the parasitoid/moth ratio was estimated to be 0.07. The control efficiency of the two parasitoids with respect to the parasitoid/host ratio was estimated using a ratio-response model. To suppress the weevil density to a level that was only 10% of the current density, the ratio was estimated to be 0.02, whereas this value was 0.14 for the Indianmeal moth. However, for the continuous suppression of the Indianmeal moth, periodic and iterative introduction of B. hebetor was required.

  11. Intraspecific variation in body size and shape in an andean highland anole species, Anolis ventrimaculatus (Squamata: Dactyloidae).

    Science.gov (United States)

    Calderón-Espinosa, Martha L; Ortega-León, Angela M; Zamora-Abrego, Joan G

    2013-03-01

    Variation in body characteristics related to lizard locomotion has been poorly studied at the intraspecific level in Anolis species. Local adaptation due to habitat heterogeneity has been reported in some island species. However, studies of mainland species are particularly scarce and suggest different patterns: high variability among highland lizards and poorly differentiated populations in one Amazonian species. We characterized inter population variation of body size and shape in the highland Andean Anolis ventrimaculatus, an endemic species from Western Colombia. A total of 15 morphometric variables were measured in specimens from the reptile collection of the Instituto de Ciencias Naturales, Universidad Nacional, Colombia. The study included individuals from seven different highland localities. We found size and shape sexual dimorphism, both of which varied among localities. Patterns of variation in body proportions among populations were different in both males and females, suggesting that either sexual or natural selective factors are different in each locality and between sexes. Since this species exhibits a fragmented distribution in highlands, genetic divergence may also be a causal factor of the observed variation. Ecological, behavioral, additional morphological as well as phylogenetic data, may help to understand the evolutionary processes behind the geographic patterns found in this species.

  12. Variation in ribosomal and mitochondrial DNA sequences demonstrates the existence of intraspecific groups in Paramecium multimicronucleatum (Ciliophora, Oligohymenophorea).

    Science.gov (United States)

    Tarcz, Sebastian; Potekhin, Alexey; Rautian, Maria; Przyboś, Ewa

    2012-05-01

    This is the first phylogenetic study of the intraspecific variability within Paramecium multimicronucleatum with the application of two-loci analysis (ITS1-5.8S-ITS2-5'LSU rDNA and COI mtDNA) carried out on numerous strains originated from different continents. The species has been shown to have a complex structure of several sibling species within taxonomic species. Our analysis revealed the existence of 10 haplotypes for the rDNA fragment and 15 haplotypes for the COI fragment in the studied material. The mean distance for all of the studied P. multimicronucleatum sequence pairs was p=0.025/0.082 (rDNA/COI). Despite the greater variation of the COI fragment, the COI-derived tree topology is similar to the tree topology constructed on the basis of the rDNA fragment. P. multimicronucleatum strains are divided into three main clades. The tree based on COI fragment analysis presents a greater resolution of the studied P. multimicronucleatum strains. Our results indicate that the strains of P. multimicronucleatum that appear in different clades on the trees could belong to different syngens. Copyright © 2012 Elsevier Inc. All rights reserved.

  13. Intraspecific differentiation of Paramecium novaurelia strains (Ciliophora, Protozoa) inferred from phylogenetic analysis of ribosomal and mitochondrial DNA variation.

    Science.gov (United States)

    Tarcz, Sebastian

    2013-01-01

    Paramecium novaurelia Beale and Schneller, 1954, was first found in Scotland and is known to occur mainly in Europe, where it is the most common species of the P. aurelia complex. In recent years, two non-European localities have been described: Turkey and the United States of America. This article presents the analysis of intraspecific variability among 25 strains of P. novaurelia with the application of ribosomal and mitochondrial loci (ITS1-5.8S-ITS2, 5' large subunit rDNA (5'LSU rDNA) and cytochrome c oxidase subunit 1 (COI) mtDNA). The mean distance observed for all of the studied P. novaurelia sequence pairs was p=0.008/0.016/0.092 (ITS1-5.8S-ITS2/5'LSU rDNA/COI). Phylogenetic trees (NJ/MP/BI) based on a comparison of all of the analysed sequences show that the studied strains of P. novaurelia form a distinct clade, separate from the P. caudatum outgroup, and are divided into two clusters (A and B) and two branches (C and D). The occurrence of substantial genetic differentiation within P. novaurelia, confirmed by the analysed DNA fragments, indicates a rapid evolution of particular species within the Paramecium genus. Copyright © 2012 Elsevier GmbH. All rights reserved.

  14. Intraspecific brood parasitism can increase the number of eggs that an individual lays in its own nest.

    Science.gov (United States)

    Ruxton, Graeme D; Broom, Mark

    2002-10-07

    Intraspecific brood parasitism involves laying eggs in the nest of another individual of the same species without subsequently caring for the eggs or hatchlings. Where individuals lay in their own nest as well as parasitically, previous works predicted that parasitism leads to fewer eggs being laid in an individual's own nest, compared with the equivalent situation without parasitism. This is predicted to occur both to reduce the effects of competition from parasitically laid individuals and because parasitism can be used to reduce competition between siblings. Here, we present a quantitative model of this situation. This model indicates that the brood-reduction prediction does not hold universally. For some plausible parameter combinations, parasitism causes an increase rather than a decrease in the number of eggs laid by an individual in its own nest. This occurs because parasitism becomes a less profitable tactic as more eggs are laid by nest owners due to increasing within-nest competition. Increasing clutch size will also increase competition between the host's own offspring, but can still be advantageous if the induced reduction in parasitism is sufficient.

  15. Intraspecific variation in flight metabolic rate in the bumblebee Bombus impatiens: repeatability and functional determinants in workers and drones.

    Science.gov (United States)

    Darveau, Charles-A; Billardon, Fannie; Bélanger, Kasandra

    2014-02-15

    The evolution of flight energetics requires that phenotypes be variable, repeatable and heritable. We studied intraspecific variation in flight energetics in order to assess the repeatability of flight metabolic rate and wingbeat frequency, as well as the functional basis of phenotypic variation in workers and drones of the bumblebee species Bombus impatiens. We showed that flight metabolic rate and wingbeat frequency were highly repeatable in workers, even when controlling for body mass variation using residual analysis. We did not detect significant repeatability in drones, but a smaller range of variation might have prevented us from finding significant values in our sample. Based on our results and previous findings, we associated the high repeatability of flight phenotypes in workers to the functional links between body mass, thorax mass, wing size, wingbeat frequency and metabolic rate. Moreover, differences between workers and drones were as predicted from these functional associations, where drones had larger wings for their size, lower wingbeat frequency and lower flight metabolic rate. We also investigated thoracic muscle metabolic phenotypes by measuring the activity of carbohydrate metabolism enzymes, and we found positive correlations between mass-independent metabolic rate and the activity of all enzymes measured, but in workers only. When comparing workers and drones that differ in flight metabolic rate, only the activity of the enzymes hexokinase and trehalase showed the predicted differences. Overall, our study indicates that there should be correlated evolution among physiological phenotypes at multiple levels of organization and morphological traits associated with flight.

  16. Role of intraspecific trait plasticity in Mikania micrantha Kunth growth and impact of its abundance on community composition

    Directory of Open Access Journals (Sweden)

    Achyut Kumar Banerjee

    2017-06-01

    Full Text Available Intraspecific trait variability, which plays an important role in community assembly, was studied in an invasive plant Mikania micrantha along with its impact on community composition. The abundance of M. micrantha and community composition were recorded in a quadrat-based study conducted on a spatial (littoral, terrestrial, and an intermediate habitat and temporal (summer, monsoon, and winter scale. Soil parameters were analyzed and some fitness-related traits of M. micrantha were estimated. Season and habitat had significant effects on M. micrantha abundance. Seasonal plasticity was evident in leaf-level traits. High laminar nitrogen and leaf dry matter content during the monsoons and a larger leaf area with high chlorophyll content during summer and winter months were responsible for maintenance of its yearlong growth. Multivariate regression analysis revealed that, after adjusting for season and habitat, none of the traits exhibited significant effect on M. micrantha abundance. Abundance of M. micrantha appeared to be the only factor responsible for decline in associated species richness. Continuous monitoring of the established population and early detection of new infestations of M. micrantha are recommended to keep a check on excessive growths to prevent it from becoming problematic in subtropical regions of the world.

  17. Intraspecific and interspecific competition in Callosobruchus maculatus (F.) and Callosobruchus subinnotatus (Pic) on stored bambara groundnut, Vigna subterranea (L.) Verdcourt.

    Science.gov (United States)

    Lale, N E.S.; Vidal, S

    2001-10-01

    Intraspecific competition was studied in Callosobruchus maculatus and Callosobruchus subinnotatus. Interspecific competition between the two bruchids was also studied to determine which of these species is likely to cause more damage to stored bambara groundnuts, Vigna subterranea in cases of joint infestation. Results showed that increasing the adult density up to 8 females per 10g of bambara groundnut seeds did not significantly reduce the mean number of eggs laid per female, the number of eggs developing to the adult stage, or the weight of emerged adults of either species. The developmental period of the two species was also not significantly affected. The adult emergence curve of C. maculatus was similar to that of C. subinnotatus and was of the scramble type. C. maculatus performed better than C. subinnotatus in interspecific competition and it achieved this through a higher egg-laying ability and a higher rate of progeny production coupled with a shorter life-cycle. The implications of these findings with respect to damage and possible loss of stored bambara groundnut are discussed.

  18. Understanding the Genomic Basis of Adaptive Response to Variable Osmotic Niches in Freshwater Prawns: A Comparative Intraspecific RNA-Seq Analysis of Macrobrachium australiense.

    Science.gov (United States)

    Moshtaghi, Azam; Rahi, Md Lifat; Mather, Peter B; Hurwood, David A

    2017-07-01

    Understanding the molecular basis of adaptive response to variable environmental conditions is a central goal of evolutionary biology. Here, we sought to identify potential outlier single nucleotide polymorphisms (SNPs) in 3 wild populations of a freshwater prawn (Macrobrachium australiense) that are exposed to differing osmotic niches by using a comparative transcriptomics approach. De novo assembly of approximately 542 million (75 nt) pair end reads collected from 10 individuals revealed 123396 longer contigs/transcripts of variable length, that showed 97.38% transcriptome assembly completeness. Differential gene expression analysis of major osmoregulatory genes revealed that calreticulin, Na+/H+ exchanger, and V-type (H+) ATPase showed the highest expression levels in the Blunder Creek (low ionic) population, while Crustacean cardiovascular peptide (CCP), Na+/K+-ATPase, Na+/K+/2Cl- co-transporter (NKCC) and Na+/HCO3- exchanger showed the highest expression levels in the Bulimba Creek (higher ionic) population. In total, 16 gene ontology term categories were functionally enriched among the 3 studied populations. We identified 4144 raw and 835 high quality filtered SNPs in the 3 M. australiense populations, of which 84 SNPs were identified as outliers. Outliers were detected in 4 important osmoregulatory genes that include: calreticulin, Na+/H+ exchanger, Na+/K+-ATPase, and V-type-(H+)-ATPase. All outliers in the osmoregulatory genes were located in noncoding regulatory regions (untranslated regions) of the gene. We hypothesize that the outlier SNPs identified here in M. australiense populations exposed naturally to different osmotic conditions influence specific gene expression patterns that allow individuals to respond to local environmental conditions. © The American Genetic Association 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  19. Phylogeographic investigation and ecological niche modelling of the endemic frog species Nanorana pleskei revealed multiple refugia in the eastern Tibetan Plateau

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    Bin Wang

    2017-09-01

    Full Text Available The largest plateau Tibetan Plateau supplied an excellent opportunity to investigate the influence of the Pleistocene events on the high-elevation species. To test for the alternative hypotheses of Pleistocene glacial refugia, we used partial sequences of two mitochondrial genes and one nuclear gene to examine the phylogeographic patterns of the endemic frog species Nanorana pleskei across its known range in the eastern Tibetan Plateau, and conducted species distribution modelling (SDM to explore changes of its distribution range through current and paleo periods. In all data sets, the species was divided into lineage north occupying open plateau platform and lineage south colonizing the mountainous plateau. The divergence of two major clades was estimated at the early Pleistocene. In mtDNA, lineage north contained northeastern and northwestern sublineages, and lineage south had two overlapping-distributed sublineages. Different lineages possessed distinct demographic characteristics, i.e., subdivision in the northeastern sublineage, historical bottleneck effects and recent expansions in the northwestern sublineage and the southeastern sublineage. SDMs depicted that stable suitable habitats had existed in the upper-middle streams of the Yellow River, Dadu River, Jinsha River and Yalong River. These regions were also recognized as the ancestral areas of different lineages. In conclusion, Nanorana pleskei lineages have probably experienced long-term separations. Stable suitable habitats existing in upper-middle streams of major rivers on the eastern Tibetan Plateau and distinct demographic dynamics of different lineages indicated that the lineages possessed independent evolutionary processes in multiple glacial refugia. The findings verified the profound effects of Pleistocene climatic fluctuations on the plateau endemic species.

  20. Phylogeographic investigation and ecological niche modelling of the endemic frog species Nanorana pleskei revealed multiple refugia in the eastern Tibetan Plateau.

    Science.gov (United States)

    Wang, Bin; Xie, Feng; Li, Jiannan; Wang, Gang; Li, Cheng; Jiang, Jianping

    2017-01-01

    The largest plateau Tibetan Plateau supplied an excellent opportunity to investigate the influence of the Pleistocene events on the high-elevation species. To test for the alternative hypotheses of Pleistocene glacial refugia, we used partial sequences of two mitochondrial genes and one nuclear gene to examine the phylogeographic patterns of the endemic frog species Nanorana pleskei across its known range in the eastern Tibetan Plateau, and conducted species distribution modelling (SDM) to explore changes of its distribution range through current and paleo periods. In all data sets, the species was divided into lineage north occupying open plateau platform and lineage south colonizing the mountainous plateau. The divergence of two major clades was estimated at the early Pleistocene. In mtDNA, lineage north contained northeastern and northwestern sublineages, and lineage south had two overlapping-distributed sublineages. Different lineages possessed distinct demographic characteristics, i.e., subdivision in the northeastern sublineage, historical bottleneck effects and recent expansions in the northwestern sublineage and the southeastern sublineage. SDMs depicted that stable suitable habitats had existed in the upper-middle streams of the Yellow River, Dadu River, Jinsha River and Yalong River. These regions were also recognized as the ancestral areas of different lineages. In conclusion, Nanorana pleskei lineages have probably experienced long-term separations. Stable suitable habitats existing in upper-middle streams of major rivers on the eastern Tibetan Plateau and distinct demographic dynamics of different lineages indicated that the lineages possessed independent evolutionary processes in multiple glacial refugia. The findings verified the profound effects of Pleistocene climatic fluctuations on the plateau endemic species.

  1. Phylogeographic and population insights of the Asian common toad (Bufo gargarizans in Korea and China: population isolation and expansions as response to the ice ages

    Directory of Open Access Journals (Sweden)

    Amaël Borzée

    2017-11-01

    Full Text Available The effects of ice ages on speciation have been well documented for many European and North American taxa. In contrast, very few studies have addressed the consequences of such environmental and topographical changes in North East Asian species. More precisely, the Korean Peninsula offers a unique model to assess patterns and processes of speciation as it hosts the northern- and eastern-most distribution limit of some widespread Asian taxa. Despite this, studies addressing phylogeographic patterns and population genetics in the peninsula and surrounding countries are few and studies for most families are lacking. Here we inferred the phylogenetic relationships of the common toad (Bufo gargarizans from South Korea and their North East Asian counterpart populations, based on mitochondrial data. Korean B. gargarizans GenBank BLASTs matched few individuals from nearby China, but the presence of a Korean clade suggests isolation on the Korean Peninsula, previous to the last glacial maximum, linked to sea level resurgence. Molecular clock calibrations within this group were used to date the divergence between clades and their relationship to paleo-climatic events in the area. Lack of genetic structure among South Korean populations and strong homogeneity between the Korean and some Chinese localities suggest weak isolation and recent expansion. Geographical projection of continuous coalescent maximum-clade-credibility trees shows an original Chinese expansion towards the Korean Peninsula through the Yellow Sea circa two million years ago with colonisation events dating circa 800 thousand years ago (K. y. a.. Following this colonisation, the data point to outgoing Korean Peninsula dispersal events throughout different periods, towards the North through land, and West through land bridge formations over the Yellow Sea during sea level falls. In accordance, demographic analyses revealed a population expansion in the Koran Peninsula circa 300 K. y. a

  2. An integrative approach to phylogeography: investigating the effects of ancient seaways, climate, and historical geology on multi-locus phylogeographic boundaries of the Arboreal Salamander (Aneides lugubris).

    Science.gov (United States)

    Reilly, Sean B; Corl, Ammon; Wake, David B

    2015-11-04

    Phylogeography is an important tool that can be used to reveal cryptic biodiversity and to better understand the processes that promote lineage diversification. We studied the phylogeographic history of the Arboreal Salamander (Aneides lugubris), a wide-ranging species endemic to the California floristic province. We used multi-locus data to reconstruct the evolutionary history of A. lugubris and to discover the geographic location of major genetic breaks within the species. We also used species distribution modeling and comparative phylogeography to better understand the environmental factors that have shaped the genetic history of A. lugubris. We found six major mitochondrial clades in A. lugubris. Nuclear loci supported the existence of at least three genetically distinct groups, corresponding to populations north of the San Francisco Bay and in the Sierra Nevada, in the Santa Cruz Mountains, and in the central coast and southern California. All of the genetic breaks in mitochondrial and nuclear loci corresponded to regions where historical barriers to dispersal have been observed in other species. Geologic or water barriers likely were the most important factors restricting gene flow among clades. Climatic unsuitability during glacial maximum may have contributed to the isolation of the mitochondrial clades in the central coast and southern California. A projection of our species distribution model to a future scenario with a moderate amount of climate change suggests that most of the range of A. lugubris will remain climatically suitable, but climatic conditions in the Sierra Nevada and low elevation areas in Southern California are likely to deteriorate. Aneides lugubris contains substantial cryptic genetic diversity as a result of historical isolation of populations. At least two (and perhaps three) evolutionarily significant units in A. lugubris merit protection; all six mitochondrial clades should be considered as management units within the species.