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Sample records for nonrandom gene flow

  1. Synonymous codon usage in different protein secondary structural classes of human genes: Implication for increased non-randomness of GC3 rich genes towards protein stability

    Indian Academy of Sciences (India)

    Pamela Mukhopadhyay; Surajit Basak; Tapash Chandra Ghosh

    2007-08-01

    The relationship between the synonymous codon usage and different protein secondary structural classes were investigated using 401 Homo sapiens proteins extracted from Protein Data Bank (PDB). A simple Chi-square test was used to assess the significance of deviation of the observed and expected frequencies of 59 codons at the level of individual synonymous families in the four different protein secondary structural classes. It was observed that synonymous codon families show non-randomness in codon usage in four different secondary structural classes. However, when the genes were classified according to their GC3 levels there was an increase in non-randomness in high GC3 group of genes. The non-randomness in codon usage was further tested among the same protein secondary structures belonging to four different protein folding classes of high GC3 group of genes. The results show that in each of the protein secondary structural unit there exist some synonymous family that shows class specific codonusage pattern. Moreover, there is an increased non-random behaviour of synonymous codons in sheet structure of all secondary structural classes in high GC3 group of genes. Biological implications of these results have been discussed.

  2. Azacytidine and decitabine induce gene-specific and non-random DNA demethylation in human cancer cell lines.

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    Sabine Hagemann

    Full Text Available The DNA methyltransferase inhibitors azacytidine and decitabine represent archetypal drugs for epigenetic cancer therapy. To characterize the demethylating activity of azacytidine and decitabine we treated colon cancer and leukemic cells with both drugs and used array-based DNA methylation analysis of more than 14,000 gene promoters. Additionally, drug-induced demethylation was compared to methylation patterns of isogenic colon cancer cells lacking both DNA methyltransferase 1 (DNMT1 and DNMT3B. We show that drug-induced demethylation patterns are highly specific, non-random and reproducible, indicating targeted remethylation of specific loci after replication. Correspondingly, we found that CG dinucleotides within CG islands became preferentially remethylated, indicating a role for DNA sequence context. We also identified a subset of genes that were never demethylated by drug treatment, either in colon cancer or in leukemic cell lines. These demethylation-resistant genes were enriched for Polycomb Repressive Complex 2 components in embryonic stem cells and for transcription factor binding motifs not present in demethylated genes. Our results provide detailed insights into the DNA methylation patterns induced by azacytidine and decitabine and suggest the involvement of complex regulatory mechanisms in drug-induced DNA demethylation.

  3. Non-random retention of protein-coding overlapping genes in Metazoa

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    Bork Peer

    2008-04-01

    Full Text Available Abstract Background Although the overlap of transcriptional units occurs frequently in eukaryotic genomes, its evolutionary and biological significance remains largely unclear. Here we report a comparative analysis of overlaps between genes coding for well-annotated proteins in five metazoan genomes (human, mouse, zebrafish, fruit fly and worm. Results For all analyzed species the observed number of overlapping genes is always lower than expected assuming functional neutrality, suggesting that gene overlap is negatively selected. The comparison to the random distribution also shows that retained overlaps do not exhibit random features: antiparallel overlaps are significantly enriched, while overlaps lying on the same strand and those involving coding sequences are highly underrepresented. We confirm that overlap is mostly species-specific and provide evidence that it frequently originates through the acquisition of terminal, non-coding exons. Finally, we show that overlapping genes tend to be significantly co-expressed in a breast cancer cDNA library obtained by 454 deep sequencing, and that different overlap types display different patterns of reciprocal expression. Conclusion Our data suggest that overlap between protein-coding genes is selected against in Metazoa. However, when retained it may be used as a species-specific mechanism for the reciprocal regulation of neighboring genes. The tendency of overlaps to involve non-coding regions of the genes leads to the speculation that the advantages achieved by an overlapping arrangement may be optimized by evolving regulatory non-coding transcripts.

  4. Deep sequencing of the murine Igh repertoire reveals complex regulation of non-random V gene rearrangement frequencies

    Science.gov (United States)

    Choi, Nancy M.; Loguercio, Salvatore; Verma-Gaur, Jiyoti; Degner, Stephanie C.; Torkamani, Ali; Su, Andrew I.; Oltz, Eugene M.; Artyomov, Maxim; Feeney, Ann J.

    2013-01-01

    A diverse antibody repertoire is formed through the rearrangement of V, D, and J segments at the immunoglobulin heavy chain (Igh) loci. The C57BL/6 murine Igh locus has over 100 functional VH gene segments that can recombine to a rearranged DJH. While the non-random usage of VH genes is well documented, it is not clear what elements determine recombination frequency. To answer this question we conducted deep sequencing of 5′-RACE products of the Igh repertoire in pro-B cells, amplified in an unbiased manner. ChIP-seq results for several histone modifications and RNA polymerase II binding, RNA-seq for sense and antisense non-coding germline transcripts, and proximity to CTCF and Rad21 sites were compared to the usage of individual V genes. Computational analyses assessed the relative importance of these various accessibility elements. These elements divide the Igh locus into four epigenetically and transcriptionally distinct domains, and our computational analyses reveal different regulatory mechanisms for each region. Proximal V genes are relatively devoid of active histone marks and non-coding RNA in general, but having a CTCF site near their RSS is critical, suggesting that being positioned near the base of the chromatin loops is important for rearrangement. In contrast, distal V genes have higher levels of histone marks and non-coding RNA, which may compensate for their poorer RSSs and for being distant from CTCF sites. Thus, the Igh locus has evolved a complex system for the regulation of V(D)J rearrangement that is different for each of the four domains that comprise this locus. PMID:23898036

  5. Nonrandom Distribution of miRNAs Genes and Single Nucleotide Variants in Keratoconus Loci.

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    Dorota M Nowak

    Full Text Available Despite numerous studies, the causes of both development and progression of keratoconus remain elusive. Previous studies of this disorder focused mainly on one or two genetic factors only. However, in the analysis of such complex diseases all potential factors should be taken into consideration. The purpose of this study was a comprehensive analysis of known keratoconus loci to uncover genetic factors involved in this disease causation in the general population, which could be omitted in the original studies. In this investigation genomic data available in various databases and experimental own data were assessed. The lists of single nucleotide variants and miRNA genes localized in reported keratoconus loci were obtained from Ensembl and miRBase, respectively. The potential impact of nonsynonymous amino acid substitutions on protein structure and function was assessed with PolyPhen-2 and SIFT. For selected protein genes the ranking was made to choose those most promising for keratoconus development. Ranking results were based on topological features in the protein-protein interaction network. High specificity for the populations in which the causative sequence variants have been identified was found. In addition, the possibility of links between previously analyzed keratoconus loci was confirmed including miRNA-gene interactions. Identified number of genes associated with oxidative stress and inflammatory agents corroborated the hypothesis of their effect on the disease etiology. Distribution of the numerous sequences variants within both exons and mature miRNA which forces you to search for a broader look at the determinants of keratoconus. Our findings highlight the complexity of the keratoconus genetics.

  6. Nonrandom Distribution of miRNAs Genes and Single Nucleotide Variants in Keratoconus Loci.

    Science.gov (United States)

    Nowak, Dorota M; Gajecka, Marzena

    2015-01-01

    Despite numerous studies, the causes of both development and progression of keratoconus remain elusive. Previous studies of this disorder focused mainly on one or two genetic factors only. However, in the analysis of such complex diseases all potential factors should be taken into consideration. The purpose of this study was a comprehensive analysis of known keratoconus loci to uncover genetic factors involved in this disease causation in the general population, which could be omitted in the original studies. In this investigation genomic data available in various databases and experimental own data were assessed. The lists of single nucleotide variants and miRNA genes localized in reported keratoconus loci were obtained from Ensembl and miRBase, respectively. The potential impact of nonsynonymous amino acid substitutions on protein structure and function was assessed with PolyPhen-2 and SIFT. For selected protein genes the ranking was made to choose those most promising for keratoconus development. Ranking results were based on topological features in the protein-protein interaction network. High specificity for the populations in which the causative sequence variants have been identified was found. In addition, the possibility of links between previously analyzed keratoconus loci was confirmed including miRNA-gene interactions. Identified number of genes associated with oxidative stress and inflammatory agents corroborated the hypothesis of their effect on the disease etiology. Distribution of the numerous sequences variants within both exons and mature miRNA which forces you to search for a broader look at the determinants of keratoconus. Our findings highlight the complexity of the keratoconus genetics.

  7. Vector integration is nonrandom and clustered and influences the fate of lymphopoiesis in SCID-X1 gene therapy.

    Science.gov (United States)

    Deichmann, Annette; Hacein-Bey-Abina, Salima; Schmidt, Manfred; Garrigue, Alexandrine; Brugman, Martijn H; Hu, Jingqiong; Glimm, Hanno; Gyapay, Gabor; Prum, Bernard; Fraser, Christopher C; Fischer, Nicolas; Schwarzwaelder, Kerstin; Siegler, Maria-Luise; de Ridder, Dick; Pike-Overzet, Karin; Howe, Steven J; Thrasher, Adrian J; Wagemaker, Gerard; Abel, Ulrich; Staal, Frank J T; Delabesse, Eric; Villeval, Jean-Luc; Aronow, Bruce; Hue, Christophe; Prinz, Claudia; Wissler, Manuela; Klanke, Chuck; Weissenbach, Jean; Alexander, Ian; Fischer, Alain; von Kalle, Christof; Cavazzana-Calvo, Marina

    2007-08-01

    Recent reports have challenged the notion that retroviruses and retroviral vectors integrate randomly into the host genome. These reports pointed to a strong bias toward integration in and near gene coding regions and, for gammaretroviral vectors, around transcription start sites. Here, we report the results obtained from a large-scale mapping of 572 retroviral integration sites (RISs) isolated from cells of 9 patients with X-linked SCID (SCID-X1) treated with a retrovirus-based gene therapy protocol. Our data showed that two-thirds of insertions occurred in or very near to genes, of which more than half were highly expressed in CD34(+) progenitor cells. Strikingly, one-fourth of all integrations were clustered as common integration sites (CISs). The highly significant incidence of CISs in circulating T cells and the nature of their locations indicate that insertion in many gene loci has an influence on cell engraftment, survival, and proliferation. Beyond the observed cases of insertional mutagenesis in 3 patients, these data help to elucidate the relationship between vector insertion and long-term in vivo selection of transduced cells in human patients with SCID-X1.

  8. Genomics of local adaptation with gene flow.

    Science.gov (United States)

    Tigano, Anna; Friesen, Vicki L

    2016-05-01

    Gene flow is a fundamental evolutionary force in adaptation that is especially important to understand as humans are rapidly changing both the natural environment and natural levels of gene flow. Theory proposes a multifaceted role for gene flow in adaptation, but it focuses mainly on the disruptive effect that gene flow has on adaptation when selection is not strong enough to prevent the loss of locally adapted alleles. The role of gene flow in adaptation is now better understood due to the recent development of both genomic models of adaptive evolution and genomic techniques, which both point to the importance of genetic architecture in the origin and maintenance of adaptation with gene flow. In this review, we discuss three main topics on the genomics of adaptation with gene flow. First, we investigate selection on migration and gene flow. Second, we discuss the three potential sources of adaptive variation in relation to the role of gene flow in the origin of adaptation. Third, we explain how local adaptation is maintained despite gene flow: we provide a synthesis of recent genomic models of adaptation, discuss the genomic mechanisms and review empirical studies on the genomics of adaptation with gene flow. Despite predictions on the disruptive effect of gene flow in adaptation, an increasing number of studies show that gene flow can promote adaptation, that local adaptations can be maintained despite high gene flow, and that genetic architecture plays a fundamental role in the origin and maintenance of local adaptation with gene flow.

  9. Targeted gene flow for conservation.

    Science.gov (United States)

    Kelly, Ella; Phillips, Ben L

    2016-04-01

    Anthropogenic threats often impose strong selection on affected populations, causing rapid evolutionary responses. Unfortunately, these adaptive responses are rarely harnessed for conservation. We suggest that conservation managers pay close attention to adaptive processes and geographic variation, with an eye to using them for conservation goals. Translocating pre-adapted individuals into recipient populations is currently considered a potentially important management tool in the face of climate change. Targeted gene flow, which involves moving individuals with favorable traits to areas where these traits would have a conservation benefit, could have a much broader application in conservation. Across a species' range there may be long-standing geographic variation in traits or variation may have rapidly developed in response to a threatening process. Targeted gene flow could be used to promote natural resistance to threats to increase species resilience. We suggest that targeted gene flow is a currently underappreciated strategy in conservation that has applications ranging from the management of invasive species and their impacts to controlling the impact and virulence of pathogens.

  10. Gene flow from glyphosate-resistant crops.

    Science.gov (United States)

    Mallory-Smith, Carol; Zapiola, Maria

    2008-04-01

    Gene flow from transgenic glyphosate-resistant crops can result in the adventitious presence of the transgene, which may negatively impact markets. Gene flow can also produce glyphosate-resistant plants that may interfere with weed management systems. The objective of this article is to review the gene flow literature as it pertains to glyphosate-resistant crops. Gene flow is a natural phenomenon not unique to transgenic crops and can occur via pollen, seed and, in some cases, vegetative propagules. Gene flow via pollen can occur in all crops, even those that are considered to be self-pollinated, because all have low levels of outcrossing. Gene flow via seed or vegetative propagules occurs when they are moved naturally or by humans during crop production and commercialization. There are many factors that influence gene flow; therefore, it is difficult to prevent or predict. Gene flow via pollen and seed from glyphosate-resistant canola and creeping bentgrass fields has been documented. The adventitious presence of the transgene responsible for glyphosate resistance has been found in commercial seed lots of canola, corn and soybeans. In general, the glyphosate-resistant trait is not considered to provide an ecological advantage. However, regulators should consider the examples of gene flow from glyphosate-resistant crops when formulating rules for the release of crops with traits that could negatively impact the environment or human health.

  11. The flow of gene expression.

    Science.gov (United States)

    Misteli, Tom

    2004-03-01

    Gene expression is a highly interconnected multistep process. A recent meeting in Iguazu Falls, Argentina, highlighted the need to uncover both the molecular details of each single step as well as the mechanisms of coordination among processes in order to fully understand the expression of genes.

  12. Complete mtDNA sequences of two millipedes suggest a new model for mitochondrial gene rearrangements: Duplication and non-random loss

    Energy Technology Data Exchange (ETDEWEB)

    Lavrov, Dennis V.; Boore, Jeffrey L.; Brown, Wesley M.

    2001-11-08

    We determined the complete mtDNA sequences of the millipedes Narceus annularus and Thyropygus sp. (Arthropoda: Diplopoda) and identified in both genomes all 37 genes typical for metazoan mtDNA. The arrangement of these genes is identical in the two millipedes, but differs from that inferred to be ancestral for arthropods by the location of four genes/gene clusters. This novel gene arrangement is unusual for animal mtDNA, in that genes with opposite transcriptional polarities are clustered in the genome and the two clusters are separated by two non-coding regions. The only exception to this pattern is the gene for cysteine tRNA, which is located in the part of the genome that otherwise contains all genes with the opposite transcriptional polarity. We suggest that a mechanism involving complete mtDNA duplication followed by the loss of genes, predetermined by their transcriptional polarity and location in the genome, could generate this gene arrangement from the one ancestral for arthropods. The proposed mechanism has important implications for phylogenetic inferences that are drawn on the basis of gene arrangement comparisons.

  13. Non-random association of the Rsa I polymorphic site 5' to the beta-globin gene with major sickle cell haplotypes.

    Science.gov (United States)

    Sharon, B; Poncz, M; Surrey, S; Schwartz, E

    1988-01-01

    There are three main African haplotypes associated with the sickle mutation on chromosome 11. We have examined an Rsa I polymorphism 550 bp 5' to the beta-globin gene to study the degree of linkage disequilibrium between this Rsa I site and the three haplotypes. This Rsa I site is contained within the 10.3 kb or less area of randomization separating the 5'- and 3'-haplotype clusters. The beta S-containing chromosomes of the Benin and Senegal haplotypes are not cut, while those of the Central African Republic are cleaved by Rsa I at this site. Possible explanations of these findings are discussed.

  14. The Nonrandom Brain: Efficiency, Economy, and Complex Dynamics

    Directory of Open Access Journals (Sweden)

    Olaf eSporns

    2011-02-01

    Full Text Available Modern anatomical tracing and imaging techniques are beginning to reveal the structural anatomy of neural circuits at small and large scales in unprecedented detail. When examined with analytic tools from graph theory and network science, neural connectivity exhibits highly nonrandom features, including high clustering and short path length, as well as modules and highly central hub nodes. These characteristic topological features of neural connections shape nonrandom dynamic interactions that occur during spontaneous activity or in response to external stimulation. Disturbances of connectivity and thus of neural dynamics are thought to underlie a number of disease states of the brain, and some evidence suggests that degraded functional performance of brain networks may be the outcome of a process of randomization affecting their nodes and edges. This article provides a survey of the nonrandom structure of neural connectivity, primarily at the large-scale of regions and pathways in the mammalian cerebral cortex. In addition, we will discuss how nonrandom connections can give rise to differentiated and complex patterns of dynamics and information flow. Finally, we will explore the idea that at least some disorders of the nervous system are associated with increased randomness of neural connections.

  15. On the relation between gene flow theory and genetic gain

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    Woolliams John A

    2000-01-01

    Full Text Available Abstract In conventional gene flow theory the rate of genetic gain is calculated as the summed products of genetic selection differential and asymptotic proportion of genes deriving from sex-age groups. Recent studies have shown that asymptotic proportions of genes predicted from conventional gene flow theory may deviate considerably from true proportions. However, the rate of genetic gain predicted from conventional gene flow theory was accurate. The current note shows that the connection between asymptotic proportions of genes and rate of genetic gain that is embodied in conventional gene flow theory is invalid, even though genetic gain may be predicted correctly from it.

  16. Nonrandom involvement of chromosomal segments in human hematologic malignancies

    Energy Technology Data Exchange (ETDEWEB)

    Rowley, J. D.

    1977-01-01

    The consistent occurrence of nonrandom chromosome changes in human malignancies suggests that they are not trivial epiphenomena. Whereas we do not understand their significance at present, one possible role which they may fulfill is to provide the chromosomally aberrant cells with a proliferative advantage as the result of alteration of the number and/or location of genes related to nucleic acid biosynthesis. It would be expected that the proliferative advantage provided by various chromosome aberrations differs in patients with different genetic constitutions.

  17. Direct and indirect estimates of gene flow among wild and managed populations of Polaskia chichipe, an endemic columnar cactus in Central Mexico.

    Science.gov (United States)

    Otero-Arnaiz, Adriana; Casas, Alejandro; Hamrick, James L

    2005-12-01

    Microsatellite markers were used to obtain direct and indirect estimates of gene flow in populations of Polaskia chichipe under different management regimes, in order to understand the genetic consequences of gene flow in the evolutionary process of domestication. P. chichipe is a columnar cactus endemic to the Tehuacan Valley, Central Mexico, and has come under domestication for its edible fruit. Morphological, phenological, physiological, and reproductive differences, apparently attributable to artificial selection, exist between wild and managed populations, which grow sympatrically. However, strong gene flow may counteract the effects of this selection. In this study, we used paternity analysis to demonstrate that although most of the pollinations occur among individuals within the same population at distances < 40 m, pollen flow from other populations is considerable (27 +/- 5%). Heterogeneity in pollen clouds sampled by mother plants (FST = 0.12) indicated nonrandom mating, which is probably due to temporal heterogeneity in pollen movement. Spatial structure on local and regional scales is consistent with an isolation-by-distance model. The similarity of indirect, direct and demographic estimates of neighbourhood size (74-250 individuals) suggests that this genetic structure is representative of an equilibrium state. These results suggest that traditional management practices have conserved the genetic resources of this species in situ, but also that gene flow is counteracting the effect of domestication to some degree. We discuss our results in the general context of genetic exchange between cultivated and wild populations during the domestication process.

  18. Speciation and gene flow between snails of opposite chirality.

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    Angus Davison

    2005-09-01

    Full Text Available Left-right asymmetry in snails is intriguing because individuals of opposite chirality are either unable to mate or can only mate with difficulty, so could be reproductively isolated from each other. We have therefore investigated chiral evolution in the Japanese land snail genus Euhadra to understand whether changes in chirality have promoted speciation. In particular, we aimed to understand the effect of the maternal inheritance of chirality on reproductive isolation and gene flow. We found that the mitochondrial DNA phylogeny of Euhadra is consistent with a single, relatively ancient evolution of sinistral species and suggests either recent "single-gene speciation" or gene flow between chiral morphs that are unable to mate. To clarify the conditions under which new chiral morphs might evolve and whether single-gene speciation can occur, we developed a mathematical model that is relevant to any maternal-effect gene. The model shows that reproductive character displacement can promote the evolution of new chiral morphs, tending to counteract the positive frequency-dependent selection that would otherwise drive the more common chiral morph to fixation. This therefore suggests a general mechanism as to how chiral variation arises in snails. In populations that contain both chiral morphs, two different situations are then possible. In the first, gene flow is substantial between morphs even without interchiral mating, because of the maternal inheritance of chirality. In the second, reproductive isolation is possible but unstable, and will also lead to gene flow if intrachiral matings occasionally produce offspring with the opposite chirality. Together, the results imply that speciation by chiral reversal is only meaningful in the context of a complex biogeographical process, and so must usually involve other factors. In order to understand the roles of reproductive character displacement and gene flow in the chiral evolution of Euhadra, it will be

  19. Polyphyly and gene flow between non-sibling Heliconius species

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    Jiggins Chris D

    2006-04-01

    Full Text Available Abstract Background The view that gene flow between related animal species is rare and evolutionarily unimportant largely antedates sensitive molecular techniques. Here we use DNA sequencing to investigate a pair of morphologically and ecologically divergent, non-sibling butterfly species, Heliconius cydno and H. melpomene (Lepidoptera: Nymphalidae, whose distributions overlap in Central and Northwestern South America. Results In these taxa, we sequenced 30–45 haplotypes per locus of a mitochondrial region containing the genes for cytochrome oxidase subunits I and II (CoI/CoII, and intron-spanning fragments of three unlinked nuclear loci: triose-phosphate isomerase (Tpi, mannose-6-phosphate isomerase (Mpi and cubitus interruptus (Ci genes. A fifth gene, dopa decarboxylase (Ddc produced sequence data likely to be from different duplicate loci in some of the taxa, and so was excluded. Mitochondrial and Tpi genealogies are consistent with reciprocal monophyly, whereas sympatric populations of the species in Panama share identical or similar Mpi and Ci haplotypes, giving rise to genealogical polyphyly at the species level despite evidence for rapid sequence divergence at these genes between geographic races of H. melpomene. Conclusion Recent transfer of Mpi haplotypes between species is strongly supported, but there is no evidence for introgression at the other three loci. Our results demonstrate that the boundaries between animal species can remain selectively porous to gene flow long after speciation, and that introgression, even between non-sibling species, can be an important factor in animal evolution. Interspecific gene flow is demonstrated here for the first time in Heliconius and may provide a route for the transfer of switch-gene adaptations for Müllerian mimicry. The results also forcefully demonstrate how reliance on a single locus may give an erroneous picture of the overall genealogical history of speciation and gene flow.

  20. Urban land use limits regional bumble bee gene flow.

    Science.gov (United States)

    Jha, Shalene; Kremen, C

    2013-05-01

    Potential declines in native pollinator communities and increased reliance on pollinator-dependent crops have raised concerns about native pollinator conservation and dispersal across human-altered landscapes. Bumble bees are one of the most effective native pollinators and are often the first to be extirpated in human-altered habitats, yet little is known about how bumble bees move across fine spatial scales and what landscapes promote or limit their gene flow. In this study, we examine regional genetic differentiation and fine-scale relatedness patterns of the yellow-faced bumble bee, Bombus vosnesenskii, to investigate how current and historic habitat composition impact gene flow. We conducted our study across a landscape mosaic of natural, agricultural and urban/suburban habitats, and we show that B. vosnesenskii exhibits low but significant levels of differentiation across the study system (F(ST) = 0.019, D(est) = 0.049). Most importantly, we reveal significant relationships between pairwise F(ST) and resistance models created from contemporary land use maps. Specifically, B. vosnesenskii gene flow is most limited by commercial, industrial and transportation-related impervious cover. Finally, our fine-scale analysis reveals significant but declining relatedness between individuals at the 1-9 km spatial scale, most likely due to local queen dispersal. Overall, our results indicate that B. vosnesenskii exhibits considerable local dispersal and that regional gene flow is significantly limited by impervious cover associated with urbanization.

  1. LONG DISTANCE POLLEN-MEDIATED GENE FLOW FROM CREEPING BENTGRASS

    Science.gov (United States)

    Researchers from USEPA WED have measured gene flow from experimental fields of Roundup? herbicide resistant genetically modified (GM) creeping bentgrass a grass used primarily on golf courses, to compatible non-crop relatives. Using a sampling design based on the estimated time ...

  2. Interspecific and interploidal gene flow in Central European Arabidopsis (Brassicaceae

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    Jørgensen Marte H

    2011-11-01

    Full Text Available Abstract Background Effects of polyploidisation on gene flow between natural populations are little known. Central European diploid and tetraploid populations of Arabidopsis arenosa and A. lyrata are here used to study interspecific and interploidal gene flow, using a combination of nuclear and plastid markers. Results Ploidal levels were confirmed by flow cytometry. Network analyses clearly separated diploids according to species. Tetraploids and diploids were highly intermingled within species, and some tetraploids intermingled with the other species, as well. Isolation with migration analyses suggested interspecific introgression from tetraploid A. arenosa to tetraploid A. lyrata and vice versa, and some interploidal gene flow, which was unidirectional from diploid to tetraploid in A. arenosa and bidirectional in A. lyrata. Conclusions Interspecific genetic isolation at diploid level combined with introgression at tetraploid level indicates that polyploidy may buffer against negative consequences of interspecific hybridisation. The role of introgression in polyploid systems may, however, differ between plant species, and even within the small genus Arabidopsis, we find very different evolutionary fates when it comes to introgression.

  3. Interspecific gene flow and maintenance of species integrity in oaks

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    Oliver Gailing

    2014-07-01

    Full Text Available Oak species show a wide variation in morphological and physiological characters, and species boundaries between closely related species are often not clear-cut. Still, despite frequent interspecific gene flow, oaks maintain distinct morphological and physiological adaptations. In sympatric stands, spatial distribution of species with different ecological requirements is not random but constrained by soil and other microenvironmental factors. Pre-zygotic isolation (e.g. cross incompatibilities, asynchrony in flowering, pollen competition and post-zygotic isolation (divergent selection contribute to the maintenance of species integrity in sympatric oak stands. The antagonistic effects of interspecific gene flow and divergent selection are reflected in the low genetic differentiation between hybridizing oak species at most genomic regions interspersed by regions with signatures of divergent selection (outlier regions. In the near future, the availability of high-density genetic linkage maps anchored to scaffolds of a sequenced Q. robur genome will allow to characterize the underlying genes in these outlier regions and their putative role in reproductive isolation between species. Reciprocal transplant experiments of seedlings between parental environments can be used to characterize selection on outlier genes. High transferability of gene-based markers will enable comparative outlier screens in different oak species.

  4. Interspecific gene flow and maintenance of species integrity in oaks

    Directory of Open Access Journals (Sweden)

    Oliver Gailing

    2014-07-01

    Full Text Available Oak species show a wide variation in morphological and physiological characters, and species boundaries between closely related species are often not clear-cut. Still, despite frequent interspecific gene flow, oaks maintain distinct morphological and physiological adaptations. In sympatric stands, spatial distribution of species with different ecological requirements is not random but constrained by soil and other microenvironmental factors. Pre-zygotic isolation (e.g. cross incompatibilities, asynchrony in flowering, pollen competition and post-zygotic isolation (divergent selection contribute to the maintenance of species integrity in sympatric oak stands. The antagonistic effects of interspecific gene flow and divergent selection are reflected in the low genetic differentiation between hybridizing oak species at most genomic regions interspersed by regions with signatures of divergent selection (outlier regions. In the near future, the availability of high-density genetic linkage maps anchored to scaffolds of a sequenced Q. robur genome will allow to characterize the underlying genes in these outlier regions and their putative role in reproductive isolation between species. Reciprocal transplant experiments of seedlings between parental environments can be used to characterize selection on outlier genes. High transferability of gene-based markers will enable comparative outlier screens in different oak species.

  5. Population structure and gene flow of Anopheles farauti s.s. (Diptera: Culicidae) among ten sites on five islands of Vanuatu: implications for malaria control.

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    Reiff, D M; Kaneko, A; Taleo, G; Amos, M; Lum, J K

    2007-07-01

    The Anopheles punctulatus (Diptera: Culicidae) group is the main vector for malaria and Bancroftian filariasis in Vanuatu. Anopheles larvae were collected from 10 localities on five islands of Vanuatu during the 2004 dry season for species identification as well as for estimating population structure and gene flow within and among islands. Species identification was determined using polymerase chain reaction-restriction fragment length polymorphism analysis of the internal transcribed spacer 2 region. Population structure and gene flow were examined by sequencing a portion of the ND4/ND5 region of the mitochondrial genome. Only one species of the An. punctulatus group, An. farauti s.s., was identified, consistent with previous studies in Vanuatu. A nonrandom distribution of An. farauti s.s. lineages was observed with one cosmopolitan lineage shared by eight sites on all five islands and a preponderance of island-specific lineages (36/40), indicating the introduction of a single main lineage into Vanuatu followed by dispersal, diversification, and limited lineage exchange between islands. Network analysis suggests a possible second introduction of An. farauti s.s. into the northern islands of Gaua and Malekula. Gene flow was high on three of the five islands, whereas Tanna and Santo have significant population structure. Among islands, gene flow was limited, indicating active mosquito dispersal only over short distances and a paucity of passive human-mediated dispersal over long distances. Minimal risk of active dispersal among these islands indicates that vector control can be effectively initiated at the island level within the archipelago of Vanuatu.

  6. Contemporary gene flow and mating system of Arabis alpina in a Central European alpine landscape

    OpenAIRE

    Buehler, D.; Graf, R; Holderegger, R; Gugerli, F.

    2017-01-01

    Background and Aims Gene flow is important in counteracting the divergence of populations but also in spreading genes among populations. However, contemporary gene flow is not well understood across alpine landscapes. The aim of this study was to estimate contemporary gene flow through pollen and to examine the realized mating system in the alpine perennial plant, Arabis alpina (Brassicaceae). Methods An entire sub-alpine to alpine landscape of 2 km2 was exhaustively sampled in the Swiss Alps...

  7. Sexual selection and magic traits in speciation with gene flow

    Institute of Scientific and Technical Information of China (English)

    Maria R.SERVEDIO; Michael KOPP

    2012-01-01

    The extent to which sexual selection is involved in speciation with gene flow remains an open question and the subject of much research.Here,we propose that some insight can be gained from considering the concept of magic traits (i.e.,traits involved in both reproductive isolation and ecological divergence).Both magic traits and other,“non-magic”,traits can contribute to speciation via a number of specific mechanisms.We argue that many of these mechanisms are likely to differ widely in the extent to which they involve sexual selection.Furthermore,in some cases where sexual selection is present,it may be prone to inhibit rather than drive speciation.Finally,there are a priori reasons to believe that certain categories of traits are much more effective than others in driving speciation.The combination of these points suggests a classification of traits that may shed light on the broader role of sexual selection in speciation with gene flow.In particular,we suggest that sexual selection can act as a driver of speciation in some scenarios,but may play a negligible role in potentially common categories of magic traits,and may be likely to inhibit speeiation in common categories of non-magic traits.

  8. Time to get moving: assisted gene flow of forest trees.

    Science.gov (United States)

    Aitken, Sally N; Bemmels, Jordan B

    2016-01-01

    Geographic variation in trees has been investigated since the mid-18th century. Similar patterns of clinal variation have been observed along latitudinal and elevational gradients in common garden experiments for many temperate and boreal species. These studies convinced forest managers that a 'local is best' seed source policy was usually safest for reforestation. In recent decades, experimental design, phenotyping methods, climatic data and statistical analyses have improved greatly and refined but not radically changed knowledge of clines. The maintenance of local adaptation despite high gene flow suggests selection for local adaptation to climate is strong. Concerns over maladaptation resulting from climate change have motivated many new genecological and population genomics studies; however, few jurisdictions have implemented assisted gene flow (AGF), the translocation of pre-adapted individuals to facilitate adaptation of planted forests to climate change. Here, we provide evidence that temperate tree species show clines along climatic gradients sufficiently similar for average patterns or climate models to guide AGF in the absence of species-specific knowledge. Composite provenancing of multiple seed sources can be used to increase diversity and buffer against future climate uncertainty. New knowledge will continue to refine and improve AGF as climates warm further.

  9. The Himalayas as a directional barrier to gene flow.

    Science.gov (United States)

    Gayden, Tenzin; Cadenas, Alicia M; Regueiro, Maria; Singh, Nanda B; Zhivotovsky, Lev A; Underhill, Peter A; Cavalli-Sforza, Luigi L; Herrera, Rene J

    2007-05-01

    High-resolution Y-chromosome haplogroup analyses coupled with Y-short tandem repeat (STR) haplotypes were used to (1) investigate the genetic affinities of three populations from Nepal--including Newar, Tamang, and people from cosmopolitan Kathmandu (referred to as "Kathmandu" subsequently)--as well as a collection from Tibet and (2) evaluate whether the Himalayan mountain range represents a geographic barrier for gene flow between the Tibetan plateau and the South Asian subcontinent. The results suggest that the Tibetans and Nepalese are in part descendants of Tibeto-Burman-speaking groups originating from Northeast Asia. All four populations are represented predominantly by haplogroup O3a5-M134-derived chromosomes, whose Y-STR-based age (+/-SE) was estimated at 8.1+/-2.9 thousand years ago (KYA), more recent than its Southeast Asian counterpart. The most pronounced difference between the two regions is reflected in the opposing high-frequency distributions of haplogroups D in Tibet and R in Nepal. With the exception of Tamang, both Newar and Kathmandu exhibit considerable similarities to the Indian Y-haplogroup distribution, particularly in their haplogroup R and H composition. These results indicate gene flow from the Indian subcontinent and, in the case of haplogroup R, from Eurasia as well, a conclusion that is also supported by the admixture analysis. In contrast, whereas haplogroup D is completely absent in Nepal, it accounts for 50.6% of the Tibetan Y-chromosome gene pool. Coalescent analyses suggest that the expansion of haplogroup D derivatives--namely, D1-M15 and D3-P47 in Tibet--involved two different demographic events (5.1+/-1.8 and 11.3+/-3.7 KYA, respectively) that are more recent than those of D2-M55 representatives common in Japan. Low frequencies, relative to Nepal, of haplogroup J and R lineages in Tibet are also consistent with restricted gene flow from the subcontinent. Yet the presence of haplogroup O3a5-M134 representatives in Nepal

  10. Inteins as Indicators of Gene Flow in the Halobacteria

    Directory of Open Access Journals (Sweden)

    Shannon Margaret Soucy

    2014-06-01

    Full Text Available This research uses inteins, a type of mobile genetic element, to infer patterns of gene transfer within the Halobacteria. We surveyed one hundred and eighteen genomes representing twenty-six genera of Halobacteria for intein sequences. We then used the presence-absence profile, sequence similarity and phylogenies from the inteins recovered to explore how intein distribution can provide insight on the dynamics of gene flow between closely related and divergent organisms. We identified twenty-four proteins in the Halobacteria that have been invaded by inteins at some point in their evolutionary history, including two proteins not previously reported to contain an intein. Furthermore, the size of an intein is used as a heuristic for the phase of the intein’s life cycle. Larger size inteins are assumed to be the canonical two domain inteins, consisting of self-splicing and homing endonuclease domains (HEN; smaller sizes are assumed to have lost the HEN domain. For many halobacterial groups the consensus phylogenetic signal derived from intein sequences is compatible with vertical inheritance or with a strong gene transfer bias creating these clusters. Regardless, the coexistence of intein-free and intein-containing alleles reveal ongoing transfer and loss of inteins within these groups. Inteins were frequently shared with other Euryarchaeota and among the Bacteria, with members of the Cyanobacteria (Cyanothece, Anabaena, Bacteriodetes (Salinibacter, Betaproteobacteria (Delftia, Acidovorax, Firmicutes (Halanaerobium, Actinobacteria (Longispora, and Deinococcus-Thermus-group.

  11. Non-random mate choice in humans: insights from a genome scan.

    Science.gov (United States)

    Laurent, R; Toupance, B; Chaix, R

    2012-02-01

    Little is known about the genetic factors influencing mate choice in humans. Still, there is evidence for non-random mate choice with respect to physical traits. In addition, some studies suggest that the Major Histocompatibility Complex may affect pair formation. Nowadays, the availability of high density genomic data sets gives the opportunity to scan the genome for signatures of non-random mate choice without prior assumptions on which genes may be involved, while taking into account socio-demographic factors. Here, we performed a genome scan to detect extreme patterns of similarity or dissimilarity among spouses throughout the genome in three populations of African, European American, and Mexican origins from the HapMap 3 database. Our analyses identified genes and biological functions that may affect pair formation in humans, including genes involved in skin appearance, morphogenesis, immunity and behaviour. We found little overlap between the three populations, suggesting that the biological functions potentially influencing mate choice are population specific, in other words are culturally driven. Moreover, whenever the same functional category of genes showed a significant signal in two populations, different genes were actually involved, which suggests the possibility of evolutionary convergences.

  12. Extensive gene flow over Europe and possible speciation

    Energy Technology Data Exchange (ETDEWEB)

    VINCENOT, Dr. LUCIE [Centre d’Ecologie Fonctionnelle et Evolutive Montpellier, France; NARA, Dr. KAZUHIDE [Department of Natural Environmental Studies, The University of Tokyo, Japan; STHULTZ, CHRISTOPHER [Centre d’Ecologie Fonctionnelle et Evolutive Montpellier, France; Labbe, Jessy L [ORNL; DUBOIS, MARIE-PIERRE [Centre d’Ecologie Fonctionnelle et Evolutive Montpellier, France; TEDERSOO, LEHO [University of Tartu, Estonia; Martin, Francis [INRA, Nancy, France; SELOSSE, Dr. MARC-ANDRE [Centre d’Ecologie Fonctionnelle et Evolutive Montpellier, France

    2012-01-01

    Biogeographical patterns and large-scale genetic structure have been little studied in ectomycorrhizal (EM) fungi, despite the ecological and economic importance of EM symbioses. We coupled population genetics and phylogenetic approaches to understand spatial structure in fungal populations on a continental scale. Using nine microsatellite markers, we characterized gene flow among 16 populations of the widespread EM basidiomycete Laccaria amethystina over Europe (i.e. over 2900 km). We also widened our scope to two additional populations from Japan (104 km away) and compared them with European populations through microsatellite markers and multilocus phylogenies, using three nuclear genes (NAR, G6PD and ribosomal DNA) and two mitochondrial ribosomal genes. European L. amethystina populations displayed limited differentiation (average FST = 0.041) and very weak isolation by distance (IBD). This panmictic European pattern may result from effective aerial dispersal of spores, high genetic diversity in populations and mutualistic interactions with multiple hosts that all facilitate migration. The multilocus phylogeny based on nuclear genes confirmed that Japanese and European specimens were closely related but clustered on a geographical basis. By using microsatellite markers, we found that Japanese populations were strongly differentiated from the European populations (FST = 0.416), more than expected by extrapolating the European pattern of IBD. Population structure analyses clearly separated the populations into two clusters, i.e. European and Japanese clusters. We discuss the possibility of IBD in a continuous population (considering some evidence for a ring species over the Northern Hemisphere) vs. an allopatric speciation over Eurasia, making L. amethystina a promising model of intercontinental species for future studies.

  13. The Himalayas: barrier and conduit for gene flow.

    Science.gov (United States)

    Gayden, Tenzin; Perez, Annabel; Persad, Patrice J; Bukhari, Areej; Chennakrishnaiah, Shilpa; Simms, Tanya; Maloney, Trisha; Rodriguez, Kristina; Herrera, Rene J

    2013-06-01

    The Himalayan mountain range is strategically located at the crossroads of the major cultural centers in Asia, the Middle East and Europe. Although previous Y-chromosome studies indicate that the Himalayas served as a natural barrier for gene flow from the south to the Tibetan plateau, this region is believed to have played an important role as a corridor for human migrations between East and West Eurasia along the ancient Silk Road. To evaluate the effects of the Himalayan mountain range in shaping the maternal lineages of populations residing on either side of the cordillera, we analyzed mitochondrial DNA variation in 344 samples from three Nepalese collections (Newar, Kathmandu and Tamang) and a general population of Tibet. Our results revealed a predominantly East Asian-specific component in Tibet and Tamang, whereas Newar and Kathmandu are both characterized by a combination of East and South Central Asian lineages. Interestingly, Newar and Kathmandu harbor several deep-rooted Indian lineages, including M2, R5, and U2, whose coalescent times from this study (U2, >40 kya) and previous reports (M2 and R5, >50 kya) suggest that Nepal was inhabited during the initial peopling of South Central Asia. Comparisons with our previous Y-chromosome data indicate sex-biased migrations in Tamang and a founder effect and/or genetic drift in Tamang and Newar. Altogether, our results confirm that while the Himalayas acted as a geographic barrier for human movement from the Indian subcontinent to the Tibetan highland, it also served as a conduit for gene flow between Central and East Asia.

  14. Sex-biased gene flow among elk in the greater Yellowstone ecosystem

    Science.gov (United States)

    , Brian K. Hand; , Shanyuan Chen; , N. Anderson; , A. Beja-Pereira; Cross, Paul C.; , M. Ebinger; , H. Edwards; , R.A. Garrott; , M.D. Kardos; Kauffman, Matthew J.; , E.L. Landguth; , A. Middleton; , B. Scurlock; , P.J. White; , P. Zager; , M.K. Schwartz; , G. Luikart

    2014-01-01

    We quantified patterns of population genetic structure to help understand gene flow among elk populations across the Greater Yellowstone Ecosystem. We sequenced 596 base pairs of the mitochondrial control region of 380 elk from eight populations. Analysis revealed high mitochondrial DNA variation within populations, averaging 13.0 haplotypes with high mean gene diversity (0.85). The genetic differentiation among populations for mitochondrial DNA was relatively high (FST = 0.161; P = 0.001) compared to genetic differentiation for nuclear microsatellite data (FST = 0.002; P = 0.332), which suggested relatively low female gene flow among populations. The estimated ratio of male to female gene flow (mm/mf = 46) was among the highest we have seen reported for large mammals. Genetic distance (for mitochondrial DNA pairwise FST) was not significantly correlated with geographic (Euclidean) distance between populations (Mantel’s r = 0.274, P = 0.168). Large mitochondrial DNA genetic distances (e.g., FST > 0.2) between some of the geographically closest populations (<65 km) suggested behavioral factors and/or landscape features might shape female gene flow patterns. Given the strong sex-biased gene flow, future research and conservation efforts should consider the sexes separately when modeling corridors of gene flow or predicting spread of maternally transmitted diseases. The growing availability of genetic data to compare male vs. female gene flow provides many exciting opportunities to explore the magnitude, causes, and implications of sex-biased gene flow likely to occur in many species

  15. Nonrandom Assignment in ANCOVA: The Alternate Ranks Design

    Science.gov (United States)

    Dalton, Starrett; Overall, John E.

    1977-01-01

    A specific form of nonrandom assignment to treatment groups, the "alternate ranks" design, was investigated. This design eliminates the possibility of a correlation between the covariate and the treatment, and rules out experimenter bias in assignment of subjects to groups. (Editor)

  16. Phenological mismatch and the effectiveness of assisted gene flow.

    Science.gov (United States)

    Wadgymar, Susana M; Weis, Arthur E

    2017-06-01

    The persistence of narrowly adapted species under climate change will depend on their ability to migrate apace with their historical climatic envelope or to adapt in place to maintain fitness. This second path to persistence can only occur if there is sufficient genetic variance for response to new selection regimes. Inadequate levels of genetic variation can be remedied through assisted gene flow (AGF), that is the intentional introduction of individuals genetically adapted to localities with historic climates similar to the current or future climate experienced by the resident population. However, the timing of reproduction is frequently adapted to local conditions. Phenological mismatch between residents and migrants can reduce resident × migrant mating frequencies, slowing the introgression of migrant alleles into the resident genetic background and impeding evolutionary rescue efforts. Focusing on plants, we devised a method to estimate the frequency of resident × migrant matings based on flowering schedules and applied it in an experiment that mimicked the first generation of an AGF program with Chamaecrista fasciculata, a prairie annual, under current and expected future temperature regimes. Phenological mismatch reduced the potential for resident × migrant matings by 40-90%, regardless of thermal treatment. The most successful migrant sires were the most resident like in their flowering time, further biasing the genetic admixture between resident and migrant populations. Other loci contributing to local adaptation-heat-tolerance genes, for instance-may be in linkage disequilibrium with phenology when residents and migrants are combined into a single mating pool. Thus, introgression of potentially adaptive migrant alleles into the resident genetic background is slowed when selection acts against migrant phenology. Successful AGF programs may require sustained high immigration rates or preliminary breeding programs when phenologically matched migrant

  17. High rates of gene flow by pollen and seed in oak populations across Europe

    NARCIS (Netherlands)

    Gerber, S.; Chadoeuf, J.; Gugerli, F.; Lascoux, M.; Buiteveld, J.; Cottrell, J.; Dounavi, A.; Fineschi, S.; Forrest, L.; Fogelqvist, J.; Goicoechea, P.G.; Jensen, J.S.; Salvini, D.; Vendramin, G.G.; Kremer, A.

    2014-01-01

    Gene flow is a key factor in the evolution of species, influencing effective population size, hybridisation and local adaptation. We analysed local gene flow in eight stands of white oak (mostly Quercus petraea and Q. robur, but also Q. pubescens and Q. faginea) distributed across Europe. Adult tree

  18. Spontaneous gene flow and population structure in wild and cultivated chicory, Cichorium intybus L

    DEFF Research Database (Denmark)

    Kiær, Lars Pødenphant; Felber, F.; Flavell, A.

    2009-01-01

    and Mediterranean Europe. The analysis used 281 AFLP markers and 75 SSAP markers giving a total of 356 polymorphic markers. Results from model based assignments with the program STRUCTURE indicated many incidents of recent gene flow. Gene flow was observed both between cultivars and wild populations, between...

  19. Euglossine bees mediate only limited long-distance gene flow in a tropical vine.

    Science.gov (United States)

    Opedal, Øystein H; Falahati-Anbaran, Mohsen; Albertsen, Elena; Armbruster, W Scott; Pérez-Barrales, Rocío; Stenøien, Hans K; Pélabon, Christophe

    2017-03-01

    Euglossine bees (Apidae: Euglossini) have long been hypothesized to act as long-distance pollinators of many low-density tropical plants. We tested this hypothesis by the analysis of gene flow and genetic structure within and among populations of the euglossine bee-pollinated vine Dalechampia scandens. Using microsatellite markers, we assessed historical gene flow by the quantification of regional-scale genetic structure and isolation by distance among 18 populations, and contemporary gene flow by the estimation of recent migration rates among populations. To assess bee-mediated pollen dispersal on a smaller scale, we conducted paternity analyses within a focal population, and quantified within-population spatial genetic structure in four populations. Gene flow was limited to certain nearby populations within continuous forest blocks, whereas drift appeared to dominate on larger scales. Limited long-distance gene flow was supported by within-population patterns; gene flow was biased towards nearby plants, and significant small-scale spatial genetic structure was detected within populations. These findings suggest that, although female euglossine bees might be effective at moving pollen within populations, and perhaps within forest blocks, their contribution to gene flow on the regional scale seems too limited to counteract genetic drift in patchily distributed tropical plants. Among-population gene flow might have been reduced following habitat fragmentation.

  20. Directional gene flow and ecological separation in Yersinia enterocolitica

    Science.gov (United States)

    Reuter, Sandra; Corander, Jukka; de Been, Mark; Harris, Simon; Cheng, Lu; Hall, Miquette; Thomson, Nicholas R.

    2015-01-01

    Yersinia enterocolitica is a common cause of food-borne gastroenteritis worldwide. Recent work defining the phylogeny of the genus Yersinia subdivided Y. enterocolitica into six distinct phylogroups. Here, we provide detailed analyses of the evolutionary processes leading to the emergence of these phylogroups. The dominant phylogroups isolated from human infections, PG3–5, show very little diversity at the sequence level, but do present marked patterns of gain and loss of functions, including those involved in pathogenicity and metabolism, including the acquisition of phylogroup-specific O-antigen loci. We tracked gene flow across the species in the core and accessory genome, and show that the non-pathogenic PG1 strains act as a reservoir for diversity, frequently acting as donors in recombination events. Analysis of the core and accessory genome also suggested that the different Y. enterocolitica phylogroups may be ecologically separated, in contrast to the long-held belief of common shared ecological niches across the Y. enterocolitica species.

  1. Spontaneous gene flow and population structure in wild and cultivated chicory, Cichorium intybus L

    DEFF Research Database (Denmark)

    Kiær, Lars Pødenphant; Felber, F.; Flavell, A.;

    2009-01-01

    Spontaneous gene flow between wild and cultivated chicory, Cichorium intybus L., may have implications for the genetic structure and evolution of populations and varieties. One aspect of this crop-wild gene flow is the dispersal of transgenes from genetically modified varieties, e.g. gene flow from...... and Mediterranean Europe. The analysis used 281 AFLP markers and 75 SSAP markers giving a total of 356 polymorphic markers. Results from model based assignments with the program STRUCTURE indicated many incidents of recent gene flow. Gene flow was observed both between cultivars and wild populations, between...... landraces and wild populations, between different wild populations as well as between cultivars. Population structure visualized by distance-based clustering showed a North–South geographical structuring of the wild populations, and a general grouping of the cultivars corresponding to known origin...

  2. Estimates of External Validity Bias When Impact Evaluations Select Sites Nonrandomly

    Science.gov (United States)

    Bell, Stephen H.; Olsen, Robert B.; Orr, Larry L.; Stuart, Elizabeth A.

    2016-01-01

    Evaluations of educational programs or interventions are typically conducted in nonrandomly selected samples of schools or districts. Recent research has shown that nonrandom site selection can yield biased impact estimates. To estimate the external validity bias from nonrandom site selection, we combine lists of school districts that were…

  3. DNA capture reveals transoceanic gene flow in endangered river sharks.

    Science.gov (United States)

    Li, Chenhong; Corrigan, Shannon; Yang, Lei; Straube, Nicolas; Harris, Mark; Hofreiter, Michael; White, William T; Naylor, Gavin J P

    2015-10-27

    For over a hundred years, the "river sharks" of the genus Glyphis were only known from the type specimens of species that had been collected in the 19th century. They were widely considered extinct until populations of Glyphis-like sharks were rediscovered in remote regions of Borneo and Northern Australia at the end of the 20th century. However, the genetic affinities between the newly discovered Glyphis-like populations and the poorly preserved, original museum-type specimens have never been established. Here, we present the first (to our knowledge) fully resolved, complete phylogeny of Glyphis that includes both archival-type specimens and modern material. We used a sensitive DNA hybridization capture method to obtain complete mitochondrial genomes from all of our samples and show that three of the five described river shark species are probably conspecific and widely distributed in Southeast Asia. Furthermore we show that there has been recent gene flow between locations that are separated by large oceanic expanses. Our data strongly suggest marine dispersal in these species, overturning the widely held notion that river sharks are restricted to freshwater. It seems that species in the genus Glyphis are euryhaline with an ecology similar to the bull shark, in which adult individuals live in the ocean while the young grow up in river habitats with reduced predation pressure. Finally, we discovered a previously unidentified species within the genus Glyphis that is deeply divergent from all other lineages, underscoring the current lack of knowledge about the biodiversity and ecology of these mysterious sharks.

  4. Calculating osmotic pressure according to nonelectrolyte Wilson nonrandom factor model.

    Science.gov (United States)

    Li, Hui; Zhan, Tingting; Zhan, Xiancheng; Wang, Xiaolan; Tan, Xiaoying; Guo, Yiping; Li, Chengrong

    2014-08-01

    Abstract The osmotic pressure of NaCl solutions was determined by the air humidity in equilibrium (AHE) method. The relationship between the osmotic pressure and the concentration was explored theoretically, and the osmotic pressure was calculated according to the nonelectrolyte Wilson nonrandom factor (N-Wilson-NRF) model from the concentration. The results indicate that the calculated osmotic pressure is comparable to the measured one.

  5. Hidden histories of gene flow in highland birds revealed with genomic markers.

    Science.gov (United States)

    Zarza, Eugenia; Faircloth, Brant C; Tsai, Whitney L E; Bryson, Robert W; Klicka, John; McCormack, John E

    2016-10-01

    Genomic studies are revealing that divergence and speciation are marked by gene flow, but it is not clear whether gene flow has played a prominent role during the generation of biodiversity in species-rich regions of the world where vicariance is assumed to be the principal mode by which new species form. We revisit a well-studied organismal system in the Mexican Highlands, Aphelocoma jays, to test for gene flow among Mexican sierras. Prior results from mitochondrial DNA (mtDNA) largely conformed to the standard model of allopatric divergence, although there was also evidence for more obscure histories of gene flow in a small sample of nuclear markers. We tested for these 'hidden histories' using genomic markers known as ultraconserved elements (UCEs) in concert with phylogenies, clustering algorithms and newer introgression tests specifically designed to detect ancient gene flow (e.g. ABBA/BABA tests). Results based on 4303 UCE loci and 2500 informative SNPs are consistent with varying degrees of gene flow among highland areas. In some cases, gene flow has been extensive and recent (although perhaps not ongoing today), whereas in other cases there is only a trace signature of ancient gene flow among species that diverged as long as 5 million years ago. These results show how a species complex thought to be a model for vicariance can reveal a more reticulate history when a broader portion of the genome is queried. As more organisms are studied with genomic data, we predict that speciation-with-bouts-of-gene-flow will turn out to be a common mode of speciation.

  6. Estimating exotic gene flow into native pine stands: zygotic vs. gametic components.

    Science.gov (United States)

    Unger, G M; Vendramin, G G; Robledo-Arnuncio, J J

    2014-11-01

    Monitoring contemporary gene flow from widespread exotic plantations is becoming an important problem in forest conservation genetics. In plants, where both seed and pollen disperse, three components of exotic gene flow with potentially unequal consequences should be, but have not been, explicitly distinguished: zygotic, male gametic and female gametic. Building on a previous model for estimating contemporary rates of zygotic and male gametic gene flow among plant populations, we present here an approach that additionally estimates the third (female gametic) gene flow component, based on a combination of uni- and biparentally inherited markers. Using this method and a combined set of chloroplast and nuclear microsatellites, we estimate gene flow rates from exotic plantations into two Iberian relict stands of maritime pine (Pinus pinaster) and Scots pine (Pinus sylvestris). Results show neither zygotic nor female gametic gene flow but moderate (6-8%) male gametic introgression for both species, implying significant dispersal of pollen, but not of seeds, from exotic plantations into native stands shortly after introduced trees reached reproductive maturity. Numerical simulation results suggest that the model yields reasonably accurate estimates for our empirical data sets, especially for larger samples. We discuss conservation management implications of observed levels of exposure to nonlocal genes and identify research needs to determine potentially associated hazards. Our approach should be useful for plant ecologists and ecosystem managers interested in the vectors of contemporary genetic connectivity among discrete plant populations.

  7. Distribution of coalescent histories under the coalescent model with gene flow.

    Science.gov (United States)

    Tian, Yuan; Kubatko, Laura S

    2016-12-01

    We propose a coalescent model for three species that allows gene flow between both pairs of sister populations. The model is designed for multilocus genomic sequence alignments, with one sequence sampled from each of the three species, and is formulated using a Markov chain representation that allows use of matrix exponentiation to compute analytical expressions for the probability density of coalescent histories. The coalescent history distribution as well as the gene tree topology distribution under this coalescent model with gene flow are then calculated via numerical integration. We analyze the model to compare the distributions of gene tree topologies and coalescent histories for species trees with differing effective population sizes and gene flow rates. Our results suggest conditions under which the species tree and associated parameters are not identifiable from the gene tree topology distribution when gene flow is present, but indicate that the coalescent history distribution may identify the species tree and associated parameters. Thus, the coalescent history distribution can be used to infer parameters such as the ancestral effective population sizes and the rates of gene flow in a maximum likelihood (ML) framework. We conduct computer simulations to evaluate the performance of our method in estimating these parameters, and we apply our method to an Afrotropical mosquito data set (Fontaine et al., 2015). Copyright © 2016 Elsevier Inc. All rights reserved.

  8. Gene Flow and the Measurement of Dispersal in Plant Populations.

    Science.gov (United States)

    Nicholls, Marc S.

    1986-01-01

    Reviews methods of estimating pollen and seed dispersals and discusses the extent and frequency of gene exchange within and between populations. Offers suggestions for designing exercises suitable for estimating dispersal distances in natural plant populations. (ML)

  9. Gene flow and herbicide resistance: Lessons learned from herbicide-resistant rice systems

    Science.gov (United States)

    Gene flow in plants is a process whereby genes are exchanged between members of the same or closely related species via pollen and become established in new populations. This natural process has long been an issue in breeding and the seed industry, but interest has increased since the deployment of ...

  10. Patterns of gene flow between crop and wild carrot, Daucus carota (Apiaceae) in the United States

    Science.gov (United States)

    Studies of gene flow between crops and their wild relatives have implications for both management practices for farming and breeding as well as understanding the risk of transgene escape. These types of studies may also yield insight into population dynamics and the evolutionary consequences of gene...

  11. Adaptive divergence with gene flow in incipient speciation of Miscanthus floridulus/sinensis complex (Poaceae).

    Science.gov (United States)

    Huang, Chao-Li; Ho, Chuan-Wen; Chiang, Yu-Chung; Shigemoto, Yasumasa; Hsu, Tsai-Wen; Hwang, Chi-Chuan; Ge, Xue-Jun; Chen, Charles; Wu, Tai-Han; Chou, Chang-Hung; Huang, Hao-Jen; Gojobori, Takashi; Osada, Naoki; Chiang, Tzen-Yuh

    2014-12-01

    Young incipient species provide ideal materials for untangling the process of ecological speciation in the presence of gene flow. The Miscanthus floridulus/sinensis complex exhibits diverse phenotypic and ecological differences despite recent divergence (approximately 1.59 million years ago). To elucidate the process of genetic differentiation during early stages of ecological speciation, we analyzed genomic divergence in the Miscanthus complex using 72 randomly selected genes from a newly assembled transcriptome. In this study, rampant gene flow was detected between species, estimated as M = 3.36 × 10(-9) to 1.20 × 10(-6) , resulting in contradicting phylogenies across loci. Nevertheless, beast analyses revealed the species identity and the effects of extrinsic cohesive forces that counteracted the non-stop introgression. As expected, early in speciation with gene flow, only 3-13 loci were highly diverged; two to five outliers (approximately 2.78-6.94% of the genome) were characterized by strong linkage disequilibrium, and asymmetrically distributed among ecotypes, indicating footprints of diversifying selection. In conclusion, ecological speciation of incipient species of Miscanthus probably followed the parapatric model, whereas allopatric speciation cannot be completely ruled out, especially between the geographically isolated northern and southern M. sinensis, for which no significant gene flow across oceanic barriers was detected. Divergence between local ecotypes in early-stage speciation began at a few genomic regions under the influence of natural selection and divergence hitchhiking that overcame gene flow.

  12. Long distance pollen-mediated flow of herbicide resistance genes in Lolium rigidum.

    Science.gov (United States)

    Busi, Roberto; Yu, Qin; Barrett-Lennard, Robert; Powles, Stephen

    2008-11-01

    Gene flow promotes genetic exchange among plant populations mediating evolutionary dynamics; yet, the importance of gene flow at distance via pollen movement is poorly understood. A field experiment at the landscape level was conducted with Lolium rigidum herbicide-susceptible individuals (population VLR1) placed into an otherwise Lolium-free bushland environment at increasing distances from adjacent large commercial crop fields infested with herbicide-resistant L. rigidum. Herbicide resistance was used as a marker to quantify the distance and the rate of pollen-mediated gene flow. About 21,245 seeds were produced on the isolated, susceptible mother plants of which 3,303 seedlings were tested for herbicide resistance and 664 seedlings were found to be resistant. Pollen-mediated gene flow occurred at 3,000 m (maximum tested distance). Both Mendelian and molecular analyses (sequencing and CAPS markers) confirmed the introgression of herbicide resistance genes. This is the first documented case of long-distance gene flow in L. rigidum. The results are important for future modeling simulations of herbicide resistance evolution and subsequent mobility. The adoption of integrated agronomic strategies, the control of potential receptor plants on fields' margins and conservative use of herbicides can be realistic options to minimize herbicide resistance spread.

  13. Adaptive divergence with gene flow in incipient speciation of Miscanthus floridulus / sinensis complex (Poaceae)

    KAUST Repository

    Huang, Chao-Li

    2014-11-11

    Young incipient species provide ideal materials for untangling the process of ecological speciation in the presence of gene flow. The Miscanthus floridulus/sinensis complex exhibits diverse phenotypic and ecological differences despite recent divergence (approximately 1.59million years ago). To elucidate the process of genetic differentiation during early stages of ecological speciation, we analyzed genomic divergence in the Miscanthus complex using 72 randomly selected genes from a newly assembled transcriptome. In this study, rampant gene flow was detected between species, estimated as M=3.36x10(-9) to 1.20x10(-6), resulting in contradicting phylogenies across loci. Nevertheless, beast analyses revealed the species identity and the effects of extrinsic cohesive forces that counteracted the non-stop introgression. As expected, early in speciation with gene flow, only 3-13 loci were highly diverged; two to five outliers (approximately 2.78-6.94% of the genome) were characterized by strong linkage disequilibrium, and asymmetrically distributed among ecotypes, indicating footprints of diversifying selection. In conclusion, ecological speciation of incipient species of Miscanthus probably followed the parapatric model, whereas allopatric speciation cannot be completely ruled out, especially between the geographically isolated northern and southern M.sinensis, for which no significant gene flow across oceanic barriers was detected. Divergence between local ecotypes in early-stage speciation began at a few genomic regions under the influence of natural selection and divergence hitchhiking that overcame gene flow.

  14. The genomic landscape underlying phenotypic integrity in the face of gene flow in crows.

    Science.gov (United States)

    Poelstra, J W; Vijay, N; Bossu, C M; Lantz, H; Ryll, B; Müller, I; Baglione, V; Unneberg, P; Wikelski, M; Grabherr, M G; Wolf, J B W

    2014-06-20

    The importance, extent, and mode of interspecific gene flow for the evolution of species has long been debated. Characterization of genomic differentiation in a classic example of hybridization between all-black carrion crows and gray-coated hooded crows identified genome-wide introgression extending far beyond the morphological hybrid zone. Gene expression divergence was concentrated in pigmentation genes expressed in gray versus black feather follicles. Only a small number of narrow genomic islands exhibited resistance to gene flow. One prominent genomic region (<2 megabases) harbored 81 of all 82 fixed differences (of 8.4 million single-nucleotide polymorphisms in total) linking genes involved in pigmentation and in visual perception-a genomic signal reflecting color-mediated prezygotic isolation. Thus, localized genomic selection can cause marked heterogeneity in introgression landscapes while maintaining phenotypic divergence. Copyright © 2014, American Association for the Advancement of Science.

  15. Forest corridors maintain historical gene flow in a tiger metapopulation in the highlands of central India.

    Science.gov (United States)

    Sharma, Sandeep; Dutta, Trishna; Maldonado, Jesús E; Wood, Thomas C; Panwar, Hemendra Singh; Seidensticker, John

    2013-09-22

    Understanding the patterns of gene flow of an endangered species metapopulation occupying a fragmented habitat is crucial for landscape-level conservation planning and devising effective conservation strategies. Tigers (Panthera tigris) are globally endangered and their populations are highly fragmented and exist in a few isolated metapopulations across their range. We used multi-locus genotypic data from 273 individual tigers (Panthera tigris tigris) from four tiger populations of the Satpura-Maikal landscape of central India to determine whether the corridors in this landscape are functional. This 45 000 km(2) landscape contains 17% of India's tiger population and 12% of its tiger habitat. We applied Bayesian and coalescent-based analyses to estimate contemporary and historical gene flow among these populations and to infer their evolutionary history. We found that the tiger metapopulation in central India has high rates of historical and contemporary gene flow. The tests for population history reveal that tigers populated central India about 10 000 years ago. Their population subdivision began about 1000 years ago and accelerated about 200 years ago owing to habitat fragmentation, leading to four spatially separated populations. These four populations have been in migration-drift equilibrium maintained by high gene flow. We found the highest rates of contemporary gene flow in populations that are connected by forest corridors. This information is highly relevant to conservation practitioners and policy makers, because deforestation, road widening and mining are imminent threats to these corridors.

  16. Considering spatial and temporal scale in landscape-genetic studies of gene flow.

    Science.gov (United States)

    Anderson, Corey Devin; Epperson, Bryan K; Fortin, Marie-Josée; Holderegger, Rolf; James, Patrick M A; Rosenberg, Michael S; Scribner, Kim T; Spear, Stephen

    2010-09-01

    Landscape features exist at multiple spatial and temporal scales, and these naturally affect spatial genetic structure and our ability to make inferences about gene flow. This article discusses how decisions about sampling of genotypes (including choices about analytical methods and genetic markers) should be driven by the scale of spatial genetic structure, the time frame that landscape features have existed in their current state, and all aspects of a species' life history. Researchers should use caution when making inferences about gene flow, especially when the spatial extent of the study area is limited. The scale of sampling of the landscape introduces different features that may affect gene flow. Sampling grain should be smaller than the average home-range size or dispersal distance of the study organism and, for raster data, existing research suggests that simplifying the thematic resolution into discrete classes may result in low power to detect effects on gene flow. Therefore, the methods used to characterize the landscape between sampling sites may be a primary determinant for the spatial scale at which analytical results are applicable, and the use of only one sampling scale for a particular statistical method may lead researchers to overlook important factors affecting gene flow. The particular analytical technique used to correlate landscape data and genetic data may also influence results; common landscape-genetic methods may not be suitable for all study systems, particularly when the rate of landscape change is faster than can be resolved by common molecular markers.

  17. Cryptic species? Patterns of maternal and paternal gene flow in eight neotropical bats.

    Directory of Open Access Journals (Sweden)

    Elizabeth L Clare

    Full Text Available Levels of sequence divergence at mitochondrial loci are frequently used in phylogeographic analysis and species delimitation though single marker systems cannot assess bi-parental gene flow. In this investigation I compare the phylogeographic patterns revealed through the maternally inherited mitochondrial COI region and the paternally inherited 7(th intron region of the Dby gene on the Y-chromosome in eight common Neotropical bat species. These species are diverse and include members of two families from the feeding guilds of sanguivores, nectarivores, frugivores, carnivores and insectivores. In each case, the currently recognized taxon is comprised of distinct, substantially divergent intraspecific mitochondrial lineages suggesting cryptic species complexes. In Chrotopterus auritus, and Saccopteryx bilineata I observed congruent patterns of divergence in both genetic regions suggesting a cessation of gene flow between intraspecific groups. This evidence supports the existence of cryptic species complexes which meet the criteria of the genetic species concept. In Glossophaga soricina two intraspecific groups with largely sympatric South American ranges show evidence for incomplete lineage sorting or frequent hybridization while a third group with a Central American distribution appears to diverge congruently at both loci suggesting speciation. Within Desmodus rotundus and Trachops cirrhosus the paternally inherited region was monomorphic and thus does not support or refute the potential for cryptic speciation. In Uroderma bilobatum, Micronycteris megalotis and Platyrrhinus helleri the gene regions show conflicting patterns of divergence and I cannot exclude ongoing gene flow between intraspecific groups. This analysis provides a comprehensive comparison across taxa and employs both maternally and paternally inherited gene regions to validate patterns of gene flow. I present evidence for previously unrecognized species meeting the criteria of

  18. Applying gene flow science to environmental policy needs: a boundary work perspective.

    Science.gov (United States)

    Ridley, Caroline E; Alexander, Laurie C

    2016-08-01

    One application of gene flow science is the policy arena. In this article, we describe two examples in which the topic of gene flow has entered into the U.S. national environmental policymaking process: regulation of genetically engineered crops and clarification of the jurisdictional scope of the Clean Water Act. We summarize both current scientific understanding and the legal context within which gene flow science has relevance. We also discuss the process by which scientific knowledge has been synthesized and communicated to decision-makers in these two contexts utilizing the concept of 'boundary work'. Boundary organizations, the work they engage in to bridge the worlds of science, policy, and practice, and the boundary objects they produce to translate scientific knowledge existed in both examples. However, the specific activities and attributes of the objects produced varied based on the needs of the decision-makers. We close with suggestions for how scientists can contribute to or engage in boundary work with policymakers.

  19. Inbreeding avoidance through non-random mating in sticklebacks.

    Science.gov (United States)

    Frommen, Joachim G; Bakker, Theo C M

    2006-06-22

    Negative effects of inbreeding are well documented in a wide range of animal taxa. Hatching success and survival of inbred offspring is reduced in many species and inbred progeny are often less attractive to potential mates. Thus, individuals should avoid mating with close kin. However, experimental evidence for inbreeding avoidance through non-random mating in vertebrates is scarce. Here, we show that gravid female three-spined sticklebacks (Gasterosteus aculeatus) when given the choice between a courting familiar brother and a courting unfamiliar non-sib prefer to mate with the non-sib and thus avoid the disadvantages of incest. We controlled for differences in males' body size and red intensity of nuptial coloration. Thus, females adjust their courting behaviour to the risk of inbreeding.

  20. Evidence for Non-Random Hydrophobicity Structures in Protein Chains

    CERN Document Server

    Irbäck, A; Potthast, F; Irb\\"ack, Anders; Peterson, Carsten; Potthast, Frank

    1996-01-01

    The question of whether proteins originate from random sequences of amino acids is addressed. A statistical analysis is performed in terms of blocked and random walk values formed by binary hydrophobic assignments of the amino acids along the protein chains. Theoretical expectations of these variables from random distributions of hydrophobicities are compared with those obtained from functional proteins. The results, which are based upon proteins in the SWISS-PROT data base, convincingly show that the amino acid sequences in proteins differ from what is expected from random sequences in a statistical significant way. By performing Fourier transforms on the random walks one obtains additional evidence for non-randomness of the distributions. We have also analyzed results from a synthetic model containing only two amino-acid types, hydrophobic and hydrophilic. With reasonable criteria on good folding properties in terms of thermodynamical and kinetic behavior, sequences that fold well are isolated. Performing t...

  1. Causal inference methods to study nonrandomized, preexisting development interventions

    Science.gov (United States)

    Arnold, Benjamin F.; Khush, Ranjiv S.; Ramaswamy, Padmavathi; London, Alicia G.; Rajkumar, Paramasivan; Ramaprabha, Prabhakar; Durairaj, Natesan; Hubbard, Alan E.; Balakrishnan, Kalpana; Colford, John M.

    2010-01-01

    Empirical measurement of interventions to address significant global health and development problems is necessary to ensure that resources are applied appropriately. Such intervention programs are often deployed at the group or community level. The gold standard design to measure the effectiveness of community-level interventions is the community-randomized trial, but the conditions of these trials often make it difficult to assess their external validity and sustainability. The sheer number of community interventions, relative to randomized studies, speaks to a need for rigorous observational methods to measure their impact. In this article, we use the potential outcomes model for causal inference to motivate a matched cohort design to study the impact and sustainability of nonrandomized, preexisting interventions. We illustrate the method using a sanitation mobilization, water supply, and hygiene intervention in rural India. In a matched sample of 25 villages, we enrolled 1,284 children <5 y old and measured outcomes over 12 mo. Although we found a 33 percentage point difference in new toilet construction [95% confidence interval (CI) = 28%, 39%], we found no impacts on height-for-age Z scores (adjusted difference = 0.01, 95% CI = −0.15, 0.19) or diarrhea (adjusted longitudinal prevalence difference = 0.003, 95% CI = −0.001, 0.008) among children <5 y old. This study demonstrates that matched cohort designs can estimate impacts from nonrandomized, preexisting interventions that are used widely in development efforts. Interpreting the impacts as causal, however, requires stronger assumptions than prospective, randomized studies. PMID:21149699

  2. Gene flow among populations of two rare co-occurring fern species differing in ploidy level.

    Science.gov (United States)

    Bucharová, Anna; Münzbergová, Zuzana

    2012-01-01

    Differences in ploidy levels among different fern species have a vast influence on their mating system, their colonization ability and on the gene flow among populations. Differences in the colonization abilities of species with different ploidy levels are well known: tetraploids, in contrast to diploids, are able to undergo intra-gametophytic selfing. Because fertilization is a post-dispersal process in ferns, selfing results in better colonization abilities in tetraploids because of single spore colonization. Considerably less is known about the gene flow among populations of different ploidy levels. The present study examines two rare fern species that differ in ploidy. While it has already been confirmed that tetraploid species are better at colonizing, the present study focuses on the gene flow among existing populations. We analyzed the genetic structure of a set of populations in a 10×10 km study region using isoenzymes. Genetic variation in tetraploid species is distributed mainly among populations; the genetic distance between populations is correlated with the geographical distance, and larger populations host more genetic diversity than smaller populations. In the diploid species, most variability is partitioned within populations; the genetic distance is not related to geographic distance, and the genetic diversity of populations is not related to the population size. This suggests that in tetraploid species, which undergo selfing, gene flow is limited. In contrast, in the diploid species, which experience outcrossing, gene flow is extensive and the whole system behaves as one large population. Our results suggest that in ferns, the ability to colonize new habitats and the gene flow among existing populations are affected by the mating system.

  3. Assessment on alien herbicide-resistant gene flow among crucifers by sexual compatibility

    Institute of Scientific and Technical Information of China (English)

    ZHAO Xiangxiang; LU Weiping; QI Cunkou; PU Huiming; XIA Qiuxia; LU Dalei; LIU Geshan; WANG Youping

    2005-01-01

    Cross-pollination and high cross-compatibility are frequently found in many cruciferous plants, which implies that there might be potential risk of alien gene flow among crucifers. In this work, the alien glyphosate-resistant gene flow between GM (Genetically modified) rapeseed variety Q3 (Brassica napus) and 6 varieties from 5 cruciferous species was assessed by sexual compatibility through aniline blue fluorescence observation, manual cross, mentor pollination with the mixture pollen and DNA identification. The results indicated that the compatibility indices of two B. napus varieties, B. juncea var. multiceps Tsen et Lee and Chinese cabbage (B. chinensis) (as female) with Q3 (as male) were 16.15, 12.77, 2.345 and 0.85, respectively. F1 plants were examined by PCR and all of these samples were confirmed as positive. Crossing between Orychophragmus violaceus, Descurainia sophia (as female) and Q3 (as male) expressed high cross-incompatibility. Fluorescence microscope observation indicated that growing of pollen tube terminated at the upper 1/3 part of the style of O. violaceus and on the stigma surface of D. sophia. The mentor plants were further analyzed by PCR and all were shown to be negative. Under the neighboring growth and natural pollination conditions, the rates of gene flow to two B. napus varieties were 2.3278% and 2.1487%, respectively, B. juncea var. multiceps Tsen et Lee and Chinese cabbage were 1.0157% and 0.9236%, respectively. No gene flow was observed in O. violaceus and D. sophia. Frequency of gene flow was highly correlated with sexual compatibility. Due to possible alien gene flow among crucifers, special consideration and care should be taken to grow GM rapeseed.

  4. Gene flow between Atlantic and Pacific Ocean basins in three lineages of deep-sea clams (Bivalvia: Vesicomyidae: Pliocardiinae) and subsequent limited gene flow within the Atlantic

    Science.gov (United States)

    LaBella, Abigail Leavitt; Van Dover, Cindy L.; Jollivet, Didier; Cunningham, Clifford W.

    2017-03-01

    Pliocardiin (vesicomyid) clams rely on microbial symbionts for nutrition and are obligate inhabitants of deep-sea chemosynthetic ecosystems. Unlike many other invertebrate hosts of chemosynthetic microbes, pliocardiin clams are found in every ocean in a variety of reducing habitats, including hydrothermal vents, cold seeps, organic falls and deep-sea fans. The global distribution of pliocardiin clams suggests historical gene flow between ocean basins. We focus on 3 pliocardiin genera-'Pliocardia' I, Calyptogena and Abyssogena-each of which has a pair of sister clades in the Atlantic and Pacific. Our work tests the hypothesis that historical gene flow between the Atlantic and Pacific Oceans within these genera was interrupted by the closure of the Panamanian seaway and tests whether isolation between the ocean basins is the result of vicariance or past colonization. These questions are investigated in the context of fossil evidence, biogeography and phylogenetics. This study revealed a set of substitution rates consistent with other invertebrate studies (μ=0.8%/My/lineage), and a set consistent with much lower rates often attributed to deep-sea organisms (μ=0.3%/My/lineage). Among the Pacific/Atlantic sister pairs, 'Pliocardia' I COI divergence per lineage is intermediate (2.5%), Calyptogena is the highest (6.1%) and Abyssogena the lowest (0.8%). The substitution rates suggest that 'Pliocardia' I and Calyptogena have histories of at least 2.8 My in the Atlantic, with Calyptogena likely older. The slower rate, however, is inconsistent with both the maximum age of the family and several well studied fossils: leaving the faster rate preferred. With the faster rate, the Abyssogena southwardae clade diverged from its Pacific sister clade around 1 Mya, which likely post-dates the closure of the Isthmus of Panama and the opening of the Bering Strait. In light of this recent divergence, we test the previously proposed hypothesis that there is a high level of ongoing gene

  5. Comparing direct vs. indirect estimates of gene flow within a population of a scattered tree species.

    Science.gov (United States)

    Oddou-Muratorio, Sylvie; Klein, Etienne K

    2008-06-01

    The comparison between historical estimates of gene flow, using variance in allelic frequencies, and contemporary estimates of gene flow, using parentage assignment, is expected to provide insights into ecological and evolutionary processes at work within and among populations. Genetic variation at six microsatellite loci was used to quantify genetic structure in the insect-pollinated, animal-dispersed, low-density tree Sorbus torminalis L. Crantz, and to derive historical estimates of gene flow. The neighbourhood size and root-mean-squared dispersal distance inferred from seedling genotypes (N(b) = 70 individuals, sigma(e) = 417 m) were similar to those inferred from adult genotypes (N(b) = 114 individuals, sigma(e) = 472 m). We also used parentage analyses and a neighbourhood model approach after an evaluation of the statistical properties of this method on simulated data. From our data, we estimated even contributions of seed- and pollen-mediated dispersal to the genetic composition of established seedlings, with both fat-tailed pollen and seed dispersal kernels, and slightly higher mean distance of pollen dispersal (248 m) as compared to seed dispersal (135 m). The resulting contemporary estimate of gene dispersal distance (sigma(c) = 211 m) was approximately twofold smaller than the historical estimates. Besides different assumptions and statistical nuances of both approaches, this discrepancy is likely to reflect a recent restriction in the scale of gene flow which requires manager's attention in a context of increasing forest fragmentation.

  6. Retroviral integration process in the human genome: is it really non-random? A new statistical approach.

    Directory of Open Access Journals (Sweden)

    Alessandro Ambrosi

    Full Text Available Retroviral vectors are widely used in gene therapy to introduce therapeutic genes into patients' cells, since, once delivered to the nucleus, the genes of interest are stably inserted (integrated into the target cell genome. There is now compelling evidence that integration of retroviral vectors follows non-random patterns in mammalian genome, with a preference for active genes and regulatory regions. In particular, Moloney Leukemia Virus (MLV-derived vectors show a tendency to integrate in the proximity of the transcription start site (TSS of genes, occasionally resulting in the deregulation of gene expression and, where proto-oncogenes are targeted, in tumor initiation. This has drawn the attention of the scientific community to the molecular determinants of the retroviral integration process as well as to statistical methods to evaluate the genome-wide distribution of integration sites. In recent approaches, the observed distribution of MLV integration distances (IDs from the TSS of the nearest gene is assumed to be non-random by empirical comparison with a random distribution generated by computational simulation procedures. To provide a statistical procedure to test the randomness of the retroviral insertion pattern, we propose a probability model (Beta distribution based on IDs between two consecutive genes. We apply the procedure to a set of 595 unique MLV insertion sites retrieved from human hematopoietic stem/progenitor cells. The statistical goodness of fit test shows the suitability of this distribution to the observed data. Our statistical analysis confirms the preference of MLV-based vectors to integrate in promoter-proximal regions.

  7. 42 CFR 421.505 - Termination and extension of non-random prepayment complex medical review.

    Science.gov (United States)

    2010-10-01

    ... a provider or supplier must be on non-random prepayment complex medical review. There is no minimum... section, a contractor must terminate a provider or supplier from non-random prepayment complex medical... complex medical review if a provider or supplier stops billing the code under review, shifts billing...

  8. Medicare Program; termination of non-random prepayment complex medical review. Final rule.

    Science.gov (United States)

    2008-09-26

    This final rule implements requirements regarding the termination of non-random prepayment complex medical review as required under the Medicare Prescription Drug, Improvement and Modernization Act of 2003. This final rule sets forth the criteria CMS contractors will use for terminating a provider or supplier from non-random prepayment complex medical review.

  9. A structured population modeling framework for quantifying and predicting gene expression noise in flow cytometry data.

    Science.gov (United States)

    Flores, Kevin B

    2013-07-01

    We formulated a structured population model with distributed parameters to identify mechanisms that contribute to gene expression noise in time-dependent flow cytometry data. The model was validated using cell population-level gene expression data from two experiments with synthetically engineered eukaryotic cells. Our model captures the qualitative noise features of both experiments and accurately fit the data from the first experiment. Our results suggest that cellular switching between high and low expression states and transcriptional re-initiation are important factors needed to accurately describe gene expression noise with a structured population model.

  10. Gene flow and pathogen transmission among bobcats (Lynx rufus) in a fragmented urban landscape

    Science.gov (United States)

    Lee, Justin S.; Ruell, Emily W.; Boydston, Erin E.; Lyren, Lisa M.; Alonso, Robert S.; Troyer, Jennifer L.; Crooks, Kevin R.; VandeWoude, Sue

    2012-01-01

    Urbanization can result in the fragmentation of once contiguous natural landscapes into a patchy habitat interspersed within a growing urban matrix. Animals living in fragmented landscapes often have reduced movement among habitat patches because of avoidance of intervening human development, which potentially leads to both reduced gene flow and pathogen transmission between patches. Mammalian carnivores with large home ranges, such as bobcats (Lynx rufus), may be particularly sensitive to habitat fragmentation. We performed genetic analyses on bobcats and their directly transmitted viral pathogen, feline immunodeficiency virus (FIV), to investigate the effects of urbanization on bobcat movement. We predicted that urban development, including major freeways, would limit bobcat movement and result in genetically structured host and pathogen populations. We analysed molecular markers from 106 bobcats and 19 FIV isolates from seropositive animals in urban southern California. Our findings indicate that reduced gene flow between two primary habitat patches has resulted in genetically distinct bobcat subpopulations separated by urban development including a major highway. However, the distribution of genetic diversity among FIV isolates determined through phylogenetic analyses indicates that pathogen genotypes are less spatially structured--exhibiting a more even distribution between habitat fragments. We conclude that the types of movement and contact sufficient for disease transmission occur with enough frequency to preclude structuring among the viral population, but that the bobcat population is structured owing to low levels of effective bobcat migration resulting in gene flow. We illustrate the utility in using multiple molecular markers that differentially detect movement and gene flow between subpopulations when assessing connectivity.

  11. Gene flow from Sorghum bicolor to its weedy relatives and its ...

    African Journals Online (AJOL)

    computer user

    2015-04-29

    Apr 29, 2015 ... drummondii, has shown natural outcrossing ranging from. 0-100% on individual ... result of artificial and natural selection for more than one level of a particular ...... Possible effects of (trans) gene flow from crops on the genetic ...

  12. Gene flow from Sorghum bicolor to its weedy relatives and its ...

    African Journals Online (AJOL)

    computer user

    2015-02-18

    Feb 18, 2015 ... more quantitative and precise methods of analyzing target DNA ... laboratory located at the College of Agriculture and Veterinary .... emitted fluorescence exceeded the standardized ..... designing effective tools to measure gene flow. .... and cultivated Sorghum bicolor (L.) Moench in Kenya: implications for.

  13. Gene flow matters in switchgrass (Panicum virgatum L.), a potential widespread biofuel feedstock.

    Science.gov (United States)

    Kwit, Charles; Stewart, C Neal

    2012-01-01

    There currently exists a large push for the use, improvement, and expansion via landscape modification of dedicated biofuel crops (feedstocks) in the United States and in many parts of the world. Ecological concerns have been voiced because many biofuel feedstocks exhibit characteristics associated with invasiveness, and due to potential negative consequences of agronomic genes in native wild populations. Seed purity concerns for biofuel feedstock cultivars whose seeds would be harvested in agronomic fields also exist from the agribusiness sector. The common thread underlying these concerns, which have regulatory implications, is gene flow; thus detailed knowledge of gene flow in biofuel crop plants is important in the formulation of environmental risk management plans. Here, we synthesize the current state of knowledge of gene flow in an exemplary biofuel crop, switchgrass (Panicum virgatum L.), which is native to eastern North America and is currently experiencing conventional and technological advances in biomass yields and ethanol production. Surprisingly little is known regarding aspects of switchgrass pollen flow and seed dispersal, and whether native populations of conspecific or congeneric relatives will readily cross with current agronomic switchgrass cultivars. We pose that filling these important gaps will be required to confront the sustainability challenges of widespread planting of biofuel feedstocks.

  14. Elevational speciation in action? Restricted gene flow associated with adaptive divergence across an altitudinal gradient

    Science.gov (United States)

    Funk, W. C.; Murphy, M.A.; Hoke, K. L.; Muths, Erin L.; Amburgey, Staci M.; Lemmon, Emily M.; Lemmon, A. R.

    2016-01-01

    Evolutionary theory predicts that divergent selection pressures across elevational gradients could cause adaptive divergence and reproductive isolation in the process of ecological speciation. Although there is substantial evidence for adaptive divergence across elevation, there is less evidence that this restricts gene flow. Previous work in the boreal chorus frog (Pseudacris maculata) has demonstrated adaptive divergence in morphological, life history and physiological traits across an elevational gradient from approximately 1500–3000 m in the Colorado Front Range, USA. We tested whether this adaptive divergence is associated with restricted gene flow across elevation – as would be expected if incipient speciation were occurring – and, if so, whether behavioural isolation contributes to reproductive isolation. Our analysis of 12 microsatellite loci in 797 frogs from 53 populations revealed restricted gene flow across elevation, even after controlling for geographic distance and topography. Calls also varied significantly across elevation in dominant frequency, pulse number and pulse duration, which was partly, but not entirely, due to variation in body size and temperature across elevation. However, call variation did not result in strong behavioural isolation: in phonotaxis experiments, low-elevation females tended to prefer an average low-elevation call over a high-elevation call, and vice versa for high-elevation females, but this trend was not statistically significant. In summary, our results show that adaptive divergence across elevation restricts gene flow in P. maculata, but the mechanisms for this potential incipient speciation remain open.

  15. Pollen and seed mediated gene flow in commercial alfalfa seed production fields

    Science.gov (United States)

    The potential for gene flow has been widely recognized since alfalfa is pollinated by bees. The Western US is a major exporter of alfalfa seed and hay and the organic dairy industry is one of the fastest growing agricultural sectors. Because of this, many alfalfa producers are impacted by market sen...

  16. [Gene flow and its ecological risks of transgenic oilseed rape ( Brassica napus)].

    Science.gov (United States)

    Tang, Guixiang; Song, Wenjian; Zhou, Weijun

    2005-12-01

    Transgenic oilseed rape Brassica napus, one of the first genetically modified crops, has now been released to commercial use in Canada and Australia. As a cross-pollinating crop, its natural crossing rate is 30%, and it is liable to cross with other Brassica species. The ecological risk of transgenic oilseed rape has been concerned by the scientists all over the world. There are two ways for the pollens flow of transgenic oilseed rape, one takes place between transgenic oilseed rape and other related wild species, and the other occurs between transgenic and nontransgenic oilseed rape. The gene may flow to other related wild species, but it is unlikely to get hybrids in field. Because the gene can really flow to the conventional oilseed rape, it is necessary to have a sufficient isolation distance in cultivating transgenic oilseed rape.

  17. Local evolution of pyrethroid resistance offsets gene flow among Aedes aegypti collections in Yucatan State, Mexico.

    Science.gov (United States)

    Saavedra-Rodriguez, Karla; Beaty, Meaghan; Lozano-Fuentes, Saul; Denham, Steven; Garcia-Rejon, Julian; Reyes-Solis, Guadalupe; Machain-Williams, Carlos; Loroño-Pino, Maria Alba; Flores-Suarez, Adriana; Ponce-Garcia, Gustavo; Beaty, Barry; Eisen, Lars; Black, William C

    2015-01-01

    The mosquito Aedes aegypti is the major vector of the four serotypes of dengue virus (DENV1-4). Previous studies have shown that Ae. aegypti in Mexico have a high effective migration rate and that gene flow occurs among populations that are up to 150 km apart. Since 2000, pyrethroids have been widely used for suppression of Ae. aegypti in cities in Mexico. In Yucatan State in particular, pyrethroids have been applied in and around dengue case households creating an opportunity for local selection and evolution of resistance. Herein, we test for evidence of local adaptation by comparing patterns of variation among 27 Ae. aegypti collections at 13 single nucleotide polymorphisms (SNPs): two in the voltage-gated sodium channel gene para known to confer knockdown resistance, three in detoxification genes previously associated with pyrethroid resistance, and eight in putatively neutral loci. The SNPs in para varied greatly in frequency among collections, whereas SNPs at the remaining 11 loci showed little variation supporting previous evidence for extensive local gene flow. Among Ae. aegypti in Yucatan State, Mexico, local adaptation to pyrethroids appears to offset the homogenizing effects of gene flow.

  18. Local Evolution of Pyrethroid Resistance Offsets Gene Flow Among Aedes aegypti Collections in Yucatan State, Mexico

    Science.gov (United States)

    Saavedra-Rodriguez, Karla; Beaty, Meaghan; Lozano-Fuentes, Saul; Denham, Steven; Garcia-Rejon, Julian; Reyes-Solis, Guadalupe; Machain-Williams, Carlos; Loroño-Pino, Maria Alba; Flores-Suarez, Adriana; Ponce-Garcia, Gustavo; Beaty, Barry; Eisen, Lars; Black, William C.

    2015-01-01

    The mosquito Aedes aegypti is the major vector of the four serotypes of dengue virus (DENV1–4). Previous studies have shown that Ae. aegypti in Mexico have a high effective migration rate and that gene flow occurs among populations that are up to 150 km apart. Since 2000, pyrethroids have been widely used for suppression of Ae. aegypti in cities in Mexico. In Yucatan State in particular, pyrethroids have been applied in and around dengue case households creating an opportunity for local selection and evolution of resistance. Herein, we test for evidence of local adaptation by comparing patterns of variation among 27 Ae. aegypti collections at 13 single nucleotide polymorphisms (SNPs): two in the voltage-gated sodium channel gene para known to confer knockdown resistance, three in detoxification genes previously associated with pyrethroid resistance, and eight in putatively neutral loci. The SNPs in para varied greatly in frequency among collections, whereas SNPs at the remaining 11 loci showed little variation supporting previous evidence for extensive local gene flow. Among Ae. aegypti in Yucatan State, Mexico, local adaptation to pyrethroids appears to offset the homogenizing effects of gene flow. PMID:25371186

  19. Monitoring gene flow from transgenic sugar beet using cytoplasmic male-sterile bait plants.

    Science.gov (United States)

    Saeglitz, C; Pohl, M; Bartsch, D

    2000-12-01

    One of the most discussed environmental effects associated with the use of transgenic plants is the flow of genes to plants in the environment. The flow of genes may occur through pollen since it is the reproductive system that is designed for gene movement. Pollen-mediated gene escape is hard to control in mating plants. Pollen from a wind pollinator can move over distances of more than 1000 m. To investigate the efficiency of transgenic pollen movement under realistic environmental conditions, the use of bait plants might be an effective tool. In this study, cytoplasmic male-sterile (CMS) sugar beets were tested with regard to their potential for monitoring transgene flow. As the pollen source, transgenic sugar beets were used that express recombinant DNA encoding viral (beet necrotic yellow vein virus) resistance, and antibiotic (kanamycin) and herbicide (glufosinate) tolerance genes. In a field trial, the effectiveness of a hemp (Cannabis sativa) stripe containment strategy was tested by measuring the frequency of pollinated CMS bait plants placed at different distances and directions from a transgenic pollen source. The results demonstrated the ineffectiveness of the containment strategy. Physiological and molecular tests confirmed the escape and production of transgenic offspring more than 200 m behind the hemp containment. Since absolute containment is unlikely to be effective, the CMS-bait plant detection system is a useful tool for other monitoring purposes.

  20. Gene flow in Prunus species in the context of novel trait risk assessment.

    Science.gov (United States)

    Cici, S Zahra H; Van Acker, Rene C

    2010-01-01

    Prunus species are important commercial fruit (plums, apricot, peach and cherries), nut (almond) and ornamental trees cultivated broadly worldwide. This review compiles information from available literature on Prunus species in regard to gene flow and hybridization within this complex of species. The review serves as a resource for environmental risk assessment related to pollen mediated gene flow and the release of transgenic Prunus. It reveals that Prunus species, especially plums and cherries show high potential for transgene flow. A range of characteristics including; genetic diversity, genetic bridging capacity, inter- and intra-specific genetic compatibility, self sterility (in most species), high frequency of open pollination, insect assisted pollination, perennial nature, complex phenotypic architecture (canopy height, heterogeneous crown, number of flowers produced in an individual plant), tendency to escape from cultivation, and the existence of ornamental and road side Prunus species suggest that there is a tremendous and complicated ability for pollen mediated gene movement among Prunus species. Ploidy differences among Prunus species do not necessarily provide genetic segregation. The characteristics of Prunu s species highlight the complexity of maintaining coexistence between GM and non-GM Prunus if there were commercial production of GM Prunus species. The results of this review suggest that the commercialization of one GM Prunus species can create coexistence issues for commercial non-GM Prunus production. Despite advances in molecular markers and genetic analysis in agroecology, there remains limited information on the ecological diversity, metapopulation nature, population dynamics, and direct measures of gene flow among different subgenera represented in the Prunus genus. Robust environmental impact, biosafety and coexistence assessments for GM Prunus species will require better understanding of the mechanisms of gene flow and hybridization

  1. Landscape features affect gene flow of Scottish Highland red deer (Cervus elaphus).

    Science.gov (United States)

    Pérez-Espona, S; Pérez-Barbería, F J; McLeod, J E; Jiggins, C D; Gordon, I J; Pemberton, J M

    2008-02-01

    Landscape features have been shown to strongly influence dispersal and, consequently, the genetic population structure of organisms. Studies quantifying the effect of landscape features on gene flow of large mammals with high dispersal capabilities are rare and have mainly been focused at large geographical scales. In this study, we assessed the influence of several natural and human-made landscape features on red deer gene flow in the Scottish Highlands by analysing 695 individuals for 21 microsatellite markers. Despite the relatively small scale of the study area (115 x 87 km), significant population structure was found using F-statistics (F(ST) = 0.019) and the program structure, with major differentiation found between populations sampled on either side of the main geographical barrier (the Great Glen). To assess the effect of landscape features on red deer population structure, the ArcMap GIS was used to create cost-distance matrices for moving between populations, using a range of cost values for each of the landscape features under consideration. Landscape features were shown to significantly affect red deer gene flow as they explained a greater proportion of the genetic variation than the geographical distance between populations. Sea lochs were found to be the most important red deer gene flow barriers in our study area, followed by mountain slopes, roads and forests. Inland lochs and rivers were identified as landscape features that might facilitate gene flow of red deer. Additionally, we explored the effect of choosing arbitrary cell cost values to construct least cost-distance matrices and described a method for improving the selection of cell cost values for a particular landscape feature.

  2. Divergence and gene flow in the globally distributed blue-winged ducks

    Science.gov (United States)

    Nelson, Joel; Wilson, Robert E.; McCracken, Kevin G.; Cumming, Graeme; Joseph, Leo; Guay, Patrick-Jean; Peters, Jeffrey

    2016-01-01

    The ability to disperse over long distances can result in a high propensity for colonizing new geographic regions, including uninhabited continents, and lead to lineage diversification via allopatric speciation. However, high vagility can also result in gene flow between otherwise allopatric populations, and in some cases, parapatric or divergence-with-gene-flow models might be more applicable to widely distributed lineages. Here, we use five nuclear introns and the mitochondrial control region along with Bayesian models of isolation with migration to examine divergence, gene flow, and phylogenetic relationships within a cosmopolitan lineage comprising six species, the blue-winged ducks (genus Anas), which inhabit all continents except Antarctica. We found two primary sub-lineages, the globally-distributed shoveler group and the New World blue-winged/cinnamon teal group. The blue-winged/cinnamon sub-lineage is composed of sister taxa from North America and South America, and taxa with parapatric distributions are characterized by low to moderate levels of gene flow. In contrast, our data support strict allopatry for most comparisons within the shovelers. However, we found evidence of gene flow from the migratory, Holarctic northern shoveler (A. clypeata) and the more sedentary, African Cape shoveler (A. smithii) into the Australasian shoveler (A. rhynchotis), although we could not reject strict allopatry. Given the diverse mechanisms of speciation within this complex, the shovelers and blue-winged/cinnamon teals can serve as an effective model system for examining how the genome diverges under different evolutionary processes and how genetic variation is partitioned among highly dispersive taxa.

  3. Beekeeping practices and geographic distance, not land use, drive gene flow across tropical bees.

    Science.gov (United States)

    Jaffé, Rodolfo; Pope, Nathaniel; Acosta, André L; Alves, Denise A; Arias, Maria C; De la Rúa, Pilar; Francisco, Flávio O; Giannini, Tereza C; González-Chaves, Adrian; Imperatriz-Fonseca, Vera L; Tavares, Mara G; Jha, Shalene; Carvalheiro, Luísa G

    2016-11-01

    Across the globe, wild bees are threatened by ongoing natural habitat loss, risking the maintenance of plant biodiversity and agricultural production. Despite the ecological and economic importance of wild bees and the fact that several species are now managed for pollination services worldwide, little is known about how land use and beekeeping practices jointly influence gene flow. Using stingless bees as a model system, containing wild and managed species that are presumed to be particularly susceptible to habitat degradation, here we examine the main drivers of tropical bee gene flow. We employ a novel landscape genetic approach to analyse data from 135 populations of 17 stingless bee species distributed across diverse tropical biomes within the Americas. Our work has important methodological implications, as we illustrate how a maximum-likelihood approach can be applied in a meta-analysis framework to account for multiple factors, and weight estimates by sample size. In contrast to previously held beliefs, gene flow was not related to body size or deforestation, and isolation by geographic distance (IBD) was significantly affected by management, with managed species exhibiting a weaker IBD than wild ones. Our study thus reveals the critical importance of beekeeping practices in shaping the patterns of genetic differentiation across bee species. Additionally, our results show that many stingless bee species maintain high gene flow across heterogeneous landscapes. We suggest that future efforts to preserve wild tropical bees should focus on regulating beekeeping practices to maintain natural gene flow and enhancing pollinator-friendly habitats, prioritizing species showing a limited dispersal ability.

  4. Next generation sequencing and FISH reveal uneven and nonrandom microsatellite distribution in two grasshopper genomes.

    Science.gov (United States)

    Ruiz-Ruano, Francisco J; Cuadrado, Ángeles; Montiel, Eugenia E; Camacho, Juan Pedro M; López-León, María Dolores

    2015-06-01

    Simple sequence repeats (SSRs), also known as microsatellites, are one of the prominent DNA sequences shaping the repeated fraction of eukaryotic genomes. In spite of their profuse use as molecular markers for a variety of genetic and evolutionary studies, their genomic location, distribution, and function are not yet well understood. Here we report the first thorough joint analysis of microsatellite motifs at both genomic and chromosomal levels in animal species, by a combination of 454 sequencing and fluorescent in situ hybridization (FISH) techniques performed on two grasshopper species. The in silico analysis of the 454 reads suggested that microsatellite expansion is not driving size increase of these genomes, as SSR abundance was higher in the species showing the smallest genome. However, the two species showed the same uneven and nonrandom location of SSRs, with clear predominance of dinucleotide motifs and association with several types of repetitive elements, mostly histone gene spacers, ribosomal DNA intergenic spacers (IGS), and transposable elements (TEs). The FISH analysis showed a dispersed chromosome distribution of microsatellite motifs in euchromatic regions, in coincidence with chromosome location patterns previously observed for many mobile elements in these species. However, some SSR motifs were clustered, especially those located in the histone gene cluster.

  5. Did Evolution Select a Nonrandom "Alphabet" of Amino Acids?

    Science.gov (United States)

    Philip, Gayle K.; Freeland, Stephen J.

    2011-04-01

    The last universal common ancestor of contemporary biology (LUCA) used a precise set of 20 amino acids as a standard alphabet with which to build genetically encoded protein polymers. Considerable evidence indicates that some of these amino acids were present through nonbiological syntheses prior to the origin of life, while the rest evolved as inventions of early metabolism. However, the same evidence indicates that many alternatives were also available, which highlights the question: what factors led biological evolution on our planet to define its standard alphabet? One possibility is that natural selection favored a set of amino acids that exhibits clear, nonrandom properties - a set of especially useful building blocks. However, previous analysis that tested whether the standard alphabet comprises amino acids with unusually high variance in size, charge, and hydrophobicity (properties that govern what protein structures and functions can be constructed) failed to clearly distinguish evolution's choice from a sample of randomly chosen alternatives. Here, we demonstrate unambiguous support for a refined hypothesis: that an optimal set of amino acids would spread evenly across a broad range of values for each fundamental property. Specifically, we show that the standard set of 20 amino acids represents the possible spectra of size, charge, and hydrophobicity more broadly and more evenly than can be explained by chance alone.

  6. Nonrandomized studies are not always found even when selection criteria for health systems intervention reviews include them: a methodological study.

    Science.gov (United States)

    Glenton, Claire; Lewin, Simon; Mayhew, Alain; Scheel, Inger; Odgaard-Jensen, Jan

    2013-04-01

    Systematic reviews within the Cochrane Effective Practice and Organisation of Care Group (EPOC) can include both randomized and nonrandomized study designs. We explored how many EPOC reviews consider and identify nonrandomized studies, and whether the proportion of nonrandomized studies identified is linked to the review topic. We recorded the study designs considered in 65 EPOC reviews. For reviews that considered nonrandomized studies, we calculated the proportion of identified studies that were nonrandomized and explored whether there were differences in the proportion of nonrandomized studies according to the review topic. Fifty-one (78.5%) reviews considered nonrandomized studies. Forty-six of these reviews found nonrandomized studies, but the proportion varied a great deal (median, 33%; interquartile range, 25--50%). Reviews of health care delivery interventions had lower proportions of nonrandomized studies than those of financial and governance interventions. Most EPOC reviews consider nonrandomized studies, but the degree to which they find them varies. As nonrandomized studies are believed to be at higher risk of bias and their inclusion entails a considerable effort, review authors should consider whether the benefits justify the inclusion of these designs. Research should explore whether it is more useful to consider nonrandomized studies in reviews of some intervention types than others. Copyright © 2013 Elsevier Inc. All rights reserved.

  7. The connectivity of Mytilus galloprovincialis in northern Morocco: A gene flow crossroads between continents

    Science.gov (United States)

    Ouagajjou, Yassine; Presa, Pablo

    2015-01-01

    Previous population genetic studies on the Mediterranean mussel Mytilus galloprovincialis have shown the existence of two well differentiated sets of populations around Southern European coasts, one Atlantic and another Mediterranean. Those two population pools are kept apart by the Almería - Oran Oceanographic Front (AOOF), an oceanographic discontinuity acting either as a cause of such differentiation or simply as a means of maintaining two historically differentiated gene pools. The role of the Gibraltar Strait at shaping mussel larval flow entering the Alboran Sea has been much less addressed, especially regarding mussel swarms inhabiting the northern coast of Morocco. The present study applies seven microsatellite markers to describing the genetic status of northern Moroccan populations of M. galloprovincialis and their relationship with the two well-characterized mussel gene pools from southern Europe. We show that the Atlantic Iberia gene pool extending continuously from the Cantabrian Sea (NE Iberia) to the Alboran Sea (SE Iberia) up to the AOOF is well differentiated from the Atlantic Moroccan mussel. Either an oceanographic barrier or a limited larval dispersal or both, are required to explain this unexpected intercontinental differentiation regarding previous studies on this species. Populations from Atlantic Morocco conformed to a single gene pool (FST ± SD = 0.012 ± 0.007) as opposed to the reported latitudinal barrier to gene flow at Cape Ghir in western Morocco. Additionally, a significant restriction to gene flow was observed between Atlantic Morocco and Alboran Morocco (FST ± SD = 0.038 ± 0.010) in contrast to the reported mussel genetic continuity along the Iberian coast up to AOOF. Three major mussel gene pools appear to meet at this crossroads between continents and between seas, namely, a Mediterranean European subpopulation, an Atlantic Iberia subpopulation including the Alboran Sea, and an Atlantic Morocco subpopulation. Knowledge on

  8. The Effect of Nonrandom Distribution of Molecules on the Equation of State for Gases

    Energy Technology Data Exchange (ETDEWEB)

    Jung, Haeyoung [DukSung Women' s Univ., Seoul (Korea, Republic of)

    2013-10-15

    Using the free volume of van der Waals equation, Carnahan-Starling equation for hard spheres, Wilson equation for nonrandom mixing of solution, NRTL equation and our equation, several new equations of states for pure gases are derived. Using these equations, compressibility factors for pure gases are calculated and compared with Nelson-Obert generalized compressibility factor charts. The equation of states using the concept of molecular nonrandom distribution gave better results than those of molecular random distribution. This shows that the molecular nonrandom distribution makes considerable effect on the equation of states.

  9. High rates of gene flow by pollen and seed in oak populations across Europe.

    Directory of Open Access Journals (Sweden)

    Sophie Gerber

    Full Text Available Gene flow is a key factor in the evolution of species, influencing effective population size, hybridisation and local adaptation. We analysed local gene flow in eight stands of white oak (mostly Quercus petraea and Q. robur, but also Q. pubescens and Q. faginea distributed across Europe. Adult trees within a given area in each stand were exhaustively sampled (range [239, 754], mean 423, mapped, and acorns were collected ([17,147], 51 from several mother trees ([3], [47], 23. Seedlings ([65,387], 178 were harvested and geo-referenced in six of the eight stands. Genetic information was obtained from screening distinct molecular markers spread across the genome, genotyping each tree, acorn or seedling. All samples were thus genotyped at 5-8 nuclear microsatellite loci. Fathers/parents were assigned to acorns and seedlings using likelihood methods. Mating success of male and female parents, pollen and seed dispersal curves, and also hybridisation rates were estimated in each stand and compared on a continental scale. On average, the percentage of the wind-borne pollen from outside the stand was 60%, with large variation among stands (21-88%. Mean seed immigration into the stand was 40%, a high value for oaks that are generally considered to have limited seed dispersal. However, this estimate varied greatly among stands (20-66%. Gene flow was mostly intraspecific, with large variation, as some trees and stands showed particularly high rates of hybridisation. Our results show that mating success was unevenly distributed among trees. The high levels of gene flow suggest that geographically remote oak stands are unlikely to be genetically isolated, questioning the static definition of gene reserves and seed stands.

  10. Gene-splitting technology: a novel approach for the containment of transgene flow in Nicotiana tabacum.

    Directory of Open Access Journals (Sweden)

    Xu-Jing Wang

    Full Text Available The potential impact of transgene escape on the environment and food safety is a major concern to the scientists and public. This work aimed to assess the effect of intein-mediated gene splitting on containment of transgene flow. Two fusion genes, EPSPSn-In and Ic-EPSPSc, were constructed and integrated into N. tabacum, using Agrobacterium tumefaciens-mediated transformation. EPSPSn-In encodes the first 295 aa of the herbicide resistance gene 5-enolpyruvyl shikimate-3-phosphate synthase (EPSPS fused with the first 123 aa of the Ssp DnaE intein (In, whereas Ic-EPSPSc encodes the 36 C-terminal aa of the Ssp DnaE intein (Ic fused to the rest of EPSPS C terminus peptide sequences. Both EPSPSn-In and Ic-EPSPSc constructs were introduced into the same N. tabacum genome by genetic crossing. Hybrids displayed resistance to the herbicide N-(phosphonomethyl-glycine (glyphosate. Western blot analysis of protein extracts from hybrid plants identified full-length EPSPS. Furthermore, all hybrid seeds germinated and grew normally on glyphosate selective medium. The 6-8 leaf hybrid plants showed tolerance of 2000 ppm glyphosate in field spraying. These results indicated that functional EPSPS protein was reassembled in vivo by intein-mediated trans-splicing in 100% of plants. In order to evaluate the effect of the gene splitting technique for containment of transgene flow, backcrossing experiments were carried out between hybrids, in which the foreign genes EPSPSn-In and Ic-EPSPSc were inserted into different chromosomes, and non-transgenic plants NC89. Among the 2812 backcrossing progeny, about 25% (664 plantlets displayed glyphosate resistance. These data indicated that transgene flow could be reduced by 75%. Overall, our findings provide a new and highly effective approach for biological containment of transgene flow.

  11. Minimally-Invasive Gene Transfection by Chemical and Physical Interaction of Atmospheric Pressure Plasma Flow

    Science.gov (United States)

    Kaneko, Toshiro

    2014-10-01

    Non-equilibrium atmospheric pressure plasma irradiated to the living-cell is investigated for medical applications such as gene transfection, which is expected to play an important role in molecular biology, gene therapy, and creation of induced pluripotent stem (iPS) cells. However, the conventional gene transfection using the plasma has some problems that the cell viability is low and the genes cannot be transferred into some specific lipid cells, which is attributed to the unknown mechanism of the gene transfection using the plasma. Therefore, the time-controlled atmospheric pressure plasma flow is generated and irradiated to the living-cell suspended solution for clarifying the transfection mechanism toward developing highly-efficient and minimally- invasive gene transfection system. In this experiment, fluorescent dye YOYO-1 is used as the simulated gene and LIVE/DEAD Stain is simultaneously used for cell viability assay. By the fluorescence image, the transfection efficiency is calculated as the ratio of the number of transferred and surviving cells to total cell count. It is clarified that the transfection efficiency is significantly increased by the short-time (cell viability (>90%). This result indicates that the physical effects such as the electric field caused by the charged particles arriving at the surface of the cell membrane, and chemical effects associated with plasma-activated products in solution act synergistically to enhance the cell-membrane transport with low-damage. This work was supported by JSPS KAKENHI Grant Number 24108004.

  12. Involvement of calcitonin gene-related peptide in migraine: regional cerebral blood flow and blood flow velocity in migraine patients

    DEFF Research Database (Denmark)

    Lassen, L.H.; Jacobsen, V.B.; Haderslev, P.A.

    2008-01-01

    g/min) or placebo for 20 min was studied in 12 patients with migraine without aura outside attacks. Xenon-133 inhalation SPECT-determined regional cerebral blood flow (rCBF) and transcranial Doppler (TCD)-determined blood velocity (V-mean) in the middle cerebral artery (MCA), as well as the heart......Calcitonin gene-related peptide (CGRP)-containing nerves are closely associated with cranial blood vessels. CGRP is the most potent vasodilator known in isolated cerebral blood vessels. CGRP can induce migraine attacks, and two selective CGRP receptor antagonists are effective in the treatment...... of migraine attacks. It is therefore important to investigate its mechanism of action in patients with migraine. We here investigate the effects of intravenous human alpha-CGRP (h alpha CGRP) on intracranial hemodynamics. In a double-blind, cross-over study, the effect of intravenous infusion of haCGRP (2 mu...

  13. Evidence for gene flow between two sympatric mealybug species (Insecta; Coccoidea; Pseudococcidae).

    Science.gov (United States)

    Kol-Maimon, Hofit; Ghanim, Murad; Franco, José Carlos; Mendel, Zvi

    2014-01-01

    Occurrence of inter-species hybrids in natural populations might be evidence of gene flow between species. In the present study we found evidence of gene flow between two sympatric, genetically related scale insect species--the citrus mealybug Planococcus citri (Risso) and the vine mealybug Planococcus ficus (Signoret). These species can be distinguished by morphological, behavioral, and molecular traits. We employed the sex pheromones of the two respective species to study their different patterns of male attraction. We also used nuclear ITS2 (internal transcribed spacer 2) and mitochondrial COI (Cytochrome c oxidase sub unit 1) DNA sequences to characterize populations of the two species, in order to demonstrate the outcome of a possible gene flow between feral populations of the two species. Our results showed attraction to P. ficus pheromones of all tested populations of P. citri males but not vice versa. Furthermore, ITS2 sequences revealed the presence of 'hybrid females' among P. citri populations but not among those of P. ficus. 'hybrid females' from P. citri populations identified as P. citri females according to COI sequences. We offer two hypotheses for these results. 1) The occurrence of phenotypic and genotypic traits of P. ficus in P. citri populations may be attributed to both ancient and contemporary gene flow between their populations; and 2) we cannot rule out that an ancient sympatric speciation by which P. ficus emerged from P. citri might have led to the present situation of shared traits between these species. In light of these findings we also discuss the origin of the studied species and the importance of the pherotype phenomenon as a tool with which to study genetic relationships between congener scale insects.

  14. The population genomics of begomoviruses: global scale population structure and gene flow

    Directory of Open Access Journals (Sweden)

    Prasanna HC

    2010-09-01

    Full Text Available Abstract Background The rapidly growing availability of diverse full genome sequences from across the world is increasing the feasibility of studying the large-scale population processes that underly observable pattern of virus diversity. In particular, characterizing the genetic structure of virus populations could potentially reveal much about how factors such as geographical distributions, host ranges and gene flow between populations combine to produce the discontinuous patterns of genetic diversity that we perceive as distinct virus species. Among the richest and most diverse full genome datasets that are available is that for the dicotyledonous plant infecting genus, Begomovirus, in the Family Geminiviridae. The begomoviruses all share the same whitefly vector, are highly recombinogenic and are distributed throughout tropical and subtropical regions where they seriously threaten the food security of the world's poorest people. Results We focus here on using a model-based population genetic approach to identify the genetically distinct sub-populations within the global begomovirus meta-population. We demonstrate the existence of at least seven major sub-populations that can further be sub-divided into as many as thirty four significantly differentiated and genetically cohesive minor sub-populations. Using the population structure framework revealed in the present study, we further explored the extent of gene flow and recombination between genetic populations. Conclusions Although geographical barriers are apparently the most significant underlying cause of the seven major population sub-divisions, within the framework of these sub-divisions, we explore patterns of gene flow to reveal that both host range differences and genetic barriers to recombination have probably been major contributors to the minor population sub-divisions that we have identified. We believe that the global Begomovirus population structure revealed here could

  15. Evidence for gene flow between two sympatric mealybug species (Insecta; Coccoidea; Pseudococcidae.

    Directory of Open Access Journals (Sweden)

    Hofit Kol-Maimon

    Full Text Available Occurrence of inter-species hybrids in natural populations might be evidence of gene flow between species. In the present study we found evidence of gene flow between two sympatric, genetically related scale insect species--the citrus mealybug Planococcus citri (Risso and the vine mealybug Planococcus ficus (Signoret. These species can be distinguished by morphological, behavioral, and molecular traits. We employed the sex pheromones of the two respective species to study their different patterns of male attraction. We also used nuclear ITS2 (internal transcribed spacer 2 and mitochondrial COI (Cytochrome c oxidase sub unit 1 DNA sequences to characterize populations of the two species, in order to demonstrate the outcome of a possible gene flow between feral populations of the two species. Our results showed attraction to P. ficus pheromones of all tested populations of P. citri males but not vice versa. Furthermore, ITS2 sequences revealed the presence of 'hybrid females' among P. citri populations but not among those of P. ficus. 'hybrid females' from P. citri populations identified as P. citri females according to COI sequences. We offer two hypotheses for these results. 1 The occurrence of phenotypic and genotypic traits of P. ficus in P. citri populations may be attributed to both ancient and contemporary gene flow between their populations; and 2 we cannot rule out that an ancient sympatric speciation by which P. ficus emerged from P. citri might have led to the present situation of shared traits between these species. In light of these findings we also discuss the origin of the studied species and the importance of the pherotype phenomenon as a tool with which to study genetic relationships between congener scale insects.

  16. DNA Repair Profiling Reveals Nonrandom Outcomes at Cas9-Mediated Breaks.

    Science.gov (United States)

    van Overbeek, Megan; Capurso, Daniel; Carter, Matthew M; Thompson, Matthew S; Frias, Elizabeth; Russ, Carsten; Reece-Hoyes, John S; Nye, Christopher; Gradia, Scott; Vidal, Bastien; Zheng, Jiashun; Hoffman, Gregory R; Fuller, Christopher K; May, Andrew P

    2016-08-18

    The repair outcomes at site-specific DNA double-strand breaks (DSBs) generated by the RNA-guided DNA endonuclease Cas9 determine how gene function is altered. Despite the widespread adoption of CRISPR-Cas9 technology to induce DSBs for genome engineering, the resulting repair products have not been examined in depth. Here, the DNA repair profiles of 223 sites in the human genome demonstrate that the pattern of DNA repair following Cas9 cutting at each site is nonrandom and consistent across experimental replicates, cell lines, and reagent delivery methods. Furthermore, the repair outcomes are determined by the protospacer sequence rather than genomic context, indicating that DNA repair profiling in cell lines can be used to anticipate repair outcomes in primary cells. Chemical inhibition of DNA-PK enabled dissection of the DNA repair profiles into contributions from c-NHEJ and MMEJ. Finally, this work elucidates a strategy for using "error-prone" DNA-repair machinery to generate precise edits.

  17. Historical divergence and gene flow: coalescent analyses of mitochondrial, autosomal and sex-linked loci in Passerina buntings.

    Science.gov (United States)

    Carling, Matthew D; Lovette, Irby J; Brumfield, Robb T

    2010-06-01

    Quantifying the role of gene flow during the divergence of closely related species is crucial to understanding the process of speciation. We collected DNA sequence data from 20 loci (one mitochondrial, 13 autosomal, and six sex-linked) for population samples of Lazuli Buntings (Passerina amoena) and Indigo Buntings (Passerina cyanea) (Aves: Cardinalidae) to test explicitly between a strict allopatric speciation model and a model in which divergence occurred despite postdivergence gene flow. Likelihood ratio tests of coalescent-based population genetic parameter estimates indicated a strong signal of postdivergence gene flow and a strict allopatric speciation model was rejected. Analyses of partitioned datasets (mitochondrial, autosomal, and sex-linked) suggest the overall gene flow patterns are driven primarily by autosomal gene flow, as there is no evidence of mitochondrial gene flow and we were unable to reject an allopatric speciation model for the sex-linked data. This pattern is consistent with either a parapatric divergence model or repeated periods of allopatry with gene flow occurring via secondary contact. These results are consistent with the low fitness of female avian hybrids under Haldane's rule and demonstrate that sex-linked loci likely are important in the initial generation of reproductive isolation, not just its maintenance.

  18. Incomplete categorical data design non-randomized response techniques for sensitive questions in surveys

    CERN Document Server

    Tian, Guo-Liang

    2013-01-01

    Respondents to survey questions involving sensitive information, such as sexual behavior, illegal drug usage, tax evasion, and income, may refuse to answer the questions or provide untruthful answers to protect their privacy. This creates a challenge in drawing valid inferences from potentially inaccurate data. Addressing this difficulty, non-randomized response approaches enable sample survey practitioners and applied statisticians to protect the privacy of respondents and properly analyze the gathered data.Incomplete Categorical Data Design: Non-Randomized Response Techniqu

  19. Gene flow from genetically modified herbicide-resistant rapeseed to cruciferous weeds

    Institute of Scientific and Technical Information of China (English)

    ZHAO Xiangxiang; XIA Qiuxia; LU Dalei; LU Weiping; QI Cunkou; PU Huiming; LIU Geshan; ZHAO Jian; WANG Youping

    2006-01-01

    The sexual compatibility between genetically modified (GM) glyphosate-resistant rapeseed variety Q3 (Brassica napus L. ) and 5 cruciferous weeds is studied through the observation of fluorescence microscopy and cross-fertility after manual pollination. The results indicated that Q3 (as male) was highly incompatible with Thlaspi arvense L., Capsella bursa-pastoris (L.) Medic, Cardamine hirsuta L. and Rorippa palustris (L.) Besser (as female). Fluorescence microscopic observation showed that growing of pollen tubes terminated on the stigma surface or at the upper 1/3 part of the style. However, B. juncea×Q3 was compatible, and the compatibility index was 1.65. Under the neighboring growth and natural pollination conditions, the rates of gene flow from Q3 to T. arvense, C.bursa-pastoris, C. hirsute and R. palustris were all 0, while it was 0.86 % for B. juncea. These results indicate that there is difference in the rate of gene flow between GM rapeseed and cruciferous wild weeds, and frequency of gene flow is highly correlated with sexual compatibility.

  20. Detecting the existence of gene flow between Spanish and North African goats through a coalescent approach

    Science.gov (United States)

    Martínez, Amparo; Manunza, Arianna; Delgado, Juan Vicente; Landi, Vincenzo; Adebambo, Ayotunde; Ismaila, Muritala; Capote, Juan; El Ouni, Mabrouk; Elbeltagy, Ahmed; Abushady, Asmaa M.; Galal, Salah; Ferrando, Ainhoa; Gómez, Mariano; Pons, Agueda; Badaoui, Bouabid; Jordana, Jordi; Vidal, Oriol; Amills, Marcel

    2016-01-01

    Human-driven migrations are one of the main processes shaping the genetic diversity and population structure of domestic species. However, their magnitude and direction have been rarely analysed in a statistical framework. We aimed to estimate the impact of migration on the population structure of Spanish and African goats. To achieve this goal, we analysed a dataset of 1,472 individuals typed with 23 microsatellites. Population structure of African and Spanish goats was moderate (mean FST = 0.07), with the exception of the Canarian and South African breeds that displayed a significant differentiation when compared to goats from North Africa and Nigeria. Measurement of gene flow with Migrate-n and IMa coalescent genealogy samplers supported the existence of a bidirectional gene flow between African and Spanish goats. Moreover, IMa estimates of the effective number of migrants were remarkably lower than those calculated with Migrate-n and classical approaches. Such discrepancies suggest that recent divergence, rather than extensive gene flow, is the main cause of the weak population structure observed in caprine breeds. PMID:27966592

  1. Detecting the existence of gene flow between Spanish and North African goats through a coalescent approach.

    Science.gov (United States)

    Martínez, Amparo; Manunza, Arianna; Delgado, Juan Vicente; Landi, Vincenzo; Adebambo, Ayotunde; Ismaila, Muritala; Capote, Juan; El Ouni, Mabrouk; Elbeltagy, Ahmed; Abushady, Asmaa M; Galal, Salah; Ferrando, Ainhoa; Gómez, Mariano; Pons, Agueda; Badaoui, Bouabid; Jordana, Jordi; Vidal, Oriol; Amills, Marcel

    2016-12-14

    Human-driven migrations are one of the main processes shaping the genetic diversity and population structure of domestic species. However, their magnitude and direction have been rarely analysed in a statistical framework. We aimed to estimate the impact of migration on the population structure of Spanish and African goats. To achieve this goal, we analysed a dataset of 1,472 individuals typed with 23 microsatellites. Population structure of African and Spanish goats was moderate (mean FST = 0.07), with the exception of the Canarian and South African breeds that displayed a significant differentiation when compared to goats from North Africa and Nigeria. Measurement of gene flow with Migrate-n and IMa coalescent genealogy samplers supported the existence of a bidirectional gene flow between African and Spanish goats. Moreover, IMa estimates of the effective number of migrants were remarkably lower than those calculated with Migrate-n and classical approaches. Such discrepancies suggest that recent divergence, rather than extensive gene flow, is the main cause of the weak population structure observed in caprine breeds.

  2. Identification of landscape features influencing gene flow: How useful are habitat selection models?

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    Roffler, Gretchen H.; Schwartz, Michael K.; Pilgrim, Kristy L.; Talbot, Sandra; Sage, Kevin; Adams, Layne G.; Luikart, Gordon

    2016-01-01

    Understanding how dispersal patterns are influenced by landscape heterogeneity is critical for modeling species connectivity. Resource selection function (RSF) models are increasingly used in landscape genetics approaches. However, because the ecological factors that drive habitat selection may be different from those influencing dispersal and gene flow, it is important to consider explicit assumptions and spatial scales of measurement. We calculated pairwise genetic distance among 301 Dall's sheep (Ovis dalli dalli) in southcentral Alaska using an intensive noninvasive sampling effort and 15 microsatellite loci. We used multiple regression of distance matrices to assess the correlation of pairwise genetic distance and landscape resistance derived from an RSF, and combinations of landscape features hypothesized to influence dispersal. Dall's sheep gene flow was positively correlated with steep slopes, moderate peak normalized difference vegetation indices (NDVI), and open land cover. Whereas RSF covariates were significant in predicting genetic distance, the RSF model itself was not significantly correlated with Dall's sheep gene flow, suggesting that certain habitat features important during summer (rugged terrain, mid-range elevation) were not influential to effective dispersal. This work underscores that consideration of both habitat selection and landscape genetics models may be useful in developing management strategies to both meet the immediate survival of a species and allow for long-term genetic connectivity.

  3. Population genetic structure, gene flow and sex-biased dispersal in frillneck lizards (Chlamydosaurus kingii).

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    Ujvari, Beata; Dowton, Mark; Madsen, Thomas

    2008-08-01

    By using both mitochondrial and nuclear multiloci markers, we explored population genetic structure, gene flow and sex-specific dispersal of frillneck lizards (Chlamydosaurus kingii) sampled at three locations, separated by 10 to 50 km, in a homogenous savannah woodland in tropical Australia. Apart from a recombinant lizard, the mitochondrial analyses revealed two nonoverlapping haplotypes/populations, while the nuclear markers showed that the frillneck lizards represented three separate clusters/populations. Due to the small population size of the mtDNA, fixation may occur via founder effects and/or drift. We therefore suggest that either of these two processes, or a combination of the two, are the most likely causes of the discordant results obtained from the mitochondrial and the nuclear markers. In contrast to the nonoverlapping mitochondrial haplotypes, in 12 out of 74 lizards, mixed nuclear genotypes were observed, hence revealing a limited nuclear gene flow. Although gene flow should ultimately result in a blending of the populations, we propose that the distinct nuclear population structure is maintained by frequent fires resulting in local bottlenecks, and concomitant spatial separation of the frillneck lizard populations. Limited mark-recapture data and the difference in distribution of the mitochondrial and nuclear markers suggest that the mixed nuclear genotypes were caused by juvenile male-biased dispersal.

  4. Spatial and temporal assessment of pollen- and seed-mediated gene flow from genetically engineered plum Prunus domestica.

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    Scorza, Ralph; Kriss, Alissa B; Callahan, Ann M; Webb, Kevin; Demuth, Mark; Gottwald, Tim

    2013-01-01

    Pollen flow from a 0.46 ha plot of genetically engineered (GE) Prunus domestica located in West Virginia, USA was evaluated from 2000-2010. Sentinel plum trees were planted at distances ranging from 132 to 854 m from the center of the GE orchard. Plots of mixed plum varieties and seedlings were located at 384, 484 and 998 m from the GE plot. Bee hives (Apis mellifera) were dispersed between the GE plum plot and the pollen flow monitoring sites. Pollen-mediated gene flow from out of the GE plum plot to non-GE plums under the study conditions was low, only occurring at all in 4 of 11 years and then in only 0.31% of the 12,116 seeds analyzed. When it occurred, gene flow, calculated as the number of GUS positive embryos/total embryos sampled, ranged from 0.215% at 132 m from the center of the GE plum plot (28 m from the nearest GE plum tree) to 0.033-0.017% at longer distances (384-998 m). Based on the percentage of GUS positive seeds per individual sampled tree the range was 0.4% to 12%. Within the GE field plot, gene flow ranged from 4.9 to 39%. Gene flow was related to distance and environmental conditions. A single year sample from a sentinel plot 132 m from the center of the GE plot accounted for 65% of the total 11-year gene flow. Spatial modeling indicated that gene flow dramatically decreased at distances over 400 m from the GE plot. Air temperature and rainfall were, respectively, positively and negatively correlated with gene flow, reflecting the effects of weather conditions on insect pollinator activity. Seed-mediated gene flow was not detected. These results support the feasibility of coexistence of GE and non-GE plum orchards.

  5. Spatial and temporal assessment of pollen- and seed-mediated gene flow from genetically engineered plum Prunus domestica.

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    Ralph Scorza

    Full Text Available Pollen flow from a 0.46 ha plot of genetically engineered (GE Prunus domestica located in West Virginia, USA was evaluated from 2000-2010. Sentinel plum trees were planted at distances ranging from 132 to 854 m from the center of the GE orchard. Plots of mixed plum varieties and seedlings were located at 384, 484 and 998 m from the GE plot. Bee hives (Apis mellifera were dispersed between the GE plum plot and the pollen flow monitoring sites. Pollen-mediated gene flow from out of the GE plum plot to non-GE plums under the study conditions was low, only occurring at all in 4 of 11 years and then in only 0.31% of the 12,116 seeds analyzed. When it occurred, gene flow, calculated as the number of GUS positive embryos/total embryos sampled, ranged from 0.215% at 132 m from the center of the GE plum plot (28 m from the nearest GE plum tree to 0.033-0.017% at longer distances (384-998 m. Based on the percentage of GUS positive seeds per individual sampled tree the range was 0.4% to 12%. Within the GE field plot, gene flow ranged from 4.9 to 39%. Gene flow was related to distance and environmental conditions. A single year sample from a sentinel plot 132 m from the center of the GE plot accounted for 65% of the total 11-year gene flow. Spatial modeling indicated that gene flow dramatically decreased at distances over 400 m from the GE plot. Air temperature and rainfall were, respectively, positively and negatively correlated with gene flow, reflecting the effects of weather conditions on insect pollinator activity. Seed-mediated gene flow was not detected. These results support the feasibility of coexistence of GE and non-GE plum orchards.

  6. Possible effects of (trans)gene flow from crops on the genetic diversity from landraces and wild relatives.

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    Gepts, Paul; Papa, Roberto

    2003-01-01

    Gene flow is a potential concern associated with the use of transgenic crops because it could affect genetic diversity of related landraces and wild relatives. This concern has taken on added importance with the looming introduction of transgenic crops in centers of crop domestication (Mexico, China) and those producing pharmaceutical compounds. For gene flow to take place among cultivars and their wild relatives, several steps have to be fulfilled, including the presence of cultivars or wild relatives within pollen or seed dispersal range, the ability to produce viable and fertile hybrids, at least partial overlap in flowering time, actual gene flow by pollen or seed, and the establishment of crop genes in the domesticated or wild recipient populations. In contrast with domestication genes, which often make crops less adapted to natural ecosystems, transgenes frequently represent gains of function, which might release wild relatives from constraints that limit their fitness. In most sexually reproducing organisms, the chromosomal region affected by selection of a single gene amounts to a small percentage of the total genome size. Because of gene flow, the level of genetic diversity present in the domesticated gene pool becomes a crucial factor affecting the genetic diversity of the wild gene pool. For some crops, such as cotton and maize, the introduction of transgenic technologies has led to a consolidation of the seed industry and a reduction in the diversity of the elite crop gene pool. Thus, diversity in improved varieties grown by farmers needs to be monitored. Several areas deserve further study, such as the actual magnitude of gene flow and its determinants in different agroecosystems, the long-term effects of gene flow on genetic diversity both across gene pools and within genomes, the expression of transgenes in new genetic backgrounds, and the effects of socio-economic factors on genetic diversity.

  7. Landscape genetics as a tool for conservation planning: predicting the effects of landscape change on gene flow.

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    van Strien, Maarten J; Keller, Daniela; Holderegger, Rolf; Ghazoul, Jaboury; Kienast, Felix; Bolliger, Janine

    2014-03-01

    For conservation managers, it is important to know whether landscape changes lead to increasing or decreasing gene flow. Although the discipline of landscape genetics assesses the influence of landscape elements on gene flow, no studies have yet used landscape-genetic models to predict gene flow resulting from landscape change. A species that has already been severely affected by landscape change is the large marsh grasshopper (Stethophyma grossum), which inhabits moist areas in fragmented agricultural landscapes in Switzerland. From transects drawn between all population pairs within maximum dispersal distance (landscape planning.

  8. Measuring gene flow from two birdsfoot trefoil (Lotus corniculatus) field trials using transgenes as tracer markers.

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    De Marchis, F; Bellucci, M; Arcioni, S

    2003-06-01

    Genetic engineering is becoming a useful tool in the improvement of plants but concern has been expressed about the potential environmental risks of releasing genetically modified (GM) organisms into the environment. Attention has focused on pollen dispersal as a major issue in the risk assessment of transgenic crop plants. In this study, pollen-mediated dispersal of transgenes via cross-fertilization was examined. Plants of Lotus corniculatus L. transformed with either the Escherichia coli asparagine synthetase gene asnA or the beta-glucuronidase gene uidA, were used as the pollen donor. Nontransgenic plants belonging to the species L. corniculatus L., L. tenuis Waldst. and Kit. ex Willd, and L. pedunculatus Cav., were utilized as recipients. Two experimental fields were established in two areas of central Italy. Plants carrying the uidA gene were partially sterile, therefore only the asnA gene was used as a tracer marker. No transgene flow between L. corniculatus transformants and the nontransgenic L. tenuis and L. pedunculatus plants was detected. As regards nontransgenic L. corniculatus plants, in one location flow of asnA transgene was detected up to 18 m from the 1.8 m2 donor plot. In the other location, pollen dispersal occurred up to 120 m from the 14 m2 pollinating plot.

  9. Detection of Gene Flow from Sexual to Asexual Lineages in Thrips tabaci (Thysanoptera: Thripidae).

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    Li, Xiao-Wei; Wang, Ping; Fail, Jozsef; Shelton, Anthony M

    2015-01-01

    Populations of Thrips tabaci are known to have two sympatric but genetically isolated reproductive modes, arrhenotoky (sexual reproduction) and thelytoky (asexual reproduction). Herein, we report behavioral, ecological and genetic studies to determine whether there is gene flow between arrhenotokous and thelytokous T. tabaci. We did not detect significant preference by arrhenotokous males to mate with females of a particular reproductive mode, nor did we detect significant behavioral differences between arrhenotokous males mated with arrhenotokous or thelytokous females in their pre-copulation, copulation duration and mating frequency. Productive gene transfer resulting from the mating between the two modes was experimentally confirmed. Gene transfer from arrhenotokous T. tabaci to thelytokous T. tabaci was further validated by confirmation of the passage of the arrhenotokous male-originated nuclear gene (histone H3 gene) allele to the F2 generation. These behavioral, ecological and genetic studies confirmed gene transfer from the sexual arrhenotokous mode to the asexual thelytokous mode of T. tabaci in the laboratory. These results demonstrate that asexual T. tabaci populations may acquire genetic variability from sexual populations, which could offset the long-term disadvantage of asexual reproduction.

  10. Detection of Gene Flow from Sexual to Asexual Lineages in Thrips tabaci (Thysanoptera: Thripidae.

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    Xiao-Wei Li

    Full Text Available Populations of Thrips tabaci are known to have two sympatric but genetically isolated reproductive modes, arrhenotoky (sexual reproduction and thelytoky (asexual reproduction. Herein, we report behavioral, ecological and genetic studies to determine whether there is gene flow between arrhenotokous and thelytokous T. tabaci. We did not detect significant preference by arrhenotokous males to mate with females of a particular reproductive mode, nor did we detect significant behavioral differences between arrhenotokous males mated with arrhenotokous or thelytokous females in their pre-copulation, copulation duration and mating frequency. Productive gene transfer resulting from the mating between the two modes was experimentally confirmed. Gene transfer from arrhenotokous T. tabaci to thelytokous T. tabaci was further validated by confirmation of the passage of the arrhenotokous male-originated nuclear gene (histone H3 gene allele to the F2 generation. These behavioral, ecological and genetic studies confirmed gene transfer from the sexual arrhenotokous mode to the asexual thelytokous mode of T. tabaci in the laboratory. These results demonstrate that asexual T. tabaci populations may acquire genetic variability from sexual populations, which could offset the long-term disadvantage of asexual reproduction.

  11. Dielectrophoresis based continuous-flow nano sorter: fast quality control of gene vaccines.

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    Viefhues, Martina; Wegener, Sonja; Rischmüller, Anja; Schleef, Martin; Anselmetti, Dario

    2013-08-01

    We present a prototype nanofluidic device, developed for the continuous-flow dielectrophoretic (DEP) fractionation, purification, and quality control of sample suspensions for gene vaccine production. The device consists of a cross injector, two operation regions, and separate outlets where the analytes are collected. In each DEP operation region, an inhomogeneous electric field is generated at a channel spanning insulating ridge. The samples are driven by ac and dc voltages that generate a dielectrophoretic potential at the ridge as well as (linear) electrokinetics. Since the DEP potential differs at the two ridges, probes of three and more species can be iteratively fully fractionated. We demonstrate the fast and efficient separation of parental plasmid, miniplasmid, and minicircle DNA, where the latter is applicable as a gene vaccine. Since the present technique is virtually label-free, it offers a fast purification and in-process quality control with low consumption, in parallel, for the production of gene vaccines.

  12. Reducing bias in survival under non-random temporary emigration

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    Peñaloza, Claudia L.; Kendall, William L.; Langtimm, Catherine Ann

    2014-01-01

    Despite intensive monitoring, temporary emigration from the sampling area can induce bias severe enough for managers to discard life-history parameter estimates toward the terminus of the times series (terminal bias). Under random temporary emigration unbiased parameters can be estimated with CJS models. However, unmodeled Markovian temporary emigration causes bias in parameter estimates and an unobservable state is required to model this type of emigration. The robust design is most flexible when modeling temporary emigration, and partial solutions to mitigate bias have been identified, nonetheless there are conditions were terminal bias prevails. Long-lived species with high adult survival and highly variable non-random temporary emigration present terminal bias in survival estimates, despite being modeled with the robust design and suggested constraints. Because this bias is due to uncertainty about the fate of individuals that are undetected toward the end of the time series, solutions should involve using additional information on survival status or location of these individuals at that time. Using simulation, we evaluated the performance of models that jointly analyze robust design data and an additional source of ancillary data (predictive covariate on temporary emigration, telemetry, dead recovery, or auxiliary resightings) in reducing terminal bias in survival estimates. The auxiliary resighting and predictive covariate models reduced terminal bias the most. Additional telemetry data was effective at reducing terminal bias only when individuals were tracked for a minimum of two years. High adult survival of long-lived species made the joint model with recovery data ineffective at reducing terminal bias because of small-sample bias. The naïve constraint model (last and penultimate temporary emigration parameters made equal), was the least efficient, though still able to reduce terminal bias when compared to an unconstrained model. Joint analysis of several

  13. Pollination between maize and teosinte: an important determinant of gene flow in Mexico.

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    Baltazar, Baltazar M; de Jesús Sánchez-Gonzalez, José; de la Cruz-Larios, Lino; Schoper, John B

    2005-02-01

    Gene flow between maize [Zea mays (L.)] and its wild relatives does occur, but at very low frequencies. Experiments were undertaken in Tapachula, Nayarit, Mexico to investigate gene flow between a hybrid maize, landraces of maize and teosinte (Z. mays ssp. mexicana, races Chalco and Central Plateau). Hybridization, flowering synchrony, pollen size and longevity, silk elongation rates, silk and trichome lengths and tassel diameter and morphology were measured. Hybrid and open-pollinated maize ears produced a mean of 8 and 11 seeds per ear, respectively, when hand-pollinated with teosinte pollen, which is approximately 1-2% of the ovules normally produced on a hybrid maize ear. Teosinte ears produced a mean of 0.2-0.3 seeds per ear when pollinated with maize pollen, which is more than one-fold fewer seeds than produced on a maize ear pollinated with teosinte pollen. The pollination rate on a per plant basis was similar in the context of a maize plant with 400-500 seeds and a teosinte plant with 30-40 inflorescences and 9-12 fruitcases per inflorescence. A number of other factors also influenced gene-flow direction: (1) between 90% and 95% of the fruitcases produced on teosinte that was fertilized by maize pollen were sterile; (2) teosinte collections were made in an area where incompatibility systems that limit fertilization are present; (3) silk longevity was much shorter for teosinte than for maize (approx. 4 days vs. approx. 11 days); (4) teosinte produced more pollen on a per plant basis than the landraces and commercial hybrid maize; (5) teosinte frequently produced lateral branches with silks close to a terminal tassel producing pollen. Collectively these factors tend to favor crossing in the direction of teosinte to maize. Our results support the hypothesis that gene flow and the subsequent introgression of maize genes into teosinte populations most probably results from crosses where teosinte first pollinates maize. The resultant hybrids then backcross with

  14. Flow-dependent regulation of vascular function and gene expression in rat superior mesenteric artery

    Institute of Scientific and Technical Information of China (English)

    XIA Shang; DENG Chang-sheng

    2009-01-01

    Background Mesenteric artery thrombosis is prone to occur at specific arterial regions with different fluid flow patterns,yet mechanistic links between blood flow and vascular function remain unclear. This study aired to investigate the role of blood flow in regulation of vascular function and gene expression in rats.Methods Isometric tension was recorded in wire myograph to examine vascular function of specific regions (trunk parts and proximal parts from the origin) with different blood flow in superior mesenteric artery (SMA). Endothelial nitric oxide syntheses (eNOS), phosphorylated-eNOS (p-eNOS), serine-threonine kinase Akt and phosphorylated-Akt (p-Akt) protein expressions in SMA were examined by Western blotting. Significance was analyzed using a Student's ttest or analysis of variance (ANOVA) followed by a Dunnett's multiple-comparison post hoc test.Results Compared with trunks, proximal parts exhibited severely impaired relaxant responses to acetylcholine (Ach) (1 nmol/L to 10 pmol/L) (P 0.05).Conclusion Critical components that drive the vascular function and influence the localization of mesenteric artery thrombosis are flow-responsive elements within the vascular endothelium.

  15. STUDY OF GENE FLOW FROM GM COTTON (Gossypium hirsutum VARIETIES IN “EL ESPINAL” (TOLIMA, COLOMBIA.

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    Alejandro Chaparro Giraldo

    2013-10-01

    Full Text Available In 2009, 4088 hectares of genetically modified (GM cotton were planted in Tolima (Colombia, however there is some uncertainty about containment measures needed to prevent the flow of pollen and seed from regulated GM fields into adjacent fields. In this study, the gene flow from GM cotton varieties to conventional or feral cotton plants via seed and pollen was evaluated. ImmunostripTM, PCR and ELISA assays were used to detect gene flow. Fifty six refuges, 27 fields with conventional cotton and four feral individuals of the enterprise “Remolinos Inc.” located in El Espinal (Tolima were analyzed in the first half of 2010. The results indicated seeds mediated gene flow in 45 refuges (80,4 % and 26 fields with conventional cotton (96 %, besides a pollen mediated gene flow in one field with conventional cotton and nine refuges. All fields cultivated with conventional cotton showed gene flow from GM cotton. Two refuges and two feral individuals did not reveal gene flow from GM cotton. 

  16. Divergence with gene flow between Ponto-Caspian refugia in an anadromous cyprinid Rutilus frisii revealed by multiple gene phylogeography.

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    Kotlík, Petr; Marková, Silvia; Choleva, Lukás; Bogutskaya, Nina G; Ekmekçi, F Guler; Ivanova, Petya P

    2008-02-01

    The Black and Caspian Seas have experienced alternating periods of isolation and interconnection over many Milankovitch climate oscillations and most recently became separated when the meltwater overflow from the Caspian Sea ceased at the end of the last glaciation. Climate-induced habitat changes have indisputably had profound impacts on distribution and demography of aquatic species, yet uncertainties remain about the relative roles of isolation and dispersal in the response of species shared between the Black and Caspian Sea basins. We examined these issues using phylogeographical analysis of an anadromous cyprinid fish Rutilus frisii. Bayesian coalescence analyses of sequence variation at two nuclear and one mitochondrial genes suggest that the Black and Caspian Seas supported separate populations of R. frisii during the last glaciation. Parameter estimates from the fitted isolation-with-migration model showed that their separation was not complete, however, and that the two populations continued to exchange genes in both directions. These analyses also suggested that majority of migrations occurred during the Pleistocene, showing that the variation shared between the Black and Caspian Seas is the result of ancient dispersal along the temporary natural connections between the basins, rather than of incomplete lineage sorting or recent human-mediated dispersal. Gene flow between the refugial populations was therefore an important source of genetic variation, and we suggest that it facilitated the evolutionary response of the populations to changing climate.

  17. Performance of vertical up-flow constructed wetlands on swine wastewater containing tetracyclines and tet genes.

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    Huang, Xu; Liu, Chaoxiang; Li, Ke; Su, Jianqiang; Zhu, Gefu; Liu, Lin

    2015-03-01

    Antibiotics and antibiotic resistance genes (ARGs) pollution in animal feeding farms received more public attention recently. Livestock wastewater contains large quantities of antibiotics and ARGs even after traditional lagoon treatment. In this study, the performance of vertical up-flow constructed wetlands (VUF-CWs) on swine wastewater containing tetracycline compounds (TCs) and tet genes was evaluated based on three aspects, TCs and tet genes removal efficiencies, residual TCs and tet genes in soils and plants, and the effect of TCs accumulation on nutrients removal and tet genes development. High removal efficiencies (69.0-99.9%) were achieved for oxytetracycline (OTC), tetracycline (TC) and chlortetracycline (CTC) with or without OTC spiked in the influent additionally. TCs concentrations in surface soils increased at first two sampling periods and then decreased after plants were harvested. Satisfactory nutrients removal efficiencies were also obtained, but TN and NH4-N removal efficiencies were significantly negative correlated with total concentration of TCs (∑TCs) in the soils (p < 0.01). The absolute abundances of all the target genes (tetO, tetM, tetW, tetA, tetX and intI1) were greatly reduced with their log units ranging from 0.26 to 3.3. However, the relative abundances of tetO, tetM and tetX in some effluent samples were significantly higher than those in the influent (p < 0.05). The relative abundances of tet genes except for tetO were significantly correlated with ∑TCs in the soils (p < 0.05). In summary, the proposed VUF-CWs are effective alternative for the removal of TCs and tet genes. But it is of great importance to prevent large accumulation of TCs in the soils. Copyright © 2014 Elsevier Ltd. All rights reserved.

  18. Gene flow between sympatric life history forms of Oncorhynchus mykiss located above and below migratory barriers.

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    Donald M Van Doornik

    Full Text Available Oncorhynchus mykiss have a diverse array of life history types, and understanding the relationship among types is important for management of the species. Patterns of gene flow between sympatric freshwater resident O. mykiss, commonly known as rainbow trout, and anadromous O. mykiss, commonly known as steelhead, populations are complex and poorly understood. In this study, we attempt to determine the occurrence and pathways of gene flow and the degree of genetic similarity between sympatric resident and anadromous O. mykiss in three river systems, and investigate whether resident O. mykiss are producing anadromous offspring in these rivers, two of which have complete barriers to upstream migration. We found that the population structure of the O. mykiss in these rivers appears to be influenced more by the presence of a barrier to upstream migration than by life history type. The sex ratio of resident O. mykiss located above a barrier, and smolts captured in screw traps was significantly skewed in favor of females, whereas the reverse was true below the barriers, suggesting that male resident O. mykiss readily migrate downstream over the barrier, and that precocious male maturation may be occurring in the anadromous populations. Through paternity analyses, we also provide direct confirmation that resident O. mykiss can produce offspring that become anadromous. Most (89% of the resident O. mykiss that produced anadromous offspring were males. Our results add to the growing body of evidence that shows that gene flow does readily occur between sympatric resident and anadromous O. mykiss life history types, and indicates that resident O. mykiss populations may be a potential repository of genes for the anadromous life history type.

  19. Molecular cloaking of H2A.Z on mortal DNA chromosomes during nonrandom segregation.

    Science.gov (United States)

    Huh, Yang Hoon; Sherley, James L

    2011-10-01

    Although nonrandom sister chromatid segregation is a singular property of distributed stem cells (DSCs) that are responsible for renewing and repairing mature vertebrate tissues, both its cellular function and its molecular mechanism remain unknown. This situation persists in part because of the lack of facile methods for detecting and quantifying nonrandom segregating cells and for identifying chromosomes with immortal DNA strands, the cellular molecules that signify nonrandom segregation. During nonrandom segregation, at each mitosis, asymmetrically self-renewing DSCs continuously cosegregate to themselves the set of chromosomes that contain immortal DNA strands, which are the oldest DNA strands. Here, we report the discovery of a molecular asymmetry between segregating sets of immortal chromosomes and opposed mortal chromosomes (i.e., containing the younger set of DNA template strands) that constitutes a new convenient biomarker for detection of cells undergoing nonrandom segregation and direct delineation of chromosomes that bear immortal DNA strands. In both cells engineered with DSC-specific properties and ex vivo-expanded mouse hair follicle stem cells, the histone H2A variant H2A.Z shows specific immunodetection on immortal DNA chromosomes. Cell fixation analyses indicate that H2A.Z is present on mortal chromosomes as well but is cloaked from immunodetection, and the cloaking entity is acid labile. The H2A.Z chromosomal asymmetry produced by molecular cloaking provides a first direct assay for nonrandom segregation and for chromosomes with immortal DNA strands. It also seems likely to manifest an important aspect of the underlying mechanism(s) responsible for nonrandom sister chromatid segregation in DSCs.

  20. UNDERSTANDING THE POPULATION GENETIC STRUCTURE OF GLEDITSIA TRIACANTHOS L.: THE SCALE AND PATTERN OF POLLEN GENE FLOW.

    Science.gov (United States)

    Schnabel, Andrew; Hamrick, J L

    1995-10-01

    Spatial and temporal patterns of gene flow determine the extent to which populations can differentiate from one another as a result of natural selection or genetic drift. In this study, we investigated pollen-mediated gene flow in two eastern Kansas populations of the subdioecious tree species, Gleditsia triacanthos L. (Leguminosae), or honeylocust. In 2 yr at each site, we used paternity-exclusion analysis to estimate the proportion of seeds sired by immigrant pollen. We also used a single-parent and parent-pair exclusion analysis on naturally established seedlings and saplings to estimate gene flow into one site over a 12-yr period and into the second site over a 22-yr period. Results of both analyses showed high minimum estimates of pollen gene flow into each site (17%-30%). In each population, we found significantly less gene flow in years of high fruit production than in years of low fruit production, but in one population, we observed little variation in gene-flow rates among age classes of seedlings and saplings. The level of pollen gene flow showed weak negative dependence on the relative isolation distances of the maternal trees sampled (140-240 m at one site vs. 85-120 m at the second site), and gene-flow estimates from naturally established juveniles were very similar at the two sites. Within populations, a multiple regression model showed that maximum-likelihood estimates of male fertility were negatively associated with distances between mates and positively associated with male size as measured by stem diameter. In neither population, however, did the regression explain more than 16% of the total variation in male fertilities. © 1995 The Society for the Study of Evolution.

  1. Gene flow from transgenic oilseed rape (Brassica napus L.) to cruciferous weeds under mentor pollen inducement

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    The alien gene flow between genetically modified glyphosate-resistant rapeseed variety Q3 ( Brassica napus L. ) and four cruciferous weeds was studied under mentor pollen inducement. The results showed that when Thlaspi arvense L., Capsella bursapastoris (L.) Medic, Cardamine hirsuta L. and Rorippa palustris (L.) Besser were pollinated with mentor pollen, the mixed Q3 and the weed, pollen grains aggregated largely and germinated quickly, and the numbers of pollen tubes penetrating into the style and the ovary were greatly increased as compared with corresponding self-pollination groups. Twenty four to forty eight hours after pollination, several pollen tubes were observed to penetrate into the ovule via micropyle in each mentor combination. However, when the mentor progenies were analyzed by PCR, all of them showed negative for the Q3 herbicide-resistant gene. Collectively, these results indicated that crossing between T. arvense, C. bursa-pastoris, C. hirsuta, R. palustris (as female) and Q3 (as male) was highly incompatible and the herbicide-resistant gene could not flow from Q3 to these four weeds.

  2. Is the Gibraltar strait a barrier to gene flow for the bat Myotis myotis (Chiroptera: Vespertilionidae)?

    Science.gov (United States)

    Castella, V; Ruedi, M; Excoffier, L; Ibáñez, C; Arlettaz, R; Hausser, J

    2000-11-01

    Because of their role in limiting gene flow, geographical barriers like mountains or seas often coincide with intraspecific genetic discontinuities. Although the Strait of Gibraltar represents such a potential barrier for both plants and animals, few studies have been conducted on its impact on gene flow. Here we test this effect on a bat species (Myotis myotis) which is apparently distributed on both sides of the strait. Six colonies of 20 Myotis myotis each were sampled in southern Spain and northern Morocco along a linear transect of 1350 km. Results based on six nuclear microsatellite loci reveal no significant population structure within regions, but a complete isolation between bats sampled on each side of the strait. Variability at 600 bp of a mitochondrial gene (cytochrome b) confirms the existence of two genetically distinct and perfectly segregating clades, which diverged several million years ago. Despite the narrowness of the Gibraltar Strait (14 km), these molecular data suggest that neither males, nor females from either region have ever reproduced on the opposite side of the strait. Comparisons of molecular divergence with bats from a closely related species (M. blythii) suggest that the North African clade is possibly a distinct taxon warranting full species rank. We provisionally refer to it as Myotis cf punicus Felten 1977, but a definitive systematic understanding of the whole Mouse-eared bat species complex awaits further genetic sampling, especially in the Eastern Mediterranean areas.

  3. Gene flow among different taxonomic units: evidence from nuclear and cytoplasmic markers in Cedrus plantation forests.

    Science.gov (United States)

    Fady, B; Lefèvre, F; Reynaud, M; Vendramin, G G; Bou Dagher-Kharrat, M; Anzidei, M; Pastorelli, R; Savouré, A; Bariteau, M

    2003-10-01

    Hybridization and introgression are important natural evolutionary processes that can be successfully investigated using molecular markers and open- and controlled-pollinated progeny. In this study, we collected open-pollinated seeds from Cedrus atlantica, Cedrus libani and C. libani x C. atlantica hybrids from three French-plantation forests. We also used pollen from C. libani and Cedrus brevifolia to pollinate C. atlantica trees. The progeny were analyzed using three different types of molecular markers: RAPDs, AFLPs and cpSSRs. Chloroplast DNA was found to be paternally inherited in Cedrus from the progeny of controlled-crosses. Heteroplasmy, although possible, could not be undoubtedly detected. There was no indication of strong reproductive isolating barriers among the three Mediterranean Cedrus taxa. Gene flow between C. atlantica and C. libani accounted for 67 to 81% of viable open-pollinated seedlings in two plantation forests. We propose that Mediterranean Cedrus taxa should be considered as units of a single collective species comprising two regional groups, North Africa and the Middle East. We recommend the use of cpSSRs for monitoring gene flow between taxa in plantation forests, especially in areas where garden specimens of one species are planted in the vicinity of selected seed-stands and gene-conservation reserves of another species.

  4. The influence of gene flow and drift on genetic and phenotypic divergence in two species of Zosterops in Vanuatu.

    Science.gov (United States)

    Clegg, Sonya M; Phillimore, Albert B

    2010-04-12

    Colonization of an archipelago sets the stage for adaptive radiation. However, some archipelagos are home to spectacular radiations, while others have much lower levels of diversification. The amount of gene flow among allopatric populations is one factor proposed to contribute to this variation. In island colonizing birds, selection for reduced dispersal ability is predicted to produce changing patterns of regional population genetic structure as gene flow-dominated systems give way to drift-mediated divergence. If this transition is important in facilitating phenotypic divergence, levels of genetic and phenotypic divergence should be associated. We consider population genetic structure and phenotypic divergence among two co-distributed, congeneric (Genus: Zosterops) bird species inhabiting the Vanuatu archipelago. The more recent colonist, Z. lateralis, exhibits genetic patterns consistent with a strong influence of distance-mediated gene flow. However, complex patterns of asymmetrical gene flow indicate variation in dispersal ability or inclination among populations. The endemic species, Z. flavifrons, shows only a partial transition towards a drift-mediated system, despite a long evolutionary history on the archipelago. We find no strong evidence that gene flow constrains phenotypic divergence in either species, suggesting that levels of inter-island gene flow do not explain the absence of a radiation across this archipelago.

  5. Gene flow and genetic diversity in cultivated and wild cacao (Theobroma cacao) in Bolivia.

    Science.gov (United States)

    Chumacero de Schawe, Claudia; Durka, Walter; Tscharntke, Teja; Hensen, Isabell; Kessler, Michael

    2013-11-01

    The role of pollen flow within and between cultivated and wild tropical crop species is little known. To study the pollen flow of cacao, we estimated the degree of self-pollination and pollen dispersal distances as well as gene flow between wild and cultivated cacao (Theobroma cacao L.). We studied pollen flow and genetic diversity of cultivated and wild cacao populations by genotyping 143 wild and 86 cultivated mature plants and 374 seedlings raised from 19 wild and 25 cultivated trees at nine microsatellite loci. A principal component analysis distinguished wild and cultivated cacao trees, supporting the notion that Bolivia harbors truly wild cacao populations. Cultivated cacao had a higher level of genetic diversity than wild cacao, presumably reflecting the varied origin of cultivated plants. Both cacao types had high outcrossing rates, but the paternity analysis revealed 7-14% self-pollination in wild and cultivated cacao. Despite the tiny size of the pollinators, pollen was transported distances up to 3 km; wild cacao showed longer distances (mean = 922 m) than cultivated cacao (826 m). Our data revealed that 16-20% of pollination events occurred between cultivated and wild populations. We found evidence of self-pollination in both wild and cultivated cacao. Pollination distances are larger than those typically reported in tropical understory tree species. The relatively high pollen exchange from cultivated to wild cacao compromises genetic identity of wild populations, calling for the protection of extensive natural forest tracts to protect wild cacao in Bolivia.

  6. Parentage versus two-generation analyses for estimating pollen-mediated gene flow in plant populations.

    Science.gov (United States)

    Burczyk, Jaroslaw; Koralewski, Tomasz E

    2005-07-01

    Assessment of contemporary pollen-mediated gene flow in plants is important for various aspects of plant population biology, genetic conservation and breeding. Here, through simulations we compare the two alternative approaches for measuring pollen-mediated gene flow: (i) the NEIGHBORHOOD model--a representative of parentage analyses, and (ii) the recently developed TWOGENER analysis of pollen pool structure. We investigate their properties in estimating the effective number of pollen parents (N(ep)) and the mean pollen dispersal distance (delta). We demonstrate that both methods provide very congruent estimates of N(ep) and delta, when the methods' assumptions considering the shape of pollen dispersal curve and the mating system follow those used in data simulations, although the NEIGHBORHOOD model exhibits generally lower variances of the estimates. The violations of the assumptions, especially increased selfing or long-distance pollen dispersal, affect the two methods to a different degree; however, they are still capable to provide comparable estimates of N(ep). The NEIGHBORHOOD model inherently allows to estimate both self-fertilization and outcrossing due to the long-distance pollen dispersal; however, the TWOGENER method is particularly sensitive to inflated selfing levels, which in turn may confound and suppress the effects of distant pollen movement. As a solution we demonstrate that in case of TWOGENER it is possible to extract the fraction of intraclass correlation that results from outcrossing only, which seems to be very relevant for measuring pollen-mediated gene flow. The two approaches differ in estimation precision and experimental efforts but they seem to be complementary depending on the main research focus and type of a population studied.

  7. Intergenic DNA sequences from the human X chromosome reveal high rates of global gene flow

    Directory of Open Access Journals (Sweden)

    Wall Jeffrey D

    2008-11-01

    Full Text Available Abstract Background Despite intensive efforts devoted to collecting human polymorphism data, little is known about the role of gene flow in the ancestry of human populations. This is partly because most analyses have applied one of two simple models of population structure, the island model or the splitting model, which make unrealistic biological assumptions. Results Here, we analyze 98-kb of DNA sequence from 20 independently evolving intergenic regions on the X chromosome in a sample of 90 humans from six globally diverse populations. We employ an isolation-with-migration (IM model, which assumes that populations split and subsequently exchange migrants, to independently estimate effective population sizes and migration rates. While the maximum effective size of modern humans is estimated at ~10,000, individual populations vary substantially in size, with African populations tending to be larger (2,300–9,000 than non-African populations (300–3,300. We estimate mean rates of bidirectional gene flow at 4.8 × 10-4/generation. Bidirectional migration rates are ~5-fold higher among non-African populations (1.5 × 10-3 than among African populations (2.7 × 10-4. Interestingly, because effective sizes and migration rates are inversely related in African and non-African populations, population migration rates are similar within Africa and Eurasia (e.g., global mean Nm = 2.4. Conclusion We conclude that gene flow has played an important role in structuring global human populations and that migration rates should be incorporated as critical parameters in models of human demography.

  8. Evidence for environmental and ecological selection in a microbe with no geographic limits to gene flow

    Science.gov (United States)

    Whittaker, Kerry A.; Rynearson, Tatiana A.

    2017-01-01

    The ability for organisms to disperse throughout their environment is thought to strongly influence population structure and thus evolution of diversity within species. A decades-long debate surrounds processes that generate and support high microbial diversity, particularly in the ocean. The debate concerns whether diversification occurs primarily through geographic partitioning (where distance limits gene flow) or through environmental selection, and remains unresolved due to lack of empirical data. Here we show that gene flow in a diatom, an ecologically important eukaryotic microbe, is not limited by global-scale geographic distance. Instead, environmental and ecological selection likely play a more significant role than dispersal in generating and maintaining diversity. We detected significantly diverged populations (FST > 0.130) and discovered temporal genetic variability at a single site that was on par with spatial genetic variability observed over distances of 15,000 km. Relatedness among populations was decoupled from geographic distance across the global ocean and instead, correlated significantly with water temperature and whole-community chlorophyll a. Correlations with temperature point to the importance of environmental selection in structuring populations. Correlations with whole-community chlorophyll a, a proxy for autotrophic biomass, suggest that ecological selection via interactions with other plankton may generate and maintain population genetic structure in marine microbes despite global-scale dispersal. Here, we provide empirical evidence for global gene flow in a marine eukaryotic microbe, suggesting that everything holds the potential to be everywhere, with environmental and ecological selection rather than geography or dispersal dictating the structure and evolution of diversity over space and time. PMID:28209775

  9. Circumpolar Genetic Structure and Recent Gene Flow of Polar Bears: A Reanalysis.

    Directory of Open Access Journals (Sweden)

    René M Malenfant

    Full Text Available Recently, an extensive study of 2,748 polar bears (Ursus maritimus from across their circumpolar range was published in PLOS ONE, which used microsatellites and mitochondrial haplotypes to apparently show altered population structure and a dramatic change in directional gene flow towards the Canadian Archipelago-an area believed to be a future refugium for polar bears as their southernmost habitats decline under climate change. Although this study represents a major international collaborative effort and promised to be a baseline for future genetics work, methodological shortcomings and errors of interpretation undermine some of the study's main conclusions. Here, we present a reanalysis of this data in which we address some of these issues, including: (1 highly unbalanced sample sizes and large amounts of systematically missing data; (2 incorrect calculation of FST and of significance levels; (3 misleading estimates of recent gene flow resulting from non-convergence of the program BayesAss. In contrast to the original findings, in our reanalysis we find six genetic clusters of polar bears worldwide: the Hudson Bay Complex, the Western and Eastern Canadian Arctic Archipelago, the Western and Eastern Polar Basin, and-importantly-we reconfirm the presence of a unique and possibly endangered cluster of bears in Norwegian Bay near Canada's expected last sea-ice refugium. Although polar bears' abundance, distribution, and population structure will certainly be negatively affected by ongoing-and increasingly rapid-loss of Arctic sea ice, these genetic data provide no evidence of strong directional gene flow in response to recent climate change.

  10. Contemporary human-altered landscapes and oceanic barriers reduce bumble bee gene flow.

    Science.gov (United States)

    Jha, S

    2015-03-01

    Much of the world's terrestrial landscapes are being altered by humans in the form of agriculture, urbanization and pastoral systems, with major implications for biodiversity. Bumble bees are one of the most effective pollinators in both natural and cultivated landscapes, but are often the first to be extirpated in human-altered habitats. Yet, little is known about the role of natural and human-altered habitats in promoting or limiting bumble bee gene flow. In this study, I closely examine the genetic structure of the yellow-faced bumble bee, Bombus vosnesenskii, across the southwestern US coast and find strong evidence that natural oceanic barriers, as well as contemporary human-altered habitats, limit bee gene flow. Heterozygosity and allelic richness were lower in island populations, while private allelic richness was higher in island populations compared to mainland populations. Genetic differentiation, measured for three indices across the 1000 km study region, was significantly greater than the null expectation (F(ST) = 0.041, F'(ST) = 0.044 and D(est) = 0.155) and correlated with geographic distance. Furthermore, genetic differentiation patterns were most strongly correlated with contemporary (2011) not past (2006, 2001) resistance maps calibrated for high dispersal limitation over oceans, impervious habitat and croplands. Despite the incorporation of dramatic elevation gradients, the analyses reveal that oceans and contemporary human land use, not mountains, are the primary dispersal barriers for B. vosnesenskii gene flow. These findings reinforce the importance of maintaining corridors of suitable habitat across the distribution range of native pollinators to promote their persistence and safeguard their ability to provide essential pollination services.

  11. Nonrandom X chromosome inactivation in natural killer cells from obligate carriers of X-linked severe combined immunodeficiency

    Energy Technology Data Exchange (ETDEWEB)

    Wengler, G.S.; Parolini, O.; Conley, M.E. (Univ. of Tennessee, Memphis (United States) St. Jude Children' s Research Hospital, Memphis, TN (United States)); Allen, R.C. (Baylor College of Medicine, Houston, TX (United States)); Smith, H. (St. Jude Children' s Research Hospital, Memphis, TN (United States))

    1993-01-15

    X-linked severe combined immunodeficiency (XSCID) is characterized by hypogammaglobulinemia, markedly reduced numbers of T cells, absent mitogen responses, decreased numbers of NK cells, and normal or elevated numbers of B cells. The abnormalities in the NK cell and B cell lineages could be attributed to dependence of these cell lineages on T cells or T cell-derived factors, or to expression of the XSCID gene defect in these cell lineages. In past experiments, the authors have examined X chromosome inactivation patterns in T cells and cultured B cells from female obligate carriers of XSCID and have found that both cell lineages demonstrate nonrandom X chromosome inactivation. This indicates that the gene defect is intrinsic to both of these cell lineages. In the present experiments, a polymerase chain reaction technique was used to evaluate X chromosome inactivation patterns in highly purified populations of freshly isolated NK cells, B cells, CD4[sup +] cells, and CD8[sup +] cells from three obligate carriers of XSCID. All four lymphoid cell populations from these three women exhibited exclusive use of a single X as the active X. In contrast, both X chromosomes were used as the active X in neutrophils and monocytes. These findings indicate that the XSCID gene is expressed in the NK cell lineage as well as in T cells and B cells. This observation makes it highly unlikely that the XSCID gene is involved in Ag receptor gene rearrangements. 21 refs., 4 figs.

  12. Systems-level chromosomal parameters represent a suprachromosomal basis for the non-random chromosomal arrangement in human interphase nuclei

    Science.gov (United States)

    Fatakia, Sarosh N.; Mehta, Ishita S.; Rao, Basuthkar J.

    2016-01-01

    Forty-six chromosome territories (CTs) are positioned uniquely in human interphase nuclei, wherein each of their positions can range from the centre of the nucleus to its periphery. A non-empirical basis for their non-random arrangement remains unreported. Here, we derive a suprachromosomal basis of that overall arrangement (which we refer to as a CT constellation), and report a hierarchical nature of the same. Using matrix algebra, we unify intrinsic chromosomal parameters (e.g., chromosomal length, gene density, the number of genes per chromosome), to derive an extrinsic effective gene density matrix, the hierarchy of which is dominated largely by extrinsic mathematical coupling of HSA19, followed by HSA17 (human chromosome 19 and 17, both preferentially interior CTs) with all CTs. We corroborate predicted constellations and effective gene density hierarchy with published reports from fluorescent in situ hybridization based microscopy and Hi-C techniques, and delineate analogous hierarchy in disparate vertebrates. Our theory accurately predicts CTs localised to the nuclear interior, which interestingly share conserved synteny with HSA19 and/or HSA17. Finally, the effective gene density hierarchy dictates how permutations among CT position represents the plasticity within its constellations, based on which we suggest that a differential mix of coding with noncoding genome modulates the same. PMID:27845379

  13. Biofluids, cell mechanics and epigenetics: Flow-induced epigenetic mechanisms of endothelial gene expression.

    Science.gov (United States)

    Davies, Peter F; Manduchi, Elisabetta; Jiménez, Juan M; Jiang, Yi-Zhou

    2017-01-04

    Epigenetics is the regulation of gene expression (transcription) in response to changes in the cell environment through genomic modifications that largely involve the non-coding fraction of the human genome and that cannot be attributed to modification of the primary DNA sequence. Epigenetics is dominant in establishing cell fate and positioning during programmed embryonic development. However the same pathways are used by mature postnatal and adult mammalian cells during normal physiology and are implicated in disease mechanisms. Recent research demonstrates that blood flow and pressure are cell environments that can influence transcription via epigenetic pathways. The principal epigenetic pathways are chemical modification of cytosine residues of DNA (DNA methylation) and of the amino tails of histone proteins associated with DNA in nucleosomes. They also encompass the post-transcriptional degradation of mRNA transcripts by non-coding RNAs (ncRNA). In vascular endothelium, epigenetic pathways respond to temporal and spatial variations of flow and pressure, particularly hemodynamic disturbed blood flow, with important consequences for gene expression. The biofluid environment is linked by mechanotransduction and solute transport to cardiovascular cell phenotypes via signaling pathways and epigenetic regulation for which there is an adequate interdisciplinary infrastructure with robust tools and methods available. Epigenetic mechanisms may be less familiar than acute genomic signaling to Investigators at the interface of biofluids, biomechanics and cardiovascular biology. Here we introduce a biofluids / cellular biomechanics readership to the principal epigenetic pathways and provide a contextual overview of endothelial epigenetic plasticity in the regulation of flow-responsive transcription. Copyright © 2016 Elsevier Ltd. All rights reserved.

  14. Modelling Gene Flow between Fields of White Clover with Honeybees as Pollen Vectors

    DEFF Research Database (Denmark)

    Løjtnant, Christina; Boelt, Birte; Clausen, Sabine Karin

    2012-01-01

    % with an estimated 95% percentile of 70%. The results show that the European Union threshold limit of 0.9% GM admixture for food and feed will likely be exceeded at times and especially organic farmers that do not accept GM admixture and often have clover and clover–grass fields might face challenges with admixture.......7%, but subjected to large uncertainty. In a worst case scenario with adjacent fields—one with a genetically modified (GM) T. repens cultivar and the other with a conventional T. repens cultivar—and where all arriving bees were expected to transfer GM pollen, the median gene flow was modelled to be 7...

  15. Asymmetrical gene flow in a hybrid zone of Hawaiian Schiedea (Caryophyllaceae species with contrasting mating systems.

    Directory of Open Access Journals (Sweden)

    Lisa E Wallace

    Full Text Available Asymmetrical gene flow, which has frequently been documented in naturally occurring hybrid zones, can result from various genetic and demographic factors. Understanding these factors is important for determining the ecological conditions that permitted hybridization and the evolutionary potential inherent in hybrids. Here, we characterized morphological, nuclear, and chloroplast variation in a putative hybrid zone between Schiedea menziesii and S. salicaria, endemic Hawaiian species with contrasting breeding systems. Schiedea menziesii is hermaphroditic with moderate selfing; S. salicaria is gynodioecious and wind-pollinated, with partially selfing hermaphrodites and largely outcrossed females. We tested three hypotheses: 1 putative hybrids were derived from natural crosses between S. menziesii and S. salicaria, 2 gene flow via pollen is unidirectional from S. salicaria to S. menziesii and 3 in the hybrid zone, traits associated with wind pollination would be favored as a result of pollen-swamping by S. salicaria. Schiedea menziesii and S. salicaria have distinct morphologies and chloroplast genomes but are less differentiated at the nuclear loci. Hybrids are most similar to S. menziesii at chloroplast loci, exhibit nuclear allele frequencies in common with both parental species, and resemble S. salicaria in pollen production and pollen size, traits important to wind pollination. Additionally, unlike S. menziesii, the hybrid zone contains many females, suggesting that the nuclear gene responsible for male sterility in S. salicaria has been transferred to hybrid plants. Continued selection of nuclear genes in the hybrid zone may result in a population that resembles S. salicaria, but retains chloroplast lineage(s of S. menziesii.

  16. Influence of gene flow on divergence dating - implications for the speciation history of Takydromus grass lizards.

    Science.gov (United States)

    Tseng, Shu-Ping; Li, Shou-Hsien; Hsieh, Chia-Hung; Wang, Hurng-Yi; Lin, Si-Min

    2014-10-01

    Dating the time of divergence and understanding speciation processes are central to the study of the evolutionary history of organisms but are notoriously difficult. The difficulty is largely rooted in variations in the ancestral population size or in the genealogy variation across loci. To depict the speciation processes and divergence histories of three monophyletic Takydromus species endemic to Taiwan, we sequenced 20 nuclear loci and combined with one mitochondrial locus published in GenBank. They were analysed by a multispecies coalescent approach within a Bayesian framework. Divergence dating based on the gene tree approach showed high variation among loci, and the divergence was estimated at an earlier date than when derived by the species-tree approach. To test whether variations in the ancestral population size accounted for the majority of this variation, we conducted computer inferences using isolation-with-migration (IM) and approximate Bayesian computation (ABC) frameworks. The results revealed that gene flow during the early stage of speciation was strongly favoured over the isolation model, and the initiation of the speciation process was far earlier than the dates estimated by gene- and species-based divergence dating. Due to their limited dispersal ability, it is suggested that geographical isolation may have played a major role in the divergence of these Takydromus species. Nevertheless, this study reveals a more complex situation and demonstrates that gene flow during the speciation process cannot be overlooked and may have a great impact on divergence dating. By using multilocus data and incorporating Bayesian coalescence approaches, we provide a more biologically realistic framework for delineating the divergence history of Takydromus.

  17. Model-based calculating tool for pollen-mediated gene flow frequencies in plants.

    Science.gov (United States)

    Lei, Wang; Bao-Rong, Lu

    2016-12-30

    The potential social-economic and environmental impacts caused by transgene flow from genetically engineered (GE) crops have stimulated worldwide biosafety concerns. To determine transgene flow frequencies resulted from pollination is the first critical step for assessing such impacts, in addition to the determination of transgene expression and fitness in crop-wild hybrid descendants. Two methods are commonly used to estimate pollen-mediated gene flow (PMGF) frequencies: field experimenting and mathematical modeling. Field experiments can provide relatively accurate results but are time/resource consuming. Modeling offers an effective complement for PMGF experimental assessment. However, many published models describe PMGF by mathematical equations and are practically not easy to use. To increase the application of PMGF modeling for the estimation of transgene flow, we established a tool to calculate PMGF frequencies based on a quasi-mechanistic PMGF model for wind-pollination species. This tool includes a calculating program displayed by an easy-operating interface. PMGF frequencies of different plant species can be quickly calculated under different environmental conditions by including a number of biological and wind speed parameters that can be measured in the fields/laboratories or obtained from published data. The tool is freely available in the public domain (http://ecology.fudan.edu.cn/userfiles/cn/files/Tool_Manual.zip). Case studies including rice, wheat, and maize demonstrated similar results between the calculated frequencies based on this tool and those from published PMGF data. This PMGF calculating tool will provide useful information for assessing and monitoring social-economic and environmental impacts caused by transgene flow from GE crops. This tool can also be applied to determine the isolation distances between GE and non-GE crops in a coexistence agro-ecosystem, and to ensure the purity of certified seeds by setting proper isolation distances

  18. Non-random assembly of bacterioplankton communities in the subtropical North Pacific Ocean

    Directory of Open Access Journals (Sweden)

    Alexander eEiler

    2011-07-01

    Full Text Available The exploration of bacterial diversity in the global ocean has revealed new taxa and previously unrecognized metabolic potential; however, our understanding of what regulates this diversity is limited. Using terminal restriction fragment length polymorphism (T-RFLP data of bacterial small-subunit ribosomal RNA genes we show that, independent of depth and time, a large fraction of bacterioplankton co-occurrence patterns are non-random in the oligotrophic North Pacific subtropical gyre (NPSG. Pair-wise correlations of all identified operational taxonomic units (OTUs revealed a high degree of significance, with 6.6% of the pair-wise co-occurrences being negatively correlated and 20.7% of them being positive. The most abundant OTUs, putatively identified as Prochlorococcus, SAR11 and SAR116 bacteria, were among the most correlated OTUs. As expected, bacterial community composition lacked statistically significant patterns of seasonality in the mostly stratified water column except in a few depth horizons of the sunlit surface waters, with higher frequency variations in community structure apparently related to populations associated with the deep chlorophyll maximum. Communities were structured vertically, with a succession from euphotic, mesopelagic, and bathylopelagic populations. Permutation based statistical analyses of T-RFLP data and their corresponding metadata revealed a broad range of putative environmental drivers controlling bacterioplankton community composition in the NPSG, including concentrations of inorganic nutrients and phytoplankton pigment. Together our results suggest that deterministic forces, such as environmental filtering and interactions among taxa, determine bacterioplankton community patterns, and consequently affect ecosystem functions in the NPSG.

  19. Pollen-mediated gene flow from glyphosate-resistant common waterhemp (Amaranthus rudis Sauer): consequences for the dispersal of resistance genes

    Science.gov (United States)

    Sarangi, Debalin; Tyre, Andrew J.; Patterson, Eric L.; Gaines, Todd A.; Irmak, Suat; Knezevic, Stevan Z.; Lindquist, John L.; Jhala, Amit J.

    2017-01-01

    Gene flow is an important component in evolutionary biology; however, the role of gene flow in dispersal of herbicide-resistant alleles among weed populations is poorly understood. Field experiments were conducted at the University of Nebraska-Lincoln to quantify pollen-mediated gene flow (PMGF) from glyphosate-resistant (GR) to -susceptible (GS) common waterhemp using a concentric donor-receptor design. More than 130,000 common waterhemp plants were screened and 26,199 plants were confirmed resistant to glyphosate. Frequency of gene flow from all distances, directions, and years was estimated with a double exponential decay model using Generalized Nonlinear Model (package gnm) in R. PMGF declined by 50% at pollen source, whereas 90% reduction was found at 88 m (maximum) depending on the direction of the pollen-receptor blocks. Amplification of the target site gene, 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), was identified as the mechanism of glyphosate resistance in parent biotype. The EPSPS gene amplification was heritable in common waterhemp and can be transferred via PMGF, and also correlated with glyphosate resistance in pseudo-F2 progeny. This is the first report of PMGF in GR common waterhemp and the results are critical in explaining the rapid dispersal of GR common waterhemp in Midwestern United States. PMID:28327669

  20. Barriers to gene flow in the marine environment: insights from two common intertidal limpet species of the Atlantic and Mediterranean.

    Science.gov (United States)

    Sá-Pinto, Alexandra; Branco, Madalena S; Alexandrino, Paulo B; Fontaine, Michaël C; Baird, Stuart J E

    2012-01-01

    Knowledge of the scale of dispersal and the mechanisms governing gene flow in marine environments remains fragmentary despite being essential for understanding evolution of marine biota and to design management plans. We use the limpets Patella ulyssiponensis and Patella rustica as models for identifying factors affecting gene flow in marine organisms across the North-East Atlantic and the Mediterranean Sea. A set of allozyme loci and a fragment of the mitochondrial gene cytochrome C oxidase subunit I were screened for genetic variation through starch gel electrophoresis and DNA sequencing, respectively. An approach combining clustering algorithms with clinal analyses was used to test for the existence of barriers to gene flow and estimate their geographic location and abruptness. Sharp breaks in the genetic composition of individuals were observed in the transitions between the Atlantic and the Mediterranean and across southern Italian shores. An additional break within the Atlantic cluster separates samples from the Alboran Sea and Atlantic African shores from those of the Iberian Atlantic shores. The geographic congruence of the genetic breaks detected in these two limpet species strongly supports the existence of transpecific barriers to gene flow in the Mediterranean Sea and Northeastern Atlantic. This leads to testable hypotheses regarding factors restricting gene flow across the study area.

  1. Genealogy-based methods for inference of historical recombination and gene flow and their application in Saccharomyces cerevisiae.

    Science.gov (United States)

    Jenkins, Paul A; Song, Yun S; Brem, Rachel B

    2012-01-01

    Genetic exchange between isolated populations, or introgression between species, serves as a key source of novel genetic material on which natural selection can act. While detecting historical gene flow from DNA sequence data is of much interest, many existing methods can be limited by requirements for deep population genomic sampling. In this paper, we develop a scalable genealogy-based method to detect candidate signatures of gene flow into a given population when the source of the alleles is unknown. Our method does not require sequenced samples from the source population, provided that the alleles have not reached fixation in the sampled recipient population. The method utilizes recent advances in algorithms for the efficient reconstruction of ancestral recombination graphs, which encode genealogical histories of DNA sequence data at each site, and is capable of detecting the signatures of gene flow whose footprints are of length up to single genes. Further, we employ a theoretical framework based on coalescent theory to test for statistical significance of certain recombination patterns consistent with gene flow from divergent sources. Implementing these methods for application to whole-genome sequences of environmental yeast isolates, we illustrate the power of our approach to highlight loci with unusual recombination histories. By developing innovative theory and methods to analyze signatures of gene flow from population sequence data, our work establishes a foundation for the continued study of introgression and its evolutionary relevance.

  2. Barriers to gene flow in the marine environment: insights from two common intertidal limpet species of the Atlantic and Mediterranean.

    Directory of Open Access Journals (Sweden)

    Alexandra Sá-Pinto

    Full Text Available Knowledge of the scale of dispersal and the mechanisms governing gene flow in marine environments remains fragmentary despite being essential for understanding evolution of marine biota and to design management plans. We use the limpets Patella ulyssiponensis and Patella rustica as models for identifying factors affecting gene flow in marine organisms across the North-East Atlantic and the Mediterranean Sea. A set of allozyme loci and a fragment of the mitochondrial gene cytochrome C oxidase subunit I were screened for genetic variation through starch gel electrophoresis and DNA sequencing, respectively. An approach combining clustering algorithms with clinal analyses was used to test for the existence of barriers to gene flow and estimate their geographic location and abruptness. Sharp breaks in the genetic composition of individuals were observed in the transitions between the Atlantic and the Mediterranean and across southern Italian shores. An additional break within the Atlantic cluster separates samples from the Alboran Sea and Atlantic African shores from those of the Iberian Atlantic shores. The geographic congruence of the genetic breaks detected in these two limpet species strongly supports the existence of transpecific barriers to gene flow in the Mediterranean Sea and Northeastern Atlantic. This leads to testable hypotheses regarding factors restricting gene flow across the study area.

  3. The large-X effect in plants: increased species divergence and reduced gene flow on the Silene X-chromosome.

    Science.gov (United States)

    Hu, Xin-Sheng; Filatov, Dmitry A

    2016-06-01

    The disproportionately large involvement of the X-chromosome in the isolation of closely related species (the large-X effect) has been reported for many animals, where X-linked genes are mostly hemizygous in the heterogametic sex. The expression of deleterious recessive mutations is thought to drive the frequent involvement of the X-chromosome in hybrid sterility, as well as to reduce interspecific gene flow for X-linked genes. Here, we evaluate the role of the X-chromosome in the speciation of two closely related plant species - the white and red campions (Silene latifolia and S. dioica) - that hybridize widely across Europe. The two species evolved separate sexes and sex chromosomes relatively recently (~10(7)  years), and unlike most animal species, most X-linked genes have intact Y-linked homologs. We demonstrate that the X-linked genes show a very small and insignificant amount of interspecific gene flow, while gene flow involving autosomal loci is significant and sufficient to homogenize the gene pools of the two species. These findings are consistent with the hypothesis of the large-X effect in Silene and comprise the first report of this effect in plants. Nonhemizygosity of many X-linked genes in Silene males indicates that exposure of recessive mutations to selection may not be essential for the occurrence of the large-X effect. Several possible causes of the large-X effect in Silene are discussed.

  4. Tocantins river as an effective barrier to gene flow in Saguinus niger populations

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    Marcelo Vallinoto

    2006-01-01

    Full Text Available The Saguinus represent the basal genus of the Callitrichinae subfamily. Traditionally this genus is divided into three groups: Hairy, Mottled and Bare-face, however, molecular data failed to validate these groups as monophyletic units, as well as raised some subspecies to the species status. This is the case of the former subspecies Saguinus midas midas and S. midas niger, which are now considered as different species. In the present study, we sequenced a portion of the D-loop mtDNA region in populations from the East bank of the Xingu and from both banks of the Tocantins river, in order to test the effectiveness of large rivers as barriers to the gene flow in Saguinus. According to our results, the populations from the East and West banks of the Tocantins river are more divergent than true species like S. mystax and S. imperator. The Tocantins river may be acting as a barrier to gene flow, and consequently these very divergent populations may represent distinct taxonomic entities (species?.

  5. Y-STR diversity and sex-biased gene flow among Caribbean populations.

    Science.gov (United States)

    Simms, Tanya M; Wright, Marisil R; Martinez, Emanuel; Regueiro, Maria; McCartney, Quinn; Herrera, Rene J

    2013-03-01

    In the present study, we report, for the first time, the allele and haplotype frequencies of 17 Y-STR (Y-filer) loci in the populations of Haiti, Jamaica and the Bahamas (Abaco, Eleuthera, Exuma, Grand Bahama, Long Island and New Providence). This investigation was undertaken to assess the paternal genetic structure of the abovementioned Caribbean islands. A total of 607 different haplotypes were identified among the 691 males examined, of which 537 (88.5%) were unique. Haplotype diversities (HD) ranged from 0.989 in Long Island to 1.000 in Grand Bahama, with limited haplotype sharing observed among these Caribbean collections. Discriminatory capacity (DC) values were also high, ranging from 79.1% to 100% in Long Island and Grand Bahama, respectively, illustrating the capacity of this set of markers to differentiate between patrilineal related individuals within each population. Phylogenetic comparison of the Bahamian, Haitian and Jamaican groups with available African, European, East Asian and Native American populations reveals strong genetic ties with the continental African collections, a finding that corroborates our earlier work using autosomal STR and Y-chromosome binary markers. In addition, various degrees of sex-biased gene flow exhibiting disproportionately higher European paternal (as compared to autosomal) influences were detected in all Caribbean islands genotyped except for Abaco and Eleuthera. We attribute the presence or absence of asymmetric gene flow to unique, island specific demographic events and family structures. Copyright © 2012 Elsevier B.V. All rights reserved.

  6. Conservation, spillover and gene flow within a network of Northern European marine protected areas.

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    Mats Brockstedt Olsen Huserbråten

    Full Text Available To ensure that marine protected areas (MPAs benefit conservation and fisheries, the effectiveness of MPA designs has to be evaluated in field studies. Using an interdisciplinary approach, we empirically assessed the design of a network of northern MPAs where fishing for European lobster (Homarusgammarus is prohibited. First, we demonstrate a high level of residency and survival (50% for almost a year (363 days within MPAs, despite small MPA sizes (0.5-1 km(2. Second, we demonstrate limited export (4.7% of lobsters tagged within MPAs (N = 1810 to neighbouring fished areas, over a median distance of 1.6 km out to maximum 21 km away from MPA centres. In comparison, median movement distance of lobsters recaptured within MPAs was 164 m, and recapture rate was high (40%. Third, we demonstrate a high level of gene flow within the study region, with an estimated F ST of less than 0.0001 over a ≈ 400 km coastline. Thus, the restricted movement of older life stages, combined with a high level of gene flow suggests that connectivity is primarily driven by larval drift. Larval export from the MPAs can most likely affect areas far beyond their borders. Our findings are of high importance for the design of MPA networks for sedentary species with pelagic early life stages.

  7. Gene flow in a Yersinia pestis vector, Oropsylla hirsuta, during a plague epizootic

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    Philip H. Jones , Leigh R. Washburn & Hugh B. Britten

    2011-09-01

    Full Text Available Background & objectives: Appreciating how Yersinia pestis, the etiological agent of plague, spreads amongblack-tailed prairie dog (Cynomys ludovicianus colonies (BTPD, is vital to wildlife conservation programsin North American grasslands. A little-studied aspect of the system is the role of Y. pestis vectors, i.e. fleas,play in the spreading of plague in natural settings. We investigated the genetic structure and variability of acommon prairie dog flea (Oropsylla hirsuta in BTPD colonies in order to examine dispersal patterns. Giventhat this research took place during a widespread plague epizootic, there was the added advantage of gaininginformation on the dynamics of sylvatic plague.Methods & Results: Oropsylla hirsuta were collected from BTPD burrows in nine colonies from May 2005 toJuly 2005, and eight polymorphic microsatellite markers were used to generate genotypic data from them.Gene flow estimates revealed low genetic differentiation among fleas sampled from different colonies. NestedPCR plague assays confirmed the presence of Y. pestis with the average Y. pestis prevalence across all ninecolonies at 12%. No significant correlations were found between the genetic variability and gene flow of O.hirsuta and Y. pestis prevalence on a per-colony basis.Conclusion: Oropsylla hirsuta dispersal among BTPD colonies was high, potentially explaining the rapidspread of Y. pestis in our study area in 2005 and 2006.

  8. Gene flow in a Yersinia pestis vector, Oropsylla hirsuta, during a plague epizootic.

    Science.gov (United States)

    Jones, Philip H; Washburn, Leigh R; Britten, Hugh B

    2011-09-01

    Appreciating how Yersinia pestis, the etiological agent of plague, spreads among black - tailed prairie dog (Cynomys ludovicianus) colonies (BTPD), is vital to wildlife conservation programs in North American grasslands. A little - studied aspect of the system is the role of Y. pestis vectors, i.e. fleas, play in the spreading of plague in natural settings. We investigated the genetic structure and variability of a common prairie dog flea (Oropsylla hirsuta) in BTPD colonies in order to examine dispersal patterns. Given that this research took place during a widespread plague epizootic, there was the added advantage of gaining information on the dynamics of sylvatic plague. Oropsylla hirsuta were collected from BTPD burrows in nine colonies from May 2005 to July 2005, and eight polymorphic microsatellite markers were used to generate genotypic data from them. Gene flow estimates revealed low genetic differentiation among fleas sampled from different colonies. NestedPCR plague assays confirmed the presence of Y. pestis with the average Y. pestis prevalence across all nine colonies at 12%. No significant correlations were found between the genetic variability and gene flow of O. hirsuta and Y. pestis prevalence on a per -colony basis. Oropsylla hirsuta dispersal among BTPD colonies was high, potentially explaining the rapid spread of Y. pestis in our study area in 2005 and 2006.

  9. Diversification and gene flow in nascent lineages of island and mainland North American tree squirrels (Tamiasciurus).

    Science.gov (United States)

    Chavez, Andreas S; Maher, Sean P; Arbogast, Brian S; Kenagy, G J

    2014-04-01

    Pleistocene climate cycles and glaciations had profound impacts on taxon diversification in the Boreal Forest Biome. Using population genetic analyses with multilocus data, we examined diversification, isolation, and hybridization in two sibling species of tree squirrels (Tamiasciurus douglasii and Tamiasciurus hudsonicus) with special attention to the geographically and genetically enigmatic population of T. hudsonicus on Vancouver Island, Canada. The two species differentiated only about 500,000 years ago, in the Late Pleistocene. The island population is phylogenetically nested within T. hudsonicus according to our nuclear analysis but within T. douglasii according to mitochondrial DNA. This conflict is more likely due to historical hybridization than to incomplete lineage sorting, and it appears that bidirectional gene flow occurred between the island population and both species on the mainland. This interpretation of our genetic analyses is consistent with our bioclimatic modeling, which demonstrates that both species were able to occupy this region throughout the Late Pleistocene. The divergence of the island population 40,000 years ago suggests that tree squirrels persisted in a refugium on Vancouver Island at the last glacial maximum, 20,000 years ago. Our observations demonstrate how Pleistocene climate change and habitat shifts have created incipient divergence in the presence of gene flow. Sequence data have been archived in GenBank—accession numbers: KF882736–KF885216.

  10. Gene flow and mode of pollination in a dry-grassland species, Filipendula vulgaris (Rosaceae).

    Science.gov (United States)

    Weidema, I R; Magnussen, L S; Philipp, M

    2000-03-01

    Filipendula vulgaris is a characteristic species of dry nonacidic grasslands in Denmark. This habitat type occurs only on marginal areas not suitable for agriculture or urbanization and that are by their nature fragmented. The population genetic structure of F. vulgaris was investigated in 17 populations within two regions of Denmark, using isozyme electrophoresis. Small populations were found to have significantly fewer polymorphic loci than larger populations, but all populations maintained the same common allelic variants. The degree of isolation of individual populations did not affect the amount of genetic variation. Offspring arrays revealed a very high outcrossing rate (0.96). The field study demonstrated a very high level of gene flow between populations considering that small insects are thought to be the main pollinators of this species. An experiment to verify whether pollen transport by wind could explain the results from the field study demonstrated long-distance transport from isolated plants to bagged plants. Filipendula vulgaris pollen grains are very small and this explains why outcrossed progeny were found using pollination bags with small pore sizes. We conclude that wind pollination is indeed possible and together with insect pollination is causing the observed patterns of genetic variation. The substantial gene flow between populations may be reducing the effects of genetic drift in the small fragmented populations of F. vulgaris.

  11. Genome-wide data substantiate Holocene gene flow from India to Australia.

    Science.gov (United States)

    Pugach, Irina; Delfin, Frederick; Gunnarsdóttir, Ellen; Kayser, Manfred; Stoneking, Mark

    2013-01-29

    The Australian continent holds some of the earliest archaeological evidence for the expansion of modern humans out of Africa, with initial occupation at least 40,000 y ago. It is commonly assumed that Australia remained largely isolated following initial colonization, but the genetic history of Australians has not been explored in detail to address this issue. Here, we analyze large-scale genotyping data from aboriginal Australians, New Guineans, island Southeast Asians and Indians. We find an ancient association between Australia, New Guinea, and the Mamanwa (a Negrito group from the Philippines), with divergence times for these groups estimated at 36,000 y ago, and supporting the view that these populations represent the descendants of an early "southern route" migration out of Africa, whereas other populations in the region arrived later by a separate dispersal. We also detect a signal indicative of substantial gene flow between the Indian populations and Australia well before European contact, contrary to the prevailing view that there was no contact between Australia and the rest of the world. We estimate this gene flow to have occurred during the Holocene, 4,230 y ago. This is also approximately when changes in tool technology, food processing, and the dingo appear in the Australian archaeological record, suggesting that these may be related to the migration from India.

  12. Meta-analysis of non-randomized studies in interventional cardiology: a critical appraisal

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    Eliano Pio Navarese

    2009-12-01

    Full Text Available Utilisation of meta-analysis is becoming more and more common in interventional cardiology. The aim of this statistical approach is to collect a large number of patients from randomized clinical studies and nonrandomized registries in order to obtain a pooled estimate of the results. Nevertheless, simply pooling these results without a correct methodological approach can easily lead to biased conclusions. In this report we analyse the possible methodological drawbacks of such an approach and we suggest a simplified check-list of items to be considered in the effort of building-up a meta-analysis from non-randomized studies.

  13. Non-random structures in universal compression and the Fermi paradox

    Science.gov (United States)

    Gurzadyan, A. V.; Allahverdyan, A. E.

    2016-02-01

    We study the hypothesis of information panspermia assigned recently among possible solutions of the Fermi paradox ("where are the aliens?"). It suggests that the expenses of alien signaling can be significantly reduced, if their messages contained compressed information. To this end we consider universal compression and decoding mechanisms ( e.g. the Lempel-Ziv-Welch algorithm) that can reveal non-random structures in compressed bit strings. The efficiency of the Kolmogorov stochasticity parameter for detection of non-randomness is illustrated, along with the Zipf's law. The universality of these methods, i.e. independence from data details, can be principal in searching for intelligent messages.

  14. Non-random structures in universal compression and the Fermi paradox

    CERN Document Server

    Gurzadyan, A V

    2016-01-01

    We study the hypothesis of information panspermia assigned recently among possible solutions of the Fermi paradox ("where are the aliens?"). It suggests that the expenses of alien signaling can be significantly reduced, if their messages contain compressed information. To this end we consider universal compression and decoding mechanisms (e.g. the Lempel-Ziv-Welch algorithm) that can reveal non-random structures in compressed bit strings. The efficiency of Kolmogorov stochasticity parameter for detection of non-randomness is illustrated, along with the Zipf's law. The universality of these methods, i.e. independence on data details, can be principal in searching for intelligent messages.

  15. Localizing F(ST) outliers on a QTL map reveals evidence for large genomic regions of reduced gene exchange during speciation-with-gene-flow.

    Science.gov (United States)

    Via, Sara; Conte, Gina; Mason-Foley, Casey; Mills, Kelly

    2012-11-01

    Populations that maintain phenotypic divergence in sympatry typically show a mosaic pattern of genomic divergence, requiring a corresponding mosaic of genomic isolation (reduced gene flow). However, mechanisms that could produce the genomic isolation required for divergence-with-gene-flow have barely been explored, apart from the traditional localized effects of selection and reduced recombination near centromeres or inversions. By localizing F(ST) outliers from a genome scan of wild pea aphid host races on a Quantitative Trait Locus (QTL) map of key traits, we test the hypothesis that between-population recombination and gene exchange are reduced over large 'divergence hitchhiking' (DH) regions. As expected under divergence hitchhiking, our map confirms that QTL and divergent markers cluster together in multiple large genomic regions. Under divergence hitchhiking, the nonoutlier markers within these regions should show signs of reduced gene exchange relative to nonoutlier markers in genomic regions where ongoing gene flow is expected. We use this predicted difference among nonoutliers to perform a critical test of divergence hitchhiking. Results show that nonoutlier markers within clusters of F(ST) outliers and QTL resolve the genetic population structure of the two host races nearly as well as the outliers themselves, while nonoutliers outside DH regions reveal no population structure, as expected if they experience more gene flow. These results provide clear evidence for divergence hitchhiking, a mechanism that may dramatically facilitate the process of speciation-with-gene-flow. They also show the power of integrating genome scans with genetic analyses of the phenotypic traits involved in local adaptation and population divergence. © 2012 Blackwell Publishing Ltd.

  16. Removal of antibiotics and antibiotic resistance genes from domestic sewage by constructed wetlands: Effect of flow configuration and plant species.

    Science.gov (United States)

    Chen, Jun; Ying, Guang-Guo; Wei, Xiao-Dong; Liu, You-Sheng; Liu, Shuang-Shuang; Hu, Li-Xin; He, Liang-Ying; Chen, Zhi-Feng; Chen, Fan-Rong; Yang, Yong-Qiang

    2016-11-15

    This study aims to investigate the removal of antibiotics and antibiotic resistance genes (ARGs) in raw domestic wastewater by various mesocosm-scale constructed wetlands (CWs) with different flow configurations or plant species including the constructed wetland with or without plant. Six mesocosm-scale CWs with three flow types (surface flow, horizontal subsurface flow and vertical subsurface flow) and two plant species (Thaliadealbata Fraser and Iris tectorum Maxim) were set up in the outdoor. 8 antibiotics including erythromycin-H2O (ETM-H2O), monensin (MON), clarithromycin (CTM), leucomycin (LCM), sulfamethoxazole (SMX), trimethoprim (TMP), sulfamethazine (SMZ) and sulfapyridine (SPD) and 12 genes including three sulfonamide resistance genes (sul1, sul2 and sul3), four tetracycline resistance genes (tetG, tetM, tetO and tetX), two macrolide resistance genes (ermB and ermC), two chloramphenicol resistance genes (cmlA and floR) and 16S rRNA (bacteria) were determined in different matrices (water, particle, substrate and plant phases) from the mesocosm-scale systems. The aqueous removal efficiencies of total antibiotics ranged from 75.8 to 98.6%, while those of total ARGs varied between 63.9 and 84.0% by the mesocosm-scale CWs. The presence of plants was beneficial to the removal of pollutants, and the subsurface flow CWs had higher pollutant removal than the surface flow CWs, especially for antibiotics. According to the mass balance analysis, the masses of all detected antibiotics during the operation period were 247,000, 4920-10,600, 0.05-0.41 and 3500-60,000μg in influent, substrate, plant and effluent of the mesocosm-scale CWs. In the CWs, biodegradation, substrate adsorption and plant uptake all played certain roles in reducing the loadings of nutrients, antibiotics and ARGs, but biodegradation was the most important process in the removal of these pollutants.

  17. Using seed purity data to estimate an average pollen mediated gene flow from crops to wild relatives.

    Science.gov (United States)

    Lavigne, C; Klein, E K; Couvet, D

    2002-01-01

    Gene flow from crops to wild related species has been recently under focus in risk-assessment studies of the ecological consequences of growing transgenic crops. However, experimental studies addressing this question are usually temporally or spatially limited. Indirect population-structure approaches can provide more global estimates of gene flow, but their assumptions appear inappropriate in an agricultural context. In an attempt to help the committees providing advice on the release of transgenic crops, we present a new method to estimate the quantity of genes migrating from crops to populations of related wild plants by way of pollen dispersal. This method provides an average estimate at a landscape level. Its originality is based on the measure of the inverse gene flow, i.e. gene flow from the wild plants to the crop. Such gene flow results in an observed level of impurities from wild plants in crop seeds. This level of impurity is usually known by the seed producers and, in any case, its measure is easier than a direct screen of wild populations because crop seeds are abundant and their genetic profile is known. By assuming that wild and cultivated plants have a similar individual pollen dispersal function, we infer the level of pollen-mediated gene flow from a crop to the surrounding wild populations from this observed level of impurity. We present an example for sugar beet data. Results suggest that under conditions of seed production in France (isolation distance of 1,000 m) wild beets produce high numbers of seeds fathered by cultivated plants.

  18. Population structure of barley landrace populations and gene-flow with modern varieties.

    Science.gov (United States)

    Bellucci, Elisa; Bitocchi, Elena; Rau, Domenico; Nanni, Laura; Ferradini, Nicoletta; Giardini, Alessandro; Rodriguez, Monica; Attene, Giovanna; Papa, Roberto

    2013-01-01

    Landraces are heterogeneous plant varieties that are reproduced by farmers as populations that are subject to both artificial and natural selection. Landraces are distinguished by farmers due to their specific traits, and different farmers often grow different populations of the same landrace. We used simple sequence repeats (SSRs) to analyse 12 barley landrace populations from Sardinia from two collections spanning 10 years. We analysed the population structure, and compared the population diversity of the landraces that were collected at field level (population). We used a representative pool of barley varieties for diversity comparisons and to analyse the effects of gene flow from modern varieties. We found that the Sardinian landraces are a distinct gene pool from those of both two-row and six-row barley varieties. There is also a low, but significant, mean level and population-dependent level of introgression from the modern varieties into the Sardinian landraces. Moreover, we show that the Sardinian landraces have the same level of gene diversity as the representative sample of modern commercial varieties grown in Italy in the last decades, even within population level. Thus, these populations represent crucial sources of germplasm that will be useful for crop improvement and for population genomics studies and association mapping, to identify genes, loci and genome regions responsible for adaptive variations. Our data also suggest that landraces are a source of valuable germplasm for sustainable agriculture in the context of future climate change, and that in-situ conservation strategies based on farmer use can preserve the genetic identity of landraces while allowing adaptation to local environments.

  19. The quality of control groups in nonrandomized studies published in the Journal of Hand Surgery.

    Science.gov (United States)

    Johnson, Shepard P; Malay, Sunitha; Chung, Kevin C

    2015-01-01

    To evaluate control group selection in nonrandomized studies published in the Journal of Hand Surgery American (JHS). We reviewed all papers published in JHS in 2013 to identify studies that used nonrandomized control groups. Data collected included type of study design and control group characteristics. We then appraised studies to determine whether authors discussed confounding and selection bias and how they controlled for confounding. Thirty-seven nonrandomized studies were published in JHS in 2013. The source of control was either the same institution as the study group, a different institution, a database, or not provided in the manuscript. Twenty-nine (78%) studies statistically compared key characteristics between control and study group. Confounding was controlled with matching, exclusion criteria, or regression analysis. Twenty-two (59%) papers explicitly discussed the threat of confounding and 18 (49%) identified sources of selection bias. In our review of nonrandomized studies published in JHS, papers had well-defined controls that were similar to the study group, allowing for reasonable comparisons. However, we identified substantial confounding and bias that were not addressed as explicit limitations, which might lead the reader to overestimate the scientific validity of the data. Incorporating a brief discussion of control group selection in scientific manuscripts should help readers interpret the study more appropriately. Authors, reviewers, and editors should strive to address this component of clinical importance. Copyright © 2015 American Society for Surgery of the Hand. Published by Elsevier Inc. All rights reserved.

  20. A nonrandomized comparison of stapes surgery with and without a vein graft in patients with otosclerosis

    NARCIS (Netherlands)

    Bittermann, A.J.; Vincent, R.; Rovers, M.M.; Heijden, G.J. van der; Tange, R.A.; Dreschler, W.A.; Grolman, W.

    2013-01-01

    OBJECTIVE: To evaluate the effectiveness of primary stapes surgery with and without a vein graft in patients with otosclerosis and to determine the differences in the postoperative gain in air-bone gap (ABG) and air-conduction (AC). STUDY DESIGN: A nonrandomized multicenter clinical evaluation.

  1. Use versus Nonuse of Repeater Examinees in Common Item Linear Equating with Nonrandom Groups.

    Science.gov (United States)

    Cope, Ronald T.

    This study considers the use of repeaters when test equating. The subjects consist of five groups of applicants to a professional certification program. Each group comprises first time examinees and repeaters. The procedures include a common item linear equating with nonrandom groups, use of equating chains, and the use of total examinee group…

  2. Quantitative assessment of unobserved confounding is mandatory in nonrandomized intervention studies

    NARCIS (Netherlands)

    Groenwold, R H H; Hak, E; Hoes, A W

    2009-01-01

    OBJECTIVE: In nonrandomized intervention studies unequal distribution of patient characteristics in the groups under study may hinder comparability of prognosis and therefore lead to confounding bias. Our objective was to review methods to control for observed confounding, as well as unobserved conf

  3. Systematic reviews incorporating evidence from nonrandomized study designs: reasons for caution when estimating health effects.

    NARCIS (Netherlands)

    Reeves, B.C.; Binsbergen, J.J. van; Weel, C. van

    2005-01-01

    Systematic reviews that include nonrandomized studies (NRS) face a number of logistical challenges. However, the greatest threat to the validity of such reviews arises from the differing susceptibility of randomized controlled trials (RCTs) and NRS to selection bias. Groups compared in NRS are unlik

  4. Checklists of Methodological Issues for Review Authors to Consider When Including Non-Randomized Studies in Systematic Reviews

    Science.gov (United States)

    Wells, George A.; Shea, Beverley; Higgins, Julian P. T.; Sterne, Jonathan; Tugwell, Peter; Reeves, Barnaby C.

    2013-01-01

    Background: There is increasing interest from review authors about including non-randomized studies (NRS) in their systematic reviews of health care interventions. This series from the Ottawa Non-Randomized Studies Workshop consists of six papers identifying methodological issues when doing this. Aim: To format the guidance from the preceding…

  5. Estimating dispersal and gene flow in the neotropical freshwater turtle Hydromedusa maximiliani (Chelidae by combining ecological and genetic methods

    Directory of Open Access Journals (Sweden)

    Souza Franco L.

    2002-01-01

    Full Text Available Hydromedusa maximiliani is a vulnerable neotropical freshwater turtle endemic to mountainous regions of the Atlantic rainforest in southeastern Brazil. Random amplified polymorphic DNA (RAPD was used to estimate the gene flow and dispersal for individuals inhabiting rivers and streams within a drainage. Nine primers generated 27 scoreable bands, of which 9 (33% were polymorphic and produced 12 RAPD phenotypes. The gene flow estimates (Nm among turtles inhabiting different rivers and streams were variable, ranging from 0.09 to 3.00 (mean: 0.60. For some loci, the rates of gene flow could offset population differentiation (Nm > 1, whereas for others random genetic drift could result in population divergence (Nm < 1. Since the genetic variation of this turtle seems to be structured according to the natural hierarchical system of rivers and streams within drainages, management programs involving translocations between different regions across the geographical range of H. maximiliani should be viewed with caution.

  6. Gene flow between wheat and wild relatives: empirical evidence from Aegilops geniculata, Ae. neglecta and Ae. triuncialis.

    Science.gov (United States)

    Arrigo, Nils; Guadagnuolo, Roberto; Lappe, Sylvain; Pasche, Sophie; Parisod, Christian; Felber, François

    2011-09-01

    Gene flow between domesticated species and their wild relatives is receiving growing attention. This study addressed introgression between wheat and natural populations of its wild relatives (Aegilops species). The sampling included 472 individuals, collected from 32 Mediterranean populations of three widespread Aegilops species (Aegilops geniculata, Ae. neglecta and Ae. triuncialis) and compared wheat field borders to areas isolated from agriculture. Individuals were characterized with amplified fragment length polymorphism fingerprinting, analysed through two computational approaches (i.e. Bayesian estimations of admixture and fuzzy clustering), and sequences marking wheat-specific insertions of transposable elements. With this combined approach, we detected substantial gene flow between wheat and Aegilops species. Specifically, Ae. neglecta and Ae. triuncialis showed significantly more admixed individuals close to wheat fields than in locations isolated from agriculture. In contrast, little evidence of gene flow was found in Ae. geniculata. Our results indicated that reproductive barriers have been regularly bypassed during the long history of sympatry between wheat and Aegilops.

  7. Fine scale gene flow and individual movements among subpopulations of Centrolene prosoblepon (Anura: Centrolenidae

    Directory of Open Access Journals (Sweden)

    Jeanne M Robertson

    2008-03-01

    Full Text Available Dispersal capabilities determine and maintain local gene flow, and this has implications for population persistence and/or recolonization following environmental perturbations (natural or anthropogenic, disease outbreaks, or other demographic collapses. To predict recolonization and understand dispersal capacity in a stream-breeding frog, we examined individual movement patterns and gene flow among four subpopulations of the Neotropical glassfrog, Centrolene prosoblepon, at a mid-elevation cloud forest site at El Copé, Panama. We measured male movement directly during a two year mark-recapture study, and indirectly with gene flow estimates from mitochondrial DNA sequences (mtDNA. Individuals of this species showed strong site fidelity: over two years, male frogs in all four headwater streams moved very little (mean = 2.33 m; mode = 0 m. Nine individuals changed streams within one or two years, moving 675-1 108 m. For those males moving more than 10 m, movement was biased upstream (p ST = 0.007, p = 0.325 but gene flow was more limited across greater distances (CT = 0.322, p = 0.065, even within the same drainage network. Lowland populations of C. prosoblepon potentially act as an important source of colonists for upland populations in this watershed. Rev. Biol. Trop. 56 (1: 13-26. Epub 2008 March 31.La capacidad de dispersión determina y mantiene el flujo genético local, y esto tiene implicaciones para la persistencia poblacional y/o la recolonización que sigue a perturbaciones ambientales. Examinamos patrones individuales de movimiento y flujo genético entre subpoblaciones de Centrolene prosoblepon (Anura: Centrolenidae en un sitio de elevación media en El Copé, Panamá. Medimos directamente el movimiento de los machos durante un estudio de marcado-recaptura, e indirectamente con estimaciones de flujo genético a partir de secuencias de ADN mitocondrial (mtDNA. Los individuos mostraron fuerte fidelidad a su lugar: por más de dos a

  8. Glyphosate drift promotes changes in fitness and transgene gene flow in canola (Brassica napus) and hybrids

    Science.gov (United States)

    Londo, Jason P.; Bautista, Nonnatus S.; Sagers, Cynthia L.; Lee, E. Henry; Watrud, Lidia S.

    2010-01-01

    Background and Aims With the advent of transgenic crops, genetically modified, herbicide-resistant Brassica napus has become a model system for examining the risks and potential ecological consequences of escape of transgenes from cultivation into wild compatible species. Escaped transgenic feral B. napus and hybrids with compatible weedy species have been identified outside of agriculture and without the apparent selection for herbicide resistance. However, herbicide (glyphosate) exposure can extend beyond crop field boundaries, and a drift-level of herbicide could function as a selective agent contributing to increased persistence of transgenes in the environment. Methods The effects of a drift level (0·1 × the field application rate) of glyphosate herbicide and varied levels of plant competition were examined on plant fitness-associated traits and gene flow in a simulated field plot, common garden experiment. Plants included transgenic, glyphosate-resistant B. napus, its weedy ancestor B. rapa, and hybrid and advanced generations derived from them. Key Results The results of this experiment demonstrate reductions in reproductive fitness for non-transgenic genotypes and a contrasting increase in plant fitness for transgenic genotypes as a result of glyphosate-drift treatments. Results also suggest that a drift level of glyphosate spray may influence the movement of transgenes among transgenic crops and weeds and alter the processes of hybridization and introgression in non-agronomic habitats by impacting flowering phenology and pollen availability within the community. Conclusions The results of this study demonstrate the potential for persistence of glyphosate resistance transgenes in weedy plant communities due to the effect of glyphosate spray drift on plant fitness. Additionally, glyphosate drift has the potential to change the gene-flow dynamics between compatible transgenic crops and weeds, simultaneously reducing direct introgression into weedy species

  9. Geographic variation in advertisement calls in a tree frog species: gene flow and selection hypotheses.

    Directory of Open Access Journals (Sweden)

    Yikweon Jang

    Full Text Available BACKGROUND: In a species with a large distribution relative to its dispersal capacity, geographic variation in traits may be explained by gene flow, selection, or the combined effects of both. Studies of genetic diversity using neutral molecular markers show that patterns of isolation by distance (IBD or barrier effect may be evident for geographic variation at the molecular level in amphibian species. However, selective factors such as habitat, predator, or interspecific interactions may be critical for geographic variation in sexual traits. We studied geographic variation in advertisement calls in the tree frog Hyla japonica to understand patterns of variation in these traits across Korea and provide clues about the underlying forces for variation. METHODOLOGY: We recorded calls of H. japonica in three breeding seasons from 17 localities including localities in remote Jeju Island. Call characters analyzed were note repetition rate (NRR, note duration (ND, and dominant frequency (DF, along with snout-to-vent length. RESULTS: The findings of a barrier effect on DF and a longitudinal variation in NRR seemed to suggest that an open sea between the mainland and Jeju Island and mountain ranges dominated by the north-south Taebaek Mountains were related to geographic variation in call characters. Furthermore, there was a pattern of IBD in mitochondrial DNA sequences. However, no comparable pattern of IBD was found between geographic distance and call characters. We also failed to detect any effects of habitat or interspecific interaction on call characters. CONCLUSIONS: Geographic variations in call characters as well as mitochondrial DNA sequences were largely stratified by geographic factors such as distance and barriers in Korean populations of H. japonica. Although we did not detect effects of habitat or interspecific interaction, some other selective factors such as sexual selection might still be operating on call characters in conjunction with

  10. Geographically weighted regression as a generalized Wombling to detect barriers to gene flow.

    Science.gov (United States)

    Diniz-Filho, José Alexandre Felizola; Soares, Thannya Nascimento; de Campos Telles, Mariana Pires

    2016-08-01

    Barriers to gene flow play an important role in structuring populations, especially in human-modified landscapes, and several methods have been proposed to detect such barriers. However, most applications of these methods require a relative large number of individuals or populations distributed in space, connected by vertices from Delaunay or Gabriel networks. Here we show, using both simulated and empirical data, a new application of geographically weighted regression (GWR) to detect such barriers, modeling the genetic variation as a "local" linear function of geographic coordinates (latitude and longitude). In the GWR, standard regression statistics, such as R(2) and slopes, are estimated for each sampling unit and thus are mapped. Peaks in these local statistics are then expected close to the barriers if genetic discontinuities exist, capturing a higher rate of population differentiation among neighboring populations. Isolation-by-Distance simulations on a longitudinally warped lattice revealed that higher local slopes from GWR coincide with the barrier detected with Monmonier algorithm. Even with a relatively small effect of the barrier, the power of local GWR in detecting the east-west barriers was higher than 95 %. We also analyzed empirical data of genetic differentiation among tree populations of Dipteryx alata and Eugenia dysenterica Brazilian Cerrado. GWR was applied to the principal coordinate of the pairwise FST matrix based on microsatellite loci. In both simulated and empirical data, the GWR results were consistent with discontinuities detected by Monmonier algorithm, as well as with previous explanations for the spatial patterns of genetic differentiation for the two species. Our analyses reveal how this new application of GWR can viewed as a generalized Wombling in a continuous space and be a useful approach to detect barriers and discontinuities to gene flow.

  11. Human-aided and natural dispersal drive gene flow across the range of an invasive mosquito.

    Science.gov (United States)

    Medley, Kim A; Jenkins, David G; Hoffman, Eric A

    2015-01-01

    Human-aided transport is responsible for many contemporary species introductions, yet the contribution of human-aided transport to dispersal within non-native regions is less clear. Understanding dispersal dynamics for invasive species can streamline mitigation efforts by targeting routes that contribute disproportionally to spread. Because of its limited natural dispersal ability, rapid spread of the Asian tiger mosquito (Aedes albopictus) has been attributed to human-aided transport, but until now, the relative roles of human-aided and natural movement have not been rigorously evaluated. Here, we use landscape genetics and information-theoretic model selection to evaluate 52 models representing 9240 pairwise dispersal paths among sites across the US range for Ae. albopictus and show that recent gene flow reflects a combination of natural and human-aided dispersal. Highways and water availability facilitate dispersal at a broad spatial scale, but gene flow is hindered by forests at the current distributional limit (range edge) and by agriculture among sites within the mosquito's native climatic niche (range core). Our results show that highways are important to genetic structure between range-edge and range-core pairs, suggesting a role for human-aided mosquito transport to the range edge. In contrast, natural dispersal is dominant at smaller spatial scales, reflecting a shifting dominance to natural movement two decades after introduction. These conclusions highlight the importance of (i) early intervention for species introductions, particularly those with readily dispersed dormant stages and short generation times, and (ii) strict monitoring of commercial shipments for transported immature stages of Ae. albopictus, particularly towards the northern edge of the US range.

  12. Geographic Variation in Advertisement Calls in a Tree Frog Species: Gene Flow and Selection Hypotheses

    Science.gov (United States)

    Jang, Yikweon; Hahm, Eun Hye; Lee, Hyun-Jung; Park, Soyeon; Won, Yong-Jin; Choe, Jae C.

    2011-01-01

    Background In a species with a large distribution relative to its dispersal capacity, geographic variation in traits may be explained by gene flow, selection, or the combined effects of both. Studies of genetic diversity using neutral molecular markers show that patterns of isolation by distance (IBD) or barrier effect may be evident for geographic variation at the molecular level in amphibian species. However, selective factors such as habitat, predator, or interspecific interactions may be critical for geographic variation in sexual traits. We studied geographic variation in advertisement calls in the tree frog Hyla japonica to understand patterns of variation in these traits across Korea and provide clues about the underlying forces for variation. Methodology We recorded calls of H. japonica in three breeding seasons from 17 localities including localities in remote Jeju Island. Call characters analyzed were note repetition rate (NRR), note duration (ND), and dominant frequency (DF), along with snout-to-vent length. Results The findings of a barrier effect on DF and a longitudinal variation in NRR seemed to suggest that an open sea between the mainland and Jeju Island and mountain ranges dominated by the north-south Taebaek Mountains were related to geographic variation in call characters. Furthermore, there was a pattern of IBD in mitochondrial DNA sequences. However, no comparable pattern of IBD was found between geographic distance and call characters. We also failed to detect any effects of habitat or interspecific interaction on call characters. Conclusions Geographic variations in call characters as well as mitochondrial DNA sequences were largely stratified by geographic factors such as distance and barriers in Korean populations of H. japoinca. Although we did not detect effects of habitat or interspecific interaction, some other selective factors such as sexual selection might still be operating on call characters in conjunction with restricted gene

  13. Gene flow and population structure in the Mexican blind cavefish complex (Astyanax mexicanus

    Directory of Open Access Journals (Sweden)

    Bradic Martina

    2012-01-01

    Full Text Available Abstract Background Cave animals converge evolutionarily on a suite of troglomorphic traits, the best known of which are eyelessness and depigmentation. We studied 11 cave and 10 surface populations of Astyanax mexicanus in order to better understand the evolutionary origins of the cave forms, the basic genetic structuring of both cave and surface populations, and the degree to which present day migration among them affects their genetic divergence. Results To assess the genetic structure within populations and the relationships among them we genotyped individuals at 26 microsatellite loci. We found that surface populations are similar to one another, despite their relatively large geographic separation, whereas the cave populations are better differentiated. The cave populations we studied span the full range of the cave forms in three separate geographic regions and have at least five separate evolutionary origins. Cave populations had lower genetic diversity than surface populations, correlated with their smaller effective population sizes, probably the result of food and space limitations. Some of the cave populations receive migrants from the surface and exchange migrants with one another, especially when geographically close. This admixture results in significant heterozygote deficiencies at numerous loci due to Wahlund effects. Cave populations receiving migrants from the surface contain small numbers of individuals that are intermediate in both phenotype and genotype, affirming at least limited gene flow from the surface. Conclusions Cave populations of this species are derived from two different surface stocks denoted "old" and "new." The old stock colonized caves at least three times independently while the new stock colonized caves at least twice independently. Thus, the similar cave phenotypes found in these caves are the result of repeated convergences. These phenotypic convergences have occurred in spite of gene flow from surface

  14. Population divergence and gene flow in an endangered and highly mobile seabird

    Science.gov (United States)

    Welch, A. J.; Fleischer, R. C.; James, H. F.; Wiley, A. E.; Ostrom, P. H.; Adams, J.; Duvall, F.; Holmes, N.; Hu, D.; Penniman, J.; Swindle, K. A.

    2012-01-01

    Seabirds are highly vagile and can disperse up to thousands of kilometers, making it difficult to identify the factors that promote isolation between populations. The endemic Hawaiian petrel (Pterodroma sandwichensis) is one such species. Today it is endangered, and known to breed only on the islands of Hawaii, Maui, Lanai and Kauai. Historical records indicate that a large population formerly bred on Molokai as well, but this population has recently been extirpated. Given the great dispersal potential of these petrels, it remains unclear if populations are genetically distinct and which factors may contribute to isolation between them. We sampled petrels from across their range, including individuals from the presumably extirpated Molokai population. We sequenced 524 bp of mitochondrial DNA, 741 bp from three nuclear introns, and genotyped 18 microsatellite loci in order to examine the patterns of divergence in this species and to investigate the potential underlying mechanisms. Both mitochondrial and nuclear data sets indicated significant genetic differentiation among all modern populations, but no differentiation was found between historic samples from Molokai and modern birds from Lanai. Population-specific nonbreeding distribution and strong natal philopatry may reduce gene flow between populations. However, the lack of population structure between extirpated Molokai birds and modern birds on Lanai indicates that there was substantial gene flow between these populations and that petrels may be able to overcome barriers to dispersal prior to complete extirpation. Hawaiian petrel populations could be considered distinct management units, however, the dwindling population on Hawaii may require translocation to prevent extirpation in the near future.

  15. Differential threshold effects of habitat fragmentation on gene flow in two widespread species of bush crickets.

    Science.gov (United States)

    Lange, Rebecca; Durka, Walter; Holzhauer, Stephanie I J; Wolters, Volkmar; Diekötter, Tim

    2010-11-01

    Effects of habitat fragmentation on genetic diversity vary among species. This may be attributed to the interacting effects of species traits and landscape structure. While widely distributed and abundant species are often considered less susceptible to fragmentation, this may be different if they are small sized and show limited dispersal. Under intensive land use, habitat fragmentation may reach thresholds at which gene flow among populations of small-sized and dispersal-limited species becomes disrupted. Here, we studied the genetic diversity of two abundant and widespread bush crickets along a gradient of habitat fragmentation in an agricultural landscape. We applied traditional (G(ST), θ) and recently developed (G'ST', D) estimators of genetic differentiation on microsatellite data from each of twelve populations of the grassland species Metrioptera roeselii and the forest-edge species Pholidoptera griseoaptera to identify thresholds of habitat fragmentation below which genetic population structure is affected. Whereas the grassland species exhibited a uniform genetic structuring (G(ST) = 0.020-0.033; D = 0.085-0.149) along the whole fragmentation gradient, the forest-edge species' genetic differentiation increased significantly from D habitat dropped below a threshold of 20% and its proximity decreased substantially at the landscape scale. The influence of fragmentation on genetic differentiation was qualitatively unaffected by the choice of estimators of genetic differentiation but quantitatively underestimated by the traditional estimators. These results indicate that even for widespread species in modern agricultural landscapes fragmentation thresholds exist at which gene flow among suitable habitat patches becomes restricted. © 2010 Blackwell Publishing Ltd.

  16. Gene Flow of a Forest-Dependent Bird across a Fragmented Landscape.

    Directory of Open Access Journals (Sweden)

    Rachael V Adams

    Full Text Available Habitat loss and fragmentation can affect the persistence of populations by reducing connectivity and restricting the ability of individuals to disperse across landscapes. Dispersal corridors promote population connectivity and therefore play important roles in maintaining gene flow in natural populations inhabiting fragmented landscapes. In the prairies, forests are restricted to riparian areas along river systems which act as important dispersal corridors for forest dependent species across large expanses of unsuitable grassland habitat. However, natural and anthropogenic barriers within riparian systems have fragmented these forested habitats. In this study, we used microsatellite markers to assess the fine-scale genetic structure of a forest-dependent species, the black-capped chickadee (Poecile atricapillus, along 10 different river systems in Southern Alberta. Using a landscape genetic approach, landscape features (e.g., land cover were found to have a significant effect on patterns of genetic differentiation. Populations are genetically structured as a result of natural breaks in continuous habitat at small spatial scales, but the artificial barriers we tested do not appear to restrict gene flow. Dispersal between rivers is impeded by grasslands, evident from isolation of nearby populations (~ 50 km apart, but also within river systems by large treeless canyons (>100 km. Significant population genetic differentiation within some rivers corresponded with zones of different cottonwood (riparian poplar tree species and their hybrids. This study illustrates the importance of considering the impacts of habitat fragmentation at small spatial scales as well as other ecological processes to gain a better understanding of how organisms respond to their environmental connectivity. Here, even in a common and widespread songbird with high dispersal potential, small breaks in continuous habitats strongly influenced the spatial patterns of genetic

  17. Gene Flow of a Forest-Dependent Bird across a Fragmented Landscape

    Science.gov (United States)

    2015-01-01

    Habitat loss and fragmentation can affect the persistence of populations by reducing connectivity and restricting the ability of individuals to disperse across landscapes. Dispersal corridors promote population connectivity and therefore play important roles in maintaining gene flow in natural populations inhabiting fragmented landscapes. In the prairies, forests are restricted to riparian areas along river systems which act as important dispersal corridors for forest dependent species across large expanses of unsuitable grassland habitat. However, natural and anthropogenic barriers within riparian systems have fragmented these forested habitats. In this study, we used microsatellite markers to assess the fine-scale genetic structure of a forest-dependent species, the black-capped chickadee (Poecile atricapillus), along 10 different river systems in Southern Alberta. Using a landscape genetic approach, landscape features (e.g., land cover) were found to have a significant effect on patterns of genetic differentiation. Populations are genetically structured as a result of natural breaks in continuous habitat at small spatial scales, but the artificial barriers we tested do not appear to restrict gene flow. Dispersal between rivers is impeded by grasslands, evident from isolation of nearby populations (~ 50 km apart), but also within river systems by large treeless canyons (>100 km). Significant population genetic differentiation within some rivers corresponded with zones of different cottonwood (riparian poplar) tree species and their hybrids. This study illustrates the importance of considering the impacts of habitat fragmentation at small spatial scales as well as other ecological processes to gain a better understanding of how organisms respond to their environmental connectivity. Here, even in a common and widespread songbird with high dispersal potential, small breaks in continuous habitats strongly influenced the spatial patterns of genetic variation. PMID

  18. Fat-tailed gene flow in the dioecious canopy tree species Fraxinus mandshurica var. japonica revealed by microsatellites.

    Science.gov (United States)

    Goto, S; Shimatani, K; Yoshimaru, H; Takahashi, Y

    2006-09-01

    Pollen flow, seed dispersal and individual reproductive success can be simultaneously estimated from the genotypes of adults and offspring using stochastic models. Using four polymorphic microsatellite loci, gene flow of the wind-pollinated and wind-seed-dispersed dioecious tree species, Fraxinus mandshurica var. japonica, was quantified in a riparian forest, in northern Japan. In a 10.5-ha plot, 74 female adults, 76 male adults and 292 current-year seedlings were mapped and genotyped, together with 200 seeds. To estimate dispersal kernels of pollen and seeds, we applied normal, exponential power, Weibull, bivariate t-distribution kernels, and two-component models consisting of two normal distribution functions, one with a small and one with a large variance. A two-component pollen flow model with a small contribution (26.1%) from short-distance dispersal (sigma = 7.2 m), and the rest from long-distance flow (sigma = 209.9 m), was chosen for the best-fitting model. The average distance that integrated pollen flows inside and outside the study plot was estimated to be 196.8 m. Tree size and flowering intensity affected reproduction, and there appeared to be critical values that distinguished reproductively successful and unsuccessful adults. In contrast, the gene flow model that estimated both pollen and seed dispersal from established seedlings resulted in extensive seed dispersal, and the expected spatial genetic structures did not satisfactorily fit with the observations, even for the selected model. Our results advanced small-scale individual-based parentage analysis for quantifying fat-tailed gene flow in wind-mediated species, but also clarified its limitations and suggested future possibilities for gene flow studies.

  19. Migration and population genetics of the grain aphid Macrosiphum miscanti (Takahashi) in relation to the geographic distance and gene flow

    Institute of Scientific and Technical Information of China (English)

    GUO Wei; SHEN Zuorui; LI Zhihong; GAO Lingwang

    2005-01-01

    The population genetics of the grain aphid Macrosiphum miscanti (Takahashi) is analyzed by microsatellite markers.Samples collected from 15 locations in China have been examined at 5 polymorphic microsatellite loci. Overall, genetic diversity displays a relation between the migration and gene flow in the grain aphid: a free and frequent gene flow is found in the eastern populations, and gene isolation occurs in the two western populations, especially Datong population and Guiyang population. The natural barriers may present an insurmountable obstacle preventing gene flow and aphid migration. However, a spatial genetic differentiation between populations is correlated with their geographical separation, indicating the geographic differentiation may play an important role in shaping the genetic structure of M. miscanti populations. In addition, most populations of grain aphids are out of Hardy-Weinberg equilibrium and there is heterozygote deficit. Based on F statistics, the average genetic differentiation among different geographical populations is relatively low. It seems that the long distance migration of the grain aphid may enhance gene flow and decrease genetic differentiation among different populations.

  20. Parallel evolution of local adaptation and reproductive isolation in the face of gene flow.

    Science.gov (United States)

    Butlin, Roger K; Saura, Maria; Charrier, Grégory; Jackson, Benjamin; André, Carl; Caballero, Armando; Coyne, Jerry A; Galindo, Juan; Grahame, John W; Hollander, Johan; Kemppainen, Petri; Martínez-Fernández, Mónica; Panova, Marina; Quesada, Humberto; Johannesson, Kerstin; Rolán-Alvarez, Emilio

    2014-04-01

    Parallel evolution of similar phenotypes provides strong evidence for the operation of natural selection. Where these phenotypes contribute to reproductive isolation, they further support a role for divergent, habitat-associated selection in speciation. However, the observation of pairs of divergent ecotypes currently occupying contrasting habitats in distinct geographical regions is not sufficient to infer parallel origins. Here we show striking parallel phenotypic divergence between populations of the rocky-shore gastropod, Littorina saxatilis, occupying contrasting habitats exposed to either wave action or crab predation. This divergence is associated with barriers to gene exchange but, nevertheless, genetic variation is more strongly structured by geography than by ecotype. Using approximate Bayesian analysis of sequence data and amplified fragment length polymorphism markers, we show that the ecotypes are likely to have arisen in the face of continuous gene flow and that the demographic separation of ecotypes has occurred in parallel at both regional and local scales. Parameter estimates suggest a long delay between colonization of a locality and ecotype formation, perhaps because the postglacial spread of crab populations was slower than the spread of snails. Adaptive differentiation may not be fully genetically independent despite being demographically parallel. These results provide new insight into a major model of ecologically driven speciation.

  1. Independent domestication of Asian rice followed by gene flow from japonica to indica.

    Science.gov (United States)

    Yang, Ching-chia; Kawahara, Yoshihiro; Mizuno, Hiroshi; Wu, Jianzhong; Matsumoto, Takashi; Itoh, Takeshi

    2012-05-01

    Results from studies on the domestication process of Asian rice Oryza sativa have been controversial because of its complicated evolutionary history. Previous studies have yielded two alternative hypotheses about the origin(s) of the two major groups of O. sativa: japonica and indica. One study proposes a single common wild ancestor, whereas the other suggests that there were multiple domestication events of different types of wild rice. Here, we provide clear evidence of the independent domestication of japonica and indica obtained via high-throughput sequencing and a large-scale comparative analysis of two wild rice accessions (W1943 and W0106) and two cultivars (a japonica cultivar called "Nipponbare" and an indica cultivar called "Guangluai-4"). The different domestication processes of the two cultivar groups appear to have led to distinct patterns of molecular evolution in protein-coding regions. The intensity of purifying selection was relaxed only in the japonica group, possibly because of a bottleneck effect. Moreover, a genome-wide comparison between Nipponbare, Guangluai-4, and another indica cultivar (93-11) suggests multiple hybridization events between japonica and indica, both before and after the divergence of the indica cultivars. We found that a large amount of genomic DNA, including domestication-related genes, was transferred from japonica to indica, which might have been important in the development of modern rice. Our study provides an overview of the dynamic process of Asian rice domestication, including independent domestication events and subsequent gene flow.

  2. Afghan Hindu Kush: where Eurasian sub-continent gene flows converge.

    Directory of Open Access Journals (Sweden)

    Julie Di Cristofaro

    Full Text Available Despite being located at the crossroads of Asia, genetics of the Afghanistan populations have been largely overlooked. It is currently inhabited by five major ethnic populations: Pashtun, Tajik, Hazara, Uzbek and Turkmen. Here we present autosomal from a subset of our samples, mitochondrial and Y- chromosome data from over 500 Afghan samples among these 5 ethnic groups. This Afghan data was supplemented with the same Y-chromosome analyses of samples from Iran, Kyrgyzstan, Mongolia and updated Pakistani samples (HGDP-CEPH. The data presented here was integrated into existing knowledge of pan-Eurasian genetic diversity. The pattern of genetic variation, revealed by structure-like and Principal Component analyses and Analysis of Molecular Variance indicates that the people of Afghanistan are made up of a mosaic of components representing various geographic regions of Eurasian ancestry. The absence of a major Central Asian-specific component indicates that the Hindu Kush, like the gene pool of Central Asian populations in general, is a confluence of gene flows rather than a source of distinctly autochthonous populations that have arisen in situ: a conclusion that is reinforced by the phylogeography of both haploid loci.

  3. Population Structure and Gene Flow of the Yellow Anaconda (Eunectes notaeus) in Northern Argentina

    Science.gov (United States)

    McCartney-Melstad, Evan; Waller, Tomás; Micucci, Patricio A.; Barros, Mariano; Draque, Juan; Amato, George; Mendez, Martin

    2012-01-01

    Yellow anacondas (Eunectes notaeus) are large, semiaquatic boid snakes found in wetland systems in South America. These snakes are commercially harvested under a sustainable management plan in Argentina, so information regarding population structuring can be helpful for determination of management units. We evaluated genetic structure and migration using partial sequences from the mitochondrial control region and mitochondrial genes cyt-b and ND4 for 183 samples collected within northern Argentina. A group of landscape features and environmental variables including several treatments of temperature and precipitation were explored as potential drivers of observed genetic patterns. We found significant population structure between most putative population comparisons and bidirectional but asymmetric migration in several cases. The configuration of rivers and wetlands was found to be significantly associated with yellow anaconda population structure (IBD), and important for gene flow, although genetic distances were not significantly correlated with the environmental variables used here. More in-depth analyses of environmental data may be needed to fully understand the importance of environmental conditions on population structure and migration. These analyses indicate that our putative populations are demographically distinct and should be treated as such in Argentina's management plan for the harvesting of yellow anacondas. PMID:22675425

  4. Continuous gene flow contributes to low global species abundance and distribution of a marine model diatom

    KAUST Repository

    Rastogi, Achal

    2017-08-15

    Unlike terrestrial ecosystems where geographical isolation often leads to a restricted gene flow between species, genetic admixing in aquatic micro-eukaryotes is likely to be frequent. Diatoms inhabit marine ecosystems since the Mesozoic period and presently constitute one of the major primary producers in the world ocean. They are a highly diversified group of eukaryotic phytoplankton with estimates of up to 200,000 species. Since decades, Phaeodactylum tricornutum is used as a model diatom species to characterize the functional pathways, physiology and evolution of diatoms in general. In the current study, using whole genome sequencing of ten P. tricornutum strains, sampled at broad geospatial and temporal scales, we show a continuous dispersal and genetic admixing between geographically isolated strains. We also describe a very high level of heterozygosity and propose it to be a consequence of frequent ancestral admixture. Our finding that P. tricornutum sequences are plausibly detectable at low but broadly distributed levels in the world ocean further suggests that high admixing between geographically isolated strains may create a significant bottleneck, thus influencing their global abundance and distribution in nature. Finally, in an attempt to understand the functional implications of genetic diversity between different P. tricornutum ecotypes, we show the effects of domestication in inducing changes in the selection pressure on many genes and metabolic pathways. We propose these findings to have significant implications for understanding the genetic structure of diatom populations in nature and provide a framework to assess the genomic underpinnings of their ecological success.

  5. A multilocus perspective on colonization accompanied by selection and gene flow.

    Science.gov (United States)

    Rosenblum, Erica Bree; Hickerson, Michael J; Moritz, Craig

    2007-12-01

    The colonization of novel habitats involves complex interactions between founder events, selection, and ongoing migration, and can lead to diverse evolutionary outcomes from local extinction to adaptation to speciation. Although there have been several studies of the demography of colonization of remote habitats, less is known about the demographic consequences of colonization of novel habitats within a continuous species range. Populations of the Eastern Fence Lizard, Sceloporus undulatus, are continuously distributed across two dramatic transitions in substrate color in southern New Mexico and have undergone rapid adaptation following colonization of these novel environments. Blanched forms inhabit the gypsum sand dunes of White Sands and melanic forms are found on the black basalt rocks of the Carrizozo lava flow. Each of these habitats formed within the last 10,000 years, allowing comparison of genetic signatures of population history for two independent colonizations from the same source population. We present evidence on phenotypic variation in lizard color, environmental variation in substrate color, and sequence variation for mitochondrial DNA and 19 independent nuclear loci. To confirm the influence of natural selection and gene flow in this system, we show that phenotypic variation is best explained by environmental variation and that neutral genetic variation is related to distance between populations, not partitioned by habitat. The historical demography of colonization was inferred using an Approximate Bayesian Computation (ABC) framework that incorporates known geological information and allows for ongoing migration with the source population. The inferences differed somewhat between mtDNA and nuclear markers, but overall provided strong evidence of historical size reductions in both white sand and black lava populations at the time of colonization. Populations in both novel habitats appear to have undergone partial but incomplete recovery from the

  6. Managing diversity: Domestication and gene flow in Stenocereus stellatus Riccob. (Cactaceae) in Mexico

    Science.gov (United States)

    Cruse-Sanders, Jennifer M; Parker, Kathleen C; Friar, Elizabeth A; Huang, Daisie I; Mashayekhi, Saeideh; Prince, Linda M; Otero-Arnaiz, Adriana; Casas, Alejandro

    2013-01-01

    Microsatellite markers (N = 5) were developed for analysis of genetic variation in 15 populations of the columnar cactus Stenocereus stellatus, managed under traditional agriculture practices in central Mexico. Microsatellite diversity was analyzed within and among populations, between geographic regions, and among population management types to provide detailed insight into historical gene flow rates and population dynamics associated with domestication. Our results corroborate a greater diversity in populations managed by farmers compared with wild ones (HE = 0.64 vs. 0.55), but with regional variation between populations among regions. Although farmers propagated S. stellatus vegetatively in home gardens to diversify their stock, asexual recruitment also occurred naturally in populations where more marginal conditions have limited sexual recruitment, resulting in lower genetic diversity. Therefore, a clear-cut relationship between the occurrence of asexual recruitment and genetic diversity was not evident. Two managed populations adjacent to towns were identified as major sources of gene movement in each sampled region, with significant migration to distant as well as nearby populations. Coupled with the absence of significant bottlenecks, this suggests a mechanism for promoting genetic diversity in managed populations through long distance gene exchange. Cultivation of S. stellatus in close proximity to wild populations has led to complex patterns of genetic variation across the landscape that reflects the interaction of natural and cultural processes. As molecular markers become available for nontraditional crops and novel analysis techniques allow us to detect and evaluate patterns of genetic diversity, genetic studies provide valuable insights into managing crop genetic resources into the future against a backdrop of global change. Traditional agriculture systems play an important role in maintaining genetic diversity for plant species. PMID:23762520

  7. Actinobacillus pleuropneumoniae genes expression in biofilms cultured under static conditions and in a drip-flow apparatus.

    Science.gov (United States)

    Tremblay, Yannick D N; Deslandes, Vincent; Jacques, Mario

    2013-05-31

    Actinobacillus pleuropneumoniae is the Gram-negative bacterium responsible for porcine pleuropneumonia. This respiratory infection is highly contagious and characterized by high morbidity and mortality. The objectives of our study were to study the transcriptome of A. pleuropneumoniae biofilms at different stages and to develop a protocol to grow an A. pleuropneumoniae biofilm in a drip-flow apparatus. This biofilm reactor is a system with an air-liquid interface modeling lung-like environment. Bacteria attached to a surface (biofilm) and free floating bacteria (plankton) were harvested for RNA isolation. Labelled cDNA was hybridized to a microarray to compare the expression profiles of planktonic cells and biofilm cells. It was observed that 47 genes were differentially expressed (22 up, 25 down) in a 4 h-static growing/maturing biofilm and 117 genes were differentially expressed (49 up, 68 down) in a 6h-static dispersing biofilm. The transcriptomes of a 4 h biofilm and a 6 h biofilm were also compared and 456 genes (235 up, 221 down) were identified as differently expressed. Among the genes identified in the 4 h vs 6h biofilm experiment, several regulators of stress response were down-regulated and energy metabolism associated genes were up-regulated. Biofilm bacteria cultured using the drip-flow apparatus differentially expressed 161 genes (68 up, 93 down) compared to the effluent bacteria. Cross-referencing of differentially transcribed genes in the different assays revealed that drip-flow biofilms shared few differentially expressed genes with static biofilms (4 h or 6 h) but shared several differentially expressed genes with natural or experimental infections in pigs. The formation of a static biofilm by A. pleuropneumoniae strain S4074 is a rapid process and transcriptional analysis indicated that dispersal observed at 6 h is driven by nutritional stresses. Furthermore, A. pleuropneumoniae can form a biofilm under low-shear force in a drip-flow apparatus and

  8. Comparison of pollen gene flow among four European beech (Fagus sylvatica L.) populations characterized by different management regimes

    NARCIS (Netherlands)

    Piotti, A.; Leonardi, S.; Buiteveld, J.; Geburek, T.; Gerber, S.; Kramer, K.; Vettori, C.; Vendramin, G.G.

    2012-01-01

    The study of the dispersal capability of a species can provide essential information for the management and conservation of its genetic variability. Comparison of gene flow rates among populations characterized by different management and evolutionary histories allows one to decipher the role of fac

  9. Dispersal and gene flow in the rare, parasitic Large Blue butterfly Maculinea arion

    DEFF Research Database (Denmark)

    Ugelvig, Line Vej; Andersen, Anne; Boomsma, Jacobus Jan

    2012-01-01

    decline throughout Europe and extinction in Britain followed by reintroduction of a seed population from the Swedish island of Öland. We find that populations are highly structured genetically, but that gene flow occurs over distances 15 times longer than the maximum distance recorded from mark...

  10. Regional gene flow and population structure of the wind-dispersed plant species Hypochaeris radicata (Asteraceae) in an agricultural landscape

    NARCIS (Netherlands)

    Mix, C.; Arens, P.F.P.; Rengelink, R.; Smulders, M.J.M.; Groenendael, van J.M.; Ouburg, J.

    2006-01-01

    Using microsatellites, we investigated population structure and gene flow of the short-lived, wind-dispersed plant species Hypochaeris radicata in a fragmented agricultural landscape where more than 99% of the nutrient-poor grasslands have disappeared over the last century. We sampled populations in

  11. EVIDENCE FOR LANDSCAPE LEVEL, POLLEN-MEDIATED GENE FLOW FROM CREEPING BENTGRASS WITH CP4 EPSPS AS A MARKER

    Science.gov (United States)

    In a landscape level study, gene flow via pollen was tracked from multiple source fields of genetically modified (GM) herbicide resistant creeping bentgrass (Agrostis stolonifera L.) to 75 of 138 sentinel plants of A. stolonifera and to 29 of 69 resident populations of Agrostis s...

  12. Empirical phylogenies and species abundance distributions are consistent with pre-equilibrium dynamics of neutral community models with gene flow

    KAUST Repository

    Bonnet-Lebrun, Anne-Sophie

    2017-03-17

    Community characteristics reflect past ecological and evolutionary dynamics. Here, we investigate whether it is possible to obtain realistically shaped modelled communities - i.e., with phylogenetic trees and species abundance distributions shaped similarly to typical empirical bird and mammal communities - from neutral community models. To test the effect of gene flow, we contrasted two spatially explicit individual-based neutral models: one with protracted speciation, delayed by gene flow, and one with point mutation speciation, unaffected by gene flow. The former produced more realistic communities (shape of phylogenetic tree and species-abundance distribution), consistent with gene flow being a key process in macro-evolutionary dynamics. Earlier models struggled to capture the empirically observed branching tempo in phylogenetic trees, as measured by the gamma statistic. We show that the low gamma values typical of empirical trees can be obtained in models with protracted speciation, in pre-equilibrium communities developing from an initially abundant and widespread species. This was even more so in communities sampled incompletely, particularly if the unknown species are the youngest. Overall, our results demonstrate that the characteristics of empirical communities that we have studied can, to a large extent, be explained through a purely neutral model under pre-equilibrium conditions. This article is protected by copyright. All rights reserved.

  13. Pollen-mediated gene flow and seed exchange in small-scale Zambian maize farming, implications for biosafety assessment

    Science.gov (United States)

    Bøhn, Thomas; Aheto, Denis W.; Mwangala, Felix S.; Fischer, Klara; Bones, Inger Louise; Simoloka, Christopher; Mbeule, Ireen; Schmidt, Gunther; Breckling, Broder

    2016-10-01

    Gene flow in agricultural crops is important for risk assessment of genetically modified (GM) crops, particularly in countries with a large informal agricultural sector of subsistence cultivation. We present a pollen flow model for maize (Zea mays), a major staple crop in Africa. We use spatial properties of fields (size, position) in three small-scale maize farming communities in Zambia and estimate rates of cross-fertilisation between fields sown with different maize varieties (e.g. conventional and transgene). As an additional factor contributing to gene flow, we present data on seed saving and sharing among farmers that live in the same communities. Our results show that: i) maize fields were small and located in immediate vicinity of neighboring fields; ii) a majority of farmers saved and shared seed; iii) modeled rates of pollen-mediated gene flow showed extensive mixing of germplasm between fields and farms and iv) as a result, segregation of GM and non-GM varieties is not likely to be an option in these systems. We conclude that the overall genetic composition of maize, in this and similar agricultural contexts, will be strongly influenced both by self-organised ecological factors (pollen flow), and by socially mediated intervention (seed recycling and sharing).

  14. Environmental implications of gene flow from sugar beet to wild beet--current status and future research needs.

    Science.gov (United States)

    Bartsch, Detlef; Cuguen, Joel; Biancardi, Enrico; Sweet, Jeremy

    2003-01-01

    Gene flow via seed or pollen is a basic biological process in plant evolution. The ecological and genetic consequences of gene flow depend on the amount and direction of gene flow as well as on the fitness of hybrids. The assessment of potential risks of transgenic plants should take into account the fact that conventional crops can often cross with wild plants. The precautionary approach in risk management of genetically modified plants (GMPs) may make it necessary to monitor significant wild and weed populations that might be affected by transgene escape. Gene flow is hard to control in wind-pollinated plants like beet (Beta vulgaris). In addition, wild beet populations potentially can undergo evolutionary changes which might expand their geographical distribution. Unintended products of cultivated beets pollinated by wild beets are weed beets that bolt and flower during their first year of planting. Weed beets cause yield losses and can delay harvest. Wild beets are important plant genetic resources and the preservation of wild beet diversity in Europe has been considered in biosafety research. We present here the methodology and research approaches that can be used for monitoring the geographical distribution and diversity of Beta populations. It has recently been shown that a century of gene flow from Beta vulgaris ssp. vulgaris has not altered the genetic diversity of wild Beta vulgaris L. ssp. maritima (L.) Arcang. in the Italian sugar beet seed production area. Future research should focus on the potential evolution of transgenic wild beet populations in comparison to these baseline data. Two monitoring models are presented describing how endpoints can be measured: (1) "Pre-post" crop commercialization against today's baseline and (2) "Parallel" to crop commercialization against GMP free reference areas/ populations. Model 2 has the advantage of taking ongoing changes in genetic diversity and population dynamics into account. Model 1 is more applicable if

  15. Inferred vs realized patterns of gene flow: an analysis of population structure in the Andros Island Rock Iguana.

    Directory of Open Access Journals (Sweden)

    Giuliano Colosimo

    Full Text Available Ecological data, the primary source of information on patterns and rates of migration, can be integrated with genetic data to more accurately describe the realized connectivity between geographically isolated demes. In this paper we implement this approach and discuss its implications for managing populations of the endangered Andros Island Rock Iguana, Cyclura cychlura cychlura. This iguana is endemic to Andros, a highly fragmented landmass of large islands and smaller cays. Field observations suggest that geographically isolated demes were panmictic due to high, inferred rates of gene flow. We expand on these observations using 16 polymorphic microsatellites to investigate the genetic structure and rates of gene flow from 188 Andros Iguanas collected across 23 island sites. Bayesian clustering of specimens assigned individuals to three distinct genotypic clusters. An analysis of molecular variance (AMOVA indicates that allele frequency differences are responsible for a significant portion of the genetic variance across the three defined clusters (Fst =  0.117, p<<0.01. These clusters are associated with larger islands and satellite cays isolated by broad water channels with strong currents. These findings imply that broad water channels present greater obstacles to gene flow than was inferred from field observation alone. Additionally, rates of gene flow were indirectly estimated using BAYESASS 3.0. The proportion of individuals originating from within each identified cluster varied from 94.5 to 98.7%, providing further support for local isolation. Our assessment reveals a major disparity between inferred and realized gene flow. We discuss our results in a conservation perspective for species inhabiting highly fragmented landscapes.

  16. Site-Specific Insertion Polymorphism of the MITE Alex-1 in the Genus Coffea Suggests Interspecific Gene Flow

    Directory of Open Access Journals (Sweden)

    Christine Dubreuil-Tranchant

    2011-01-01

    Full Text Available Miniature Inverted-repeat Transposable Elements (MITEs are small nonautonomous class-II transposable elements distributed throughout eukaryotic genomes. We identified a novel family of MITEs (named Alex in the Coffea canephora genome often associated with expressed sequences. The Alex-1 element is inserted in an intron of a gene at the CcEIN4 locus. Its mobility was demonstrated by sequencing the insertion site in C. canephora accessions and Coffea species. Analysis of the insertion polymorphism of Alex-1 at this locus in Coffea species and in C. canephora showed that there was no relationship between the geographical distribution of the species, their phylogenetic relationships, and insertion polymorphism. The intraspecific distribution of C. canephora revealed an original situation within the E diversity group. These results suggest possibly greater gene flow between species than previously thought. This MITE family will enable the study of the C. canephora genome evolution, phylogenetic relationships, and possible gene flows within the Coffea genus.

  17. Head Transcriptomes of Two Closely Related Species of Fruit Flies of the Anastrepha fraterculus Group Reveals Divergent Genes in Species with Extensive Gene Flow

    Directory of Open Access Journals (Sweden)

    Victor Borges Rezende

    2016-10-01

    Full Text Available Several fruit flies species of the Anastrepha fraterculus group are of great economic importance for the damage they cause to a variety of fleshy fruits. Some species in this group have diverged recently, with evidence of introgression, showing similar morphological attributes that render their identification difficult, reinforcing the relevance of identifying new molecular markers that may differentiate species. We investigated genes expressed in head tissues from two closely related species: A. obliqua and A. fraterculus, aiming to identify fixed single nucleotide polymorphisms (SNPs and highly differentiated transcripts, which, considering that these species still experience some level of gene flow, could indicate potential candidate genes involved in their differentiation process. We generated multiple libraries from head tissues of these two species, at different reproductive stages, for both sexes. Our analyses indicate that the de novo transcriptome assemblies are fairly complete. We also produced a hybrid assembly to map each species’ reads, and identified 67,470 SNPs in A. fraterculus, 39,252 in A. obliqua, and 6386 that were common to both species. We identified 164 highly differentiated unigenes that had a mean interspecific index (D¯ of at least 0.94. We selected unigenes that had Ka/Ks higher than 0.5, or had at least three or more highly differentiated SNPs as potential candidate genes for species differentiation. Among these candidates, we identified proteases, regulators of redox homeostasis, and an odorant-binding protein (Obp99c, among other genes. The head transcriptomes described here enabled the identification of thousands of genes hitherto unavailable for these species, and generated a set of candidate genes that are potentially important to genetically identify species and understand the speciation process in the presence of gene flow of A. obliqua and A. fraterculus.

  18. Hierarchical structure of mitochondrial DNA gene flow among humpback whales Megaptera novaeangliae, world-wide.

    Science.gov (United States)

    Baker, C S; Slade, R W; Bannister, J L; Abernethy, R B; Weinrich, M T; Lien, J; Urban, J; Corkeron, P; Calmabokidis, J; Vasquez, O

    1994-08-01

    The genetic structure of humpback whale populations and subpopulation divisions is described by restriction fragment length analysis of the mitochondrial (mt) DNA from samples of 230 whales collected by biopsy darting in 11 seasonal habitats representing six subpopulations, or 'stocks', world-wide. The hierarchical structure of mtDNA haplotype diversity among population subdivisions is described using the analysis of molecular variance (AMOVA) procedure, the analysis of gene identity, and the genealogical relationship of haplotypes as constructed by parsimony analysis and distance clustering. These analyses revealed: (i) significant partitioning of world-wide genetic variation among oceanic populations, among subpopulations or 'stocks' within oceanic populations and among seasonal habitats within stocks; (ii) fixed categorical segregation of haplotypes on the south-eastern Alaska and central California feeding grounds of the North Pacific; (iii) support for the division of the North Pacific population into a central stock which feeds in Alaska and winters in Hawaii, and an eastern or 'American' stock which feeds along the coast of California and winters near Mexico; (iv) evidence of genetic heterogeneity within the Gulf of Maine feeding grounds and among the sampled feeding and breeding grounds of the western North Atlantic; and (v) support for the historical division between the Group IV (Western Australia) and Group V (eastern Australia, New Zealand and Tonga) stocks in the Southern Oceans. Overall, our results demonstrate a striking degree of genetic structure both within and between oceanic populations of humpback whales, despite the nearly unlimited migratory potential of this species. We suggest that the humpback whale is a suitable demographic and genetic model for the management of less tractable species of baleen whales and for the general study of gene flow among long-lived, mobile vertebrates in the marine ecosystem.

  19. Relating diseases by integrating gene associations and information flow through protein interaction network.

    Science.gov (United States)

    Hamaneh, Mehdi Bagheri; Yu, Yi-Kuo

    2014-01-01

    Identifying similar diseases could potentially provide deeper understanding of their underlying causes, and may even hint at possible treatments. For this purpose, it is necessary to have a similarity measure that reflects the underpinning molecular interactions and biological pathways. We have thus devised a network-based measure that can partially fulfill this goal. Our method assigns weights to all proteins (and consequently their encoding genes) by using information flow from a disease to the protein interaction network and back. Similarity between two diseases is then defined as the cosine of the angle between their corresponding weight vectors. The proposed method also provides a way to suggest disease-pathway associations by using the weights assigned to the genes to perform enrichment analysis for each disease. By calculating pairwise similarities between 2534 diseases, we show that our disease similarity measure is strongly correlated with the probability of finding the diseases in the same disease family and, more importantly, sharing biological pathways. We have also compared our results to those of MimMiner, a text-mining method that assigns pairwise similarity scores to diseases. We find the results of the two methods to be complementary. It is also shown that clustering diseases based on their similarities and performing enrichment analysis for the cluster centers significantly increases the term association rate, suggesting that the cluster centers are better representatives for biological pathways than the diseases themselves. This lends support to the view that our similarity measure is a good indicator of relatedness of biological processes involved in causing the diseases. Although not needed for understanding this paper, the raw results are available for download for further study at ftp://ftp.ncbi.nlm.nih.gov/pub/qmbpmn/DiseaseRelations/.

  20. Meta-analyses including non-randomized studies of therapeutic interventions: a methodological review

    Directory of Open Access Journals (Sweden)

    Timor Faber

    2016-03-01

    Full Text Available Abstract Background There is an increasing number of meta-analyses including data from non-randomized studies for therapeutic evaluation. We aimed to systematically assess the methods used in meta-analyses including non-randomized studies evaluating therapeutic interventions. Methods For this methodological review, we searched MEDLINE via PubMed, from January 1, 2013 to December 31, 2013 for meta-analyses including at least one non-randomized study evaluating therapeutic interventions. Etiological assessments and meta-analyses with no comparison group were excluded. Two reviewers independently assessed the general characteristics and key methodological components of the systematic review process and meta-analysis methods. Results One hundred eighty eight meta-analyses were selected: 119 included both randomized controlled trials (RCTs and non-randomized studies of interventions (NRSI and 69 only NRSI. Half of the meta-analyses (n = 92, 49 % evaluated non-pharmacological interventions. “Grey literature” was searched for 72 meta-analyses (38 %. An assessment of methodological quality or risk of bias was reported in 135 meta-analyses (72 % but this assessment considered the risk of confounding bias in only 33 meta-analyses (18 %. In 130 meta-analyses (69 %, the design of each NRSI was not clearly specified. In 131 (70 %, whether crude or adjusted estimates of treatment effect for NRSI were combined was unclear or not reported. Heterogeneity across studies was assessed in 182 meta-analyses (97 % and further explored in 157 (84 %. Reporting bias was assessed in 127 (68 %. Conclusions Some key methodological components of the systematic review process—search for grey literature, description of the type of NRSI included, assessment of risk of confounding bias and reporting of whether crude or adjusted estimates were combined—are not adequately carried out or reported in meta-analyses including NRSI.

  1. Implications of nonrandom seed abscission and global stilling for migration of wind-dispersed plant species.

    Science.gov (United States)

    Thompson, Sally E; Katul, Gabriel G

    2013-06-01

    Migration of plant populations is a potential survival response to climate change that depends critically on seed dispersal. Biological and physical factors determine dispersal and migration of wind-dispersed species. Recent field and wind tunnel studies demonstrate biological adaptations that bias seed release toward conditions of higher wind velocity, promoting longer dispersal distances and faster migration. However, another suite of international studies also recently highlighted a global decrease in near-surface wind speeds, or 'global stilling'. This study assessed the implications of both factors on potential plant population migration rates, using a mechanistic modeling framework. Nonrandom abscission was investigated using models of three seed release mechanisms: (i) a simple drag model; (ii) a seed deflection model; and (iii) a 'wear and tear' model. The models generated a single functional relationship between the frequency of seed release and statistics of the near-surface wind environment, independent of the abscission mechanism. An Inertial-Particle, Coupled Eulerian-Lagrangian Closure model (IP-CELC) was used to investigate abscission effects on seed dispersal kernels and plant population migration rates under contemporary and potential future wind conditions (based on reported global stilling trends). The results confirm that nonrandom seed abscission increased dispersal distances, particularly for light seeds. The increases were mitigated by two physical feedbacks: (i) although nonrandom abscission increased the initial acceleration of seeds from rest, the sensitivity of the seed dispersal to this initial condition declined as the wind speed increased; and (ii) while nonrandom abscission increased the mean dispersal length, it reduced the kurtosis of seasonal dispersal kernels, and thus the chance of long-distance dispersal. Wind stilling greatly reduced the modeled migration rates under biased seed release conditions. Thus, species that require

  2. Discerning between recurrent gene flow and recent divergence under a finite-site mutation model applied to North Atlantic and Mediterranean Sea fin whale (Balaenoptera physalus) populations

    NARCIS (Netherlands)

    Palsboll, PJ; Berube, M; Aguilar, A; Notarbartolo-Di-Sciara, G; Nielsen, R

    2004-01-01

    Genetic divergence among conspecific subpopulations can be due to either low recurrent gene flow or recent divergence and no gene flow. Here we present a modification of an earlier method developed by Nielsen and Wakeley (2001), which accommodates a finite-site mutation model, to assess which of the

  3. Investigating Pollen and Gene Flow of WYMV-Resistant Transgenic Wheat N12-1 Using a Dwarf Male-Sterile Line as the Pollen Receptor.

    Directory of Open Access Journals (Sweden)

    Shanshan Dong

    Full Text Available Pollen-mediated gene flow (PMGF is the main mode of transgene flow in flowering plants. The study of pollen and gene flow of transgenic wheat can help to establish the corresponding strategy for preventing transgene escape and contamination between compatible genotypes in wheat. To investigate the pollen dispersal and gene flow frequency in various directions and distances around the pollen source and detect the association between frequency of transgene flow and pollen density from transgenic wheat, a concentric circle design was adopted to conduct a field experiment using transgenic wheat with resistance to wheat yellow mosaic virus (WYMV as the pollen donor and dwarf male-sterile wheat as the pollen receptor. The results showed that the pollen and gene flow of transgenic wheat varied significantly among the different compass sectors. A higher pollen density and gene flow frequency was observed in the downwind SW and W sectors, with average frequencies of transgene flow of 26.37 and 23.69% respectively. The pollen and gene flow of transgenic wheat declined dramatically with increasing distance from its source. Most of the pollen grains concentrated within 5 m and only a few pollen grains were detected beyond 30 m. The percentage of transgene flow was the highest where adjacent to the pollen source, with an average of 48.24% for all eight compass directions at 0 m distance. Transgene flow was reduced to 50% and 95% between 1.61 to 3.15 m, and 10.71 to 20.93 m, respectively. Our results suggest that climate conditions, especially wind direction, may significantly affect pollen dispersal and gene flow of wheat. The isolation-by-distance model is one of the most effective methods for achieving stringent transgene confinement in wheat. The frequency of transgene flow is directly correlated with the relative density of GM pollen grains in air currents, and pollen competition may be a major factor influencing transgene flow.

  4. Frugivores bias seed-adult tree associations through nonrandom seed dispersal: a phylogenetic approach.

    Science.gov (United States)

    Razafindratsima, Onja H; Dunham, Amy E

    2016-08-01

    Frugivores are the main seed dispersers in many ecosystems, such that behaviorally driven, nonrandom patterns of seed dispersal are a common process; but patterns are poorly understood. Characterizing these patterns may be essential for understanding spatial organization of fruiting trees and drivers of seed-dispersal limitation in biodiverse forests. To address this, we studied resulting spatial associations between dispersed seeds and adult tree neighbors in a diverse rainforest in Madagascar, using a temporal and phylogenetic approach. Data show that by using fruiting trees as seed-dispersal foci, frugivores bias seed dispersal under conspecific adults and under heterospecific trees that share dispersers and fruiting time with the dispersed species. Frugivore-mediated seed dispersal also resulted in nonrandom phylogenetic associations of dispersed seeds with their nearest adult neighbors, in nine out of the 16 months of our study. However, these nonrandom phylogenetic associations fluctuated unpredictably over time, ranging from clustered to overdispersed. The spatial and phylogenetic template of seed dispersal did not translate to similar patterns of association in adult tree neighborhoods, suggesting the importance of post-dispersal processes in structuring plant communities. Results suggest that frugivore-mediated seed dispersal is important for structuring early stages of plant-plant associations, setting the template for post-dispersal processes that influence ultimate patterns of plant recruitment. Importantly, if biased patterns of dispersal are common in other systems, frugivores may promote tree coexistence in biodiverse forests by limiting the frequency and diversity of heterospecific interactions of seeds they disperse.

  5. Self-recruitment and sweepstakes reproduction amid extensive gene flow in a coral-reef fish.

    Science.gov (United States)

    Christie, Mark R; Johnson, Darren W; Stallings, Christopher D; Hixon, Mark A

    2010-03-01

    Identifying patterns of larval dispersal within marine metapopulations is vital for effective fisheries management, appropriate marine reserve design, and conservation efforts. We employed genetic markers (microsatellites) to determine dispersal patterns in bicolour damselfish (Pomacentridae: Stegastes partitus). Tissue samples of 751 fish were collected in 2004 and 2005 from 11 sites encompassing the Exuma Sound, Bahamas. Bayesian parentage analysis identified two parent-offspring pairs, which is remarkable given the large population sizes and 28 day pelagic larval duration of bicolour damselfish. The two parent-offspring pairs directly documented self-recruitment at the two northern-most sites, one of which is a long-established marine reserve. Principal coordinates analyses of pair-wise relatedness values further indicated that self-recruitment was common in all sampled populations. Nevertheless, measures of genetic differentiation (F(ST)) and results from assignment methods suggested high levels of gene flow among populations. Comparisons of heterozygosity and relatedness among samples of adults and recruits indicated spatially and temporally independent sweepstakes events, whereby only a subset of adults successfully contribute to subsequent generations. These results indicate that self-recruitment and sweepstakes reproduction are the predominant, ecologically-relevant processes that shape patterns of larval dispersal in this system.

  6. Gene flow and maintenance of genetic diversity in invasive mosquitofish (Gambusia holbrooki.

    Directory of Open Access Journals (Sweden)

    David Díez-del-Molino

    Full Text Available Genetic analyses contribute to studies of biological invasions by mapping the origin and dispersal patterns of invasive species occupying new territories. Using microsatellite loci, we assessed the genetic diversity and spatial population structure of mosquitofish (Gambusia holbrooki that had invaded Spanish watersheds, along with the American locations close to the suspected potential source populations. Mosquitofish populations from the Spanish streams that were studied had similar levels of genetic diversity to the American samples; therefore, these populations did not appear to have undergone substantial losses of genetic diversity during the invasion process. Population structure analyses indicated that the Spanish populations fell into four main clusters, which were primarily associated with hydrography. Dispersal patterns indicated that local populations were highly connected upstream and downstream through active dispersal, with an average of 21.5% fish from other locations in each population. After initially introducing fish to one location in a given basin, such dispersal potential might contribute to the spread and colonization of suitable habitats throughout the entire river basin. The two-dimension isolation-by-distance pattern here obtained, indicated that the human-mediated translocation of mosquitofish among the three study basins is a regular occurrence. Overall, both phenomena, high natural dispersal and human translocation, favor gene flow among river basins and the retention of high genetic diversity, which might help retain the invasive potential of mosquitofish populations.

  7. Spatial genetic structure and restricted gene flow in bed bugs (Cimex lectularius) populations in France.

    Science.gov (United States)

    Akhoundi, Mohammad; Kengne, Pierre; Cannet, Arnaud; Brengues, Cécile; Berenger, Jean-Michel; Izri, Arezki; Marty, Pierre; Simard, Frederic; Fontenille, Didier; Delaunay, Pascal

    2015-08-01

    Bed bugs (Cimex lectularius) are resurgent blood-sucking ectoparasites that are currently increasing at a rapid rate, particularly in industrialized countries, such as France. Despite the rapid spread of bed bugs, there is a lack of knowledge concerning the population structure and gene flow among C. lectularius populations in France. To fill this gap, a genetic study was conducted using 183 C. lectularius from 14 populations of bed bugs collected in a hotel and in individual apartments in the French Riviera and in the Saint Ouen suburb of Paris. The samples were genotyped using an isolated set of six polymorphic microsatellite loci, including five new loci which were newly isolated and chosen based on prior successful amplification, and one previously described loci (bb15b). The low genetic diversity observed in the samples (of one to five alleles) suggested that most of prospected populations were established by only a few individuals, possibly from a single mated female. The overall genetic differentiation was high and statistically significant (FST=0.556, plectularius populations in France; however, the available information should be expanded in further studies.

  8. Adaptation with gene flow across the landscape in a dune sunflower.

    Science.gov (United States)

    Andrew, Rose L; Ostevik, Katherine L; Ebert, Daniel P; Rieseberg, Loren H

    2012-05-01

    Isolation by adaptation increases divergence at neutral loci when natural selection against immigrants reduces the rate of gene flow between different habitats. This can occur early in the process of adaptive divergence and is a key feature of ecological speciation. Despite the ability of isolation by distance (IBD) and other forms of landscape resistance to produce similar patterns of neutral divergence within species, few studies have used landscape genetics to control for these other forces. We have studied the divergence of Helianthus petiolaris ecotypes living in active sand dunes and adjacent non-dune habitat, using landscape genetics approaches, such as circuit theory and multiple regression of distance matrices, in addition to coalescent modelling. Divergence between habitats was significant, but not strong, and was shaped by IBD. We expected that increased resistance owing to patchy and unfavourable habitat in the dunes would contribute to divergence. Instead, we found that landscape resistance models with lower resistance in the dunes performed well as predictors of genetic distances among subpopulations. Nevertheless, habitat class remained a strong predictor of genetic distance when controlling for isolation by resistance and IBD. We also measured environmental variables at each site and confirmed that specific variables, especially soil nitrogen and vegetation cover, explained a greater proportion of variance in genetic distance than did landscape or the habitat classification alone. Asymmetry in effective population sizes and numbers of migrants per generation was detected using coalescent modelling with Bayesian inference, which is consistent with incipient ecological speciation being driven by the dune habitat.

  9. Matching genetics with oceanography: directional gene flow in a Mediterranean fish species.

    Science.gov (United States)

    Schunter, C; Carreras-Carbonell, J; Macpherson, E; Tintoré, J; Vidal-Vijande, E; Pascual, A; Guidetti, P; Pascual, M

    2011-12-01

    Genetic connectivity and geographic fragmentation are two opposing mechanisms determining the population structure of species. While the first homogenizes the genetic background across populations the second one allows their differentiation. Therefore, knowledge of processes affecting dispersal of marine organisms is crucial to understand their genetic distribution patterns and for the effective management of their populations. In this study, we use genetic analyses of eleven microsatellites in combination with oceanographic satellite and dispersal simulation data to determine distribution patterns for Serranus cabrilla, a ubiquitous demersal broadcast spawner, in the Mediterranean Sea. Pairwise population F(ST) values ranged between -0.003 and 0.135. Two genetically distinct clusters were identified, with a clear division located between the oceanographic discontinuities at the Ibiza Channel (IC) and the Almeria-Oran Front (AOF), revealing an admixed population in between. The Balearic Front (BF) also appeared to dictate population structure. Directional gene flow on the Spanish coast was observed as S. cabrilla dispersed from west to east over the AOF, from north to south on the IC and from south of the IC towards the Balearic Islands. Correlations between genetic and oceanographic data were highly significant. Seasonal changes in current patterns and the relationship between ocean circulation patterns and spawning season may also play an important role in population structure around oceanographic fronts. © 2011 Blackwell Publishing Ltd.

  10. Gene flow between insular, coastal and interior populations of brown bears in Alaska.

    Science.gov (United States)

    Paetkau, D; Shields, G F; Strobeck, C

    1998-10-01

    The brown bears of coastal Alaska have been recently regarded as comprising from one to three distinct genetic groups. We sampled brown bears from each of the regions for which hypotheses of genetic uniqueness have been made, including the bears of the Kodiak Archipelago and the bears of Admiralty, Baranof and Chichagof (ABC) Islands in southeast Alaska. These samples were analysed with a suite of nuclear microsatellite markers. The 'big brown bears' of coastal Alaska were found to be part of the continuous continental distribution of brown bears, and not genetically isolated from the physically smaller 'grizzly bears' of the interior. By contrast, Kodiak brown bears appear to have experienced little or no genetic exchange with continental populations in recent generations. The bears of the ABC Islands, which have previously been shown to undergo little or no female-mediated gene flow with mainland populations, were found not to be genetically isolated from mainland bears. The data from the four insular populations indicate that female and male dispersal can be reduced or eliminated by water barriers of 2-4 km and 7 km in width, respectively.

  11. Non-random spatial coupling induces desynchronization, chaos and multistability in a predator-prey-resource system.

    Science.gov (United States)

    Suzuki, Kenta; Yoshida, Takehito

    2012-05-07

    The metacommunity perspective has attracted much attention recently, but the understanding of how dispersal between local communities alters their ecological dynamics is still limited, especially regarding the effect of non-random, unequal dispersal of organisms. This is a study of a three-trophic-level (predator-prey-resource) system that is connected by different manners of dispersal. The model is based on a well-studied experimental system cultured in chemostats (continuous flow-through culture), which consists of rotifer predator, algal prey and nutrient. In the model, nutrient dispersal can give rise to multistability when the two systems are connected by nutrient dispersal, whereas three-trophic-level systems tend to show a rich dynamical behavior, e.g. antisynchronous or asynchronous oscillations including chaos. Although the existence of multistability was already known in two-trophic-level (predator-prey) systems, it was confined to a small range of dispersal rate. In contrast, the multistability in the three-trophic-level system is found in a broader range of dispersal rate. The results suggest that, in three-trophic-level systems, the dispersal of nutrient not only alters population dynamics of local systems but can also cause regime shifts such as a transition to different oscillation phases.

  12. Genetics, Gene Flow, and Glaciation: The Case of the South American Limpet Nacella mytilina

    Science.gov (United States)

    González-Wevar, Claudio A.; Rosenfeld, Sebastián; Segovia, Nicolás I.; Hüne, Mathias; Gérard, Karin; Ojeda, Jaime; Mansilla, Andrés; Brickle, Paul; Díaz, Angie; Poulin, Elie

    2016-01-01

    Glacial episodes of the Quaternary, and particularly the Last Glacial Maximum (LGM) drastically altered the distribution of the Southern-Hemisphere biota, principally at higher latitudes. The irregular coastline of Patagonia expanding for more than 84.000 km constitutes a remarkable area to evaluate the effect of Quaternary landscape and seascape shifts over the demography of near-shore marine benthic organisms. Few studies describing the biogeographic responses of marine species to the LGM have been conducted in Patagonia, but existing data from coastal marine species have demonstrated marked genetic signatures of post-LGM recolonization and expansion. The kelp-dweller limpet Nacella mytilina is broadly distributed along the southern tip of South America and at the Falkland/Malvinas Islands. Considering its distribution, abundance, and narrow bathymetry, N. mytilina represents an appropriate model to infer how historical and contemporary processes affected the distribution of intraspecific genetic diversity and structure along the southern tip of South America. At the same time, it will be possible to determine how life history traits and the ecology of the species are responsible for the current pattern of gene flow and connectivity across the study area. We conducted phylogeographic and demographic inference analyses in N. mytilina from 12 localities along Pacific Patagonia (PP) and one population from the Falkland/Malvinas Islands (FI). Analyses of the mitochondrial gene COI in 300 individuals of N. mytilina revealed low levels of genetic polymorphism and the absence of genetic differentiation along PP. In contrast, FI showed a strong and significant differentiation from Pacific Patagonian populations. Higher levels of genetic diversity were also recorded in the FI population, together with a more expanded genealogy supporting the hypothesis of glacial persistence of the species in these islands. Haplotype genealogy, and mismatch analyses in the FI population

  13. The impact of pollination syndrome and habitat on gene flow: a comparative study of two Streptocarpus (Gesneriaceae) species.

    Science.gov (United States)

    Hughes, Mark; Möller, Michael; Edwards, Trevor J; Bellstedt, Dirk U; Villiers, Margaret de

    2007-10-01

    Gene flow through pollen and seed dispersal is important in terms of population differentiation and eventually speciation. Seed and pollen flow are affected in turn by habitats and pollen vectors. We examined the effect of different pollinators and habitats on gene flow by comparing two species of Streptocarpus, using microsatellite and chloroplast RFLP markers. Populations of the forest-dwelling S. primulifolius were highly differentiated according to nuclear microsatellite data and had mutually exclusive chloroplast haplotypes. This result is congruent with infrequent seed dispersal and limited between-population foraging by the long-tongued fly pollinator Stenobasipteron wiedemanni. In contrast, populations of S. dunnii growing in exposed crags had lower levels of population differentiation according to both nuclear and chloroplast data, congruent with a hypothesis of more effective between population seed dispersal and greater pollen-mediated gene flow due to the sunbird pollinator Nectarinia famosa. The population genetic behavior of these species is reflected in their taxonomy and phylogenetic position; S. primulifolius belongs to a taxonomically complex clade in which recent speciation is evident, while the clade containing S. dunnii is characterized by taxonomically well-defined species on longer phylogenetic branches. Our study shows that pollinator movements and seed dispersal patterns are a major determinant of the evolutionary trajectories of these species.

  14. Migration between continents: geographical structure and long-distance gene flow in Porpidia flavicunda (lichen-forming Ascomycota).

    Science.gov (United States)

    Buschbom, Jutta

    2007-05-01

    Historical and contemporary geographical distribution ranges with their associated gene flow patterns interact to produce the genetic diversity observed today. Often it is not possible to separate out the impacts of historical events, e.g. past fragmentation, and contemporary gene flow, e.g. long-distance dispersal. Porpidia flavicunda is a lichen-forming ascomycete occurring circumpolar in the boreal to arctic zones for which vegetation history suggests that its distribution pattern has stayed broadly the same over the past millennia. DNA-sequence diversity in P. flavicunda can, thus, be expected to predominantly represent geographical population differentiation and its contemporary migration rates. The population sample consists of 110 specimens collected in Northern Québec, Baffin Island, Western Greenland and Northern Scandinavia. DNA-sequence data sets of three nuclear gene fragments (LSU, RPB2 and beta-tubulin) were analysed for genetic diversity within, and differentiation between, geographical regions. Tests of population subdivision employing analyses of molecular variance and exact tests of haplotype frequency distributions showed significant structure between the geographical regions. However, the lack of fixed nucleotide polymorphisms and the wide sharing of identical haplotypes between geographical regions suggest recurrent long-distance gene flow of propagules. Still, the means by which propagules are dispersed remain to be discovered. Inference of migration rates shows that in many cases a sufficiently high amount of migrants is exchanged between geographical regions to prevent drastic population differentiation through genetic drift. The observed haplotype distributions and migration rates point to a gene flow model of isolation by distance.

  15. The impact of selection, gene flow and demographic history on heterogeneous genomic divergence: three-spine sticklebacks in divergent environments.

    Science.gov (United States)

    Ferchaud, Anne-Laure; Hansen, Michael M

    2016-01-01

    Heterogeneous genomic divergence between populations may reflect selection, but should also be seen in conjunction with gene flow and drift, particularly population bottlenecks. Marine and freshwater three-spine stickleback (Gasterosteus aculeatus) populations often exhibit different lateral armour plate morphs. Moreover, strikingly parallel genomic footprints across different marine-freshwater population pairs are interpreted as parallel evolution and gene reuse. Nevertheless, in some geographic regions like the North Sea and Baltic Sea, different patterns are observed. Freshwater populations in coastal regions are often dominated by marine morphs, suggesting that gene flow overwhelms selection, and genomic parallelism may also be less pronounced. We used RAD sequencing for analysing 28 888 SNPs in two marine and seven freshwater populations in Denmark, Europe. Freshwater populations represented a variety of environments: river populations accessible to gene flow from marine sticklebacks and large and small isolated lakes with and without fish predators. Sticklebacks in an accessible river environment showed minimal morphological and genomewide divergence from marine populations, supporting the hypothesis of gene flow overriding selection. Allele frequency spectra suggested bottlenecks in all freshwater populations, and particularly two small lake populations. However, genomic footprints ascribed to selection could nevertheless be identified. No genomic regions were consistent freshwater-marine outliers, and parallelism was much lower than in other comparable studies. Two genomic regions previously described to be under divergent selection in freshwater and marine populations were outliers between different freshwater populations. We ascribe these patterns to stronger environmental heterogeneity among freshwater populations in our study as compared to most other studies, although the demographic history involving bottlenecks should also be considered in the

  16. Population variability in Chironomus (Camptochironomus) species (Diptera, Nematocera) with a Holarctic distribution: evidence of mitochondrial gene flow.

    Science.gov (United States)

    Martin, J; Guryev, V; Blinov, A

    2002-10-01

    Phylogenetic analysis of DNA sequences from mitochondrial (mt) genes (Cytochrome b and Cytochrome oxidase I) and one nuclear gene (globin 2b) was used for the investigation of Nearctic and Palearctic populations representing four Chironomus species of the subgenus Camptochironomus, namely C. biwaprimus, C. pallidivittatus, C. tentans sensu stricto and C. dilutus (the last two species constitute Holarctic C. tentans sensu lato). Phenograms constructed on the basis of mt sequences were not congruent with trees based on nuclear genes, or with morphological and cytological data. The mt tree divided the populations by continental region, rather than by the species groupings recognized by the other data sets. The incongruence is explained by mt gene flow resulting from hybridization between the sympatric species on each continent. Calculation of divergence times, based on the sequence data, suggest that C. tentans (s.l.) and C. pallidivittatus have both been in North America for about 2.5 My.

  17. Localization of male-specifically expressed MROS genes of Silene latifolia by PCR on flow-sorted sex chromosomes and autosomes.

    OpenAIRE

    Kejnovský, E; Vrána, J; Matsunaga, S.; Soucek, P.; Siroký, J; Dolezel, J; Vyskot, B

    2001-01-01

    The dioecious white campion Silene latifolia (syn. Melandrium album) has heteromorphic sex chromosomes, XX in females and XY in males, that are larger than the autosomes and enable their separation by flow sorting. The group of MROS genes, the first male-specifically expressed genes in dioecious plants, was recently identified in S. latifolia. To localize the MROS genes, we used the flow-sorted X chromosomes and autosomes as a template for PCR with internal primers. Our results indicate that ...

  18. The Self-Made Puzzle: Integrating Self-Assembly and Pattern Formation Under Non-Random Genetic Regulation

    Science.gov (United States)

    Doursat, René

    On the one hand, research in self-assembling systems, whether natural or artificial, has traditionally focused on pre-existing components endowed with fixed shapes. Biological development, by contrast, dynamically creates new cells that acquire selective adhesion properties through differentiation induced by their neighborhood. On the other hand, pattern formation phenomena are generally construed as orderly states of activity on top of a continuous 2-D or 3-D substrate. Yet, again, the spontaneous patterning of an organism into domains of gene expression arises within a multicellular medium in perpetual expansion and reshaping. Finally, both phenomena are often thought in terms of stochastic events, whether mixed components that randomly collide in self-assembly, or spots and stripes that occur unpredictably from instabilities in pattern formation. Here too, these notions need significant revision if they are to be extended and applied to embryogenesis. Cells are not randomly mixed but pre-positioned where cell division occurs. Genetic identity domains are not randomly distributed but highly regulated in number and position. In this work, I present a computational model of program-mable and reproducible artificial morphogenesis that integrates self-assembly and pattern formation under the control of a nonrandom gene regulatory network. The specialized properties of cells (division, adhesion, migration) are determined by the gene expression domains to which they belong, while at the same time these domains further expand and segment into subdomains due to the self-assembly of specialized cells. Through this model, I also promote a new discipline, embryomorphic engineering to solve the paradox of "meta-designing" decentralized, autonomous systems.

  19. Genetic analysis of local Vietnamese chickens provides evidence of gene flow from wild to domestic populations

    Directory of Open Access Journals (Sweden)

    Chi C Vu

    2009-01-01

    between Ha Giang chickens and junglefowl, as well as the results of a Bayesian clustering analysis, suggest that gene flow has been taking place from junglefowl to Ha Giang chickens.

  20. Gene flow, subspecies composition, and dengue virus-2 susceptibility among Aedes aegypti collections in Senegal.

    Directory of Open Access Journals (Sweden)

    Massamba Sylla

    Full Text Available BACKGROUND: Aedes aegypti, the "yellow fever mosquito", is the primary vector to humans of the four serotypes of dengue viruses (DENV1-4 and yellow fever virus (YFV and is a known vector of Chikungunya virus. There are two recognized subspecies of Ae. aegypti sensu latu (s.l.: the presumed ancestral form, Ae. aegypti formosus (Aaf, a primarily sylvan mosquito in sub-Saharan Africa, and Ae. aegypti aegypti (Aaa, found globally in tropical and subtropical regions typically in association with humans. The designation of Ae. aegypti s.l. subspecies arose from observations made in East Africa in the late 1950s that the frequency of pale "forms" of Ae. aegypti was higher in populations in and around human dwellings than in those of the nearby bush. But few studies have been made of Ae. aegypti s.l. in West Africa. To address this deficiency we have been studying the population genetics, subspecies composition and vector competence for DENV-2 of Ae. aegypti s.l. in Senegal. METHODS AND FINDINGS: A population genetic analysis of gene flow was conducted among 1,040 Aedes aegypti s.l. from 19 collections distributed across the five phytogeographic regions of Senegal. Adults lacking pale scales on their first abdominal tergite were classified as Aedes aegypti formosus (Aaf following the original description of the subspecies and the remainder were classified as Aedes aegypti aegypti (Aaa. There was a clear northwest-southeast cline in the abundance of Aaa and Aaf. Collections from the northern Sahelian region contained only Aaa while southern Forest gallery collections contained only Aaf. The two subspecies occurred in sympatry in four collections north of the Gambia in the central Savannah region and Aaa was a minor component of two collections from the Forest gallery area. Mosquitoes from 11 collections were orally challenged with DENV-2 virus. In agreement with the early literature, Aaf had significantly lower vector competence than Aaa. Among pure Aaa

  1. Gene flow rise with habitat fragmentation in the bog fritillary butterfly (Lepidoptera: Nymphalidae

    Directory of Open Access Journals (Sweden)

    Descimon Henri

    2008-03-01

    Full Text Available Abstract Background The main components of the spatial genetic structure of the populations are neighbourhood size and isolation by distance. These may be inferred from the allele frequencies across a series of populations within a region. Here, the spatial population structure of Proclossiana eunomia was investigated in two mountainous areas of southern Europe (Asturias, Spain and Pyrenees, France and in two areas of intermediate elevation (Morvan, France and Ardennes, Belgium. Results A total of eight polymorphic loci were scored by allozyme electrophoresis, revealing a higher polymorphism in the populations of southern Europe than in those of central Europe. Isolation by distance effect was much stronger in the two mountain ranges (Pyrenees and Asturias than in the two areas of lower elevation (Ardennes and Morvan. By contrast, the neighbourhood size estimates were smaller in the Ardennes and in the Morvan than in the two high mountain areas, indicating more common movements between neighbouring patches in the mountains than in plains. Conclusion Short and long dispersal events are two phenomena with distinct consequences in the population genetics of natural populations. The differences in level of population differentiation within each the four regions may be explained by change in dispersal in lowland recently fragmented landscapes: on average, butterflies disperse to a shorter distance but the few ones which disperse long distance do so more efficiently. Habitat fragmentation has evolutionary consequences exceeding by far the selection of dispersal related traits: the balance between local specialisation and gene flow would be perturbed, which would modify the extent to which populations are adapted to heterogeneous environments.

  2. Differentiation and Gene Flow among European Populations of Leishmania infantum MON-1

    Science.gov (United States)

    Kuhls, Katrin; Chicharro, Carmen; Cañavate, Carmen; Cortes, Sofia; Campino, Lenea; Haralambous, Christos; Soteriadou, Ketty; Pratlong, Francine; Dedet, Jean-Pierre; Mauricio, Isabel; Miles, Michael; Schaar, Matthias; Ochsenreither, Sebastian; Radtke, Oliver A.; Schönian, Gabriele

    2008-01-01

    Background Leishmania infantum is the causative agent of visceral and cutaneous leishmaniasis in the Mediterranean region, South America, and China. MON-1 L. infantum is the predominating zymodeme in all endemic regions, both in humans and dogs, the reservoir host. In order to answer important epidemiological questions it is essential to discriminate strains of MON-1. Methodology/Principal Findings We have used a set of 14 microsatellite markers to analyse 141 strains of L. infantum mainly from Spain, Portugal, and Greece of which 107 strains were typed by MLEE as MON-1. The highly variable microsatellites have the potential to discriminate MON-1 strains from other L. infantum zymodemes and even within MON-1 strains. Model- and distance-based analysis detected a considerable amount of structure within European L. infantum. Two major monophyletic groups—MON-1 and non-MON-1—could be distinguished, with non-MON-1 being more polymorphic. Strains of MON-98, 77, and 108 were always part of the MON-1 group. Among MON-1, three geographically determined and genetically differentiated populations could be identified: (1) Greece; (2) Spain islands–Majorca/Ibiza; (3) mainland Portugal/Spain. All four populations showed a predominantly clonal structure; however, there are indications of occasional recombination events and gene flow even between MON-1 and non-MON-1. Sand fly vectors seem to play an important role in sustaining genetic diversity. No correlation was observed between Leishmania genotypes, host specificity, and clinical manifestation. In the case of relapse/re-infection, only re-infections by a strain with a different MLMT profile can be unequivocally identified, since not all strains have individual MLMT profiles. Conclusion In the present study for the first time several key epidemiological questions could be addressed for the MON-1 zymodeme, because of the high discriminatory power of microsatellite markers, thus creating a basis for further epidemiological

  3. How much gene flow is needed to avoid inbreeding depression in wild tiger populations?

    Science.gov (United States)

    Kenney, John; Allendorf, Fred W; McDougal, Charles; Smith, James L D

    2014-08-22

    The number and size of tiger populations continue to decline owing to habitat loss, habitat fragmentation and poaching of tigers and their prey. As a result, tiger populations have become small and highly structured. Current populations have been isolated since the early 1970s or for approximately seven generations. The objective of this study is to explore how inbreeding may be affecting the persistence of remaining tiger populations and how dispersal, either natural or artificial, may reduce the potentially detrimental effect of inbreeding depression. We developed a tiger simulation model and used published levels of genetic load in mammals to simulate inbreeding depression. Following a 50 year period of population isolation, we introduced one to four dispersing male tigers per generation to explore how gene flow from nearby populations may reduce the negative impact of inbreeding depression. For the smallest populations, even four dispersing male tigers per generation did not increase population viability, and the likelihood of extinction is more than 90% within 30 years. Unless habitat connectivity is restored or animals are artificially introduced in the next 70 years, medium size wild populations are also likely to go extinct, with only four to five of the largest wild tiger populations likely to remain extant in this same period without intervention. To reduce the risk of local extinction, habitat connectivity must be pursued concurrently with efforts to increase population size (e.g. enhance habitat quality, increase habitat availability). It is critical that infrastructure development, dam construction and other similar projects are planned appropriately so that they do not erode the extent or quality of habitat for these populations so that they can truly serve as future source populations. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

  4. Prezygotic barriers to gene flow between Taraxacum ceratophorum and the invasive Taraxacum officinale (Asteraceae).

    Science.gov (United States)

    Brock, Marcus T

    2009-08-01

    Prezygotic reproductive barriers limit interspecific gene flow between congeners. Here, I examine the strength of floral isolation and interspecific pollen-pistil barriers between an invasive apomictic, Taraxacum officinale, and the indigenous sexual alpine dandelion, Taraxacum ceratophorum. Experimental arrays of either native inflorescences or a mixture of native and exotic inflorescences were used to examine insect preference and to track movement of a pollen analog. Using hand-pollinations, conspecific and heterospecific pollen germination success on native stigmas was compared. To additionally test for interspecific pollen competition, T. ceratophorum plants received one of three possible hand-pollinations: control conspecific pollination, concomitant conspecific and heterospecific pollination (mixed), or conspecific pollen followed by heterospecific pollen 15 min later (staggered). Floral isolation was negligible as no insect preference was detected. On a presence/absence basis, florets on native inflorescences received slightly less pollen analog from heterospecific donors than from conspecific donors; however, the amount of dye particles transferred from either Taraxacum species to stigmas on recipient T. ceratophorum inflorescences was equivalent. In contrast to weak floral isolation, strong pollen germination and pollen competition barriers should reduce the potential for hybridization. Heterospecific T. officinale pollen exhibited reduced germination success on T. ceratophorum stigmas in comparison to conspecific pollen. Furthermore, a significant pollen-competition effect on the percentage of hybrid offspring was detected only when T. officinale preceded T. ceratophorum pollen by 15 min. This result indicates that conspecific pollen out-competes heterospecific pollen but further suggests that biotic and abiotic factors reducing pollen accrual rates may partially remove barriers to natural hybridization.

  5. Genetic differentiation and gene flow among six sheep breeds of Mongolian group in China

    Institute of Scientific and Technical Information of China (English)

    Yan GENG; Zhangping YANG; Hong CHANG; Yongjiang MAO; Wei SUN; Xiaoya GUO; Dongyan QU

    2008-01-01

    The level of genetic differentiation,gene flow and the relationship between geographical distance and genetic differentiation among six sheep populations of Mongolian group in China (Tong sheep,small-tailed Han sheep,Hu sheep,Tan sheep,Ujumuqin sheep and Bayinbuluk sheep) were analyzed using seven microsatellites.The trees were constructed from diversity coefficient (DC) distances among the six sheep populations.The overall heterozygote deficit across all the populations (Fit) was between 0.167 (OarAE101) and 0.044 (MAF33).The overall significant deficit of heterozygote,because of inbreeding within breeds,(Fis) was between 0.089 (OarFCB304) and 0.005 (MAF33).The coefficient of genetic differentiation (Fst) was between 0.100 (OarAE101) and 0.022 (Oar-FCB48).It indicated that 3.9% of the total genetic variation could be explained by breed differences and the remaining 96.1% by differences among individuals for each population.This illustrated that most variations existed within breeds and genetic differentiation level were very low among sheep breeds of the Mongolian Group in China.The average number of effective migrants exchanged per generation (Nem) ranged from 2.7369 (Tan sheep and Bayinbuluk sheep) to 44.3928 (Tong sheep and Hu sheep),and the mean value was 11.25213.Significantly positive relationships between the level of genetic differentiation and geographical distance and genetic distances were detected.It is concluded that genetic differentiation of sheep breeds of Mongolian group in China is mainly the result of natural selection (different living conditions).

  6. Divergence with gene flow across a speciation continuum of Heliconius butterflies.

    Science.gov (United States)

    Supple, Megan A; Papa, Riccardo; Hines, Heather M; McMillan, W Owen; Counterman, Brian A

    2015-09-24

    A key to understanding the origins of species is determining the evolutionary processes that drive the patterns of genomic divergence during speciation. New genomic technologies enable the study of high-resolution genomic patterns of divergence across natural speciation continua, where taxa pairs with different levels of reproductive isolation can be used as proxies for different stages of speciation. Empirical studies of these speciation continua can provide valuable insights into how genomes diverge during speciation. We examine variation across a handful of genomic regions in parapatric and allopatric populations of Heliconius butterflies with varying levels of reproductive isolation. Genome sequences were mapped to 2.2-Mb of the H. erato genome, including 1-Mb across the red color pattern locus and multiple regions unlinked to color pattern variation. Phylogenetic analyses reveal a speciation continuum of pairs of hybridizing races and incipient species in the Heliconius erato clade. Comparisons of hybridizing pairs of divergently colored races and incipient species reveal that genomic divergence increases with ecological and reproductive isolation, not only across the locus responsible for adaptive variation in red wing coloration, but also at genomic regions unlinked to color pattern. We observe high levels of divergence between the incipient species H. erato and H. himera, suggesting that divergence may accumulate early in the speciation process. Comparisons of genomic divergence between the incipient species and allopatric races suggest that limited gene flow cannot account for the observed high levels of divergence between the incipient species. Our results provide a reconstruction of the speciation continuum across the H. erato clade and provide insights into the processes that drive genomic divergence during speciation, establishing the H. erato clade as a powerful framework for the study of speciation.

  7. Differentiation and gene flow among European populations of Leishmania infantum MON-1.

    Science.gov (United States)

    Kuhls, Katrin; Chicharro, Carmen; Cañavate, Carmen; Cortes, Sofia; Campino, Lenea; Haralambous, Christos; Soteriadou, Ketty; Pratlong, Francine; Dedet, Jean-Pierre; Mauricio, Isabel; Miles, Michael; Schaar, Matthias; Ochsenreither, Sebastian; Radtke, Oliver A; Schönian, Gabriele

    2008-07-09

    Leishmania infantum is the causative agent of visceral and cutaneous leishmaniasis in the Mediterranean region, South America, and China. MON-1 L. infantum is the predominating zymodeme in all endemic regions, both in humans and dogs, the reservoir host. In order to answer important epidemiological questions it is essential to discriminate strains of MON-1. We have used a set of 14 microsatellite markers to analyse 141 strains of L. infantum mainly from Spain, Portugal, and Greece of which 107 strains were typed by MLEE as MON-1. The highly variable microsatellites have the potential to discriminate MON-1 strains from other L. infantum zymodemes and even within MON-1 strains. Model- and distance-based analysis detected a considerable amount of structure within European L. infantum. Two major monophyletic groups-MON-1 and non-MON-1-could be distinguished, with non-MON-1 being more polymorphic. Strains of MON-98, 77, and 108 were always part of the MON-1 group. Among MON-1, three geographically determined and genetically differentiated populations could be identified: (1) Greece; (2) Spain islands-Majorca/Ibiza; (3) mainland Portugal/Spain. All four populations showed a predominantly clonal structure; however, there are indications of occasional recombination events and gene flow even between MON-1 and non-MON-1. Sand fly vectors seem to play an important role in sustaining genetic diversity. No correlation was observed between Leishmania genotypes, host specificity, and clinical manifestation. In the case of relapse/re-infection, only re-infections by a strain with a different MLMT profile can be unequivocally identified, since not all strains have individual MLMT profiles. In the present study for the first time several key epidemiological questions could be addressed for the MON-1 zymodeme, because of the high discriminatory power of microsatellite markers, thus creating a basis for further epidemiological investigations.

  8. Differentiation and gene flow among European populations of Leishmania infantum MON-1.

    Directory of Open Access Journals (Sweden)

    Katrin Kuhls

    Full Text Available BACKGROUND: Leishmania infantum is the causative agent of visceral and cutaneous leishmaniasis in the Mediterranean region, South America, and China. MON-1 L. infantum is the predominating zymodeme in all endemic regions, both in humans and dogs, the reservoir host. In order to answer important epidemiological questions it is essential to discriminate strains of MON-1. METHODOLOGY/PRINCIPAL FINDINGS: We have used a set of 14 microsatellite markers to analyse 141 strains of L. infantum mainly from Spain, Portugal, and Greece of which 107 strains were typed by MLEE as MON-1. The highly variable microsatellites have the potential to discriminate MON-1 strains from other L. infantum zymodemes and even within MON-1 strains. Model- and distance-based analysis detected a considerable amount of structure within European L. infantum. Two major monophyletic groups-MON-1 and non-MON-1-could be distinguished, with non-MON-1 being more polymorphic. Strains of MON-98, 77, and 108 were always part of the MON-1 group. Among MON-1, three geographically determined and genetically differentiated populations could be identified: (1 Greece; (2 Spain islands-Majorca/Ibiza; (3 mainland Portugal/Spain. All four populations showed a predominantly clonal structure; however, there are indications of occasional recombination events and gene flow even between MON-1 and non-MON-1. Sand fly vectors seem to play an important role in sustaining genetic diversity. No correlation was observed between Leishmania genotypes, host specificity, and clinical manifestation. In the case of relapse/re-infection, only re-infections by a strain with a different MLMT profile can be unequivocally identified, since not all strains have individual MLMT profiles. CONCLUSION: In the present study for the first time several key epidemiological questions could be addressed for the MON-1 zymodeme, because of the high discriminatory power of microsatellite markers, thus creating a basis for further

  9. Evidence of long-term gene flow and selection during domestication from analyses of Eurasian wild and domestic pig genomes.

    Science.gov (United States)

    Frantz, Laurent A F; Schraiber, Joshua G; Madsen, Ole; Megens, Hendrik-Jan; Cagan, Alex; Bosse, Mirte; Paudel, Yogesh; Crooijmans, Richard P M A; Larson, Greger; Groenen, Martien A M

    2015-10-01

    Traditionally, the process of domestication is assumed to be initiated by humans, involve few individuals and rely on reproductive isolation between wild and domestic forms. We analyzed pig domestication using over 100 genome sequences and tested whether pig domestication followed a traditional linear model or a more complex, reticulate model. We found that the assumptions of traditional models, such as reproductive isolation and strong domestication bottlenecks, are incompatible with the genetic data. In addition, our results show that, despite gene flow, the genomes of domestic pigs have strong signatures of selection at loci that affect behavior and morphology. We argue that recurrent selection for domestic traits likely counteracted the homogenizing effect of gene flow from wild boars and created 'islands of domestication' in the genome. Our results have major ramifications for the understanding of animal domestication and suggest that future studies should employ models that do not assume reproductive isolation.

  10. Crossing the threshold: gene flow, dominance and the critical level of standing genetic variation required for adaptation to novel environments.

    Science.gov (United States)

    Nuismer, S L; MacPherson, A; Rosenblum, E B

    2012-12-01

    Genetic architecture plays an important role in the process of adaptation to novel environments. One example is the role of allelic dominance, where advantageous recessive mutations have a lower probability of fixation than advantageous dominant mutations. This classic observation, termed 'Haldane's sieve', has been well explored theoretically for single isolated populations adapting to new selective regimes. However, the role of dominance is less well understood for peripheral populations adapting to novel environments in the face of recurrent and maladaptive gene flow. Here, we use a combination of analytical approximations and individual-based simulations to explore how dominance influences the likelihood of adaptation to novel peripheral environments. We demonstrate that in the face of recurrent maladaptive gene flow, recessive alleles can fuel adaptation only when their frequency exceeds a critical threshold within the ancestral range.

  11. Gene flow among Anopheles albimanus populations in Central America, South America, and the Caribbean assessed by microsatellites and mitochondrial DNA.

    Science.gov (United States)

    Molina-Cruz, Alvaro; de Mérida, Ana María P; Mills, Katherine; Rodríguez, Fernando; Schoua, Carolina; Yurrita, María Marta; Molina, Eduviges; Palmieri, Margarita; Black, William C

    2004-09-01

    Gene flow was examined among Anopheles albimanus populations from Cuba, Mexico, Guatemala, El Salvador, Nicaragua, Costa Rica, Panama, Colombia, and Venezuela by examining variation at four microsatellite (MS) loci and a mitochondrial DNA (mtDNA) marker. There was little variation among Central American populations and weak isolation by distance was only observed with the MS loci. There was moderate to large variation between Central and South American populations, suggesting a barrier to gene flow between Central and South America. However, Panamanian and Pacific Costa Rican populations differed with respect to western Central America, suggesting that there may be another barrier within Central America. There was small to moderate variation among Caribbean and continental populations. Phylogenetic and diversity analyses of mtDNA indicate that more ancestral and diverse haplotypes were present in the Caribbean population, suggesting that current continental An. albimanus populations may have originated from the Caribbean.

  12. Flow Cytometry-Assisted Cloning of Specific Sequence Motifs from Complex 16S rRNA Gene Libraries

    DEFF Research Database (Denmark)

    Nielsen, Jeppe Lund; Schramm, Andreas; Bernhard, Anne E.

    2004-01-01

      FLOW CYTOMETRY-ASSISTED CLONING OF SPECIFIC SEQUENCE MOTIFS FROM COMPLEX 16S RRNA GENE LIBRARIES Jeppe L. Nielsen,1 Andreas Schramm,1,2 Anne E. Bernhard,1 Gerrit J. van den Engh,3 and David A. Stahl1* Department of Civil and Environmental Engineering, University of Washington,1 and Institute...... for Systems Biology,3 Seattle, Washington, and Department of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany2 A flow cytometry method was developed for rapid screening and recovery of cloned DNA containing common sequence motifs. This approach, termed fluorescence-activated cell sorting......-assisted cloning, was used to recover sequences affiliated with a unique lineage within the Bacteroidetes not abundant in a clone library of environmental 16S rRNA genes.  ...

  13. Migratory flyway and geographical distance are barriers to the gene flow of influenza virus among North American birds

    Science.gov (United States)

    Lam, T. T. -Y.; Ip, H. S.; Ghedin, E.; Wentworth, D. E.; Halpin, R. A.; Stockwell, T. B.; Spiro, D. J.; Dusek, R. J.; Bortner, J. B.; Hoskins, J.; Bales, B. D.; Yparraguirre, D. R.; Holmes, E. C.

    2012-01-01

    Despite the importance of migratory birds in the ecology and evolution of avian influenza virus (AIV), there is a lack of information on the patterns of AIV spread at the intra-continental scale. We applied a variety of statistical phylogeographic techniques to a plethora of viral genome sequence data to determine the strength, pattern and determinants of gene flow in AIV sampled from wild birds in North America. These analyses revealed a clear isolation-by-distance of AIV among sampling localities. In addition, we show that phylogeographic models incorporating information on the avian flyway of sampling proved a better fit to the observed sequence data than those specifying homogeneous or random rates of gene flow among localities. In sum, these data strongly suggest that the intra-continental spread of AIV by migratory birds is subject to major ecological barriers, including spatial distance and avian flyway. ?? 2011 Blackwell Publishing Ltd/CNRS.

  14. Comparison of pollen gene flow among four European beech (Fagus sylvatica L.) populations characterized by different management regimes.

    Science.gov (United States)

    Piotti, A; Leonardi, S; Buiteveld, J; Geburek, T; Gerber, S; Kramer, K; Vettori, C; Vendramin, G G

    2012-03-01

    The study of the dispersal capability of a species can provide essential information for the management and conservation of its genetic variability. Comparison of gene flow rates among populations characterized by different management and evolutionary histories allows one to decipher the role of factors such as isolation and tree density on gene movements. We used two paternity analysis approaches and different strategies to handle the possible presence of genotyping errors to obtain robust estimates of pollen flow in four European beech (Fagus sylvatica L.) populations from Austria and France. In each country one of the two plots is located in an unmanaged forest; the other plots are managed with a shelterwood system and inside a colonization area (in Austria and France, respectively). The two paternity analysis approaches provided almost identical estimates of gene flow. In general, we found high pollen immigration (~75% of pollen from outside), with the exception of the plot from a highly isolated forest remnant (~50%). In the two unmanaged plots, the average within-population pollen dispersal distances (from 80 to 184 m) were higher than previously estimated for beech. From the comparison between the Austrian managed and unmanaged plots, that are only 500 m apart, we found no evidence that either gene flow or reproductive success distributions were significantly altered by forest management. The investigated phenotypic traits (crown area, height, diameter and flowering phenology) were not significantly related with male reproductive success. Shelterwood seems to have an effect on the distribution of within-population pollen dispersal distances. In the managed plot, pollen dispersal distances were shorter, possibly because adult tree density is three-fold (163 versus 57 trees per hectare) with respect to the unmanaged one.

  15. Evidence for panmixia despite barriers to gene flow in the southern African endemic, Caffrogobius caffer (Teleostei: Gobiidae

    Directory of Open Access Journals (Sweden)

    von der Heyden Sophie

    2008-12-01

    Full Text Available Abstract Background Oceanography and life-history characteristics are known to influence the genetic structure of marine species, however the relative role that these factors play in shaping phylogeographic patterns remains unresolved. The population genetic structure of the endemic, rocky shore dwelling Caffrogobius caffer was investigated across a known major oceanographic barrier, Cape Agulhas, which has previously been shown to strongly influence genetic structuring of South African rocky shore and intertidal marine organisms. Given the variable and dynamic oceanographical features of the region, we further sought to test how the pattern of gene flow between C. caffer populations is affected by the dominant Agulhas and Benguela current systems of the southern oceans. Results The variable 5' region of the mtDNA control region was amplified for 242 individuals from ten localities spanning the distributional range of C. caffer. Fifty-five haplotypes were recovered and in stark contrast to previous phylogeographic studies of South African marine species, C. caffer showed no significant population genetic structuring along 1300 km of coastline. The parsimony haplotype network, AMOVA and SAMOVA analyses revealed panmixia. Coalescent analyses reveal that gene flow in C. caffer is strongly asymmetrical and predominantly affected by the Agulhas Current. Notably, there was no gene flow between the east coast and all other populations, although all other analyses detect no significant population structure, suggesting a recent divergence. The mismatch distribution suggests that C. caffer underwent a population expansion at least 14 500 years ago. Conclusion We propose several possible life-history adaptations that could have enabled C. caffer to maintain gene flow across its distributional range, including a long pelagic larval stage. We have shown that life-history characteristics can be an important contributing factor to the phylogeography of marine

  16. Adaptive traits are maintained on steep selective gradients despite gene flow and hybridization in the intertidal zone.

    Directory of Open Access Journals (Sweden)

    Gerardo I Zardi

    Full Text Available Gene flow among hybridizing species with incomplete reproductive barriers blurs species boundaries, while selection under heterogeneous local ecological conditions or along strong gradients may counteract this tendency. Congeneric, externally-fertilizing fucoid brown algae occur as distinct morphotypes along intertidal exposure gradients despite gene flow. Combining analyses of genetic and phenotypic traits, we investigate the potential for physiological resilience to emersion stressors to act as an isolating mechanism in the face of gene flow. Along vertical exposure gradients in the intertidal zone of Northern Portugal and Northwest France, the mid-low shore species Fucus vesiculosus, the upper shore species Fucus spiralis, and an intermediate distinctive morphotype of F. spiralis var. platycarpus were morphologically characterized. Two diagnostic microsatellite loci recovered 3 genetic clusters consistent with prior morphological assignment. Phylogenetic analysis based on single nucleotide polymorphisms in 14 protein coding regions unambiguously resolved 3 clades; sympatric F. vesiculosus, F. spiralis, and the allopatric (in southern Iberia population of F. spiralis var. platycarpus. In contrast, the sympatric F. spiralis var. platycarpus (from Northern Portugal was distributed across the 3 clades, strongly suggesting hybridization/introgression with both other entities. Common garden experiments showed that physiological resilience following exposure to desiccation/heat stress differed significantly between the 3 sympatric genetic taxa; consistent with their respective vertical distribution on steep environmental clines in exposure time. Phylogenetic analyses indicate that F. spiralis var. platycarpus is a distinct entity in allopatry, but that extensive gene flow occurs with both higher and lower shore species in sympatry. Experimental results suggest that strong selection on physiological traits across steep intertidal exposure gradients

  17. Local adaptation with high gene flow: temperature parameters drive adaptation to altitude in the common frog (Rana temporaria)

    OpenAIRE

    2014-01-01

    Both environmental and genetic influences can result in phenotypic variation. Quantifying the relative contributions of local adaptation and phenotypic plasticity to phenotypes is key to understanding the effect of environmental variation on populations. Identifying the selective pressures that drive divergence is an important, but often lacking, next step. High gene flow between high- and low-altitude common frog (Rana temporaria) breeding sites has previously been demonstrated in Scotland. ...

  18. Adaptive Traits Are Maintained on Steep Selective Gradients despite Gene Flow and Hybridization in the Intertidal Zone

    Science.gov (United States)

    Canovas, Fernando; Ferreira Costa, Joana; Serrão, Ester A.; Pearson, Gareth A.

    2011-01-01

    Gene flow among hybridizing species with incomplete reproductive barriers blurs species boundaries, while selection under heterogeneous local ecological conditions or along strong gradients may counteract this tendency. Congeneric, externally-fertilizing fucoid brown algae occur as distinct morphotypes along intertidal exposure gradients despite gene flow. Combining analyses of genetic and phenotypic traits, we investigate the potential for physiological resilience to emersion stressors to act as an isolating mechanism in the face of gene flow. Along vertical exposure gradients in the intertidal zone of Northern Portugal and Northwest France, the mid-low shore species Fucus vesiculosus, the upper shore species Fucus spiralis, and an intermediate distinctive morphotype of F. spiralis var. platycarpus were morphologically characterized. Two diagnostic microsatellite loci recovered 3 genetic clusters consistent with prior morphological assignment. Phylogenetic analysis based on single nucleotide polymorphisms in 14 protein coding regions unambiguously resolved 3 clades; sympatric F. vesiculosus, F. spiralis, and the allopatric (in southern Iberia) population of F. spiralis var. platycarpus. In contrast, the sympatric F. spiralis var. platycarpus (from Northern Portugal) was distributed across the 3 clades, strongly suggesting hybridization/introgression with both other entities. Common garden experiments showed that physiological resilience following exposure to desiccation/heat stress differed significantly between the 3 sympatric genetic taxa; consistent with their respective vertical distribution on steep environmental clines in exposure time. Phylogenetic analyses indicate that F. spiralis var. platycarpus is a distinct entity in allopatry, but that extensive gene flow occurs with both higher and lower shore species in sympatry. Experimental results suggest that strong selection on physiological traits across steep intertidal exposure gradients acts to maintain

  19. Adaptive traits are maintained on steep selective gradients despite gene flow and hybridization in the intertidal zone.

    Science.gov (United States)

    Zardi, Gerardo I; Nicastro, Katy R; Canovas, Fernando; Costa, Joana Ferreira; Serrão, Ester A; Pearson, Gareth A

    2011-01-01

    Gene flow among hybridizing species with incomplete reproductive barriers blurs species boundaries, while selection under heterogeneous local ecological conditions or along strong gradients may counteract this tendency. Congeneric, externally-fertilizing fucoid brown algae occur as distinct morphotypes along intertidal exposure gradients despite gene flow. Combining analyses of genetic and phenotypic traits, we investigate the potential for physiological resilience to emersion stressors to act as an isolating mechanism in the face of gene flow. Along vertical exposure gradients in the intertidal zone of Northern Portugal and Northwest France, the mid-low shore species Fucus vesiculosus, the upper shore species Fucus spiralis, and an intermediate distinctive morphotype of F. spiralis var. platycarpus were morphologically characterized. Two diagnostic microsatellite loci recovered 3 genetic clusters consistent with prior morphological assignment. Phylogenetic analysis based on single nucleotide polymorphisms in 14 protein coding regions unambiguously resolved 3 clades; sympatric F. vesiculosus, F. spiralis, and the allopatric (in southern Iberia) population of F. spiralis var. platycarpus. In contrast, the sympatric F. spiralis var. platycarpus (from Northern Portugal) was distributed across the 3 clades, strongly suggesting hybridization/introgression with both other entities. Common garden experiments showed that physiological resilience following exposure to desiccation/heat stress differed significantly between the 3 sympatric genetic taxa; consistent with their respective vertical distribution on steep environmental clines in exposure time. Phylogenetic analyses indicate that F. spiralis var. platycarpus is a distinct entity in allopatry, but that extensive gene flow occurs with both higher and lower shore species in sympatry. Experimental results suggest that strong selection on physiological traits across steep intertidal exposure gradients acts to maintain

  20. Gene Flow Results in High Genetic Similarity Between Sibiraea (Rosaceae species in the Qinghai-Tibetan Plateau

    Directory of Open Access Journals (Sweden)

    Peng-Cheng Fu

    2016-10-01

    Full Text Available Studying closely related species and divergent populations provides insight into the process of speciation. Previous studies showed that the Sibiraea complex's evolutionary history on the Qinghai-Tibetan Plateau (QTP was confusing and could not be distinguishable on the molecular level. In this study, the genetic structure and gene flow of S. laevigata and S. angustata on the QTP was examined across 45 populations using 8 microsatellite loci. Microsatellites revealed high genetic diversity in Sibiraea populations. Most of the variance was detected within populations (87.45% rather than between species (4.39%. We found no significant correlations between genetic and geographical distances among populations. Bayesian cluster analysis grouped all individuals in the sympatric area of Sibiraea into one cluster and other individuals of S. angustata into another. Divergence history analysis based on the approximate Bayesian computation method indicated that the populations of S. angustata at the sympatric area derived from the admixture of 2 species. The assignment test assigned all individuals to populations of their own species rather than its congeneric species. Consistently, intraspecies were detected rather than interspecies first-generation migrants. The bidirectional gene flow in long-term patterns between the 2 species was asymmetric, with more from S. angustata to S. laevigata. In conclusion, the Sibiraea complex was distinguishable on the molecular level using microsatellite loci. We found that the high genetic similarity of these 2 species resulted from huge bidirectional gene flow, especially on the sympatric area where population admixtures between the species occurred.

  1. Genetic structure, mating system, and long-distance gene flow in heart of palm (Euterpe edulis Mart.).

    Science.gov (United States)

    Gaiotto, F A; Grattapaglia, D; Vencovsky, R

    2003-01-01

    We report a detailed analysis of the population genetic structure, mating system, and gene flow of heart of palm (Euterpe edulis Mart.-Arecaceae) in central Brazil. This palm is considered a keystone species because it supplies fruits for birds and rodents all year and is intensively harvested for culinary purposes. Two populations of this palm tree were examined, using 18 microsatellite loci. The species displays a predominantly outcrossed mating system (tm = 0.94), with a probability of full sibship greater than 70% within open-pollinated families. The following estimates of interpopulation genetic variation were calculated and found significant: FIT = 0.17, FIS = 0.12, FST = 0.06, and RST = 0.07. This low but significant level of interpopulation genetic variation indicates high levels of gene flow. Two adult trees were identified as likely seed parents (P > 99.9%) of juveniles located at a distance of 22 km. Gene flow over such distances has not been reported before for tropical tree species. The establishment and management of in situ genetic reserves or ex situ conservation and breeding populations for E. edulis should contemplate the collection of several hundreds open-pollinated maternal families from relatively few distant populations to maximize the genetic sampling of a larger number of pollen parents.

  2. Limited contemporary gene flow and high self-replenishment drives peripheral isolation in an endemic coral reef fish.

    Science.gov (United States)

    van der Meer, Martin H; Horne, John B; Gardner, Michael G; Hobbs, Jean-Paul A; Pratchett, Morgan; van Herwerden, Lynne

    2013-06-01

    Extensive ongoing degradation of coral reef habitats worldwide has lead to declines in abundance of coral reef fishes and local extinction of some species. Those most vulnerable are ecological specialists and endemic species. Determining connectivity between locations is vital to understanding recovery and long-term persistence of these species following local extinction. This study explored population connectivity in the ecologically-specialized endemic three-striped butterflyfish (Chaetodon tricinctus) using mt and msatDNA (nuclear microsatellites) to distinguish evolutionary versus contemporary gene flow, estimate self-replenishment and measure genetic diversity among locations at the remote Australian offshore coral reefs of Middleton Reef (MR), Elizabeth Reef (ER), Lord Howe Island (LHI), and Norfolk Island (NI). Mt and msatDNA suggested genetic differentiation of the most peripheral location (NI) from the remaining three locations (MR, ER, LHI). Despite high levels of mtDNA gene flow, there is limited msatDNA gene flow with evidence of high levels of self-replenishment (≥76%) at all four locations. Taken together, this suggests prolonged population recovery times following population declines. The peripheral population (NI) is most vulnerable to local extinction due to its relative isolation, extreme levels of self-replenishment (95%), and low contemporary abundance.

  3. A search theory model of patch-to-patch forager movement with application to pollinator-mediated gene flow.

    Science.gov (United States)

    Hoyle, Martin; Cresswell, James E

    2007-09-07

    We present a spatially implicit analytical model of forager movement, designed to address a simple scenario common in nature. We assume minimal depression of patch resources, and discrete foraging bouts, during which foragers fill to capacity. The model is particularly suitable for foragers that search systematically, foragers that deplete resources in a patch only incrementally, and for sit-and-wait foragers, where harvesting does not affect the rate of arrival of forage. Drawing on the theory of job search from microeconomics, we estimate the expected number of patches visited as a function of just two variables: the coefficient of variation of the rate of energy gain among patches, and the ratio of the expected time exploiting a randomly chosen patch and the expected time travelling between patches. We then consider the forager as a pollinator and apply our model to estimate gene flow. Under model assumptions, an upper bound for animal-mediated gene flow between natural plant populations is approximately proportional to the probability that the animal rejects a plant population. In addition, an upper bound for animal-mediated gene flow in any animal-pollinated agricultural crop from a genetically modified (GM) to a non-GM field is approximately proportional to the proportion of fields that are GM and the probability that the animal rejects a field.

  4. Local adaptation with high gene flow: temperature parameters drive adaptation to altitude in the common frog (Rana temporaria).

    Science.gov (United States)

    Muir, A P; Biek, R; Thomas, R; Mable, B K

    2014-02-01

    Both environmental and genetic influences can result in phenotypic variation. Quantifying the relative contributions of local adaptation and phenotypic plasticity to phenotypes is key to understanding the effect of environmental variation on populations. Identifying the selective pressures that drive divergence is an important, but often lacking, next step. High gene flow between high- and low-altitude common frog (Rana temporaria) breeding sites has previously been demonstrated in Scotland. The aim of this study was to assess whether local adaptation occurs in the face of high gene flow and to identify potential environmental selection pressures that drive adaptation. Phenotypic variation in larval traits was quantified in R. temporaria from paired high- and low-altitude sites using three common temperature treatments. Local adaptation was assessed using Q(ST)-F(ST) analyses, and quantitative phenotypic divergence was related to environmental parameters using Mantel tests. Although evidence of local adaptation was found for all traits measured, only variation in larval period and growth rate was consistent with adaptation to altitude. Moreover, this was only evident in the three mountains with the highest high-altitude sites. This variation was correlated with mean summer and winter temperatures, suggesting that temperature parameters are potentially strong selective pressures maintaining local adaptation, despite high gene flow.

  5. Landscape-scale deforestation decreases gene flow distance of a keystone tropical palm, Euterpe edulis Mart (Arecaceae).

    Science.gov (United States)

    Santos, Alesandro S; Cazetta, Eliana; Dodonov, Pavel; Faria, Deborah; Gaiotto, Fernanda A

    2016-09-01

    Habitat loss represents one of the main threats to tropical forests, which have reached extremely high rates of species extinction. Forest loss negatively impacts biodiversity, affecting ecological (e.g., seed dispersal) and genetic (e.g., genetic diversity and structure) processes. Therefore, understanding how deforestation influences genetic resources is strategic for conservation. Our aim was to empirically evaluate the effects of landscape-scale forest reduction on the spatial genetic structure and gene flow of Euterpe edulis Mart (Arecaceae), a palm tree considered a keystone resource for many vertebrate species. This study was carried out in nine forest remnants in the Atlantic Forest, northeastern Brazil, located in landscapes within a gradient of forest cover (19-83%). We collected leaves of 246 adults and 271 seedlings and performed genotyping using microsatellite markers. Our results showed that the palm populations had low spatial genetic structure, indicating that forest reduction did not influence this genetic parameter for neither seedlings nor adults. However, forest loss decreased the gene flow distance, which may negatively affect the genetic diversity of future generations by increasing the risk of local extinction of this keystone palm. For efficient strategies of genetic variability conservation and maintenance of gene flow in E. edulis, we recommend the maintenance of landscapes with intermediary to high levels of forest cover, that is, forest cover above 40%.

  6. Risk assessment of gene flow from genetically engineered virus resistant cassava to wild relatives in Africa: an expert panel report.

    Science.gov (United States)

    Hokanson, Karen E; Ellstrand, Norman C; Dixon, Alfred G O; Kulembeka, Heneriko P; Olsen, Kenneth M; Raybould, Alan

    2016-02-01

    The probability and consequences of gene flow to wild relatives is typically considered in the environmental risk assessment of genetically engineered crops. This is a report from a discussion by a group of experts who used a problem formulation approach to consider existing information for risk assessment of gene flow from cassava (Manihot esculenta) genetically engineered for virus resistance to the 'wild' (naturalized) relative M. glaziovii in East Africa. Two environmental harms were considered in this case: (1) loss of genetic diversity in the germplasm pool, and (2) loss of valued species, ecosystem resources, or crop yield and quality due to weediness or invasiveness of wild relatives. Based on existing information, it was concluded that gene flow will occur, but it is not likely that this will reduce the genetic diversity in the germplasm pool. There is little existing information about the impact of the virus in natural populations that could be used to inform a prediction about whether virus resistance would lead to an increase in reproduction or survival, hence abundance of M. glaziovii. However, an increase in the abundance of M. glaziovii should be manageable, and would not necessarily lead to the identified environmental harms.

  7. Exceptional diversity, non-random distribution, and rapid evolution of retroelements in the B73 maize genome.

    Directory of Open Access Journals (Sweden)

    Regina S Baucom

    2009-11-01

    Full Text Available Recent comprehensive sequence analysis of the maize genome now permits detailed discovery and description of all transposable elements (TEs in this complex nuclear environment. Reiteratively optimized structural and homology criteria were used in the computer-assisted search for retroelements, TEs that transpose by reverse transcription of an RNA intermediate, with the final results verified by manual inspection. Retroelements were found to occupy the majority (>75% of the nuclear genome in maize inbred B73. Unprecedented genetic diversity was discovered in the long terminal repeat (LTR retrotransposon class of retroelements, with >400 families (>350 newly discovered contributing >31,000 intact elements. The two other classes of retroelements, SINEs (four families and LINEs (at least 30 families, were observed to contribute 1,991 and approximately 35,000 copies, respectively, or a combined approximately 1% of the B73 nuclear genome. With regard to fully intact elements, median copy numbers for all retroelement families in maize was 2 because >250 LTR retrotransposon families contained only one or two intact members that could be detected in the B73 draft sequence. The majority, perhaps all, of the investigated retroelement families exhibited non-random dispersal across the maize genome, with LINEs, SINEs, and many low-copy-number LTR retrotransposons exhibiting a bias for accumulation in gene-rich regions. In contrast, most (but not all medium- and high-copy-number LTR retrotransposons were found to preferentially accumulate in gene-poor regions like pericentromeric heterochromatin, while a few high-copy-number families exhibited the opposite bias. Regions of the genome with the highest LTR retrotransposon density contained the lowest LTR retrotransposon diversity. These results indicate that the maize genome provides a great number of different niches for the survival and procreation of a great variety of retroelements that have evolved to

  8. Exceptional diversity, non-random distribution, and rapid evolution of retroelements in the B73 maize genome.

    Science.gov (United States)

    Baucom, Regina S; Estill, James C; Chaparro, Cristian; Upshaw, Naadira; Jogi, Ansuya; Deragon, Jean-Marc; Westerman, Richard P; Sanmiguel, Phillip J; Bennetzen, Jeffrey L

    2009-11-01

    Recent comprehensive sequence analysis of the maize genome now permits detailed discovery and description of all transposable elements (TEs) in this complex nuclear environment. Reiteratively optimized structural and homology criteria were used in the computer-assisted search for retroelements, TEs that transpose by reverse transcription of an RNA intermediate, with the final results verified by manual inspection. Retroelements were found to occupy the majority (>75%) of the nuclear genome in maize inbred B73. Unprecedented genetic diversity was discovered in the long terminal repeat (LTR) retrotransposon class of retroelements, with >400 families (>350 newly discovered) contributing >31,000 intact elements. The two other classes of retroelements, SINEs (four families) and LINEs (at least 30 families), were observed to contribute 1,991 and approximately 35,000 copies, respectively, or a combined approximately 1% of the B73 nuclear genome. With regard to fully intact elements, median copy numbers for all retroelement families in maize was 2 because >250 LTR retrotransposon families contained only one or two intact members that could be detected in the B73 draft sequence. The majority, perhaps all, of the investigated retroelement families exhibited non-random dispersal across the maize genome, with LINEs, SINEs, and many low-copy-number LTR retrotransposons exhibiting a bias for accumulation in gene-rich regions. In contrast, most (but not all) medium- and high-copy-number LTR retrotransposons were found to preferentially accumulate in gene-poor regions like pericentromeric heterochromatin, while a few high-copy-number families exhibited the opposite bias. Regions of the genome with the highest LTR retrotransposon density contained the lowest LTR retrotransposon diversity. These results indicate that the maize genome provides a great number of different niches for the survival and procreation of a great variety of retroelements that have evolved to differentially

  9. Experimental evidence of genome-wide impact of ecological selection during early stages of speciation-with-gene-flow.

    Science.gov (United States)

    Egan, Scott P; Ragland, Gregory J; Assour, Lauren; Powell, Thomas H Q; Hood, Glen R; Emrich, Scott; Nosil, Patrik; Feder, Jeffrey L

    2015-08-01

    Theory predicts that speciation-with-gene-flow is more likely when the consequences of selection for population divergence transitions from mainly direct effects of selection acting on individual genes to a collective property of all selected genes in the genome. Thus, understanding the direct impacts of ecologically based selection, as well as the indirect effects due to correlations among loci, is critical to understanding speciation. Here, we measure the genome-wide impacts of host-associated selection between hawthorn and apple host races of Rhagoletis pomonella (Diptera: Tephritidae), a model for contemporary speciation-with-gene-flow. Allele frequency shifts of 32 455 SNPs induced in a selection experiment based on host phenology were genome wide and highly concordant with genetic divergence between co-occurring apple and hawthorn flies in nature. This striking genome-wide similarity between experimental and natural populations of R. pomonella underscores the importance of ecological selection at early stages of divergence and calls for further integration of studies of eco-evolutionary dynamics and genome divergence. © 2015 The Authors Ecology Letters published by John Wiley & Sons Ltd and CNRS.

  10. Environmental selection on transcriptome-derived SNPs in a high gene flow marine fish, the Atlantic herring (Clupea harengus)

    DEFF Research Database (Denmark)

    Limborg, Morten; Helyar, S.J.; de Bruyn, M.;

    2012-01-01

    High gene flow is considered the norm for most marine organisms and is expected to limit their ability to adapt to local environments. Few studies have directly compared the patterns of differentiation at neutral and selected gene loci in marine organisms. We analysed a transcriptome-derived panel...... of 281 SNPs in Atlantic herring (Clupea harengus), a highly migratory small pelagic fish, for elucidating neutral and selected genetic variation among populations and to identify candidate genes for environmental adaptation. We analysed 607 individuals from 18 spawning locations in the northeast Atlantic......, including two temperature clines (5–12 C) and two salinity clines (5–35&). By combining genome scan and landscape genetic analyses, four genetically distinct groups of herring were identified: Baltic Sea, Baltic–North Sea transition area, North Sea ⁄ British Isles and North Atlantic; notably, samples...

  11. A systematic review of nonrandomized controlled trials on the curative effects of aquatic exercise

    Directory of Open Access Journals (Sweden)

    Kamioka H

    2011-03-01

    Full Text Available Hiroharu Kamioka1, Kiichiro Tsutani2, Yoshiteru Mutoh3, Hiroyasu Okuizum4, Miho Ohta5, Shuichi Handa4, Shinpei Okada6, Jun Kitayuguchi7, Masamitsu Kamada7, Nobuyoshi Shiozawa8, Sang-Jun Park4, Takuya Honda4, Shoko Moriyama41Faculty of Regional Environment Science, Tokyo University of Agriculture, Tokyo, Japan; 2Department of Drug Policy and Management, Graduate School of Pharmaceutical Sciences, 3Department of Physical and Health Education, Graduate School of Education, The University of Tokyo, Tokyo, Japan; 4Mimaki Onsen (Spa Clinic, Tomi City, Japan; 5Laboratory of Aqua, Health, and Sports Medicine, 6Physical Education and Medicine Research Foundation, Nagano, Japan; 7Physical Education and Medicine Research Center Unnan, Unnan City, Japan; 8Department of Longevity and Social Medicine, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, JapanBackground: The objectives of this review were to integrate the evidence of curative effects through aquatic exercise and assess the quality of studies based on a review of nonrandomized controlled trials (nRCTs.Methods: Study design was a systematic review of nonrandomized controlled trials. Trials were eligible if they were nonrandomized clinical trials. Studies included one treatment group in which aquatic exercise was applied. We searched the following databases from 2000 up to July 20, 2009: MEDLINE via PubMed, CINAHL, and Ichushi-Web.Results: Twenty-one trials met all inclusion criteria. Languages included were English (N = 9, Japanese (N = 11, and Korean (N = 1. Target diseases were knee and/or hip osteoarthritis, poliomyelitis, chronic kidney disease, discomforts of pregnancy, cardiovascular diseases, and rotator cuff tears. Many studies on nonspecific disease (healthy participants were included. All studies reported significant effectiveness in at least one or more outcomes. However results of evaluations with the TREND and CLEAR-NPT checklists generally

  12. Patterns of Nonrandom Mating Within and Across 11 Major Psychiatric Disorders

    Science.gov (United States)

    Nordsletten, Ashley E.; Larsson, Henrik; Crowley, James J.; Almqvist, Catarina; Lichtenstein, Paul; Mataix-Cols, David

    2016-01-01

    IMPORTANCE Psychiatric disorders are heritable, polygenic traits, which often share risk alleles and for which nonrandom mating has been suggested. However, despite the potential etiological implications, the scale of nonrandom mating within and across major psychiatric conditions remains unclear. OBJECTIVE To quantify the nature and extent of nonrandom mating within and across a broad range of psychiatric conditions at the population level. DESIGN, SETTING, AND PARTICIPANTS Population-based cohort using Swedish population registers. Participants were all Swedish residents with a psychiatric diagnosis of interest (attention-deficit/hyperactivity disorder, autism spectrum disorder, schizophrenia, bipolar disorder, major depression, generalized anxiety disorder, agoraphobia, social phobia, obsessive-compulsive disorder, anorexia, or substance abuse), along with their mates. Individuals with select nonpsychiatric disorders (Crohn’s disease, type 1 and type 2 diabetes mellitus, multiple sclerosis, or rheumatoid arthritis) were included for comparison. General population samples were also derived and matched 1:5 with each case proband. Inpatient and outpatient diagnostic data were derived from the Swedish National Patient Register (1973-2009), with analyses conducted between June 2014 and May 2015. MAIN OUTCOMES AND MEASURES Correlation in the diagnostic status of mates both within and across disorders. Conditional logistic regression was used to quantify the odds of each diagnosis in the mates of cases relative to matched population controls. RESULTS Across cohorts, data corresponded to 707 263 unique case individuals, with women constituting 45.7% of the full population. Positive correlations in diagnostic status were evident between mates. Within-disorder correlations were marginally higher (range, 0.11-0.48) than cross-disorder correlations (range, 0.01-0.42). Relative to matched populations, the odds of psychiatric case probands having an affected mate were

  13. Anderson transition in low-dimensional disordered systems driven by long-range nonrandom hopping.

    Science.gov (United States)

    Rodríguez, A; Malyshev, V A; Sierra, G; Martín-Delgado, M A; Rodríguez-Laguna, J; Domínguez-Adame, F

    2003-01-17

    The single-parameter scaling hypothesis predicts the absence of delocalized states for noninteracting quasiparticles in low-dimensional disordered systems. We show analytically, using a supersymmetric method combined with a renormalization group analysis, as well as numerically that extended states may occur in the one- and two-dimensional Anderson model with a nonrandom hopping falling off as some power of the distance between sites. The different size scaling of the bare level spacing and the renormalized magnitude of the disorder seen by the quasiparticles finally results in the delocalization of states at one of the band edges of the quasiparticle energy spectrum.

  14. Soluble epoxide hydrolase gene deletion improves blood flow and reduces infarct size after cerebral ischemia in reproductively senescent female mice

    Directory of Open Access Journals (Sweden)

    Kristen L Zuloaga

    2015-01-01

    Full Text Available Soluble epoxide hydrolase (sEH, a key enzyme in the metabolism of vasodilatory epoxyeicosatrienoic acids (EETs, is sexually dimorphic, suppressed by estrogen, and contributes to underlying sex differences in cerebral blood flow and injury after cerebral ischemia. We tested the hypothesis that sEH inhibition or gene deletion in reproductively senescent (RS female mice would increase cerebral perfusion and decrease infarct size following stroke. RS (15-18 month old and young (3-4 month old female sEH knockout (sEHKO mice and wild type (WT mice were subjected to 45 min middle cerebral artery occlusion (MCAO with laser Doppler perfusion monitoring. WT mice were treated with vehicle or a sEH inhibitor t-AUCB at the time of reperfusion and every 24hrs thereafter for 3 days. Differences in regional cerebral blood flow were measured in vivo using optical microangiography. Infarct size was measured 3 days after reperfusion. Infarct size and cerebral perfusion 24h after MCAO were not altered by age. Both sEH gene deletion and sEH inhibition increased cortical perfusion 24h after MCAO. Neither sEH gene deletion nor sEH inhibition reduced infarct size in young mice. However, sEH gene deletion, but not sEH inhibition of the hydrolase domain of the enzyme, decreased infarct size in RS mice. Results of these studies show that sEH gene deletion and sEH inhibition enhance cortical perfusion following MCAO and sEH gene deletion reduces damage after ischemia in RS female mice; however this neuroprotection in absent is young mice.

  15. Long distance pollen-mediated gene flow at a landscape level: the weed beet as a case study.

    Science.gov (United States)

    Fénart, Stéphane; Austerlitz, Frédéric; Cuguen, Joël; Arnaud, Jean-François

    2007-09-01

    Gene flow is a crucial parameter that can affect the organization of genetic diversity in plant species. It has important implications in terms of conservation of genetic resources and of gene exchanges between crop to wild relatives and within crop species complex. In the Beta vulgaris complex, hybridization between crop and wild beets in seed production areas is well documented and the role of the ensuing hybrids, weed beets, as bridges towards wild forms in sugar beet production areas have been shown. Indeed, in contrast to cultivated beets that are bi-annual, weed beets can bolt, flower and reproduce in the same crop season. Nonetheless, the extent of pollen gene dispersal through weedy lineages remains unknown. In this study, the focus is directed towards weed-to-weed gene flow, and we report the results of a pollen-dispersal analysis within an agricultural landscape composed of five sugar beet fields with different levels of infestation by weed beets. Our results, based on paternity analysis of 3240 progenies from 135 maternal plants using 10 microsatellite loci, clearly demonstrate that even if weedy plants are mostly pollinated by individuals from the same field, some mating events occur between weed beets situated several kilometres apart (up to 9.6 km), with rates of interfield-detected paternities ranging from 11.3% to 17.5%. Moreover, we show that pollen flow appears to be more restricted when individuals are aggregated as most mating events occurred only for short-distance classes. The best-fit dispersal curves were fat-tailed geometric functions for populations exhibiting low densities of weed beets and thin-tailed Weibull function for fields with weed beet high densities. Thus, weed beet populations characterized by low density with geographically isolated individuals may be difficult to detect but are likely to act as pollen traps for pollen emitted by close and remote fields. Hence, it appears evident that interfield pollen-mediated gene flow

  16. Reactive particles in random flows.

    Science.gov (United States)

    Károlyi, György; Tél, Tamás; de Moura, Alessandro P S; Grebogi, Celso

    2004-04-30

    We study the dynamics of chemically or biologically active particles advected by open flows of chaotic time dependence, which can be modeled by a random time dependence of the parameters on a stroboscopic map. We develop a general theory for reactions in such random flows, and derive the reaction equation for this case. We show that there is a singular enhancement of the reaction in random flows, and this enhancement is increased as compared to the nonrandom case. We verify our theory in a model flow generated by four point vortices moving chaotically.

  17. Informal "seed" systems and the management of gene flow in traditional agroecosystems: the case of cassava in Cauca, Colombia.

    Science.gov (United States)

    Dyer, George A; González, Carolina; Lopera, Diana Carolina

    2011-01-01

    Our ability to manage gene flow within traditional agroecosystems and their repercussions requires understanding the biology of crops, including farming practices' role in crop ecology. That these practices' effects on crop population genetics have not been quantified bespeaks lack of an appropriate analytical framework. We use a model that construes seed-management practices as part of a crop's demography to describe the dynamics of cassava (Manihot esculenta Crantz) in Cauca, Colombia. We quantify several management practices for cassava--the first estimates of their kind for a vegetatively-propagated crop--describe their demographic repercussions, and compare them to those of maize, a sexually-reproduced grain crop. We discuss the implications for gene flow, the conservation of cassava diversity, and the biosafety of vegetatively-propagated crops in centers of diversity. Cassava populations are surprisingly open and dynamic: farmers exchange germplasm across localities, particularly improved varieties, and distribute it among neighbors at extremely high rates vis-à-vis maize. This implies that a large portion of cassava populations consists of non-local germplasm, often grown in mixed stands with local varieties. Gene flow from this germplasm into local seed banks and gene pools via pollen has been documented, but its extent remains uncertain. In sum, cassava's biology and vegetative propagation might facilitate pre-release confinement of genetically-modified varieties, as expected, but simultaneously contribute to their diffusion across traditional agroecosystems if released. Genetically-modified cassava is unlikely to displace landraces or compromise their diversity; but rapid diffusion of improved germplasm and subsequent incorporation into cassava landraces, seed banks or wild populations could obstruct the tracking and eradication of deleterious transgenes. Attempts to regulate traditional farming practices to reduce the risks could compromise cassava

  18. Informal "seed" systems and the management of gene flow in traditional agroecosystems: the case of cassava in Cauca, Colombia.

    Directory of Open Access Journals (Sweden)

    George A Dyer

    Full Text Available Our ability to manage gene flow within traditional agroecosystems and their repercussions requires understanding the biology of crops, including farming practices' role in crop ecology. That these practices' effects on crop population genetics have not been quantified bespeaks lack of an appropriate analytical framework. We use a model that construes seed-management practices as part of a crop's demography to describe the dynamics of cassava (Manihot esculenta Crantz in Cauca, Colombia. We quantify several management practices for cassava--the first estimates of their kind for a vegetatively-propagated crop--describe their demographic repercussions, and compare them to those of maize, a sexually-reproduced grain crop. We discuss the implications for gene flow, the conservation of cassava diversity, and the biosafety of vegetatively-propagated crops in centers of diversity. Cassava populations are surprisingly open and dynamic: farmers exchange germplasm across localities, particularly improved varieties, and distribute it among neighbors at extremely high rates vis-à-vis maize. This implies that a large portion of cassava populations consists of non-local germplasm, often grown in mixed stands with local varieties. Gene flow from this germplasm into local seed banks and gene pools via pollen has been documented, but its extent remains uncertain. In sum, cassava's biology and vegetative propagation might facilitate pre-release confinement of genetically-modified varieties, as expected, but simultaneously contribute to their diffusion across traditional agroecosystems if released. Genetically-modified cassava is unlikely to displace landraces or compromise their diversity; but rapid diffusion of improved germplasm and subsequent incorporation into cassava landraces, seed banks or wild populations could obstruct the tracking and eradication of deleterious transgenes. Attempts to regulate traditional farming practices to reduce the risks could

  19. Non-random biodiversity loss underlies predictable increases in viral disease prevalence.

    Science.gov (United States)

    Lacroix, Christelle; Jolles, Anna; Seabloom, Eric W; Power, Alison G; Mitchell, Charles E; Borer, Elizabeth T

    2014-03-06

    Disease dilution (reduced disease prevalence with increasing biodiversity) has been described for many different pathogens. Although the mechanisms causing this phenomenon remain unclear, the disassembly of communities to predictable subsets of species, which can be caused by changing climate, land use or invasive species, underlies one important hypothesis. In this case, infection prevalence could reflect the competence of the remaining hosts. To test this hypothesis, we measured local host species abundance and prevalence of four generalist aphid-vectored pathogens (barley and cereal yellow dwarf viruses) in a ubiquitous annual grass host at 10 sites spanning 2000 km along the North American West Coast. In laboratory and field trials, we measured viral infection as well as aphid fecundity and feeding preference on several host species. Virus prevalence increased as local host richness declined. Community disassembly was non-random: ubiquitous hosts dominating species-poor assemblages were among the most competent for vector production and virus transmission. This suggests that non-random biodiversity loss led to increased virus prevalence. Because diversity loss is occurring globally in response to anthropogenic changes, such work can inform medical, agricultural and veterinary disease research by providing insights into the dynamics of pathogens nested within a complex web of environmental forces.

  20. Gene expression responses of HeLa cells to chemical species generated by an atmospheric plasma flow

    Energy Technology Data Exchange (ETDEWEB)

    Yokoyama, Mayo, E-mail: yokoyama@plasma.ifs.tohoku.ac.jp [Institute of Fluid Science, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577 (Japan); Johkura, Kohei, E-mail: kohei@shinshu-u.ac.jp [Department of Histology and Embryology, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto 390-8621 (Japan); Sato, Takehiko, E-mail: sato@ifs.tohoku.ac.jp [Institute of Fluid Science, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577 (Japan)

    2014-08-08

    Highlights: • Response of HeLa cells to a plasma-irradiated medium was revealed by DNA microarray. • Gene expression pattern was basically different from that in a H{sub 2}O{sub 2}-added medium. • Prominently up-/down-regulated genes were partly shared by the two media. • Gene ontology analysis showed both similar and different responses in the two media. • Candidate genes involved in response to ROS were detected in each medium. - Abstract: Plasma irradiation generates many factors able to affect the cellular condition, and this feature has been studied for its application in the field of medicine. We previously reported that hydrogen peroxide (H{sub 2}O{sub 2}) was the major cause of HeLa cell death among the chemical species generated by high level irradiation of a culture medium by atmospheric plasma. To assess the effect of plasma-induced factors on the response of live cells, HeLa cells were exposed to a medium irradiated by a non-lethal plasma flow level, and their gene expression was broadly analyzed by DNA microarray in comparison with that in a corresponding concentration of 51 μM H{sub 2}O{sub 2}. As a result, though the cell viability was sufficiently maintained at more than 90% in both cases, the plasma-medium had a greater impact on it than the H{sub 2}O{sub 2}-medium. Hierarchical clustering analysis revealed fundamentally different cellular responses between these two media. A larger population of genes was upregulated in the plasma-medium, whereas genes were downregulated in the H{sub 2}O{sub 2}-medium. However, a part of the genes that showed prominent differential expression was shared by them, including an immediate early gene ID2. In gene ontology analysis of upregulated genes, the plasma-medium showed more diverse ontologies than the H{sub 2}O{sub 2}-medium, whereas ontologies such as “response to stimulus” were common, and several genes corresponded to “response to reactive oxygen species.” Genes of AP-1 proteins, e.g., JUN

  1. Gene flow between sexual and facultatively asexual lineages of an aphid species and the maintenance of reproductive mode variation.

    Science.gov (United States)

    Halkett, F; Plantegenest, M; Bonhomme, J; Simon, J-C

    2008-06-01

    Many organisms considered as strictly clonal may in fact experience some rare events of sexual reproduction with their sexual relatives. However, the rate of sexual-asexual gene flow has rarely been assessed mainly because its evaluation is difficult to achieve in the field. In the cyclically parthenogenetic aphid Rhopalosiphum padi, two main sets of lineages, differing in their investment in sexual reproduction and in their genetic attributes, co-exist even at a very fine scale: the 'sexual' lineages which have a full commitment to the sexual reproduction, and the 'facultatively asexual' lineages, which allocate investment in the sexual and parthenogenetic reproduction. This system offers a unique opportunity to tackle the genetic interactions between two contrasting reproductive modes. Here, we provide evidence that gene flow occurred between sexual and facultatively asexual lineages of R. padi. We carefully examined the shuffling in phenotypic and genotypic variation following a sexual reproduction event that took place in the field. Combining genotypic data and phenotypic measurements showed that this gene mixing led to the production of a wide array of reproductive modes, including strictly asexual lineages. Finally, we discuss the central role played by facultatively asexual lineages on the maintenance of reproductive mode variation.

  2. Flow Cytometry-assisted Cloning of Specific Sequence Motifs fromComplex 16S ribosomal RNA Gene Libraries.

    Energy Technology Data Exchange (ETDEWEB)

    Nielsen, J.L.; Schramm, A.; Bernhard, A.E.; van den Engh, G.J.; Stahl, D.A.

    2004-07-21

    A flow cytometry method was developed for rapid screeningand recovery of cloned DNA containing common sequence motifs. Thisapproach, termed fluorescence-activated cell sorting-assisted cloning,was used to recover sequences affiliated with a unique lineage within theBacteroidetes not abundant in a clone library of environmental 16S rRNAgenes. Retrieval and sequence analysis of phylogenetically informativegenes has become a standard cultivation-independent technique toinvestigate microbial diversity in nature (7, 18). Genes encoding the 16SrRNA, because of the relative ease of their selective amplification, havebeen most frequently employed for general diversity surveys (16).Environmental studies have also focused on specific subpopulationsaffiliated with a phylogenetic group or identified by genes encodingspecific metabolic functions (e.g., ammonia oxidation, sulfaterespiration, and nitrate reduction) (8,15,20). However, specificpopulations may be of low abundance (1,23), or the genes encodingspecific metabolic functions may be insufficiently conserved to providepriming sites for general PCR amplification. Three general approacheshave been used to obtain 16S rRNA sequence information from low-abundancepopulations: screening hundreds to thousands of clones in a general 16SrRNA gene library (21), flow cytometric sorting of a subpopulation ofenvironmentally derived cells labeled by fluorescent in situhybridization (FISH) (27), or selective PCR amplification using primersspecific for the subpopulation (2,23). While the first approach is simplytime-consuming and tedious, the second has been restricted to fairlylarge and strongly fluorescent cells from aquatic samples (5, 27). Thethird approach often generates fragments of only a few hundred bases dueto the limited number of specific priming sites. Partial sequenceinformation often degrades analysis, obscuring or distorting thephylogenetic placement of the new sequences (11, 20). A more robustcharacterization of environ

  3. High-Resolution Gene Flow Model for Assessing Environmental Impacts of Transgene Escape Based on Biological Parameters and Wind Speed.

    Science.gov (United States)

    Wang, Lei; Haccou, Patsy; Lu, Bao-Rong

    2016-01-01

    Environmental impacts caused by transgene flow from genetically engineered (GE) crops to their wild relatives mediated by pollination are longstanding biosafety concerns worldwide. Mathematical modeling provides a useful tool for estimating frequencies of pollen-mediated gene flow (PMGF) that are critical for assessing such environmental impacts. However, most PMGF models are impractical for this purpose because their parameterization requires actual data from field experiments. In addition, most of these models are usually too general and ignored the important biological characteristics of concerned plant species; and therefore cannot provide accurate prediction for PMGF frequencies. It is necessary to develop more accurate PMGF models based on biological and climatic parameters that can be easily measured in situ. Here, we present a quasi-mechanistic PMGF model that only requires the input of biological and wind speed parameters without actual data from field experiments. Validation of the quasi-mechanistic model based on five sets of published data from field experiments showed significant correlations between the model-simulated and field experimental-generated PMGF frequencies. These results suggest accurate prediction for PMGF frequencies using this model, provided that the necessary biological parameters and wind speed data are available. This model can largely facilitate the assessment and management of environmental impacts caused by transgene flow, such as determining transgene flow frequencies at a particular spatial distance, and establishing spatial isolation between a GE crop and its coexisting non-GE counterparts and wild relatives.

  4. Testing the role of meander cutoff in promoting gene flow across a riverine barrier in ground skinks (Scincella lateralis.

    Directory of Open Access Journals (Sweden)

    Nathan D Jackson

    Full Text Available Despite considerable attention, the long-term impact of rivers on species diversification remains uncertain. Meander loop cutoff (MLC is one river phenomenon that may compromise a river's diversifying effects by passively transferring organisms from one side of the river to the other. However, the ability of MLC to promote gene flow across rivers has not been demonstrated empirically. Here, we test several predictions of MLC-mediated gene flow in populations of North American ground skinks (Scincella lateralis separated by a well-established riverine barrier, the Mississippi River: 1 individuals collected from within meander cutoffs should be more closely related to individuals across the river than on the same side, 2 individuals within meander cutoffs should contain more immigrants than individuals away from meander cutoffs, 3 immigration rates estimated across the river should be highest in the direction of the cutoff event, and 4 the distribution of alleles native to one side of the river should be better predicted by the historical rather than current path of the river. To test these predictions we sampled 13 microsatellite loci and mitochondrial DNA from ground skinks collected near three ancient meander loops. These predictions were generally supported by genetic data, although support was stronger for mtDNA than for microsatellite data. Partial support for genetic divergence of samples within ancient meander loops also provides evidence for the MLC hypothesis. Although a role for MLC-mediated gene flow was supported here for ground skinks, the transient nature of river channels and morphologies may limit the long-term importance of MLC in stemming population divergence across major rivers.

  5. Seed-mediated gene flow promotes genetic diversity of weedy rice within populations: implications for weed management.

    Science.gov (United States)

    He, Zhuoxian; Jiang, Xiaoqi; Ratnasekera, Disna; Grassi, Fabrizio; Perera, Udugahapattuwage; Lu, Bao-Rong

    2014-01-01

    Increased infestation of weedy rice-a noxious agricultural pest has caused significant reduction of grain yield of cultivated rice (Oryza sativa) worldwide. Knowledge on genetic diversity and structure of weedy rice populations will facilitate the design of effective methods to control this weed by tracing its origins and dispersal patterns in a given region. To generate such knowledge, we studied genetic diversity and structure of 21 weedy rice populations from Sri Lanka based on 23 selected microsatellite (SSR) loci. Results indicated an exceptionally high level of within-population genetic diversity (He = 0.62) and limited among-population differentiation (Fst = 0.17) for this predominantly self-pollinating weed. UPGMA analysis showed a loose genetic affinity of the weedy rice populations in relation to their geographical locations, and no obvious genetic structure among populations across the country. This phenomenon was associated with the considerable amount of gene flow between populations. Limited admixture from STRUCTURE analyses suggested a very low level of hybridization (pollen-mediated gene flow) between populations. The abundant within-population genetic diversity coupled with limited population genetic structure and differentiation is likely caused by the considerable seed-mediated gene flow of weedy rice along with the long-distance exchange of farmer-saved rice seeds between weedy-rice contaminated regions in Sri Lanka. In addition to other effective weed management strategies, promoting the application of certified rice seeds with no weedy rice contamination should be the immediate action to significantly reduce the proliferation and infestation of this weed in rice ecosystems in countries with similar rice farming styles as in Sri Lanka.

  6. Limited divergence among populations of rice striped stem borer in southeast China caused by gene flow: Implications for resistance management

    Institute of Scientific and Technical Information of China (English)

    Chao YANG; Xiao YANG; Qiang FU; Kai XU; Bao-Rong LU

    2012-01-01

    Rice striped stem borer (RSSB,Chilo suppressalis) is a serious lepidopteron pest occurring in rice ecosystems of Asia and Europe.Genetically modified (GM) insect-resistant Bt rice has been developed to deter lepidopteron pests including RSSB.The concern of resistance evolution to the Bt toxin by the pests under commercial cultivation of GM Bt rice and the need of effective management of the resistance encourage the studies of genetic variation and divergence,as well as gene flow of RSSB populations.We analyzed 13 RSSB populations fed on water-oats or rice plants,respectively,from southeast China applying the fluorescent amplified fragment length polymorphism fingerprints.A generally moderate level of genetic variation was detected in the populations,as estimated by Nei's genetic diversity (0.27) and Shannon's index (0.42).The FsT- and AMOVA values indicated a low level (~ 12%) of genetic divergence among the RSSB populations.A relatively frequent gene flow (an average Nm =2.62) was detected among the 12 RSSB populations,which may explain the limited genetic divergence among the rice-feeding populations.This explanation gains support by the assignment test of the corresponding populations,suggesting that a considerable proportion of individuals was contributed from non-native populations.Our results revealed that the moderate level of genetic diversity combined with relatively frequent gene flow among RSSB populations across a large geographical range may slow down the resistance evolution of the RSSB populations,given that a proper measure of resistance management is taken.

  7. Impact of life history traits on gene flow: A multispecies systematic review across oceanographic barriers in the Mediterranean Sea

    KAUST Repository

    Pascual, Marta

    2017-05-10

    Marine species can demonstrate strong genetic differentiation and population structure despite the hypothesis of open seas and high connectivity. Some suggested drivers causing the genetic breaks are oceanographic barriers and the species\\' biology. We assessed the relevance of seven major oceanographic fronts on species connectivity while considering their dispersal capacity and life strategy.We systematically reviewed the scientific articles reporting population genetic differentiation along the Mediterranean Sea and across the Atlantic-Mediterranean transition. We retained those considering at least one sampling locality at each side of an oceanographic front, and at least two localities with no-front between them to correctly assess the effect of the front. To estimate the impact of life history characteristics affecting connectivity we considered the planktonic larval duration (PLD) and adult life strategy.Oceanographic barriers in the Mediterranean Sea seem to reduce gene flow globally; however, this effect is not homogeneous considering the life history traits of the species. The effect of the oceanographic fronts reduces gene flow in highly mobile species with PLD larger than 2-4 weeks. Benthic sessile species and/or with short PLD (< 2 weeks) have more significant genetic breaks between localities than species with higher motility; however, genetic differentiation occurs independently of the presence of a front.Genetic connectivity is important for populations to recover from anthropogenic or natural impacts. We show that species with low mobility, mostly habitat-formers, have high genetic differentiation but low gene flow reduction mediated by the front, therefore, considering the importance of these species, we emphasize the vulnerability of the Mediterranean ecosystems and the necessity of protection strategies based on the whole ecosystem.

  8. Workers select mates for queens: a possible mechanism of gene flow restriction between supercolonies of the invasive Argentine ant

    Science.gov (United States)

    Sunamura, Eiriki; Hoshizaki, Sugihiko; Sakamoto, Hironori; Fujii, Takeshi; Nishisue, Koji; Suzuki, Shun; Terayama, Mamoru; Ishikawa, Yukio; Tatsuki, Sadahiro

    2011-05-01

    Some invasive ants form large networks of mutually non-aggressive nests, i.e., supercolonies. The Argentine ant Linepithema humile forms much larger supercolonies in introduced ranges than in its native range. In both cases, it has been shown that little gene flow occurs between supercolonies of this species, though the mechanism of gene flow restriction is unknown. In this species, queens do not undertake nuptial flight, and males have to travel to foreign nests and cope with workers before gaining access to alien queens. In this study, we hypothesized that male Argentine ants receive interference from workers of alien supercolonies. To test this hypothesis, we conducted behavioral and chemical experiments using ants from two supercolonies in Japan. Workers attacked males from alien supercolonies but not those from their own supercolonies. The level of aggression against alien males was similar to that against alien workers. The frequency of severe aggression against alien males increased as the number of recipient workers increased. Cuticular hydrocarbon profiles, which serve as cues for nestmate recognition, of workers and males from the same supercolony were very similar. Workers are likely to distinguish alien males from males of their own supercolony using the profiles. It is predicted that males are subject to considerable aggression from workers when they intrude into the nests of alien supercolonies. This may be a mechanism underlying the restricted gene flow between supercolonies of Argentine ants. The Argentine ant may possess a distinctive reproductive system, where workers participate in selecting mates for their queens. We argue that the aggression of workers against alien males is a novel form of reproductive interference.

  9. Population genetic structure in Sabatieria (Nematoda) reveals intermediary gene flow and admixture between distant cold seeps from the Mediterranean Sea.

    Science.gov (United States)

    De Groote, Annelies; Hauquier, Freija; Vanreusel, Ann; Derycke, Sofie

    2017-07-01

    There is a general lack of information on the dispersal and genetic structuring for populations of small-sized deep-water taxa, including free-living nematodes which inhabit and dominate the seafloor sediments. This is also true for unique and scattered deep-sea habitats such as cold seeps. Given the limited dispersal capacity of marine nematodes, genetic differentiation between such geographically isolated habitat patches is expected to be high. Against this background, we examined genetic variation in both mitochondrial (COI) and nuclear (18S and 28S ribosomal) DNA markers of 333 individuals of the genus Sabatieria, abundantly present in reduced cold-seep sediments. Samples originated from four Eastern Mediterranean cold seeps, separated by hundreds of kilometers, and one seep in the Southeast Atlantic. Individuals from the Mediterranean and Atlantic were divided into two separate but closely-related species clades. Within the Eastern Mediterranean, all specimens belonged to a single species, but with a strong population genetic structure (ΦST = 0.149). The haplotype network of COI contained 19 haplotypes with the most abundant haplotype (52% of the specimens) shared between all four seeps. The number of private haplotypes was high (15), but the number of mutations between haplotypes was low (1-8). These results indicate intermediary gene flow among the Mediterranean Sabatieria populations with no evidence of long-term barriers to gene flow. The presence of shared haplotypes and multiple admixture events indicate that Sabatieria populations from disjunct cold seeps are not completely isolated, with gene flow most likely facilitated through water current transportation of individuals and/or eggs. Genetic structure and molecular diversity indices are comparable to those of epiphytic shallow-water marine nematodes, while no evidence of sympatric cryptic species was found for the cold-seep Sabatieria.

  10. Genetic diversity and gene flow in the morphologically variable, rare endemics Begonia dregei and Begonia homonyma (Begoniaceae).

    Science.gov (United States)

    Matolweni, L O; Balkwill, K; McLellan, T

    2000-03-01

    Begonia dregei and B. homonyma (Begoniaceae), rare plants endemic to coastal forests of eastern South Africa, are two closely related species with high levels of variation among populations in the shape of leaves. Distribution of genetic variation and genetic relatedness were investigated in 12 populations of B. dregei and seven of B. homonyma using polyacrylamide gel electrophoresis. Twelve of the 15 enzyme loci examined were polymorphic, but only seven loci were polymorphic within at least one population. Genetic diversity measures indicated that the among-population gene differentiation represents >90% of the total genetic component in both species considered individually or combined. This indicated restricted gene flow, consistent with the limited dispersal abilities of Begonia generally and the ancient separation of isolated forest patches. Genetic distances among populations are much higher than usually found within species. Allozyme data provide no support for the recognition of B. dregei and B. homonyma as distinct species.

  11. Genomic signatures of local directional selection in a high gene flow marine organism, the Atlantic cod (Gadus morhua)

    DEFF Research Database (Denmark)

    Eg Nielsen, Einar; Hansen, Jakob Hemmer; Poulsen, Nina Aagaard;

    2009-01-01

    Background: Marine fishes have been shown to display low levels of genetic structuring and associated high levels of gene flow, suggesting shallow evolutionary trajectories and, possibly, limited or lacking adaptive divergence among local populations. We investigated variation in 98 gene...... selection in local demes, or closely linked to loci under selection. Likewise, on a regional south/north transect of central and eastern Atlantic populations, seven loci displayed strongly elevated levels of genetic differentiation. Selection patterns among populations appeared to be relatively widespread...... archived otoliths from a Faeroese population demonstrated stability of the intra-population variation over 24 years. An exploratory landscape genetic analysis was used to elucidate potential effects of the most likely environmental factors responsible for the signatures of local adaptation. We found...

  12. Non-equilibrium estimates of gene flow inferred from nuclear genealogies suggest that Iberian and North African wall lizards (Podarcis spp. are an assemblage of incipient species

    Directory of Open Access Journals (Sweden)

    Harris D James

    2008-02-01

    Full Text Available Abstract Background The study of recently-diverged species offers significant challenges both in the definition of evolutionary entities and in the estimation of gene flow among them. Iberian and North African wall lizards (Podarcis constitute a cryptic species complex for which previous assessments of mitochondrial DNA (mtDNA and allozyme variation are concordant in describing the existence of several highly differentiated evolutionary units. However, these studies report important differences suggesting the occurrence of gene flow among forms. Here we study sequence variation in two nuclear introns, β-fibint7 and 6-Pgdint7, to further investigate overall evolutionary dynamics and test hypotheses related to species delimitation within this complex. Results Both nuclear gene genealogies fail to define species as monophyletic. To discriminate between the effects of incomplete lineage sorting and gene flow in setting this pattern, we estimated migration rates among species using both FST-based estimators of gene flow, which assume migration-drift equilibrium, and a coalescent approach based on a model of divergence with gene flow. Equilibrium estimates of gene flow suggest widespread introgression between species, but coalescent estimates describe virtually zero admixture between most (but not all species pairs. This suggests that although gene flow among forms may have occurred the main cause for species polyphyly is incomplete lineage sorting, implying that most forms have been isolated since their divergence. This observation is therefore in accordance with previous reports of strong differentiation based on mtDNA and allozyme data. Conclusion These results corroborate most forms of Iberian and North African Podarcis as differentiated, although incipient, species, supporting a gradual view of speciation, according to which species may persist as distinct despite some permeability to genetic exchange and without having clearly definable genetic

  13. Genomic signatures of local directional selection in a high gene flow marine organism; the Atlantic cod (Gadus morhua

    Directory of Open Access Journals (Sweden)

    Mittelholzer Christian

    2009-12-01

    Full Text Available Abstract Background Marine fishes have been shown to display low levels of genetic structuring and associated high levels of gene flow, suggesting shallow evolutionary trajectories and, possibly, limited or lacking adaptive divergence among local populations. We investigated variation in 98 gene-associated single nucleotide polymorphisms (SNPs for evidence of selection in local populations of Atlantic cod (Gadus morhua L. across the species distribution. Results Our global genome scan analysis identified eight outlier gene loci with very high statistical support, likely to be subject to directional selection in local demes, or closely linked to loci under selection. Likewise, on a regional south/north transect of central and eastern Atlantic populations, seven loci displayed strongly elevated levels of genetic differentiation. Selection patterns among populations appeared to be relatively widespread and complex, i.e. outlier loci were generally not only associated with one of a few divergent local populations. Even on a limited geographical scale between the proximate North Sea and Baltic Sea populations four loci displayed evidence of adaptive evolution. Temporal genome scan analysis applied to DNA from archived otoliths from a Faeroese population demonstrated stability of the intra-population variation over 24 years. An exploratory landscape genetic analysis was used to elucidate potential effects of the most likely environmental factors responsible for the signatures of local adaptation. We found that genetic variation at several of the outlier loci was better correlated with temperature and/or salinity conditions at spawning grounds at spawning time than with geographic distance per se. Conclusion These findings illustrate that adaptive population divergence may indeed be prevalent despite seemingly high levels of gene flow, as found in most marine fishes. Thus, results have important implications for our understanding of the interplay of

  14. Non-random food-web assembly at habitat edges increases connectivity and functional redundancy.

    Science.gov (United States)

    Peralta, Guadalupe; Frost, Carol M; Didham, Raphael K; Rand, Tatyana A; Tylianakis, Jason M

    2017-04-01

    Habitat fragmentation dramatically alters the spatial configuration of landscapes, with the creation of artificial edges affecting community structure and dynamics. Despite this, it is not known how the different food webs in adjacent habitats assemble at their boundaries. Here we demonstrate that the composition and structure of herbivore-parasitoid food webs across edges between native and plantation forests are not randomly assembled from those of the adjacent communities. Rather, elevated proportions of abundant, interaction-generalist parasitoid species at habitat edges allowed considerable interaction rewiring, which led to higher linkage density and less modular networks, with higher parasitoid functional redundancy. This was despite high overlap in host composition between edges and interiors. We also provide testable hypotheses for how food webs may assemble between habitats with lower species overlap. In an increasingly fragmented world, non-random assembly of food webs at edges may increasingly affect community dynamics at the landscape level.

  15. Evidence for landscape-level, pollen-mediated gene flow from genetically modified creeping bentgrass with CP4 EPSPS as a marker

    Science.gov (United States)

    Watrud, L.S.; Lee, E.H.; Fairbrother, A.; Burdick, C.; Reichman, J.R.; Bollman, M.; Storm, M.; King, G.; Van De Water, Peter K.

    2004-01-01

    Sampling methods and results of a gene flow study are described that will be of interest to plant scientists, evolutionary biologists, ecologists, and stakeholders assessing the environmental safety of transgenic crops. This study documents gene flow on a landscape level from creeping bentgrass (Agrostis stolonifera L.), one of the first wind-pollinated, perennial, and highly outcrossing transgenic crops being developed for commercial use. Most of the gene flow occurred within 2 km in the direction of prevailing winds. The maximal gene flow distances observed were 21 km and 14 km in sentinel and resident plants, respectively, that were located in primarily nonagronomic habitats. The selectable marker used in these studies was the CP4 EPSPS gene derived from Agrobacterium spp. strain CP4 that encodes 5-enol-pyruvylshikimate-3-phosphate synthase and confers resistance to glyphosate herbicide. Evidence for gene flow to 75 of 138 sentinel plants of A. stolonifera and to 29 of 69 resident Agrostis plants was based on seedling progeny survival after spraying with glyphosate in greenhouse assays and positive TraitChek, PCR, and sequencing results. Additional studies are needed to determine whether introgression will occur and whether it will affect the ecological fitness of progeny or the structure of plant communities in which transgenic progeny may become established.

  16. Patterns of genetic structure and evidence of gene flow among Tunisian Citrus species based on informative nSSR markers.

    Science.gov (United States)

    Ben Romdhane, Meriam; Riahi, Leila; Selmi, Ayet; Zoghlami, Nejia

    2016-01-01

    This study investigates the extent of genetic diversity, phylogenetic relationships and the amount of gene flow among Tunisian Citrus species based on a set of 15 informative nuclear SSR molecular markers. Genotyping data highlighted an allelic richness among Tunisian Citrus species and has allowed the detection of 168 alleles among them 104.19 were effective. The partition of the total genetic diversity (HT=0.832) showed that the highest amount of variation within the Citrus species is HS=0.550, while the relative amount of the between-species genetic diversity GST does not exceed 0.338. This pattern of genetic structure was supported by low-to-moderate FST pairwise values and the presence of a gene flow (Nm) among the eight Citrus species. The lowest genetic differentiation was revealed between the species C. sinensis and C. insitorum (FST=0.111, Nm=1.99), while the highest genetic differentiation was recorded between the species C. aurantifolia and C. paradisi (FST=0.367, Nm=0.43). The established Neighbor Joining analysis showed that all genotypes were widely discriminated and clearly pooled according to their species of origin, with minor exceptions. Copyright © 2016 Académie des sciences. Published by Elsevier SAS. All rights reserved.

  17. Limited gene flow and partial isolation phylogeography of Himalayan snowcock Tetraogallus himalayensis based on part mitochondrial D-loop sequences

    Institute of Scientific and Technical Information of China (English)

    Xiaoli WANG; Jiangyong QU; Naifa LIU; Xinkang BAO; Sen SONG

    2011-01-01

    Himalayan snowcock Tetraogallus himalayensis are distributed in alpine and subalpine areas in China.We used mitochondrial DNA control-region data to investigate the origin and past demographic change in sixty-seven Himalayan snowcock T.himalayensis.The fragments of 1155 nucleotides from the control region of mitochondrial DNA were sequenced,and 57 polymorphic positions defined 37 haplotypes.A high level of genetic diversity was detected in all populations sampled and may be associated isolation of the mountains and habitat fragmentation and deterioration from Quaternary glaciations.In the phylogenetic tree,all haplotypes grouped into four groups:clade A (Kunlun Mountains clade),clade B (Northern Qinghai-Tibetan Plateau clade),clade C (Tianshan Mountains clade) and clade D (Kalakunlun Mountains clade).We found a low level of gene flow and significant genetic differentiation among all populations.Based on divergence time we suggest that the divergence of Himalayan snowcock occurred in the middle Pleistocene inter-glaciation,and expansion occurred in the glaciation.Analysis of mtDNA D-loop sequences confirmed demographic population expansion,as did our non-significant mismatch distribution analysis.In conclusion,limited gene flow and a pattern of partial isolation phylogeographic was found in geographic populations of T.himalayansis based on the analysis on mtDNA D-loop sequences [Current Zoology 57 (6):758-767,2011 ].

  18. Genetic structure and indirect estimates of gene flow in three taxa of Cucurbita (Cucurbitaceae) in western Mexico.

    Science.gov (United States)

    Montes-Hernandez, Salvador; Eguiarte, Luis E

    2002-07-01

    Cultivated squash (Cucurbita argyrosperma ssp. argyrosperma and C. moschata) are important in the Mexican traditional agroecosystem. They are typically cultivated within maize fields where adjacent populations of a wild, close relative, C. argyrosperma ssp. sororia, occur. Consequently, there are ample opportunities for gene flow between domesticated and free-living Cucurbita populations. We used allozymes to examine genetic variation and gene flow among these three Cucurbita taxa in the state of Jalisco in Western Mexico. Twelve polymorphic allozyme loci were used to calculate genetic diversity for 16 populations of Cucurbita. We found high levels of genetic variation: polymorphism of 0.96, mean allelic diversity of 2.08, average expected heterozygosity 0.407, and little differentiation among conspecific populations (D = 0.081; F(ST) = 0.087; N(e)m = 5.22). These findings indicate that Cucurbita possess a high pollen dispersal potential, a somewhat surprising result considering they have specialist pollinators. Unweighted pair group method with arithmetic means (UPGMA) analysis of allozymes suggests the existence of at least two distinct groups of populations, one consisting of both subspecies of C. argyrosperma and another consisting of C. moschata.

  19. High gene flow due to pelagic larval dispersal among South Pacific archipelagos in two amphidromous gastropods (Neritomorpha: Neritidae).

    Science.gov (United States)

    Crandall, E D; Taffel, J R; Barber, P H

    2010-06-01

    The freshwater stream fauna of tropical oceanic islands is dominated by amphidromous species, whose larvae are transported to the ocean and develop in the plankton before recruiting back to freshwater habitat as juveniles. Because stream habitat is relatively scarce and unstable on oceanic islands, this life history would seem to favor either the retention of larvae to their natal streams, or the ability to delay metamorphosis until new habitat is encountered. To distinguish between these hypotheses, we used population genetic methods to estimate larval dispersal among five South Pacific archipelagos in two amphidromous species of Neritid gastropod (Neritina canalis and Neripteron dilatatus). Sequence data from mitochondrial cytochrome oxidase I (COI) revealed that neither species is genetically structured throughout the Western Pacific, suggesting that their larvae have a pelagic larval duration (PLD) of at least 8 weeks, longer than many marine species. In addition, the two species have recently colonized isolated Central Pacific archipelagos in three independent events. Since colonization, there has been little or no gene flow between the Western and Central Pacific archipelagos in N. canalis, and high levels of gene flow across the same region in N. dilatatus. Both species show departures from neutrality and recent dates for colonization of the Central Pacific archipelagos, which is consistent with frequent extinction and recolonization of stream populations in this area. Similar results from other amphidromous species suggest that unstable freshwater habitats promote long-distance dispersal capabilities.

  20. Genetic structure and gene flow in the endangered aquatic economic crop Brasenia schreberi J. F. Gmel. (Nymphaeaceae) in China

    Science.gov (United States)

    Dong, Yuan-Huo; Wahiti Gituru, Robert

    Inter-simple sequence repeat (ISSR) markers were used to measure the levels of genetic variation and patterns of population structure within and among five extant populations of Brasenia schreberi, an endangered aquatic plant in China. Six primers selected from sixty ISSR primers were used in the study which amplified 49 reproducible bands with 22 (44.9%) being polymorphic, indicating low levels of genetic diversity at the species level. AMOVA analysis revealed that most genetic variation (85.64%) is present among populations. The low level of gene flow (Nm = 0.1) is estimated among five remaining populations. A Mantel test show significant relationship between genetic distance and geographic distance (r = 0.91). Several factors including clonal growth, habitat fragment, population isolation, restricted gene flow among populations and agricultural practices, might have played an important role in maintaining the genetic structure of B. schreberi populations in China. In view of the limited genetic information currently available for B. schreberi, we recommend in situ preservation of the remaining population.

  1. Effect of selective logging on genetic diversity and gene flow in Cariniana legalis sampled from a cacao agroforestry system.

    Science.gov (United States)

    Leal, J B; Santos, R P; Gaiotto, F A

    2014-01-28

    The fragments of the Atlantic Forest of southern Bahia have a long history of intense logging and selective cutting. Some tree species, such as jequitibá rosa (Cariniana legalis), have experienced a reduction in their populations with respect to both area and density. To evaluate the possible effects of selective logging on genetic diversity, gene flow, and spatial genetic structure, 51 C. legalis individuals were sampled, representing the total remaining population from the cacao agroforestry system. A total of 120 alleles were observed from the 11 microsatellite loci analyzed. The average observed heterozygosity (0.486) was less than the expected heterozygosity (0.721), indicating a loss of genetic diversity in this population. A high fixation index (FIS = 0.325) was found, which is possibly due to a reduction in population size, resulting in increased mating among relatives. The maximum (1055 m) and minimum (0.095 m) distances traveled by pollen or seeds were inferred based on paternity tests. We found 36.84% of unique parents among all sampled seedlings. The progenitors of the remaining seedlings (63.16%) were most likely out of the sampled area. Positive and significant spatial genetic structure was identified in this population among classes 10 to 30 m away with an average coancestry coefficient between pairs of individuals of 0.12. These results suggest that the agroforestry system of cacao cultivation is contributing to maintaining levels of diversity and gene flow in the studied population, thus minimizing the effects of selective logging.

  2. Gene flow and geographic variation in natural populations of Alnus acuminata ssp. arguta (Fagales: Betulaceae in Costa Rica and Panama

    Directory of Open Access Journals (Sweden)

    Olman Murillo

    1999-12-01

    Full Text Available Seventeen natural populations in Costa Rica and Panama were used to asses gene flow and geographic patterns of genetic variation in this tree species. Gene flow analysis was based on the methods of rare alleles and FST (Index of genetic similarity M, using the only four polymorphic gene loci among 22 investigated (PGI-B, PGM-A, MNR-A and IDH-A. The geographic variation analysis was based on Pearson`s correlations between four geographic and 14 genetic variables. Some evidence of isolation by distance and a weak gene flow among geographic regions was found. Patterns of clinal variation in relation to altitude (r = -0.62 for genetic diversity and latitude (r= -0.77 for PGI-B3 were also observed, supporting the hypothesis of isolation by distance. No private alleles were found at the single population level.Diecisiete poblaciones naturales de esta especie forestal en Costa Rica y Panamá, fueron investigadas en relación con sus patrones de flujo genético y de variación geográfica. El análisis de flujo genético fue basado en los métodos de los alelos raros y de FST (Indice de similaridad genética M. Los análisis fueron a su vez basados en los únicos cuatro loci genéticos de un total de 22 investigados que mostraron polimorfismo (PGI-B, PGM-A, MNR-A and IDH-A. Los análisis de variación geográfica fueron basados en el desarrollo de correlaciones de Pearson entre 4 variables geográficas y 14 variables genéticas. Alguna evidencia de aislamiento por distancia así como un débil flujo genético entre regiones geográficas fue encontrado. Fueron también observados patrones de variación clinal en relación con la altitud (r = -0.62 para la diversidad genética y latitud (r= -0.77 en PGI-B3, que apoyan la hipotesis de aislamiento por distancia para esta especie. No se encontraron alelos privados en ninguna de las poblaciones investigadas.

  3. Plastid 16S rRNA gene diversity among eukaryotic picophytoplankton sorted by flow cytometry from the South Pacific Ocean.

    Science.gov (United States)

    Shi, Xiao Li; Lepère, Cécile; Scanlan, David J; Vaulot, Daniel

    2011-04-28

    The genetic diversity of photosynthetic picoeukaryotes was investigated in the South East Pacific Ocean. Genetic libraries of the plastid 16S rRNA gene were constructed on picoeukaryote populations sorted by flow cytometry, using two different primer sets, OXY107F/OXY1313R commonly used to amplify oxygenic organisms, and PLA491F/OXY1313R, biased towards plastids of marine algae. Surprisingly, the two sets revealed quite different photosynthetic picoeukaryote diversity patterns, which were moreover different from what we previously reported using the 18S rRNA nuclear gene as a marker. The first 16S primer set revealed many sequences related to Pelagophyceae and Dictyochophyceae, the second 16S primer set was heavily biased toward Prymnesiophyceae, while 18S sequences were dominated by Prasinophyceae, Chrysophyceae and Haptophyta. Primer mismatches with major algal lineages is probably one reason behind this discrepancy. However, other reasons, such as DNA accessibility or gene copy numbers, may be also critical. Based on plastid 16S rRNA gene sequences, the structure of photosynthetic picoeukaryotes varied along the BIOSOPE transect vertically and horizontally. In oligotrophic regions, Pelagophyceae, Chrysophyceae, and Prymnesiophyceae dominated. Pelagophyceae were prevalent at the DCM depth and Chrysophyceae at the surface. In mesotrophic regions Pelagophyceae were still important but Chlorophyta contribution increased. Phylogenetic analysis revealed a new clade of Prasinophyceae (clade 16S-IX), which seems to be restricted to hyper-oligotrophic stations. Our data suggest that a single gene marker, even as widely used as 18S rRNA, provides a biased view of eukaryotic communities and that the use of several markers is necessary to obtain a complete image.

  4. Plastid 16S rRNA gene diversity among eukaryotic picophytoplankton sorted by flow cytometry from the South Pacific Ocean.

    Directory of Open Access Journals (Sweden)

    Xiao Li Shi

    Full Text Available The genetic diversity of photosynthetic picoeukaryotes was investigated in the South East Pacific Ocean. Genetic libraries of the plastid 16S rRNA gene were constructed on picoeukaryote populations sorted by flow cytometry, using two different primer sets, OXY107F/OXY1313R commonly used to amplify oxygenic organisms, and PLA491F/OXY1313R, biased towards plastids of marine algae. Surprisingly, the two sets revealed quite different photosynthetic picoeukaryote diversity patterns, which were moreover different from what we previously reported using the 18S rRNA nuclear gene as a marker. The first 16S primer set revealed many sequences related to Pelagophyceae and Dictyochophyceae, the second 16S primer set was heavily biased toward Prymnesiophyceae, while 18S sequences were dominated by Prasinophyceae, Chrysophyceae and Haptophyta. Primer mismatches with major algal lineages is probably one reason behind this discrepancy. However, other reasons, such as DNA accessibility or gene copy numbers, may be also critical. Based on plastid 16S rRNA gene sequences, the structure of photosynthetic picoeukaryotes varied along the BIOSOPE transect vertically and horizontally. In oligotrophic regions, Pelagophyceae, Chrysophyceae, and Prymnesiophyceae dominated. Pelagophyceae were prevalent at the DCM depth and Chrysophyceae at the surface. In mesotrophic regions Pelagophyceae were still important but Chlorophyta contribution increased. Phylogenetic analysis revealed a new clade of Prasinophyceae (clade 16S-IX, which seems to be restricted to hyper-oligotrophic stations. Our data suggest that a single gene marker, even as widely used as 18S rRNA, provides a biased view of eukaryotic communities and that the use of several markers is necessary to obtain a complete image.

  5. Hydrologic controls on nitrogen cycling processes and functional gene abundance in sediments of a groundwater flow-through lake

    Science.gov (United States)

    Stoliker, Deborah L.; Repert, Deborah A.; Smith, Richard L.; Song, Bongkeun; LeBlanc, Denis R.; McCobb, Timothy D.; Conaway, Christopher; Hyun, Sung Pil; Koh, Dong-Chan; Moon, Hee Sun; Kent, Douglas B.

    2016-01-01

    The fate and transport of inorganic nitrogen (N) is a critically important issue for human and aquatic ecosystem health because discharging N-contaminated groundwater can foul drinking water and cause algal blooms. Factors controlling N-processing were examined in sediments at three sites with contrasting hydrologic regimes at a lake on Cape Cod, MA. These factors included water chemistry, seepage rates and direction of groundwater flow, and the abundance and potential rates of activity of N-cycling microbial communities. Genes coding for denitrification, anaerobic ammonium oxidation (anammox), and nitrification were identified at all sites regardless of flow direction or groundwater dissolved oxygen concentrations. Flow direction was, however, a controlling factor in the potential for N-attenuation via denitrification in the sediments. Potential rates of denitrification varied from 6 to 4500 pmol N/g/h from the inflow to the outflow side of the lake, owing to fundamental differences in the supply of labile organic matter. The results of laboratory incubations suggested that when anoxia and limiting labile organic matter prevailed, the potential existed for concomitant anammox and denitrification. Where oxic lake water was downwelling, potential rates of nitrification at shallow depths were substantial (1640 pmol N/g/h). Rates of anammox, denitrification, and nitrification may be linked to rates of organic N-mineralization, serving to increase N-mobility and transport downgradient.

  6. TRACKING GENE FLOW FROM A GENETICALLY MODIFIED CREEPING BENTGRASS -- METHODS, MEASURES AND LESSONS LEARNED

    Science.gov (United States)

    Creeping bentgrass (CBG) expressing an engineered gene for resistance to glyphosate herbicide is one of the first genetically modified (GM) perennial crops to undergo regulatory review for commercial release by the US Department of Agriculture Animal Plant Health and Inspection S...

  7. Population genetic studies revealed local adaptation in a high gene-flow marine fish, the small yellow croaker (Larimichthys polyactis.

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    Le Wang

    Full Text Available The genetic differentiation of many marine fish species is low. Yet local adaptation may be common in marine fish species as the vast and changing marine environment provides more chances for natural selection. Here, we used anonymous as well as known protein gene linked microsatellites and mitochondrial DNA to detect the population structure of the small yellow croaker (Larimichthys polyactis in the Northwest Pacific marginal seas. Among these loci, we detected at least two microsatellites, anonymous H16 and HSP27 to be clearly under diversifying selection in outlier tests. Sequence cloning and analysis revealed that H16 was located in the intron of BAHCC1 gene. Landscape genetic analysis showed that H16 mutations were significantly associated with temperature, which further supported the diversifying selection at this locus. These marker types presented different patterns of population structure: (i mitochondrial DNA phylogeny showed no evidence of genetic divergence and demonstrated only one glacial linage; (ii population differentiation using putatively neutral microsatellites presented a pattern of high gene flow in the L. polyactis. In addition, several genetic barriers were identified; (iii the population differentiation pattern revealed by loci under diversifying selection was rather different from that revealed by putatively neutral loci. The results above suggest local adaptation in the small yellow croaker. In summary, population genetic studies based on different marker types disentangle the effects of demographic history, migration, genetic drift and local adaptation on population structure and also provide valuable new insights for the design of management strategies in L. polyactis.

  8. Assessment of Gene Flow Through Detection of Sexual Compatibility Between Transgenic Rice with bar and Echinochloa crusgalli var. mitis

    Institute of Scientific and Technical Information of China (English)

    SONG Xiao-ling; QIANG Sheng; LIU Lin-li; XU Yan-hong

    2002-01-01

    The possibility of gene flow between two varieties of transgenic rice with bar gene (Y0003 and 99-t) (male) and barnyard grass(Echinochloa crusgalli var. mitis ) (female) was studied by means of reproductive biology. The germination and growth of rice pollen grains on barnyard grass stigmas at 30 rmin, and 1 -4 h after crossing by hand were observed with an optical microscope. The results were compared with the germination and growth of barnyard grass pollen grains at the corresponding time after self-pollination. The results showed that germination and growth of the pollen grains of the two varieties were similar on barnyard grass stigmas, but differed significantly from self-pollination of barnyard grass. Pollen grains germinated and pollen tubes penetrated stigmas normally, and the number of pollen grains being condensing or releasing their inclusions or having released them increased with the time after self-pollination. Pollen grains of transgenic rice on the stigmas of barnyard grass couldn't germinate or grow normally after crossing, neither could they penetrate the stigmas of barnyard grass. Therefore, it could be concluded that the sexual incompatibility between transgenic rice with bar gene and barnyard grass is due to the rice pollen being unable to penetrate the stigma of barnyard grass. Further proof of incompatibility lies in the fact that the emasculated barnyard grass pollinated with the rice pollen grains could not seed.

  9. Evaluation of polymeric gene delivery nanoparticles by nanoparticle tracking analysis and high-throughput flow cytometry.

    Science.gov (United States)

    Shmueli, Ron B; Bhise, Nupura S; Green, Jordan J

    2013-03-01

    Non-viral gene delivery using polymeric nanoparticles has emerged as an attractive approach for gene therapy to treat genetic diseases(1) and as a technology for regenerative medicine(2). Unlike viruses, which have significant safety issues, polymeric nanoparticles can be designed to be non-toxic, non-immunogenic, non-mutagenic, easier to synthesize, chemically versatile, capable of carrying larger nucleic acid cargo and biodegradable and/or environmentally responsive. Cationic polymers self-assemble with negatively charged DNA via electrostatic interaction to form complexes on the order of 100 nm that are commonly termed polymeric nanoparticles. Examples of biomaterials used to form nanoscale polycationic gene delivery nanoparticles include polylysine, polyphosphoesters, poly(amidoamines)s and polyethylenimine (PEI), which is a non-degradable off-the-shelf cationic polymer commonly used for nucleic acid delivery(1,3) . Poly(beta-amino ester)s (PBAEs) are a newer class of cationic polymers(4) that are hydrolytically degradable(5,6) and have been shown to be effective at gene delivery to hard-to-transfect cell types such as human retinal endothelial cells (HRECs)(7), mouse mammary epithelial cells(8), human brain cancer cells(9) and macrovascular (human umbilical vein, HUVECs) endothelial cells(10). A new protocol to characterize polymeric nanoparticles utilizing nanoparticle tracking analysis (NTA) is described. In this approach, both the particle size distribution and the distribution of the number of plasmids per particle are obtained(11). In addition, a high-throughput 96-well plate transfection assay for rapid screening of the transfection efficacy of polymeric nanoparticles is presented. In this protocol, poly(beta-amino ester)s (PBAEs) are used as model polymers and human retinal endothelial cells (HRECs) are used as model human cells. This protocol can be easily adapted to evaluate any polymeric nanoparticle and any cell type of interest in a multi

  10. Development of an interventional pain management specific instrument for methodologic quality assessment of nonrandomized studies of interventional techniques.

    Science.gov (United States)

    Manchikanti, Laxmaiah; Hirsch, Joshua A; Heavner, James E; Cohen, Steven P; Benyamin, Ramsin M; Sehgal, Nalini; Falco, Frank J E; Vallejo, Ricardo; Onyewu, Obi; Zhu, Jie; Kaye, Alan D; Boswell, Mark V; Helm, Standiford; Candido, Kenneth D; Diwan, Sudhir; Simopoulos, Thomas T; Singh, Vijay; Pampati, Vidyasagar; Racz, Gabor B; Raj, P Prithvi

    2014-01-01

    The major component of a systematic review is assessment of the methodologic quality and bias of randomized and nonrandomized trials. While there are multiple instruments available to assess the methodologic quality and bias for randomized controlled trials (RCTs), there is a lack of extensively utilized instruments for observational studies, specifically for interventional pain management (IPM) techniques. Even Cochrane review criteria for randomized trials is considered not to be a "gold standard," but merely an indication of the current state of the art review methodology. Recently a specific instrument to assess the methodologic quality of randomized trials has been developed for interventional techniques. Our objective was to develop an IPM specific instrument to assess the methodological quality of nonrandomized trials or observational studies of interventional techniques. The item generation for the instrument was based on a definition of quality, to the extent to which the design and conduct of the trial were congruent with the objectives of the study. Applicability was defined as the extent to which procedures produced by the study could be applied using contemporary IPM techniques. Multiple items based on Cochrane review criteria and Interventional Pain Management Techniques - Quality Appraisal of Reliability and Risk of Bias Assessment for Nonrandomized Studies (IPM-QRBNR) were utilized. A total of 16 items were developed which formed the IPM-QRBNR tool. The assessment was performed in multiple stages. The final assessment was 4 nonrandomized studies. The inter-rater agreement was moderate to good for IPM-QRBNR criteria. Limited validity or accuracy assessment of the instrument and the large number of items to be scored were limitations. We have developed a new comprehensive instrument to assess the methodological quality of nonrandomized studies of interventional techniques. This instrument provides extensive information specific to interventional

  11. Influence of long-distance seed dispersal on the genetic diversity of seed rain in fragmented Pinus densiflora populations relative to pollen-mediated gene flow.

    Science.gov (United States)

    Ozawa, Hajime; Watanabe, Atsushi; Uchiyama, Kentaro; Saito, Yoko; Ide, Yuji

    2013-01-01

    Long-distance dispersal (LDD) of seeds has a critical impact on species survival in patchy landscapes. However, relative to pollen dispersal, empirical data on how seed LDD affects genetic diversity in fragmented populations have been poorly reported. Thus, we attempted to indirectly evaluate the influence of seed LDD by estimating maternal and paternal inbreeding in the seed rain of fragmented 8 Pinus densiflora populations. In total, the sample size was 458 seeds and 306 adult trees. Inbreeding was estimated by common parentage analysis to evaluate gene flow within populations and by sibship reconstruction analysis to estimate gene flow within and among populations. In the parentage analysis, the observed probability that sampled seeds had the same parents within populations was significantly larger than the expected probability in many populations. This result suggested that gene dispersal was limited to within populations. In the sibship reconstruction, many donors both within and among populations appeared to contribute to sampled seeds. Significant differences in sibling ratios were not detected between paternity and maternity. These results suggested that seed-mediated gene flow and pollen-mediated gene flow from outside population contributed some extent to high genetic diversity of the seed rain (H E > 0.854). We emphasize that pine seeds may have excellent potential for gene exchange within and among populations.

  12. Regional gene flow and population structure of the wind-dispersed plant species Hypochaeris radicata (Asteraceae) in an agricultural landscape.

    Science.gov (United States)

    Mix, C; Arens, P F P; Rengelink, R; Smulders, M J M; Van Groenendael, J M; Ouborg, N J

    2006-06-01

    Using microsatellites, we investigated population structure and gene flow of the short-lived, wind-dispersed plant species Hypochaeris radicata in a fragmented agricultural landscape where more than 99% of the nutrient-poor grasslands have disappeared over the last century. We sampled populations in the few remaining high density populations in conservation areas, as well as individuals that occurred, with lower densities, in linear landscape elements, at two spatial scales. In a re-inventory of the landscape, after 3 years, both extinctions and colonizations of populations were observed. Contrary to expectations, no differences in genetic diversity between high and low density populations were observed. Both types of populations had relatively high levels of diversity. Overall genetic differentiation (theta) was 0.04 and significantly different from zero (P aerodynamic models on seed dispersal of H. radicata. We discuss the consequences of these results for an evaluation of the probability of persistence of this species in the fragmented landscape.

  13. Effect of non-random dispersal strategies on spatial coexistence mechanisms.

    Science.gov (United States)

    Amarasekare, Priyanga

    2010-01-01

    1. Random dispersal leads to spatial coexistence via two mechanisms (emigration-mediated and source-sink), both of which involve the movement of organisms from areas of higher to lower fitness. What is not known is whether such coexistence would occur if organisms dispersed non-randomly, using cues such as density and habitat quality to gauge fitness differences between habitats. Here, I conduct a comparative analysis of random and non-random dispersal strategies in a foodweb with a basal resource, top predator, and two intermediate consumers that exhibit a trade-off between competitive ability and predator susceptibility. 2. I find a striking contrast between density- and habitat-dependent dispersal in their effects on spatial coexistence. Dispersal in response to competitor and predator density facilitates coexistence while dispersal in response to habitat quality (resource productivity and predator pressure) inhibits it. Moreover, density-dependent dispersal changes species' distribution patterns from interspecific segregation to interspecific aggregation, while habitat-dependent dispersal preserves the interspecific segregation observed in the absence of dispersal. Under density-dependent dispersal, widespread spatial coexistence results in an overall decline in the abundance of the inferior competitor that is less susceptible to predation and an overall increase in the abundance of the superior competitor that is more susceptible to predation. Under habitat-dependent dispersal, restricted spatial coexistence results in species' abundances being essentially unchanged from those observed in the absence of dispersal. 3. A key outcome is that when the superior competitor moves in the direction of increasing fitness but the inferior competitor does not, spatial coexistence is possible in both resource-poor and resource-rich habitats. However, when the inferior competitor moves in the direction of increasing fitness but the superior competitor does not, spatial

  14. Intravenous Immunoglobulin Therapy in Pediatric Narcolepsy: A Nonrandomized, Open-Label, Controlled, Longitudinal Observational Study

    Science.gov (United States)

    Lecendreux, Michel; Berthier, Johanna; Corny, Jennifer; Bourdon, Olivier; Dossier, Claire; Delclaux, Christophe

    2017-01-01

    Study Objectives: Previous case reports of intravenous immunoglobulins (IVIg) in pediatric narcolepsy have shown contradictory results. Methods: This was a nonrandomized, open-label, controlled, longitudinal observational study of IVIg use in pediatric narcolepsy with retrospective data collection from medical files obtained from a single pediatric national reference center for the treatment of narcolepsy in France. Of 56 consecutively referred patients with narcolepsy, 24 received IVIg (3 infusions administered at 1-mo intervals) in addition to standard care (psychostimulants and/or anticataplectic agents), and 32 continued on standard care alone (controls). Results: For two patients in each group, medical files were unavailable. Of the 22 IVIg patients, all had cerebrospinal fluid (CSF) hypocretin ≤ 110 pg/mL and were HLA-DQB1*06:02 positive. Of the 30 control patients, 29 were HLA-DQB1*06:02 positive and of those with available CSF measurements, all 12 had hypocretin ≤ 110 pg/mL. Compared with control patients, IVIg patients had shorter disease duration, shorter latency to sleep onset, and more had received H1N1 vaccination. Mean (standard deviation) follow-up length was 2.4 (1.1) y in the IVIg group and 3.9 (1.7) y in controls. In multivariate-adjusted linear mixed-effects analyses of change from baseline in Ullanlinna Narcolepsy Scale (UNS) scores, high baseline UNS, but not IVIg treatment, was associated with a reduction in narcolepsy symptoms. On time-to-event analysis, among patients with high baseline UNS scores, control patients achieved a UNS score narcolepsy symptoms were not significantly reduced by IVIg. However, in patients with high baseline symptoms, a subset of IVIg-treated patients achieved remission more rapidly than control patients. Commentary: A commentary on this article appears in this issue on page 363. Citation: Lecendreux M, Berthier J, Corny J, Bourdon O, Dossier C, Delclaux C. Intravenous immunoglobulin therapy in pediatric

  15. Inference of Gene Flow in the Process of Speciation: An Efficient Maximum-Likelihood Method for the Isolation-with-Initial-Migration Model

    Science.gov (United States)

    Costa, Rui J.; Wilkinson-Herbots, Hilde

    2017-01-01

    The isolation-with-migration (IM) model is commonly used to make inferences about gene flow during speciation, using polymorphism data. However, it has been reported that the parameter estimates obtained by fitting the IM model are very sensitive to the model’s assumptions—including the assumption of constant gene flow until the present. This article is concerned with the isolation-with-initial-migration (IIM) model, which drops precisely this assumption. In the IIM model, one ancestral population divides into two descendant subpopulations, between which there is an initial period of gene flow and a subsequent period of isolation. We derive a very fast method of fitting an extended version of the IIM model, which also allows for asymmetric gene flow and unequal population sizes. This is a maximum-likelihood method, applicable to data on the number of segregating sites between pairs of DNA sequences from a large number of independent loci. In addition to obtaining parameter estimates, our method can also be used, by means of likelihood-ratio tests, to distinguish between alternative models representing the following divergence scenarios: (a) divergence with potentially asymmetric gene flow until the present, (b) divergence with potentially asymmetric gene flow until some point in the past and in isolation since then, and (c) divergence in complete isolation. We illustrate the procedure on pairs of Drosophila sequences from ∼30,000 loci. The computing time needed to fit the most complex version of the model to this data set is only a couple of minutes. The R code to fit the IIM model can be found in the supplementary files of this article. PMID:28193727

  16. Altruism can proliferate through population viscosity despite high random gene flow.

    Directory of Open Access Journals (Sweden)

    Roberto H Schonmann

    Full Text Available The ways in which natural selection can allow the proliferation of cooperative behavior have long been seen as a central problem in evolutionary biology. Most of the literature has focused on interactions between pairs of individuals and on linear public goods games. This emphasis has led to the conclusion that even modest levels of migration would pose a serious problem to the spread of altruism through population viscosity in group structured populations. Here we challenge this conclusion, by analyzing evolution in a framework which allows for complex group interactions and random migration among groups. We conclude that contingent forms of strong altruism that benefits equally all group members, regardless of kinship and without greenbeard effects, can spread when rare under realistic group sizes and levels of migration, due to the assortment of genes resulting only from population viscosity. Our analysis combines group-centric and gene-centric perspectives, allows for arbitrary strength of selection, and leads to extensions of Hamilton's rule for the spread of altruistic alleles, applicable under broad conditions.

  17. Genetic diversity in Oryza glumaepatula wild rice populations in Costa Rica and possible gene flow from O. sativa

    Science.gov (United States)

    Meneses Martínez, Allan; Calvo, Amanda; Muñoz, Melania

    2016-01-01

    Wild crop relatives are an important source of genetic diversity for crop improvement. Diversity estimates are generally lacking for many wild crop relatives. The objective of the present study was to analyze how genetic diversity is distributed within and among populations of the wild rice species Oryza glumaepatula in Costa Rica. We also evaluated the likelihood of gene flow between wild and commercial rice species because the latter is commonly sympatric with wild rice populations. Introgression may change wild species by incorporating alleles from domesticated species, increasing the risk of losing original variation. Specimens from all known O. glumaepatula populations in Costa Rica were analyzed with 444 AFLP markers to characterize genetic diversity and structure. We also compared genetic diversity estimates between O. glumaepatula specimens and O. sativa commercial rice. Our results showed that O. glumaepatula populations in Costa Rica have moderately high levels of genetic diversity, comparable to those found in South American populations. Despite the restricted distribution of this species in Costa Rica, populations are fairly large, reducing the effects of drift on genetic diversity. We found a dismissible but significant structure (θ = 0.02 ± 0.001) among populations. A Bayesian structure analysis suggested that some individuals share a significant proportion of their genomes with O. sativa. These results suggest that gene flow from cultivated O. sativa populations may have occurred in the recent past. These results expose an important biohazard: recurrent hybridization may reduce the genetic diversity of this wild rice species. Introgression may transfer commercial traits into O. glumaepatula, which in turn could alter genetic diversity and increase the likelihood of local extinction. These results have important implications for in situ conservation strategies of the only wild populations of O. glumaepatula in Costa Rica. PMID:27077002

  18. Genetic diversity in Oryza glumaepatula wild rice populations in Costa Rica and possible gene flow from O. sativa

    Directory of Open Access Journals (Sweden)

    Eric J. Fuchs

    2016-04-01

    Full Text Available Wild crop relatives are an important source of genetic diversity for crop improvement. Diversity estimates are generally lacking for many wild crop relatives. The objective of the present study was to analyze how genetic diversity is distributed within and among populations of the wild rice species Oryza glumaepatula in Costa Rica. We also evaluated the likelihood of gene flow between wild and commercial rice species because the latter is commonly sympatric with wild rice populations. Introgression may change wild species by incorporating alleles from domesticated species, increasing the risk of losing original variation. Specimens from all known O. glumaepatula populations in Costa Rica were analyzed with 444 AFLP markers to characterize genetic diversity and structure. We also compared genetic diversity estimates between O. glumaepatula specimens and O. sativa commercial rice. Our results showed that O. glumaepatula populations in Costa Rica have moderately high levels of genetic diversity, comparable to those found in South American populations. Despite the restricted distribution of this species in Costa Rica, populations are fairly large, reducing the effects of drift on genetic diversity. We found a dismissible but significant structure (θ = 0.02 ± 0.001 among populations. A Bayesian structure analysis suggested that some individuals share a significant proportion of their genomes with O. sativa. These results suggest that gene flow from cultivated O. sativa populations may have occurred in the recent past. These results expose an important biohazard: recurrent hybridization may reduce the genetic diversity of this wild rice species. Introgression may transfer commercial traits into O. glumaepatula, which in turn could alter genetic diversity and increase the likelihood of local extinction. These results have important implications for in situ conservation strategies of the only wild populations of O. glumaepatula in Costa Rica.

  19. Allele distributions at hybrid incompatibility loci facilitate the potential for gene flow between cultivated and weedy rice in the US.

    Science.gov (United States)

    Craig, Stephanie M; Reagon, Michael; Resnick, Lauren E; Caicedo, Ana L

    2014-01-01

    The accumulation of independent mutations over time in two populations often leads to reproductive isolation. Reproductive isolation between diverging populations may be reinforced by barriers that occur either pre- or postzygotically. Hybrid sterility is the most common form of postzygotic isolation in plants. Four postzygotic sterility loci, comprising three hybrid sterility systems (Sa, s5, DPL), have been recently identified in Oryza sativa. These loci explain, in part, the limited hybridization that occurs between the domesticated cultivated rice varieties, O. sativa spp. japonica and O. sativa spp. indica. In the United States, cultivated fields of japonica rice are often invaded by conspecific weeds that have been shown to be of indica origin. Crop-weed hybrids have been identified in crop fields, but at low frequencies. Here we examined the possible role of these hybrid incompatibility loci in the interaction between cultivated and weedy rice. We identified a novel allele at Sa that seemingly prevents loss of fertility in hybrids. Additionally, we found wide-compatibility type alleles at strikingly high frequencies at the Sa and s5 loci in weed groups, and a general lack of incompatible alleles between crops and weeds at the DPL loci. Our results suggest that weedy individuals, particularly those of the SH and BRH groups, should be able to freely hybridize with the local japonica crop, and that prezygotic factors, such as differences in flowering time, have been more important in limiting weed-crop gene flow in the past. As the selective landscape for weedy rice changes due to increased use of herbicide resistant strains of cultivated rice, the genetic barriers that hinder indica-japonica hybridization cannot be counted on to limit the flow of favorable crop genes into weeds.

  20. Allele distributions at hybrid incompatibility loci facilitate the potential for gene flow between cultivated and weedy rice in the US.

    Directory of Open Access Journals (Sweden)

    Stephanie M Craig

    Full Text Available The accumulation of independent mutations over time in two populations often leads to reproductive isolation. Reproductive isolation between diverging populations may be reinforced by barriers that occur either pre- or postzygotically. Hybrid sterility is the most common form of postzygotic isolation in plants. Four postzygotic sterility loci, comprising three hybrid sterility systems (Sa, s5, DPL, have been recently identified in Oryza sativa. These loci explain, in part, the limited hybridization that occurs between the domesticated cultivated rice varieties, O. sativa spp. japonica and O. sativa spp. indica. In the United States, cultivated fields of japonica rice are often invaded by conspecific weeds that have been shown to be of indica origin. Crop-weed hybrids have been identified in crop fields, but at low frequencies. Here we examined the possible role of these hybrid incompatibility loci in the interaction between cultivated and weedy rice. We identified a novel allele at Sa that seemingly prevents loss of fertility in hybrids. Additionally, we found wide-compatibility type alleles at strikingly high frequencies at the Sa and s5 loci in weed groups, and a general lack of incompatible alleles between crops and weeds at the DPL loci. Our results suggest that weedy individuals, particularly those of the SH and BRH groups, should be able to freely hybridize with the local japonica crop, and that prezygotic factors, such as differences in flowering time, have been more important in limiting weed-crop gene flow in the past. As the selective landscape for weedy rice changes due to increased use of herbicide resistant strains of cultivated rice, the genetic barriers that hinder indica-japonica hybridization cannot be counted on to limit the flow of favorable crop genes into weeds.

  1. High gene flow in reef fishes and its implications for ad-hoc no-take marine reserves.

    Science.gov (United States)

    Matias, Ambrocio Melvin A; Anticamara, Jonathan A; Quilang, Jonas P

    2013-10-01

    Integration of genetic connectivity information in effective marine reserve (MR) design is important in sustaining marine biodiversity. Here, genetic connectivity based on mitochondrial DNA (mtDNA) of three reef fish species, namely Epinephelus merra (n = 67; 32 from Bolinao, 14 from Alaminos, and 21 from Masinloc), Parupeneus multifasciatus (n = 23; 12 from Bolinao and 11 from Masinloc), and Odonus niger (n = 35; 21 from Mabini and 14 from Tingloy), sampled across western Luzon, Philippines, was inferred by assessing their genetic diversity, population genetic structure, and historical demography. The results show high haplotype and nucleotide diversity in the three species. Tests for population structure indicate high gene flow and no spatial genetic structuring for the three species. Mismatch analyses suggest unimodal distribution for E. merra and P. multifasciatus, but bimodal distribution for O. niger. Even with differences in mismatch distributions, all the three species exhibit low raggedness index indicating demographic population expansion. The bimodal distribution of O. niger could be attributed to the mixing of two isolated populations. High gene flow between sampling locations implies genetic exchanges and connectivity between many small MRs and fishing grounds in western Luzon, Philippines, at a scale similar to our study. This research is among the first few to elucidate the high genetic connectivity of reef fish communities across the Philippines (here western Luzon), but it also calls for more support (i.e. government and academia) for genetic research that aims to (1) understand the maintenance of megadiversity of the country and (2) search for effective biodiversity conservation options for the coral reefs.

  2. Low crop plant population densities promote pollen-mediated gene flow in spring wheat (Triticum aestivum L.).

    Science.gov (United States)

    Willenborg, Christian J; Brûlé-Babel, Anita L; Van Acker, Rene C

    2009-12-01

    Transgenic wheat is currently being field tested with the intent of eventual commercialization. The development of wheat genotypes with novel traits has raised concerns regarding the presence of volunteer wheat populations and the role they may play in facilitating transgene movement. Here, we report the results of a field experiment that investigated the potential of spring wheat plant population density and crop height to minimize gene flow from a herbicide-resistant (HR) volunteer population to a non-HR crop. Pollen-mediated gene flow (PMGF) between the HR volunteer wheat population and four conventional spring wheat genotypes varying in height was assessed over a range of plant population densities. Natural hybridization events between the two cultivars were detected by phenotypically scoring plants in F(1) populations followed by verification with Mendelian segregation ratios in the F(1:2) families. PMGF was strongly associated with crop yield components, but showed no association with flowering synchrony. Maximum observed PMGF was always less than 0.6%, regardless of crop height and density. The frequency of PMGF in spring wheat decreased exponentially with increasing plant population density, but showed no dependence on either crop genotype or height. However, increasing plant densities beyond the recommended planting rate of 300 cropped wheat plants m(-2) provided no obvious benefit to reducing PMGF. Nevertheless, our results demonstrate a critical plant density of 175-200 cropped wheat plants m(-2) below which PMGF frequencies rise exponentially with decreasing plant density. These results will be useful in the development of mechanistic models and best management practices that collectively facilitate the coexistence of transgenic and nontransgenic wheat crops.

  3. Genetic differentiation of eastern wolves in Algonquin Park despite bridging gene flow between coyotes and grey wolves.

    Science.gov (United States)

    Rutledge, L Y; Garroway, C J; Loveless, K M; Patterson, B R

    2010-12-01

    Distinguishing genetically differentiated populations within hybrid zones and determining the mechanisms by which introgression occurs are crucial for setting effective conservation policy. Extensive hybridization among grey wolves (Canis lupus), eastern wolves (C. lycaon) and coyotes (C. latrans) in eastern North America has blurred species distinctions, creating a Canis hybrid swarm. Using complementary genetic markers, we tested the hypotheses that eastern wolves have acted as a conduit of sex-biased gene flow between grey wolves and coyotes, and that eastern wolves in Algonquin Provincial Park (APP) have differentiated following a history of introgression. Mitochondrial, Y chromosome and autosomal microsatellite genetic data provided genotypes for 217 canids from three geographic regions in Ontario, Canada: northeastern Ontario, APP and southern Ontario. Coyote mitochondrial DNA (mtDNA) haplotypes were common across regions but coyote-specific Y chromosome haplotypes were absent; grey wolf mtDNA was absent from southern regions, whereas grey wolf Y chromosome haplotypes were present in all three regions. Genetic structuring analyses revealed three distinct clusters within a genetic cline, suggesting some gene flow among species. In APP, however, 78.4% of all breeders and 11 of 15 known breeding pairs had assignment probability of Q0.8 to the Algonquin cluster, and the proportion of eastern wolf Y chromosome haplotypes in APP breeding males was higher than expected from random mating within the park (Pwolves remain genetically distinct despite providing a sex-biased genetic bridge between coyotes and grey wolves. We speculate that ongoing hybridization within the park is limited by pre-mating reproductive barriers.

  4. Efficient removal of antibiotics in surface-flow constructed wetlands, with no observed impact on antibiotic resistance genes.

    Science.gov (United States)

    Berglund, Björn; Khan, Ghazanfar Ali; Weisner, Stefan E B; Ehde, Per Magnus; Fick, Jerker; Lindgren, Per-Eric

    2014-04-01

    Recently, there have been growing concerns about pharmaceuticals including antibiotics as environmental contaminants. Antibiotics of concentrations commonly encountered in wastewater have been suggested to affect bacterial population dynamics and to promote dissemination of antibiotic resistance. Conventional wastewater treatment processes do not always adequately remove pharmaceuticals causing environmental dissemination of low levels of these compounds. Using constructed wetlands as an additional treatment step after sewage treatment plants have been proposed as a cheap alternative to increase reduction of wastewater contaminants, however this means that the natural microbial community of the wetlands becomes exposed to elevated levels of antibiotics. In this study, experimental surface-flow wetlands in Sweden were continuously exposed to antibiotics of concentrations commonly encountered in wastewater. The aim was to assess the antibiotic removal efficiency of constructed wetlands and to evaluate the impact of low levels of antibiotics on bacterial diversity, resistance development and expression in the wetland bacterial community. Antibiotic concentrations were measured using liquid chromatography-mass spectrometry and the effect on the bacterial diversity was assessed with 16S rRNA-based denaturing gradient gel electrophoresis. Real-time PCR was used to detect and quantify antibiotic resistance genes and integrons in the wetlands, during and after the exposure period. The results indicated that the antibiotic removal efficiency of constructed wetlands was comparable to conventional wastewater treatment schemes. Furthermore, short-term treatment of the constructed wetlands with environmentally relevant concentrations (i.e. 100-2000 ng×l(-1)) of antibiotics did not significantly affect resistance gene concentrations, suggesting that surface-flow constructed wetlands are well-suited for wastewater treatment purposes.

  5. Contrasting demographic history and gene flow patterns of two mangrove species on either side of the Central American Isthmus.

    Science.gov (United States)

    Cerón-Souza, Ivania; Gonzalez, Elena G; Schwarzbach, Andrea E; Salas-Leiva, Dayana E; Rivera-Ocasio, Elsie; Toro-Perea, Nelson; Bermingham, Eldredge; McMillan, W Owen

    2015-08-01

    Comparative phylogeography offers a unique opportunity to understand the interplay between past environmental events and life-history traits on diversification of unrelated but co-distributed species. Here, we examined the effects of the quaternary climate fluctuations and palaeomarine currents and present-day marine currents on the extant patterns of genetic diversity in the two most conspicuous mangrove species of the Neotropics. The black (Avicennia germinans, Avicenniaceae) and the red (Rhizophora mangle, Rhizophoraceae) mangroves have similar geographic ranges but are very distantly related and show striking differences on their life-history traits. We sampled 18 Atlantic and 26 Pacific locations for A. germinans (N = 292) and R. mangle (N = 422). We performed coalescence simulations using microsatellite diversity to test for evidence of population change associated with quaternary climate fluctuations. In addition, we examined whether patterns of genetic variation were consistent with the directions of major marine (historical and present day) currents in the region. Our demographic analysis was grounded within a phylogeographic framework provided by the sequence analysis of two chloroplasts and one flanking microsatellite region in a subsample of individuals. The two mangrove species shared similar biogeographic histories including: (1) strong genetic breaks between Atlantic and Pacific ocean basins associated with the final closure of the Central American Isthmus (CAI), (2) evidence for simultaneous population declines between the mid-Pleistocene and early Holocene, (3) asymmetric historical migration with higher gene flow from the Atlantic to the Pacific oceans following the direction of the palaeomarine current, and (4) contemporary gene flow between West Africa and South America following the major Atlantic Ocean currents. Despite the remarkable differences in life-history traits of mangrove species, which should have had a strong influence on seed

  6. Fine-scale population differentiation and gene flow in a terrestrial salamander (Plethodon cinereus) living in continuous habitat.

    Science.gov (United States)

    Cabe, P R; Page, R B; Hanlon, T J; Aldrich, M E; Connors, L; Marsh, D M

    2007-01-01

    Several recent studies have shown that amphibian populations may exhibit high genetic subdivision in areas with recent fragmentation and urban development. Less is known about the potential for genetic differentiation in continuous habitats. We studied genetic differentiation of red-backed salamanders (Plethodon cinereus) across a 2-km transect through continuous forest in Virginia, USA. Mark-recapture studies suggest very little dispersal for this species, whereas homing experiments and post-Pleistocene range expansion both suggest greater dispersal abilities. We used six microsatellite loci to examine genetic population structure and differentiation between eight subpopulations of red-backed salamanders at distances from 200 m to 2 km. We also used several methods to extrapolate dispersal frequencies and test for sex-biased dispersal. We found small, but detectable differentiation among populations, even at distances as small as 200 m. Differentiation was closely correlated with distance and both Mantel tests and assignment tests were consistent with an isolation-by-distance model for the population. Extrapolations of intergenerational variance in spatial position (sigma(2)<15 m(2)) and pair-wise dispersal frequencies (4 Nm < 25 for plots separated by 300 m) both suggest limited gene flow. Additionally, tests for sex-biased dispersal imply that dispersal frequency is similarly low for both sexes. We suggest that these low levels of gene flow and the infrequent dispersal observed in mark-recapture studies may be reconciled with homing ability and range expansion if dispersing animals rarely succeed in breeding in saturated habitats, if dispersal is flexible depending on the availability of habitat, or if dispersal frequency varies across the geographic range of red-backed salamanders.

  7. A multiscale analysis of gene flow for the New England cottontail, an imperiled habitat specialist in a fragmented landscape.

    Science.gov (United States)

    Fenderson, Lindsey E; Kovach, Adrienne I; Litvaitis, John A; O'Brien, Kathleen M; Boland, Kelly M; Jakubas, Walter J

    2014-05-01

    Landscape features of anthropogenic or natural origin can influence organisms' dispersal patterns and the connectivity of populations. Understanding these relationships is of broad interest in ecology and evolutionary biology and provides key insights for habitat conservation planning at the landscape scale. This knowledge is germane to restoration efforts for the New England cottontail (Sylvilagus transitionalis), an early successional habitat specialist of conservation concern. We evaluated local population structure and measures of genetic diversity of a geographically isolated population of cottontails in the northeastern United States. We also conducted a multiscale landscape genetic analysis, in which we assessed genetic discontinuities relative to the landscape and developed several resistance models to test hypotheses about landscape features that promote or inhibit cottontail dispersal within and across the local populations. Bayesian clustering identified four genetically distinct populations, with very little migration among them, and additional substructure within one of those populations. These populations had private alleles, low genetic diversity, critically low effective population sizes (3.2-36.7), and evidence of recent genetic bottlenecks. Major highways and a river were found to limit cottontail dispersal and to separate populations. The habitat along roadsides, railroad beds, and utility corridors, on the other hand, was found to facilitate cottontail movement among patches. The relative importance of dispersal barriers and facilitators on gene flow varied among populations in relation to landscape composition, demonstrating the complexity and context dependency of factors influencing gene flow and highlighting the importance of replication and scale in landscape genetic studies. Our findings provide information for the design of restoration landscapes for the New England cottontail and also highlight the dual influence of roads, as both

  8. Occurrence of alfalfa (Medicago sativa L.) populations along roadsides in southern Manitoba, Canada and their potential role in intraspecific gene flow.

    Science.gov (United States)

    Bagavathiannan, Muthukumar V; Gulden, Robert H; Van Acker, Rene C

    2011-04-01

    Alfalfa is a highly outcrossing perennial species that can be noticed in roadsides as feral populations. There remains little information available on the extent of feral alfalfa populations in western Canadian prairies and their role in gene flow. The main objectives of this study were (a) to document the occurrence of feral alfalfa populations, and (b) to estimate the levels of outcrossing facilitated by feral populations. A roadside survey confirmed widespread occurrence of feral alfalfa populations, particularly in alfalfa growing regions. The feral populations were dynamic and their frequency ranged from 0.2 to 1.7 populations km(-1). In many cases, the nearest feral alfalfa population from alfalfa production field was located within a distance sufficient for outcrossing in alfalfa. The gene flow study confirmed that genes can move back and forth between feral and cultivated alfalfa populations. In this study, the estimated outcrossing levels were 62% (seed fields to feral), 78% (feral to seed fields), 82% (hay fields to feral) and 85% (feral to feral). Overall, the results show that feral alfalfa plants are prevalent in alfalfa producing regions in western Canada and they can serve as bridges for gene flow at landscape level. Management of feral populations should be considered, if gene flow is a concern. Emphasis on preventing seed spill/escapes and intentional roadside planting of alfalfa cultivars will be particularly helpful. Further, realistic and pragmatic threshold levels should be established for markets sensitive to the presence of GE traits.

  9. Gene flow analysis demonstrates that Phytophthora fragariae var. rubi constitutes a distinct species, Phytophthora rubi comb. nov.

    Science.gov (United States)

    Man in 't Veld, Willem A

    2007-01-01

    Isozyme analysis and cytochrome oxidase sequences were used to examine whether differentiation of P. fragariae var. fragariae and P. fragariae var. rubi at the variety level is justified. In isozyme studies six strains of both P. fragariae varieties were analyzed with malate dehydrogenase (MDH), glucose phosphate isomerase (GPI), aconitase (ACO), isocitrate dehydrogenase (IDH) and phosphogluconate dehydrogenase (PGD), comprising altogether seven putative loci. Five unique alleles (Mdh-1(A), Mdh-2(B), Gpi(A), Aco(B) and Idh-1(B)) were found in strains of P. fragariae var. fragariae, whereas five unique alleles (Mdh-1(B), Mdh-2(A), Gpi(B), Aco(A) and Idh-1(A)) were present in strains of P. fragariae var. rubi. It was inferred from these data that there is no gene flow between the two P. fragariae varieties. Cytochrome oxidase I (Cox I) sequences showed consistent differences at 15 positions between strains of Fragaria and Rubus respectively. Based on isozyme data, cytochrome oxidase I sequences, and previously published differences in restyriction enzyme patterns of mitochondrial DNA, sequences of nuclear and mitochondrial genes, AFLP patterns and pathogenicity, it was concluded that both specific pathogenic varieties of P. fragariae are reproductively isolated and constitute a distinct species. Consequently strains isolated from Rubus idaeus are assigned to Phytophthora rubi comb. nov.

  10. Ancestral Gene Flow and Parallel Organellar Genome Capture Result in Extreme Phylogenomic Discord in a Lineage of Angiosperms.

    Science.gov (United States)

    Folk, Ryan A; Mandel, Jennifer R; Freudenstein, John V

    2016-09-16

    While hybridization has recently received a resurgence of attention from systematists and evolutionary biologists, there remains a dearth of case studies on ancient, diversified hybrid lineages-clades of organisms that originated through reticulation. Studies on these groups are valuable in that they would speak to the long-term phylogenetic success of lineages following gene flow between species. We present a phylogenomic view of Heuchera, long known for frequent hybridization, incorporating all three independent genomes: targeted nuclear (~400,000 bp), plastid (~160,000 bp), and mitochondrial (~470,000 bp) data. We analyze these data using multiple concatenation and coalescence strategies. The nuclear phylogeny is consistent with previous work and with morphology, confidently suggesting a monophyletic Heuchera By contrast, analyses of both organellar genomes recover a grossly polyphyletic Heuchera,consisting of three primary clades with relationships extensively rearranged within these as well. A minority of nuclear loci also exhibit phylogenetic discord; yet these topologies remarkably never resemble the pattern of organellar loci and largely present low levels of discord inter alia Two independent estimates of the coalescent branch length of the ancestor of Heuchera using nuclear data suggest rare or nonexistent incomplete lineage sorting with related clades, inconsistent with the observed gross polyphyly of organellar genomes (confirmed by simulation of gene trees under the coalescent). These observations, in combination with previous work, strongly suggest hybridization as the cause of this phylogenetic discord. [Ancient hybridization; chloroplast capture; incongruence; phylogenomics; reticulation.].

  11. Cytogenetic aberrations in osteosarcomas. Nonrandom deletions, rings, and double-minute chromosomes.

    Science.gov (United States)

    Fletcher, J A; Gebhardt, M C; Kozakewich, H P

    1994-10-01

    Relatively few karyotypes have been reported from short-term cultures and/or direct harvests of osteosarcomas. We describe clonal aberrations in 17 high-grade osteosarcoma specimens and in one low-grade osteosarcoma. The high-grade osteosarcomas were karyotyped after direct harvest (four cases) or after short-term culture periods of osteosarcoma and two lung metastases, were from the same patient and shared a number of clonal aberrations. No consistent chromosome translocations were identified in the overall group of high-grade osteosarcomas, but potential nonrandom deletions involved 6q21-->qter, 9p21-->pter, chromosome 10, chromosome 13, 17p12-pter, and chromosome 20. Ring chromosomes were detected in three cases, and double-minute (dmin) chromosomes were detected in six. All high-grade osteosarcomas had numerous nonclonal chromosome aberrations superimposed on complex clonal events. The single low-grade osteosarcoma was characterized by a balanced, nonconstitutional, t(5;10) (p13;p14-15), together with an addition to the short arm of chromosome X. This is the first translocation reported in low-grade osteosarcoma, and the simplicity of the karyotype contrasts strikingly with those in the high-grade osteosarcomas.

  12. Assessing the impacts of nonrandom seed dispersal by multiple frugivore partners on plant recruitment.

    Science.gov (United States)

    Razafindratsima, Onja H; Dunham, Amy E

    2015-01-01

    Directed dispersal is defined as enhanced dispersal of seeds into suitable microhabitats, resulting in higher recruitment than if seeds were dispersed randomly. While this constitutes one of the main explanations for the adaptive value of frugivore-mediated seed dispersal, the generality of this advantage has received little study, particularly when multiple dispersers are involved. We used probability recruitment models of a long-lived rainforest tree in Madagascar to compare recruitment success under dispersal by multiple frugivores, no dispersal, and random dispersal. Models were parameterized using a three-year recruitment experiment and observational data of dispersal events by three frugivorous lemur species that commonly disperse its seeds. Frugivore-mediated seed dispersal was nonrandom with respect to canopy cover and increased modeled per-seed sapling recruitment fourfold compared to no dispersal. Seeds dispersed by one frugivore, Eulemur rubriventer, had higher modeled recruitment probability than seeds dispersed randomly. However, as a group, our models suggest that seeds dispersed by lemurs would have lower recruitment than if dispersal were random. Results demonstrate the importance of evaluating the contribution of multiple frugivores to plant recruitment for understanding plant population dynamics and the ecological and evolutionary significance of seed dispersal.

  13. Evidence for non-random sampling in randomised, controlled trials by Yuhji Saitoh.

    Science.gov (United States)

    Carlisle, J B; Loadsman, J A

    2017-01-01

    A large number of randomised trials authored by Yoshitaka Fujii have been retracted, in part as a consequence of a previous analysis finding a very low probability of random sampling. Dr Yuhji Saitoh co-authored 34 of those trials and he was corresponding author for eight of them. We found a number of additional randomised, controlled trials that included baseline data, with Saitoh as corresponding author, that Fujii did not co-author. We used Monte Carlo simulations to analyse the baseline data from 32 relevant trials in total as well as an outcome (muscle twitch recovery ratios) reported in several. We also compared a series of muscle twitch recovery graphs appearing in a number of Saitoh's publications. The baseline data in 14/32 randomised, controlled trials had p sampling. Combining the continuous and categorical probabilities of the 32 included trials, we found a very low likelihood of random sampling: p = 1.27 × 10(-8) (1 in 100,000,000). The high probability of non-random sampling and the repetition of lines in multiple graphs suggest that further scrutiny of Saitoh's work is warranted. © 2016 The Association of Anaesthetists of Great Britain and Ireland.

  14. Offender and offense characteristics of a nonrandom sample of adolescent mass murderers.

    Science.gov (United States)

    Meloy, J R; Hempel, A G; Mohandie, K; Shiva, A A; Gray, B T

    2001-06-01

    The authors conducted a descriptive, archival study of adolescent (mass murderers-subjects who intentionally killed three or more victims in one event-to identify demographic, clinical, and forensic characteristics. A nonrandom sample of convenience of adolescent mass murderers was utilized. Thirty-four subjects, acting alone or in pairs, committed 27 mass murders between 1958 and 1999. The sample consisted of males with a median age of 17. A majority were described as "loners" and abused alcohol or drugs; almost half were bullied by others, preoccupied with violent fantasy, and violent by history. Although 23% had a documented psychiatric history, only 6% were judged to have been psychotic at the time of the mass murder. Depressive symptoms and historical antisocial behaviors were predominant. There was a precipitating event in most cases--usually a perceived failure in love or school--and most subjects made threatening statements regarding the mass murder to third parties. The majority of the sample clustered into three types: the family annihilator, the classroom avenger, and the criminal opportunist. The adolescent mass murderer is often predatorily rather than affectively violent and typically does not show any sudden or highly emotional warning signs. Although the act of mass murder is virtually impossible to predict because of its extremely low frequency, certain clinical and forensic findings can alert the clinician to the need for further, intensified primary care, including family, school, community, law enforcement, and mental health intervention.

  15. A new non-randomized model for analysing sensitive questions with binary outcomes.

    Science.gov (United States)

    Tian, Guo-Liang; Yu, Jun-Wu; Tang, Man-Lai; Geng, Zhi

    2007-10-15

    We propose a new non-randomized model for assessing the association of two sensitive questions with binary outcomes. Under the new model, respondents only need to answer a non-sensitive question instead of the original two sensitive questions. As a result, it can protect a respondent's privacy, avoid the usage of any randomizing device, and be applied to both the face-to-face interview and mail questionnaire. We derive the constrained maximum likelihood estimates of the cell probabilities and the odds ratio for two binary variables associated with the sensitive questions via the EM algorithm. The corresponding standard error estimates are then obtained by bootstrap approach. A likelihood ratio test and a chi-squared test are developed for testing association between the two binary variables. We discuss the loss of information due to the introduction of the non-sensitive question, and the design of the co-operative parameters. Simulations are performed to evaluate the empirical type I error rates and powers for the two tests. In addition, a simulation is conducted to study the relationship between the probability of obtaining valid estimates and the sample size for any given cell probability vector. A real data set from an AIDS study is used to illustrate the proposed methodologies.

  16. Nonrandom seedling establishment corresponds with distance-dependent decline in mycorrhizal abundance in two terrestrial orchids.

    Science.gov (United States)

    Waud, Michael; Wiegand, Thorsten; Brys, Rein; Lievens, Bart; Jacquemyn, Hans

    2016-07-01

    In plant species that critically rely on mycorrhizal symbionts for germination and seedling establishment, distance-dependent decline of mycorrhizal fungi in the soil can be hypothesized to lead to significant spatial clustering as a result of nonrandom spatial patterns of seedling establishment. To test this hypothesis, we investigated the abundance and distribution of mycorrhizal fungi in the soil and how they relate to spatial patterns of adults and seedling recruitment in two related orchid species. We combined assessments of spatial variation in fungal abundance using quantitative PCR (qPCR) with spatial point pattern analyses based on long-term demographic data and cluster point process models. qPCR analyses showed that fungal abundance declined rapidly with distance from the adult host plants. Spatial point pattern analyses showed that successful recruitment in both species was clustered significantly around adult plants and that the decline in the neighborhood density of recruits around adults coincided with the decline of fungal abundance around adult plants. Overall, these results indicate that the distribution and abundance of fungal associates in the soil may have a strong impact on the aboveground distribution of its partner.

  17. Impact of Integrated Services on HIV Testing: A Nonrandomized Trial among Kenyan Family Planning Clients.

    Science.gov (United States)

    Church, Kathryn; Warren, Charlotte E; Birdthistle, Isolde; Ploubidis, George B; Tomlin, Keith; Zhou, Weiwei; Kimani, James; Abuya, Timothy; Ndwiga, Charity; Sweeney, Sedona; Mayhew, Susannah H

    2017-06-01

    The impact of integrated reproductive health and HIV services on HIV testing and counseling (HTC) uptake was assessed among 882 Kenyan family planning clients using a nonrandomized cohort design within six intervention and six "comparison" facilities. The effect of integration on HTC goals (two tests over two years) was assessed using conditional logistic regression to test four "integration" exposures: a training and reorganization intervention; receipt of reproductive health and HIV services at recruitment; a functional measure of facility integration at recruitment; and a woman's cumulative exposure to functionally integrated care across different facilities over time. While recent receipt of HTC increased rapidly at intervention facilities, achievement of HTC goals was higher at comparison facilities. Only high cumulative exposure to integrated care over two years had a significant effect on HTC goals after adjustment (aOR 2.94, 95%CI 1.73-4.98), and programs should therefore make efforts to roll out integrated services to ensure repeated contact over time. © 2017 The Population Council, Inc.

  18. Synaptic signal streams generated by ex vivo neuronal networks contain non-random, complex patterns.

    Science.gov (United States)

    Lee, Sangmook; Zemianek, Jill M; Shultz, Abraham; Vo, Anh; Maron, Ben Y; Therrien, Mikaela; Courtright, Christina; Guaraldi, Mary; Yanco, Holly A; Shea, Thomas B

    2014-11-01

    Cultured embryonic neurons develop functional networks that transmit synaptic signals over multiple sequentially connected neurons as revealed by multi-electrode arrays (MEAs) embedded within the culture dish. Signal streams of ex vivo networks contain spikes and bursts of varying amplitude and duration. Despite the random interactions inherent in dissociated cultures, neurons are capable of establishing functional ex vivo networks that transmit signals among synaptically connected neurons, undergo developmental maturation, and respond to exogenous stimulation by alterations in signal patterns. These characteristics indicate that a considerable degree of organization is an inherent property of neurons. We demonstrate herein that (1) certain signal types occur more frequently than others, (2) the predominant signal types change during and following maturation, (3) signal predominance is dependent upon inhibitory activity, and (4) certain signals preferentially follow others in a non-reciprocal manner. These findings indicate that the elaboration of complex signal streams comprised of a non-random distribution of signal patterns is an emergent property of ex vivo neuronal networks.

  19. Identification of varieties and gene flow in Douglas fir exemplified in artificially established stands in Germany

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    Barbara Fussi

    2013-12-01

    Full Text Available Douglas-fir [Pseudotsuga menziesii (Mirb. Franco] is an economically valuable non-native tree species in Germany and is considered very promising in view of global climate change. Therefore, the genetic characterization of Douglas-fir populations and seed stands in Germany is essential. We studied coastal and interior Douglas-fir varieties, both present in Germany, by using eleven isoenzyme and four microsatellite loci. By analyzing eight reference populations of known origin we were able to identify the two varieties on the population level using Bayesian and distance based methods. Seven populations present in Bavaria were then successfully assigned to one of the two varieties. Within varieties we found stronger grouping within the interior variety than within the coastal one. Despite lower differences within coastal Douglas-fir we have first indications for the origin of two populations. For two Bavarian populations, natural regeneration was included and genetic data revealed no significant genetic difference between adults and offspring. The parentage analysis for one of the studied stands revealed that a large proportion of adults took part in the reproduction, but some trees were more successful than others in transferring their genes to the next generation. Our study was able to improve variety identification of Douglas-fir using isoenzyme markers and nuclear microsatellites and study reproductive patterns, both are important issues for the management of Douglas-fir stands in Bavaria.

  20. Identification of varieties and gene flow in Douglas fir exemplified in artificially established stands in Germany

    Directory of Open Access Journals (Sweden)

    Barbara Fussi

    2013-12-01

    Full Text Available Douglas-fir [Pseudotsuga menziesii (Mirb. Franco] is an economically valuable non-native tree species in Germany and is considered very promising in view of global climate change. Therefore, the genetic characterization of Douglas-fir populations and seed stands in Germany is essential. We studied coastal and interior Douglas-fir varieties, both present in Germany, by using eleven isoenzyme and four microsatellite loci. By analyzing eight reference populations of known origin we were able to identify the two varieties on the population level using Bayesian and distance based methods. Seven populations present in Bavaria were then successfully assigned to one of the two varieties. Within varieties we found stronger grouping within the interior variety than within the coastal one. Despite lower differences within coastal Douglas-fir we have first indications for the origin of two populations. For two Bavarian populations, natural regeneration was included and genetic data revealed no significant genetic difference between adults and offspring. The parentage analysis for one of the studied stands revealed that a large proportion of adults took part in the reproduction, but some trees were more successful than others in transferring their genes to the next generation. Our study was able to improve variety identification of Douglas-fir using isoenzyme markers and nuclear microsatellites and study reproductive patterns, both are important issues for the management of Douglas-fir stands in Bavaria.

  1. Contrasting patterns of gene flow between sister plant species in the understorey of African moist forests - the case of sympatric and parapatric Marantaceae species.

    Science.gov (United States)

    Ley, A C; Hardy, O J

    2014-08-01

    Gene flow within and between species is a fundamental process shaping the evolutionary history of taxa. However, the extent of hybridization and reinforcement is little documented in the tropics. Here we explore the pattern of gene flow between three sister species from the herbaceous genus Marantochloa (Marantaceae), sympatrically distributed in the understorey of the African rainforest, using data from the chloroplast and nuclear genomes (DNA sequences and AFLP). We found highly contrasting patterns: while there was no evidence of gene flow between M. congensis and M. monophylla, species identity between M. monophylla and M. incertifolia was maintained despite considerable gene flow. We hypothesize that M. incertifolia originated from an ancient hybridization event between M. congensis and M. monophylla, considering the current absence of hybridization between the two assumed parent species, the rare presence of shared haplotypes between all three species and the high percentage of haplotypes shared by M. incertifolia with each of the two parent species. This example is contrasted with two parapatrically distributed species from the same family in the genus Haumania forming a hybrid zone restricted to the area of overlap. This work illustrates the diversity of speciation/introgression patterns that can potentially occur in the flora of tropical Africa.

  2. Functional redundancy patterns reveal non-random assembly rules in a species-rich marine assemblage.

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    Nicolas Guillemot

    Full Text Available The relationship between species and the functional diversity of assemblages is fundamental in ecology because it contains key information on functional redundancy, and functionally redundant ecosystems are thought to be more resilient, resistant and stable. However, this relationship is poorly understood and undocumented for species-rich coastal marine ecosystems. Here, we used underwater visual censuses to examine the patterns of functional redundancy for one of the most diverse vertebrate assemblages, the coral reef fishes of New Caledonia, South Pacific. First, we found that the relationship between functional and species diversity displayed a non-asymptotic power-shaped curve, implying that rare functions and species mainly occur in highly diverse assemblages. Second, we showed that the distribution of species amongst possible functions was significantly different from a random distribution up to a threshold of ∼90 species/transect. Redundancy patterns for each function further revealed that some functions displayed fast rates of increase in redundancy at low species diversity, whereas others were only becoming redundant past a certain threshold. This suggested non-random assembly rules and the existence of some primordial functions that would need to be fulfilled in priority so that coral reef fish assemblages can gain a basic ecological structure. Last, we found little effect of habitat on the shape of the functional-species diversity relationship and on the redundancy of functions, although habitat is known to largely determine assemblage characteristics such as species composition, biomass, and abundance. Our study shows that low functional redundancy is characteristic of this highly diverse fish assemblage, and, therefore, that even species-rich ecosystems such as coral reefs may be vulnerable to the removal of a few keystone species.

  3. Outcome of Percutaneous Release of Tennis Elbow: A Non-Randomized Controlled Trial Study

    Science.gov (United States)

    Khatri, Kishor; Kharel, Krishna; Byanjankar, Subin; Shrestha, Rahul; Sharma, Jay R; Vaishya, Raju; Agarwal, Amit kumar; Vijay, Vipul

    2017-01-01

    Background Tennis elbow is a common disorder of the upper extremity. It can be treated conservatively in the majority of patients, but some resistant cases eventually can be treated by percutaneous release with good functional outcome. Materials and methods This non-randomized control trial was conducted at the Department of Orthopaedics Surgery in a tertiary care hospital from July 2015 to June 2016 on 50 patients who underwent percutaneous release of the common extensor origin using an 18 gauge hypodermic needle. These patients did not respond to conservative treatment including rest, nonsteroidal anti-inflammatory drugs (NSAIDS) and local steroid injections. The outcome was graded as Excellent, Good, Fair, and Poor. Results Fifty patients (50 elbows) were included in the study. Thirty-two patients were female (64%), and 18 were male (36%). The right side was affected in 37 patients (74%) and left side in 13 (26%). The time taken to achieve a completely pain-free elbow ranged from one day to two months (average of 26.2 days). Those who did not achieve a pain-free elbow had a residual pain of 1.5 to six on the visual analogue scale (VAS) (average 2.32). Excellent outcome was noticed in 24 patients (48%); Good result in eight patients (36% ); Fair in four patients (eight percent) and Poor in four patients (eight percent). Conclusion Tennis elbow probably results from the degenerative tear of the common extensor origin, and a percutaneous tenotomy using an 18 gauge hypodermic needle is a simple, safe, patient-friendly, efficient, and easily reproducible method of treating tennis elbow in those who are resistant to conservative treatment, and it can be done as an outpatient procedure. PMID:28168130

  4. Cortical microtubule arrays are initiated from a nonrandom prepattern driven by atypical microtubule initiation.

    Science.gov (United States)

    Lindeboom, Jelmer J; Lioutas, Antonios; Deinum, Eva E; Tindemans, Simon H; Ehrhardt, David W; Emons, Anne Mie C; Vos, Jan W; Mulder, Bela M

    2013-03-01

    The ordered arrangement of cortical microtubules in growing plant cells is essential for anisotropic cell expansion and, hence, for plant morphogenesis. These arrays are dismantled when the microtubule cytoskeleton is rearranged during mitosis and reassembled following completion of cytokinesis. The reassembly of the cortical array has often been considered as initiating from a state of randomness, from which order arises at least partly through self-organizing mechanisms. However, some studies have shown evidence for ordering at early stages of array assembly. To investigate how cortical arrays are initiated in higher plant cells, we performed live-cell imaging studies of cortical array assembly in tobacco (Nicotiana tabacum) Bright Yellow-2 cells after cytokinesis and drug-induced disassembly. We found that cortical arrays in both cases did not initiate randomly but with a significant overrepresentation of microtubules at diagonal angles with respect to the cell axis, which coincides with the predominant orientation of the microtubules before their disappearance from the cell cortex in preprophase. In Arabidopsis (Arabidopsis thaliana) root cells, recovery from drug-induced disassembly was also nonrandom and correlated with the organization of the previous array, although no diagonal bias was observed in these cells. Surprisingly, during initiation, only about one-half of the new microtubules were nucleated from locations marked by green fluorescent protein-γ-tubulin complex protein2-tagged γ-nucleation complexes (γ-tubulin ring complex), therefore indicating that a large proportion of early polymers was initiated by a noncanonical mechanism not involving γ-tubulin ring complex. Simulation studies indicate that the high rate of noncanonical initiation of new microtubules has the potential to accelerate the rate of array repopulation.

  5. Strategies for improving postpartum contraceptive use: evidence from non-randomized studies.

    Science.gov (United States)

    Lopez, Laureen M; Grey, Thomas W; Chen, Mario; Hiller, Janet E

    2014-11-27

    Nearly two-thirds of women in their first postpartum year have an unmet need for family planning. Adolescents often have repeat pregnancies within a year of giving birth. Women may receive counseling on family planning both antepartum and postpartum. Decisions about contraceptive use made right after counseling may differ considerably from actual postpartum use. In earlier work, we found limited evidence of effectiveness from randomized trials on postpartum contraceptive counseling. For educational interventions, non-randomized studies may be conducted more often than randomized trials. We reviewed non-randomized studies of educational strategies to improve postpartum contraceptive use. Our intent was to examine associations between specific interventions and postpartum contraceptive use or subsequent pregnancy. We searched for eligible non-randomized studies until 3 November 2014. Sources included CENTRAL, PubMed, POPLINE, and Web of Science. We also sought current trials via ClinicalTrials.gov and ICTRP. For additional citations, we examined reference lists of relevant reports and reviews. The studies had to be comparative, i.e., have intervention and comparison groups. The educational component could be counseling or another behavioral strategy to improve contraceptive use among postpartum women. The intervention had to include contact within six weeks postpartum. The comparison condition could be another behavioral strategy to improve contraceptive use, usual care, other health education, or no intervention. Our primary outcomes were postpartum contraceptive use and subsequent pregnancy. Two authors evaluated abstracts for eligibility and extracted data from included studies. We computed the Mantel-Haenszel odds ratio (OR) for dichotomous outcomes and the mean difference (MD) for continuous measures, both with 95% Confidence Intervals (CI). Where studies used adjusted analyses for continuous outcomes, we presented the results as reported by the investigators

  6. Fuzzy boundaries: color and gene flow patterns among parapatric lineages of the western shovel-nosed snake and taxonomic implication

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    Wood, Dustin A.; Fisher, Robert N.; Vandergast, Amy G.

    2014-01-01

    Accurate delineation of lineage diversity is increasingly important, as species distributions are becoming more reduced and threatened. During the last century, the subspecies category was often used to denote phenotypic variation within a species range and to provide a framework for understanding lineage differentiation, often considered incipient speciation. While this category has largely fallen into disuse, previously recognized subspecies often serve as important units for conservation policy and management when other information is lacking. In this study, we evaluated phenotypic subspecies hypotheses within shovel-nosed snakes on the basis of genetic data and considered how evolutionary processes such as gene flow influenced possible incongruence between phenotypic and genetic patterns. We used both traditional phylogenetic and Bayesian clustering analyses to infer range-wide genetic structure and spatially explicit analyses to detect possible boundary locations of lineage contact. Multilocus analyses supported three historically isolated groups with low to moderate levels of contemporary gene exchange. Genetic data did not support phenotypic subspecies as exclusive groups, and we detected patterns of discordance in areas where three subspecies are presumed to be in contact. Based on genetic and phenotypic evidence, we suggested that species-level diversity is underestimated in this group and we proposed that two species be recognized, Chionactis occipitalis and C. annulata. In addition, we recommend retention of two subspecific designations within C. annulata (C. a. annulata and C. a. klauberi) that reflect regional shifts in both genetic and phenotypic variation within the species. Our results highlight the difficultly in validating taxonomic boundaries within lineages that are evolving under a time-dependent, continuous process.

  7. Botanical Files on Lettuce (Lactuca sativa). On the chance for gene flow between wild and cultivated Lettuce (Lactuca sativa L. including L. serriola L., Compositae) and the generalized implications for risk-assessments on genetically modified plants

    NARCIS (Netherlands)

    Frietema de Vries, F.T.; Meijden, van der R.; Brandenburg, W.A.

    1994-01-01

    In Botanical Files, a study of the real chances for gene flow from cultivated plants to the wild a system of dispersal codes (Dpdf) was introduced (see text box Dpdf).³7 They are indications of already occurring gene flow from cultivated plants to the wild flora, as can be deduced from herbarium col

  8. Directional dispersal between mid-ocean ridges: deep-ocean circulation and gene flow in Ridgeia piscesae.

    Science.gov (United States)

    Young, C R; Fujio, S; Vrijenhoek, R C

    2008-04-01

    This study examined relationships between bathymetrically induced deep-ocean currents and the dispersal of the hydrothermal vent tubeworm Ridgeia piscesae along the northeast Pacific ridge system. A robust diagnostic model of deep-ocean circulation in this region predicted strong southeasterly currents following contours of the Blanco Transform Fault, a 450-km lateral offset that separates the Gorda and Juan de Fuca ridge systems. Such currents should facilitate the southward dispersal of R. piscesae larvae. Immigration rates for populations north and south of the Blanco Transform Fault were estimated from molecular population genetic data. Mitochondrial DNA evidence revealed population subdivision across the Blanco Transform Fault, and a strong directional bias in gene flow that was consistent with predictions of the circulation model. The distribution of mitochondrial diversity between the northern and southern populations of R. piscesae suggests that the Gorda Ridge tubeworms have maintained larger effective population sizes than the northern populations, a pattern that also exists in co-occurring limpets. Together, these data suggest that the northern vent fields may experience a higher frequency of habitat turnover and consequently more rapid losses of genetic diversity.

  9. High levels of interspecific gene flow in an endemic cichlid fish adaptive radiation from an extreme lake environment.

    Science.gov (United States)

    Ford, Antonia G P; Dasmahapatra, Kanchon K; Rüber, Lukas; Gharbi, Karim; Cezard, Timothee; Day, Julia J

    2015-07-01

    Studying recent adaptive radiations in isolated insular systems avoids complicating causal events and thus may offer clearer insight into mechanisms generating biological diversity. Here, we investigate evolutionary relationships and genomic differentiation within the recent radiation of Alcolapia cichlid fish that exhibit extensive phenotypic diversification, and which are confined to the extreme soda lakes Magadi and Natron in East Africa. We generated an extensive RAD data set of 96 individuals from multiple sampling sites and found evidence for genetic admixture between species within Lake Natron, with the highest levels of admixture between sympatric populations of the most recently diverged species. Despite considerable environmental separation, populations within Lake Natron do not exhibit isolation by distance, indicating panmixia within the lake, although individuals within lineages clustered by population in phylogenomic analysis. Our results indicate exceptionally low genetic differentiation across the radiation despite considerable phenotypic trophic variation, supporting previous findings from smaller data sets; however, with the increased power of densely sampled SNPs, we identify genomic peaks of differentiation (FST outliers) between Alcolapia species. While evidence of ongoing gene flow and interspecies hybridization in certain populations suggests that Alcolapia species are incompletely reproductively isolated, the identification of outlier SNPs under diversifying selection indicates the radiation is undergoing adaptive divergence.

  10. Incipient speciation with gene flow on a continental island: Species delimitation of the Hainan Hwamei (Leucodioptron canorum owstoni, Passeriformes, Aves).

    Science.gov (United States)

    Wang, Ning; Liang, Bin; Wang, Jichao; Yeh, Chia-Fen; Liu, Yang; Liu, Yanlin; Liang, Wei; Yao, Cheng-Te; Li, Shou-Hsien

    2016-09-01

    Because of their isolation, continental islands (e.g., Madagascar) are often thought of as ideal systems to study allopatric speciation. However, many such islands have been connected intermittently to their neighboring continent during recent periods of glaciation, which may cause frequent contact between the diverging populations on the island and continent. As a result, the speciation processes on continental islands may not meet the prerequisites for strictly allopatric speciation. We used multiple lines of evidence to re-evaluate the taxonomic status of the Hainan Hwamei (Leucodioptron canorum owstoni), which is endemic to Hainan, the largest continental island in the South China Sea. Our analysis of mitochondrial DNA and twelve nuclear loci suggests that the Hainan Hwamei can be regarded as an independent species (L. owstoni); the morphological traits of the Hainan Hwamei also showed significant divergence from those of their mainland sister taxon, the Chinese Hwamei (L. canorum). We also inferred the divergence history of the Hainan and Chinese Hwamei to see whether their divergence was consistent with a strictly allopatric model. Our results suggest that the two Hwameis split only 0.2 million years ago with limited asymmetrical post-divergence gene flow. This implies that the Hainan Hwamei is an incipient species and that speciation occurred through ecologically divergent selection and/or assortative mating rather than a strictly allopatric process.

  11. Genetic diversity and gene flow in a Caribbean tree Pterocarpus officinalis Jacq.: a study based on chloroplast and nuclear microsatellites.

    Science.gov (United States)

    Muller, F; Voccia, M; Bâ, A; Bouvet, J-M

    2009-03-01

    We analysed the molecular diversity of Pterocarpus officinalis, a tree species distributed in Caribbean islands, South and Central America to quantify the genetic variation within island, to assess the pattern of differentiation and infer levels of gene flow; with the overall goal of defining a strategy of conservation. Two hundred two individuals of 9 populations were analysed using three chloroplast and six nuclear microsatellite markers. The observed heterozygosity varied markedly among the populations for nuclear (H(Onuc )= 0.20-0.50) and chloroplast microsatellites (H (cp )= 0.22-0.68). The continental population from French Guyana showed a higher value of H(Onuc) than island populations, and the differences were significant in some cases. The fixation index F (IS) ranged from -0.043 to 0.368; a significant heterozygote deficit was detected in 7 populations. The heterozygosity excess method suggested that two populations in Guadeloupe have undergone a recent bottleneck. Global and pairwise F (ST) were high for both nuclear (F(STnuc )= 0.29) and chloroplast microsatellites (F(STcp )= 0.58). The neighbour-joining tree based on both markers, presented a differentiation pattern that can be explained by the seed dispersal by flotation and marine stream. The comparison of Bayesian approach and the method based on allelic frequency demonstrate a very limited number of migrants between populations.

  12. Multiple introductions and gene flow in subtropical South American populations of the fireweed, Senecio madagascariensis(Asteraceae

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    Geraldo Mäder

    2016-03-01

    Full Text Available Abstract Non-indigenous plants exhibit different attributes that make them aggressive competitors with indigenous plants and serious threats to biodiversity.Senecio madagascariensis (fireweed, Asteraceae, a native from southern Africa, is a strong competitor in agricultural activities and has toxic alkaloids that may result in high cattle mortality. In Brazil, this weed was collected for the first time in 1995 and has since spread quickly throughout the Pampas region. To better understand the invasion of the fireweed in South America, we used a genetic characterization with internal transcribed spacer (ITS and microsatellite markers. Based on the ITS data, the southern Brazil populations of S. madagascariensis shared genetic homology with samples taken from the Hawaiian Islands and South Africa. Microsatellite analysis showed the genetic diversity split in two clusters, perhaps intimating the independent introduction of each species into South America. Although fireweed was introduced recently in southern Brazil, the considerable levels of genetic diversity, gene flow, and inbreeding may indicate success in the species establishment in this environment.

  13. Ascertaining gene flow patterns in livestock populations of developing countries: a case study in Burkina Faso goat

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    Traoré Amadou

    2012-05-01

    Full Text Available Abstract Background Introgression of Sahel livestock genes southwards in West Africa may be favoured by human activity and the increase of the duration of the dry seasons since the 1970’s. The aim of this study is to assess the gene flow patterns in Burkina Faso goat and to ascertain the most likely factors influencing geographic patterns of genetic variation in the Burkina Faso goat population. Results A total of 520 goat were sampled in 23 different locations of Burkina Faso and genotyped for a set of 19 microsatellites. Data deposited in the Dryad repository: http://dx.doi.org/10.5061/dryad.41h46j37. Although overall differentiation is poor (FST = 0.067 ± 0.003, the goat population of Burkina Faso is far from being homogeneous. Barrier analysis pointed out the existence of: a genetic discontinuities in the Central and Southeast Burkina Faso; and b genetic differences within the goat sampled in the Sahel or the Sudan areas of Burkina Faso. Principal component analysis and admixture proportion scores were computed for each population sampled and used to construct interpolation maps. Furthermore, Population Graph analysis revealed that the Sahel and the Sudan environmental areas of Burkina Faso were connected through a significant number of extended edges, which would be consistent with the hypothesis of long-distance dispersal. Genetic variation of Burkina Faso goat followed a geographic-related pattern. This pattern of variation is likely to be related to the presence of vectors of African animal trypanosomosis. Partial Mantel test identified the present Northern limit of trypanosome vectors as the most significant landscape boundary influencing the genetic variability of Burkina Faso goat (p = 0.008. The contribution of Sahel goat genes to the goat populations in the Northern and Eastern parts of the Sudan-Sahel area of Burkina Faso was substantial. The presence of perennial streams explains the existence of trypanosome vectors. The South

  14. Determination of protein expression and plasmid copy number from cloned genes in Escherichia coli by flow injection analysis using an enzyme indicator vector.

    Science.gov (United States)

    Schendel, F J; Baude, E J; Flickinger, M C

    1989-10-20

    On-line determination of expression rates from cloned genes in Escherichia coli and of plasmid copy number would be useful for monitoring accumulation of non-secreted proteins. As an initial model for monitoring gene expression in intact cells, a non-gene-fusion enzyme-based indicator plasmid has been constructed containing the phoA gene coding for alkaline phosphatase (AP) in pUCIS and pACYC184. The activity of AP can be rapidly determined in permeabilized cells. A flow injection analysis (FIA) assay has been developed which allows the direct real-time measurement of the AP activity during cell growth. A model target gene coding for E. coli cyanase (cynS) has been inserted in order to determine the ratio between the expression of the target and indicator, AP. A linear relationship has been found between plasmid copy number and AP activity for the high-copy pUC vector. To minimize indicator expression, transcription terminators have been inserted between the cynS and phoA genes, altering the target-to-indicator ratio by 10- to 40-fold. These vectors may be useful for the rapid continuous determination of plasmid copy number and target gene expression for nonsecreted proteins and would overcome the limitations of in situ probe biosensors for real-time determination of the accumulation of proteins from cloned genes in E. coli.

  15. Asymmetry of gene flow and differential geographical structure of molecular diversity in wild and domesticated common bean (Phaseolus vulgaris L.) from Mesoamerica.

    Science.gov (United States)

    Papa, R; Gepts, P

    2003-01-01

    Using amplified fragment length polymorphisms (AFLPs), we analyzed the genetic structure of wild and domesticated common bean (Phaseolus vulgaris L.) from Mesoamerica at different geographical levels to test the hypothesis of asymmetric gene flow and investigate the origin of weedy populations. We showed both by phenetic and admixture population analyses that gene flow is about three- to four-fold higher from domesticated to wild populations than in the reverse direction. This result, combined with other work, points to a displacement of genetic diversity in wild populations due to gene flow from the domesticated populations. The weedy populations appear to be genetically intermediate between domesticated and wild populations, suggesting that they originated by hybridization between wild and domesticated types rather than by escape from cultivation. In addition, the domesticated bean races were genetically similar confirming a single domestication event for the Mesoamerican gene pool. Finally, the genetic diversity of the domesticated bean population showed a lower level of geographic structure in comparison to that of the wild populations.

  16. Rock magnetic evidence of non-random raw material selection criteria in Cerro Toledo Obsidian Artifacts from Valles Caldera, New Mexico

    Science.gov (United States)

    Gregovich, A.; Feinberg, J. M.; Steffen, A.; Sternberg, R. S.

    2014-12-01

    Stone tools are one of the most enduring forms of ancient human behavior available to anthropologists. The geologic materials that comprise stone tools are a reflection of the rocks that were available locally or through trade, as are the intended use of the tools and the knapping technology needed to produce them. Investigation of the rock magnetic and geochemical characteristics of the artifacts and the geological source materials provides a baseline to explore these past behaviors. This study uses rock magnetic properties to explore the raw material selection criteria involved in the production of obsidian tools in the region around Valles Caldera in northern New Mexico. Obsidian is locally abundant and was traded by tribes across the central United States. Here we compare the rock magnetic properties of a sample of obsidian projectile points (N =25) that have been geochemically sourced to the Cerro Toledo obsidian flow with geological samples collected from four sites within the same flow (N =135). This collection of archaeological artifacts, albeit small, contains representatives of at least 8 different point styles that were used over 6000 years from the Archaic into the Late Prehistoric. Bulk rock hysteresis parameters (Mr, Ms, Bc, and Bcr) and low-field susceptibility (Χ) measurements show that the projectile points generally contain a lower concentration of magnetic minerals than the geologic samples. For example, the artifacts' median Ms value is 2.9 x 10-3 Am2kg-1, while that of the geological samples is 6.5 x 10-3 Am2kg-1. The concentration of magnetic minerals in obsidian is a proxy for the concentration of microlites in general, and this relationship suggests that although obsidian was locally abundant, toolmakers employed non-random selection criteria resulting in generally lower concentrations of microlites in their obsidian tools.

  17. Cortical atrophy patterns in multiple sclerosis are non-random and clinically relevant.

    Science.gov (United States)

    Steenwijk, Martijn D; Geurts, Jeroen J G; Daams, Marita; Tijms, Betty M; Wink, Alle Meije; Balk, Lisanne J; Tewarie, Prejaas K; Uitdehaag, Bernard M J; Barkhof, Frederik; Vrenken, Hugo; Pouwels, Petra J W

    2016-01-01

    cortical atrophy in multiple sclerosis occurs largely in a non-random manner and develops (at least partly) according to distinct anatomical patterns. In addition, these cortical atrophy patterns showed stronger associations with clinical (especially cognitive) dysfunction than global cortical atrophy.

  18. Multidisciplinary intervention reducing readmissions in medical inpatients: a prospective, non-randomized study

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    Torisson G

    2013-09-01

    Full Text Available Gustav Torisson,1 Lennart Minthon,1 Lars Stavenow,2 Elisabet Londos1 1Clinical Memory Research Unit, Department of Clinical Sciences, Lund University, 2Department of Internal Medicine, Skåne University Hospital, Malmö, Sweden Background: The purpose of this study was to examine whether a multidisciplinary intervention targeting drug-related problems, cognitive impairment, and discharge miscommunication could reduce readmissions in a general hospital population. Methods: This prospective, non-randomized intervention study was carried out at the department of general internal medicine at a tertiary university hospital. Two hundred medical inpatients living in the community and aged over 60 years were included. Ninety-nine patients received interventions and 101 received standard care. Control/intervention allocation was determined by geographic selection. Interventions consisted of a comprehensive medication review, improved discharge planning, post-discharge telephone follow-up, and liaison with the patient's general practitioner. The main outcome measures recorded were readmissions and hospital nights 12 months after discharge. Separate analyses were made for 12-month survivors and from an intention-to-treat perspective. Comparative analyses were made between groups as well as within groups over time. Results: After 12 months, survivors in the control group had 125 readmissions in total, compared with 58 in the intervention group (Mann–Whitney U test, P = 0.02. For hospital nights, the numbers were 1,228 and 492, respectively (P = 0.009. Yearly admissions had increased from the previous year in the control group from 77 to 125 (Wilcoxon signed-rank test, P = 0.002 and decreased from 75 to 58 in the intervention group (P = 0.25. From the intention-to-treat perspective, the same general pattern was observed but was not significant (1,827 versus 1,008 hospital nights, Mann–Whitney test, P = 0.054. Conclusion: A multidisciplinary approach

  19. Non-random genomic integration - an intrinsic property of retrogenes in Drosophila?

    Directory of Open Access Journals (Sweden)

    Metta Muralidhar

    2010-04-01

    Full Text Available Abstract Background The Drosophila X-chromosome shows a significant underrepresentation of genes with male-biased gene expression (demasculinization. This trend is matched by retrogenes, which typically have a male biased gene expression pattern and show a significant movement bias from X-chromosomes to autosomes. It is currently assumed that these patterns are best explained by selection, either mediated by male meiotic sex chromosome inactivation (MSCI or sexually antagonistic forces. We scrutinized the evolutionary dynamics of retroposition by focusing on retrogenes for which the parental copy has degenerated. Results Consistent with a functional substitution of the degenerated gene by the retrogene, patterns of sequence evolution and gene expression were similar between retroposed and parental genes. Like previous studies, our set of retrogenes showed a significant movement off the X-chromosome. In contrast to data sets where retroposition caused gene duplication, the genes in our study showed primarily female-biased or unbiased gene expression. Conclusions Based on our results, the biased transposition pattern cannot be explained by MSCI and probably not by sexual antagonism. Rather, we propose that the movement away from the X-chromosome represents a general property of retroposition in Drosophila.

  20. Gene

    Data.gov (United States)

    U.S. Department of Health & Human Services — Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes,...

  1. Recent and projected increases in atmospheric CO2 concentration can enhance gene flow between wild and genetically altered rice (Oryza sativa.

    Directory of Open Access Journals (Sweden)

    Lewis H Ziska

    Full Text Available Although recent and projected increases in atmospheric carbon dioxide can alter plant phenological development, these changes have not been quantified in terms of floral outcrossing rates or gene transfer. Could differential phenological development in response to rising CO(2 between genetically modified crops and wild, weedy relatives increase the spread of novel genes, potentially altering evolutionary fitness? Here we show that increasing CO(2 from an early 20(th century concentration (300 µmol mol(-1 to current (400 µmol mol(-1 and projected, mid-21(st century (600 µmol mol(-1 values, enhanced the flow of genes from wild, weedy rice to the genetically altered, herbicide resistant, cultivated population, with outcrossing increasing from 0.22% to 0.71% from 300 to 600 µmol mol(-1. The increase in outcrossing and gene transfer was associated with differential increases in plant height, as well as greater tiller and panicle production in the wild, relative to the cultivated population. In addition, increasing CO(2 also resulted in a greater synchronicity in flowering times between the two populations. The observed changes reported here resulted in a subsequent increase in rice dedomestication and a greater number of weedy, herbicide-resistant hybrid progeny. Overall, these data suggest that differential phenological responses to rising atmospheric CO(2 could result in enhanced flow of novel genes and greater success of feral plant species in agroecosystems.

  2. Flow-FISH analysis and isolation of clostridial strains in an anaerobic semi-solid bio-hydrogen producing system by hydrogenase gene target.

    Science.gov (United States)

    Jen, Chang Jui; Chou, Chia-Hung; Hsu, Ping-Chi; Yu, Sian-Jhong; Chen, Wei-En; Lay, Jiunn-Jyi; Huang, Chieh-Chen; Wen, Fu-Shyan

    2007-04-01

    By using hydrogenase gene-targeted polymerase chain reaction (PCR) and reverse transcriptase PCR (RT-PCR), the predominant clostridial hydrogenase that may have contributed to biohydrogen production in an anaerobic semi-solid fermentation system has been monitored. The results revealed that a Clostridium pasteurianum-like hydrogenase gene sequence can be detected by both PCR and RT-PCR and suggested that the bacterial strain possessing this specific hydrogenase gene was dominant in hydrogenase activity and population. Whereas another Clostridium saccharobutylicum-like hydrogenase gene can be detected only by RT-PCR and suggest that the bacterial strain possessing this specific hydrogenase gene may be less dominant in population. In this study, hydrogenase gene-targeted fluorescence in situ hybridization (FISH) and flow cytometry analysis confirmed that only 6.6% of the total eubacterial cells in a hydrogen-producing culture were detected to express the C. saccharobutylicum-like hydrogenase, whereas the eubacteria that expressed the C. pasteurianum-like hydrogenase was 25.6%. A clostridial strain M1 possessing the identical nucleotide sequences of the C. saccharobutylicum-like hydrogenase gene was then isolated and identified as Clostridium butyricum based on 16S rRNA sequence. Comparing to the original inoculum with mixed microflora, either using C. butyricum M1 as the only inoculum or co-culturing with a Bacillus thermoamylovorans isolate will guarantee an effective and even better production of hydrogen from brewery yeast waste.

  3. Impacts of selective logging on inbreeding and gene flow in two Amazonian timber species with contrasting ecological and reproductive characteristics.

    Science.gov (United States)

    Vinson, C C; Kanashiro, M; Harris, S A; Boshier, D H

    2015-01-01

    Selective logging in Brazil allows for the removal of up to 90% of trees above 50 cm diameter of a given timber species, independent of a species' life history characteristics or how quickly it will recover. The genetic and demographic effects of selective logging on two Amazonian timber species (Dipteryx odorata Leguminosae, Jacaranda copaia Bignoniaceae) with contrasting ecological and reproductive characteristics were assessed in the same forest. Genetic diversity and gene flow were characterized by genotyping adults and seed sampled before and after logging, using hypervariable microsatellite markers. Overall, there were no short-term genetic impacts on the J. copaia population, with commercial application of current Brazilian forest management regulations. In contrast, for D. Odorata, selective logging showed a range of genetic impacts, with a 10% loss of alleles, and reductions in siring by pollen from trees within the 546-ha study area (23-11%) and in the number of pollen donors per progeny array (2.8-1.6), illustrating the importance of the surrounding landscape. Asynchrony in flowering between D. odorata trees led to trees with no breeding partners, which could limit the species reproduction and regeneration under current regulations. The results are summarized with other published studies from the same site and the implications for forest management discussed. The different types and levels of impacts associated with each species support the idea that ecological and genetic information by species, ecological guild or reproductive group is essential in helping to derive sustainable logging guidelines for tropical forests.

  4. Combining flow cytometry and 16S rRNA gene pyrosequencing: a promising approach for drinking water monitoring and characterization.

    Science.gov (United States)

    Prest, E I; El-Chakhtoura, J; Hammes, F; Saikaly, P E; van Loosdrecht, M C M; Vrouwenvelder, J S

    2014-10-15

    The combination of flow cytometry (FCM) and 16S rRNA gene pyrosequencing data was investigated for the purpose of monitoring and characterizing microbial changes in drinking water distribution systems. High frequency sampling (5 min intervals for 1 h) was performed at the outlet of a treatment plant and at one location in the full-scale distribution network. In total, 52 bulk water samples were analysed with FCM, pyrosequencing and conventional methods (adenosine-triphosphate, ATP; heterotrophic plate count, HPC). FCM and pyrosequencing results individually showed that changes in the microbial community occurred in the water distribution system, which was not detected with conventional monitoring. FCM data showed an increase in the total bacterial cell concentrations (from 345 ± 15 × 10(3) to 425 ± 35 × 10(3) cells mL(-1)) and in the percentage of intact bacterial cells (from 39 ± 3.5% to 53 ± 4.4%) during water distribution. This shift was also observed in the FCM fluorescence fingerprints, which are characteristic of each water sample. A similar shift was detected in the microbial community composition as characterized with pyrosequencing, showing that FCM and genetic fingerprints are congruent. FCM and pyrosequencing data were subsequently combined for the calculation of cell concentration changes for each bacterial phylum. The results revealed an increase in cell concentrations of specific bacterial phyla (e.g., Proteobacteria), along with a decrease in other phyla (e.g., Actinobacteria), which could not be concluded from the two methods individually. The combination of FCM and pyrosequencing methods is a promising approach for future drinking water quality monitoring and for advanced studies on drinking water distribution pipeline ecology. Copyright © 2014 Elsevier Ltd. All rights reserved.

  5. Combining flow cytometry and 16S rRNA gene pyrosequencing: A promising approach for drinking water monitoring and characterization

    KAUST Repository

    Prest, Emmanuelle I E C

    2014-10-01

    The combination of flow cytometry (FCM) and 16S rRNA gene pyrosequencing data was investigated for the purpose of monitoring and characterizing microbial changes in drinking water distribution systems. High frequency sampling (5min intervals for 1h) was performed at the outlet of a treatment plant and at one location in the full-scale distribution network. In total, 52 bulk water samples were analysed with FCM, pyrosequencing and conventional methods (adenosine-triphosphate, ATP; heterotrophic plate count, HPC). FCM and pyrosequencing results individually showed that changes in the microbial community occurred in the water distribution system, which was not detected with conventional monitoring. FCM data showed an increase in the total bacterial cell concentrations (from 345±15×103 to 425±35×103cellsmL-1) and in the percentage of intact bacterial cells (from 39±3.5% to 53±4.4%) during water distribution. This shift was also observed in the FCM fluorescence fingerprints, which are characteristic of each water sample. A similar shift was detected in the microbial community composition as characterized with pyrosequencing, showing that FCM and genetic fingerprints are congruent. FCM and pyrosequencing data were subsequently combined for the calculation of cell concentration changes for each bacterial phylum. The results revealed an increase in cell concentrations of specific bacterial phyla (e.g., Proteobacteria), along with a decrease in other phyla (e.g., Actinobacteria), which could not be concluded from the two methods individually. The combination of FCM and pyrosequencing methods is a promising approach for future drinking water quality monitoring and for advanced studies on drinking water distribution pipeline ecology. © 2014 Elsevier Ltd.

  6. Combined analyses of kinship and FST suggest potential drivers of chaotic genetic patchiness in high gene-flow populations.

    Science.gov (United States)

    Iacchei, Matthew; Ben-Horin, Tal; Selkoe, Kimberly A; Bird, Christopher E; García-Rodríguez, Francisco J; Toonen, Robert J

    2013-07-01

    We combine kinship estimates with traditional F-statistics to explain contemporary drivers of population genetic differentiation despite high gene flow. We investigate range-wide population genetic structure of the California spiny (or red rock) lobster (Panulirus interruptus) and find slight, but significant global population differentiation in mtDNA (ΦST = 0.006, P = 0.001; D(est_Chao) = 0.025) and seven nuclear microsatellites (F(ST) = 0.004, P < 0.001; D(est_Chao) = 0.03), despite the species' 240- to 330-day pelagic larval duration. Significant population structure does not correlate with distance between sampling locations, and pairwise FST between adjacent sites often exceeds that among geographically distant locations. This result would typically be interpreted as unexplainable, chaotic genetic patchiness. However, kinship levels differ significantly among sites (pseudo-F(16,988) = 1.39, P = 0.001), and ten of 17 sample sites have significantly greater numbers of kin than expected by chance (P < 0.05). Moreover, a higher proportion of kin within sites strongly correlates with greater genetic differentiation among sites (D(est_Chao), R(2) = 0.66, P < 0.005). Sites with elevated mean kinship were geographically proximate to regions of high upwelling intensity (R(2) = 0.41, P = 0.0009). These results indicate that P. interruptus does not maintain a single homogenous population, despite extreme dispersal potential. Instead, these lobsters appear to either have substantial localized recruitment or maintain planktonic larval cohesiveness whereby siblings more likely settle together than disperse across sites. More broadly, our results contribute to a growing number of studies showing that low F(ST) and high family structure across populations can coexist, illuminating the foundations of cryptic genetic patterns and the nature of marine dispersal.

  7. Landscape genetics, historical isolation and cross-Andean gene flow in the wax palm, Ceroxylon echinulatum (Arecaceae).

    Science.gov (United States)

    Trénel, Philipp; Hansen, Michael M; Normand, Signe; Borchsenius, Finn

    2008-08-01

    Knowledge of the role of landscapes in shaping genetic connectivity and divergence is essential for understanding patterns of biogeography and diversity. This is particularly relevant for the Andes region, a major biodiversity hotspot of relatively recent origin. We examined the phylogeography and landscape genetics of the Andean wax palm Ceroxylon echinulatum (Arecaceae) that occurs in two narrow bands of montane forests on each side of the Andes in Ecuador and northeastern Peru. First, we tested the hypothesis of C. echinulatum being a geographic cline species crossing the Andes in the Amotape-Huancabamba zone (AHZ) of southern Ecuador/northern Peru, as indicated by observations on fruit morphology. Second, we assessed the timeframe of cross-Andean divergence, and third, we investigated the impact of contemporary and historical landscape features on observed spatio-genetic patterns. Individual-based Bayesian clustering (BC) identified a northeastern, southeastern, southwestern, and northwestern cluster, with areas of genetic discontinuity coinciding with the Andes and the Giron-Paute deflection. F-statistics derived from BC suggested an east-to-west dispersal history. Population-based analyses revealed strong genetic structuring at both small and large geographic scales. Interpopulation relationships and Mantel tests strongly supported the cline model with cross-Andean dispersal in the AHZ. Along the cline, gene flow measured as F(ST) was mainly limited by distance, with less but significant impact of climatic friction. Coalescent analysis revealed that cross-Andean divergence took place during the Quaternary. Significant historical isolation (R(ST) > F(ST)) was found in the southwestern population. The current study illustrates a joint effect of founder dynamics, divergence by distance and historical isolation on patterns of Andean diversity and distribution.

  8. Hybridizing Daphnia communities from ten neighbouring lakes: spatio-temporal dynamics, local processes, gene flow and invasiveness.

    Science.gov (United States)

    Yin, Mingbo; Gießler, Sabine; Griebel, Johanna; Wolinska, Justyna

    2014-04-12

    In natural communities of cyclical parthenogens, rapid response to environmental change is enabled by switching between two reproduction modes. While long periods of asexual reproduction allow some clones to outcompete others, and may result in "clonal erosion", sexual reproduction restores genetic variation in such systems. Moreover, sexual reproduction may result in the formation of interspecific hybrids. These hybrids can then reach high abundances, through asexual clonal reproduction. In the present study, we explored genetic variation in water fleas of the genus Daphnia. The focus was on the short-term dynamics within several clonal assemblages from the hybridizing Daphnia longispina complex and the impact of gene flow at small spatial scales. Daphnia individuals belonged either to the parental species D. galeata and D. longispina, or to different hybrid classes, as identified by 15 microsatellite markers. The distribution and genotypic structure of parental species, but not hybrids, corresponded well with the geographical positions of the lakes. Within parental species, the genetic distance among populations of D. galeata was lower than among populations of D. longispina. Moreover, D. galeata dominance was associated with higher phosphorous load. Finally, there was no evidence for clonal erosion. Our results suggest that the contemporary structure of hybridizing Daphnia communities from ten nearby lakes is influenced by colonization events from neighbouring habitats as well as by environmental factors. Unlike the parental species, however, there was little evidence for successful dispersal of hybrids, which seem to be produced locally. Finally, in contrast to temporary Daphnia populations, in which a decrease in clonal diversity was sometimes detectable over a single growing season, the high clonal diversity and lack of clonal erosion observed here might result from repeated hatching of sexually produced offspring. Overall, our study provides insights into

  9. Habitat availability and gene flow influence diverging local population trajectories under scenarios of climate change: a place-based approach.

    Science.gov (United States)

    Schwalm, Donelle; Epps, Clinton W; Rodhouse, Thomas J; Monahan, William B; Castillo, Jessica A; Ray, Chris; Jeffress, Mackenzie R

    2016-04-01

    Ecological niche theory holds that species distributions are shaped by a large and complex suite of interacting factors. Species distribution models (SDMs) are increasingly used to describe species' niches and predict the effects of future environmental change, including climate change. Currently, SDMs often fail to capture the complexity of species' niches, resulting in predictions that are generally limited to climate-occupancy interactions. Here, we explore the potential impact of climate change on the American pika using a replicated place-based approach that incorporates climate, gene flow, habitat configuration, and microhabitat complexity into SDMs. Using contemporary presence-absence data from occupancy surveys, genetic data to infer connectivity between habitat patches, and 21 environmental niche variables, we built separate SDMs for pika populations inhabiting eight US National Park Service units representing the habitat and climatic breadth of the species across the western United States. We then predicted occurrence probability under current (1981-2010) and three future time periods (out to 2100). Occurrence probabilities and the relative importance of predictor variables varied widely among study areas, revealing important local-scale differences in the realized niche of the American pika. This variation resulted in diverse and - in some cases - highly divergent future potential occupancy patterns for pikas, ranging from complete extirpation in some study areas to stable occupancy patterns in others. Habitat composition and connectivity, which are rarely incorporated in SDM projections, were influential in predicting pika occupancy in all study areas and frequently outranked climate variables. Our findings illustrate the importance of a place-based approach to species distribution modeling that includes fine-scale factors when assessing current and future climate impacts on species' distributions, especially when predictions are intended to manage and

  10. Restriction to large-scale gene flow vs. regional panmixia among cold seep Escarpia spp. (Polychaeta, Siboglinidae).

    Science.gov (United States)

    Cowart, Dominique A; Huang, Chunya; Arnaud-Haond, Sophie; Carney, Susan L; Fisher, Charles R; Schaeffer, Stephen W

    2013-08-01

    The history of colonization and dispersal in fauna distributed among deep-sea chemosynthetic ecosystems remains enigmatic and poorly understood because of an inability to mark and track individuals. A combination of molecular, morphological and environmental data improves understanding of spatial and temporal scales at which panmixia, disruption of gene flow or even speciation may occur. Vestimentiferan tubeworms of the genus Escarpia are important components of deep -sea cold seep ecosystems, as they provide long-term habitat for many other taxa. Three species of Escarpia, Escarpia spicata [Gulf of California (GoC)], Escarpia laminata [Gulf of Mexico (GoM)] and Escarpia southwardae (West African Cold Seeps), have been described based on morphology, but are not discriminated through the use of mitochondrial markers (cytochrome oxidase subunit 1; large ribosomal subunit rDNA, 16S; cytochrome b). Here, we also sequenced the exon-primed intron-crossing Haemoglobin subunit B2 intron and genotyped 28 microsatellites to (i) determine the level of genetic differentiation, if any, among the three geographically separated entities and (ii) identify possible population structure at the regional scale within the GoM and West Africa. Results at the global scale support the occurrence of three genetically distinct groups. At the regional scale among eight sampling sites of E. laminata (n = 129) and among three sampling sites of E. southwardae (n = 80), no population structure was detected. These findings suggest that despite the patchiness and isolation of seep habitats, connectivity is high on regional scales. © 2013 John Wiley & Sons Ltd.

  11. Microstructural descriptors and cellular automata simulation of the effects of non-random nuclei location on recrystallization in two dimensions

    Directory of Open Access Journals (Sweden)

    Paulo Rangel Rios

    2006-06-01

    Full Text Available The effect of non-random nuclei location and the efficiency of microstructural descriptors in assessing such a situation are studied. Cellular automata simulation of recrystallization in two dimensions is carried out to simulate microstrutural evolution for nuclei distribution ranging from a periodic arrangement to clusters of nuclei. The simulation results are compared in detail with microstrutural descriptors normally used to follow transformation evolution. It is shown that the contiguity is particularly relevant to detect microstructural deviations from randomness. This work focuses on recrystallization but its results are applicable to any nucleation and growth transformation.

  12. Association genetics of oleoresin flow in loblolly pine: discovering genes and predicting phenotype for improved resistance to bark beetles and bioenergy potential.

    Science.gov (United States)

    Westbrook, Jared W; Resende, Marcio F R; Munoz, Patricio; Walker, Alejandro R; Wegrzyn, Jill L; Nelson, C Dana; Neale, David B; Kirst, Matias; Huber, Dudley A; Gezan, Salvador A; Peter, Gary F; Davis, John M

    2013-07-01

    Rapidly enhancing oleoresin production in conifer stems through genomic selection and genetic engineering may increase resistance to bark beetles and terpenoid yield for liquid biofuels. We integrated association genetic and genomic prediction analyses of oleoresin flow (g 24 h(-1)) using 4854 single nucleotide polymorphisms (SNPs) in expressed genes within a pedigreed population of loblolly pine (Pinus taeda) that was clonally replicated at three sites in the southeastern United States. Additive genetic variation in oleoresin flow (h(2) ≈ 0.12-0.30) was strongly correlated between years in which precipitation varied (r(a) ≈ 0.95), while the genetic correlation between sites declined from 0.8 to 0.37 with increasing differences in soil and climate among sites. A total of 231 SNPs were significantly associated with oleoresin flow, of which 81% were specific to individual sites. SNPs in sequences similar to ethylene signaling proteins, ABC transporters, and diterpenoid hydroxylases were associated with oleoresin flow across sites. Despite this complex genetic architecture, we developed a genomic prediction model to accelerate breeding for enhanced oleoresin flow that is robust to environmental variation. Results imply that breeding could increase oleoresin flow 1.5- to 2.4-fold in one generation.

  13. Molecular markers as a complementary tool in risk assessments: quantifying interspecific gene flow from triticale to spring wheat and durum wheat.

    Science.gov (United States)

    Kavanagh, Vanessa B; Hills, Melissa J; Goyal, Aakash; Randhawa, Harpinder S; Topinka, A Keith; Eudes, Francois; Hall, Linda M

    2013-08-01

    Triticale is being considered as a bioindustrial crop in Canada using genetic modification. Because related spring wheat (Triticum aestivum) and durum wheat (T. durum) may exhibit synchronous flowering and grow in proximity, determination of interspecific gene flow when triticale is the pollen donor is necessary to evaluate potential risk. Pollen-mediated gene flow risk assessments generally rely on phenotypic markers to detect hybridization but DNA markers could be powerful and less ambiguous in quantifying rare interspecific gene flow. Six cultivars representing four species [spring wheat, durum wheat, triticale and rye (Secale cereale)] were screened with 235 spring wheat and 27 rye SSR markers to evaluate transferability and polymorphism. Fifty-five polymorphic markers were used in conjunction with morphological characterization to quantify interspecific gene flow from a blue aleurone (BA) triticale line to two spring wheat cultivars (AC Barrie and AC Crystal) and one durum wheat cultivar (AC Avonlea). Approximately 1.9 Million seeds from small plot experiments were visually screened in comparison with known hybrid seed. In total 2031 putative hybrids were identified and 448 germinated. Morphological analysis of putative hybrid plants identified five hybrids while molecular analysis identified 11 hybrids and two were common to both. Combined, 14 hybrids were confirmed: 10 spring wheat × triticale (0.0008 % of harvested seed): seven AC Barrie × BA triticale (0.001 %) and three AC Crystal × BA triticale (0.0005 %); and four durum wheat × triticale (0.0006 %). The occurrence of rare hybrids does not present a substantial risk to the development of GM triticale.

  14. Population genetic structure in Myrtus communis L. in a chronically fragmented landscape in the Mediterranean: can gene flow counteract habitat perturbation?

    Science.gov (United States)

    Albaladejo, R G; Carrillo, L F; Aparicio, A; Fernández-Manjarrés, J F; González-Varo, J P

    2009-05-01

    Ancient managed landscapes provide ideal opportunities to assess the consequences of habitat fragmentation on the patterns of genetic diversity and gene flow in long-lived plant species. Using amplified fragment length polymorphism (AFLP) and allozyme markers, we quantified seed-mediated gene flow and population genetic diversity and structure in 14 populations of Myrtus communis (myrtle), a common endozoochorous shrub species of forest patches in lowland agricultural Mediterranean areas. Overall, allozyme diversity for myrtle was low (P(95) = 25%; A = 1.411; H(e) = 0.085) compared to other known populations, and a significant portion of populations (57%) had lower levels of allelic diversity and/or heterozygosity than expected at random, as shown by simulated resampling of the whole diversity of the landscape. We found significant correlations between allozyme variability and population size and patch isolation, but no significant inbreeding in any population. Genetic differentiation among populations for both allozyme and AFLP markers was significant (Phi(ST) = 0.144 and Phi(ST) = 0.142, respectively) but an isolation-by-distance pattern was not detected. Assignment tests on AFLP data indicated a high immigration rate in the populations (ca. 20-22%), likely through effective seed dispersal across the landscape by birds and mammals. Our results suggest that genetic isolation is not the automatic outcome of habitat destruction since substantial levels of seed-mediated gene flow are currently detectable. However, even moderate rates of gene flow seem insufficient in this long-lived species to counteract the genetic erosion and differentiation imposed by chronic habitat destruction.

  15. Adaptation to a seasonally varying environment: a strong latitudinal cline in reproductive diapause combined with high gene flow in Drosophila montana

    Science.gov (United States)

    Tyukmaeva, Venera I; Salminen, Tiina S; Kankare, Maaria; Knott, K Emily; Hoikkala, Anneli

    2011-01-01

    Adaptation to seasonal changes in the northern hemisphere includes an ability to predict the forthcoming cold season from gradual changes in environmental cues early enough to prepare for the harsh winter conditions. The magnitude and speed of changes in these cues vary between the latitudes, which induces strong selection pressures for local adaptation. We studied adaptation to seasonal changes in Drosophila montana, a northern maltfly, by defining the photoperiodic conditions leading to adult reproductive diapause along a latitudinal cline in Finland and by measuring genetic differentiation and the amount of gene flow between the sampling sites with microsatellites. Our data revealed a clear correlation between the latitude and the critical day length (CDL), in which half of the females of different cline populations enter photoperiodic reproductive diapause. There was no sign of limited gene flow between the cline populations, even though these populations showed isolation by distance. Our results show that local adaptation may occur even in the presence of high gene flow, when selection for locally adaptive life-history traits is strong. A wide range of variation in the CDLs of the fly strains within and between the cline populations may be partly due to gene flow and partly due to the opposing selection pressures for fly reproduction and overwinter survival. This variation in the timing of diapause will enhance populations’ survival over the years that differ in the severity of the winter and in the length of the warm period and may also help them respond to long-term changes in environmental conditions. PMID:22393492

  16. CHO-S Antibody Titers >1 Gram/Liter Using Flow Electroporation-Mediated Transient Gene Expression followed by Rapid Migration to High-Yield Stable Cell Lines

    OpenAIRE

    Steger, Krista; Brady, James; WANG, WEILI; Duskin, Meg; Donato, Karen; Peshwa, Madhusudan

    2015-01-01

    In recent years, researchers have turned to transient gene expression (TGE) as an alternative to CHO stable cell line generation for early-stage antibody development. Despite advances in transfection methods and culture optimization, the majority of CHO-based TGE systems produce insufficient antibody titers for extensive use within biotherapeutic development pipelines. Flow electroporation using the MaxCyte STX Scalable Transfection System is a highly efficient, scalable means of CHO-based TG...

  17. Landscape features influence gene flow as measured by cost-distance and genetic analyses: a case study for giant pandas in the Daxiangling and Xiaoxiangling Mountains

    OpenAIRE

    Wei Fuwen; Zhang Shanning; Meng Tao; Zhan Xiangjiang; Zhu Lifeng

    2010-01-01

    Abstract Background Gene flow maintains genetic diversity within a species and is influenced by individual behavior and the geographical features of the species' habitat. Here, we have characterized the geographical distribution of genetic patterns in giant pandas (Ailuropoda melanoleuca) living in four isolated patches of the Xiaoxiangling and Daxiangling Mountains. Three geographic distance definitions were used with the "isolation by distance theory": Euclidean distance (EUD), least-cost p...

  18. Contrasting Effects of Historical Sea Level Rise and Contemporary Ocean Currents on Regional Gene Flow of Rhizophora racemosa in Eastern Atlantic Mangroves.

    Science.gov (United States)

    Ngeve, Magdalene N; Van der Stocken, Tom; Menemenlis, Dimitris; Koedam, Nico; Triest, Ludwig

    2016-01-01

    Mangroves are seafaring taxa through their hydrochorous propagules that have the potential to disperse over long distances. Therefore, investigating their patterns of gene flow provides insights on the processes involved in the spatial genetic structuring of populations. The coastline of Cameroon has a particular geomorphological history and coastal hydrology with complex contemporary patterns of ocean currents, which we hypothesize to have effects on the spatial configuration and composition of present-day mangroves within its spans. A total of 982 trees were sampled from 33 transects (11 sites) in 4 estuaries. Using 11 polymorphic SSR markers, we investigated genetic diversity and structure of Rhizophora racemosa, a widespread species in the region. Genetic diversity was low to moderate and genetic differentiation between nearly all population pairs was significant. Bayesian clustering analysis, PCoA, estimates of contemporary migration rates and identification of barriers to gene flow were used and complemented with estimated dispersal trajectories of hourly released virtual propagules, using high-resolution surface current from a mesoscale and tide-resolving ocean simulation. These indicate that the Cameroon Volcanic Line (CVL) is not a present-day barrier to gene flow. Rather, the Inter-Bioko-Cameroon (IBC) corridor, formed due to sea level rise, allows for connectivity between two mangrove areas that were isolated during glacial times by the CVL. Genetic data and numerical ocean simulations indicated that an oceanic convergence zone near the Cameroon Estuary complex (CEC) presents a strong barrier to gene flow, resulting in genetic discontinuities between the mangrove areas on either side. This convergence did not result in higher genetic diversity at the CEC as we had hypothesized. In conclusion, the genetic structure of Rhizophora racemosa is maintained by the contrasting effects of the contemporary oceanic convergence and historical climate change

  19. Simultaneous evaluation of paternal and maternal immigrant gene flow and the implications for the overall genetic composition of Pinus densiflora dispersed seeds.

    Science.gov (United States)

    Iwaizumi, Masakazu G; Takahashi, Makoto; Watanabe, Atsushi; Ubukata, Masatoshi

    2010-01-01

    When considering the genetic implications of immigrant gene flow, it is important to evaluate both the proportions of immigrant gametes and their genetic composition. We simultaneously investigated paternal and maternal gene flow in dispersed seeds in a natural population of Pinus densiflora located along a ridge. The paternity and maternity of a total of 454 dispersed seeds (in 2004 and 2005) were accurately and separately assigned to 454 candidate adult trees, by analyzing the nuclear DNA of both diploid biparentally derived embryos and haploid maternally derived megagametophytes of the seeds. The relative genetic diversities and differences between within-population and immigrant groups of both paternally and maternally derived gametes (4 groups) that formed the genotypes of the seeds were evaluated. Using 8 microsatellite markers, we found that 64.0-72.6% of paternally derived gametes, and 17.8-20.2% of maternally derived gametes, were from other populations. Principal coordinate analysis showed that the 4 gamete groups tended to be plotted at different locations on the scattergram, indicating that they each have different genetic compositions. Substantial paternal and maternal immigrant gene flow occurred in this population, and therefore, the overall genetic variation of dispersed seeds is enhanced by both paternally and maternally derived immigrant gametes.

  20. The Mediterranean Sea as a barrier to gene flow: evidence from variation in and around the F7 and F12 genomic regions

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    Stoneking Mark

    2010-03-01

    Full Text Available Abstract Background The Mediterranean has a long history of interactions among different peoples. In this study, we investigate the genetic relationships among thirteen population samples from the broader Mediterranean region together with three other groups from the Ivory Coast and Bolivia with a particular focus on the genetic structure between North Africa and South Europe. Analyses were carried out on a diverse set of neutral and functional polymorphisms located in and around the coagulation factor VII and XII genomic regions (F7 and F12. Results Principal component analysis revealed a significant clustering of the Mediterranean samples into North African and South European groups consistent with the results from the hierarchical AMOVA, which showed a low but significant differentiation between groups from the two shores. For the same range of geographic distances, populations from each side of the Mediterranean were found to differ genetically more than populations within the same side. To further investigate this differentiation, we carried out haplotype analyses, which provided partial evidence that sub-Saharan gene flow was higher towards North Africa than South Europe. Conclusions As there is no consensus between the two genomic regions regarding gene flow through the Sahara, it is hard to reach a solid conclusion about its role in the differentiation between the two Mediterranean shores and more data are necessary to reach a definite conclusion. However our data suggest that the Mediterranean Sea was at least partially a barrier to gene flow between the two shores.

  1. The Mediterranean Sea as a barrier to gene flow: evidence from variation in and around the F7 and F12 genomic regions.

    Science.gov (United States)

    Athanasiadis, Georgios; González-Pérez, Emili; Esteban, Esther; Dugoujon, Jean-Michel; Stoneking, Mark; Moral, Pedro

    2010-03-27

    The Mediterranean has a long history of interactions among different peoples. In this study, we investigate the genetic relationships among thirteen population samples from the broader Mediterranean region together with three other groups from the Ivory Coast and Bolivia with a particular focus on the genetic structure between North Africa and South Europe. Analyses were carried out on a diverse set of neutral and functional polymorphisms located in and around the coagulation factor VII and XII genomic regions (F7 and F12). Principal component analysis revealed a significant clustering of the Mediterranean samples into North African and South European groups consistent with the results from the hierarchical AMOVA, which showed a low but significant differentiation between groups from the two shores. For the same range of geographic distances, populations from each side of the Mediterranean were found to differ genetically more than populations within the same side. To further investigate this differentiation, we carried out haplotype analyses, which provided partial evidence that sub-Saharan gene flow was higher towards North Africa than South Europe. As there is no consensus between the two genomic regions regarding gene flow through the Sahara, it is hard to reach a solid conclusion about its role in the differentiation between the two Mediterranean shores and more data are necessary to reach a definite conclusion. However our data suggest that the Mediterranean Sea was at least partially a barrier to gene flow between the two shores.

  2. Genetic Variation, Structure, and Gene Flow in a Sloth Bear (Melursus ursinus Meta-Population in the Satpura-Maikal Landscape of Central India.

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    Trishna Dutta

    Full Text Available Sloth bears (Melursus ursinus are endemic to the Indian subcontinent. As a result of continued habitat loss and degradation over the past century, sloth bear populations have been in steady decline and now exist only in isolated or fragmented habitat across the entire range. We investigated the genetic connectivity of the sloth bear meta-population in five tiger reserves in the Satpura-Maikal landscape of central India. We used noninvasively collected fecal and hair samples to obtain genotypic information using a panel of seven polymorphic loci. Out of 194 field collected samples, we identified 55 individuals in this meta-population. We found that this meta-population has moderate genetic variation, and is subdivided into two genetic clusters. Further, we identified five first-generation migrants and signatures of contemporary gene flow. We found evidence of sloth bears in the corridor between the Kanha and Pench Tiger Reserves, and our results suggest that habitat connectivity and corridors play an important role in maintaining gene flow in this meta-population. These corridors face several anthropogenic and infrastructure development threats that have the potential to sever ongoing gene flow, if policies to protect them are not put into action immediately.

  3. Genetic Variation, Structure, and Gene Flow in a Sloth Bear (Melursus ursinus) Meta-Population in the Satpura-Maikal Landscape of Central India.

    Science.gov (United States)

    Dutta, Trishna; Sharma, Sandeep; Maldonado, Jesús E; Panwar, Hemendra Singh; Seidensticker, John

    2015-01-01

    Sloth bears (Melursus ursinus) are endemic to the Indian subcontinent. As a result of continued habitat loss and degradation over the past century, sloth bear populations have been in steady decline and now exist only in isolated or fragmented habitat across the entire range. We investigated the genetic connectivity of the sloth bear meta-population in five tiger reserves in the Satpura-Maikal landscape of central India. We used noninvasively collected fecal and hair samples to obtain genotypic information using a panel of seven polymorphic loci. Out of 194 field collected samples, we identified 55 individuals in this meta-population. We found that this meta-population has moderate genetic variation, and is subdivided into two genetic clusters. Further, we identified five first-generation migrants and signatures of contemporary gene flow. We found evidence of sloth bears in the corridor between the Kanha and Pench Tiger Reserves, and our results suggest that habitat connectivity and corridors play an important role in maintaining gene flow in this meta-population. These corridors face several anthropogenic and infrastructure development threats that have the potential to sever ongoing gene flow, if policies to protect them are not put into action immediately.

  4. Intracorneal Rings (INTACS SK) Might be Beneficial in Keratoconus; A Prospective Nonrandomized Study.

    Science.gov (United States)

    A Ibrahim, Tarek; Elmor, Osama

    2013-01-01

    In order to determine the effect of intracorneal rings (Intacs SK), when implanted in keratoconic patients, on corneal curvature, Uncorrected Visual Acuity (UCVA), Best Corrected Visual Acuity (BCVA) and on the progression of the cone through three years follow-up period. In this prospective nonrandomized study 114 eyes of 71 keratoconic patients (38 females and 33 males) were implanted with Intacs SK. Incisions were always made in the steep meridian. UCVA, BCVA, Corneal Topography (TMS) were measured pre and postoperatively and at intervals of 1, 3, 6 & 12 months then yearly for 3 consecutive years. Preoperative mean k-reading was 52.53 and 48.18, 49.56, 49.17, 48.51, 48.15 & 48.01 at 1, 3, 6, 12, 24 & 36 months postoperatively (P‹0.01). In terms of UCVA, 15.64% of patients gained more than 3 lines and 69.73% gained 1-3 lines with a total of 85.37% of patients gaining lines compared to their preoperative UCVA (P‹0.01) while 14.63% of cases did not gain any lines at 1 month postoperative. At three months postoperatively, 12.64% gained more than 3 lines, 71.15% gained 1-3 lines with a total of 83.79% while 16.21% did not gain any lines. Three years postoperative 11.82% of cases gained more than 3 lines, 73.23% gained 1-3 lines with a total of 85.05% while 14.95% did not gain any lines (P‹0.01). With regard to BCVA, 19.73% gained more than 3 lines, 68.26% gained 1-3 lines with a total of 87.99% of cases gaining lines compared to their preoperative BCVA (P‹0.01) while 12.01% did not gained any lines at 1 month postoperative. At three months postoperatively, 14.96% gained more than 3 lines, 70.19% gained 1-3 lines with a total of 85.15% while 14.85% did not gain any lines. Three years postoperative, 12.17% gained more than 3 lines, 71.78% gained 1-3 lines with a total of 83.95% (P‹0.01) while 16.05% did not gain any lines. No eyes lost any lines as it pertained to UCVA & BCVA. Despite the fluctuation of k-readings, UCVA and BCVA in the first 3 months, which

  5. The phylogeographic importance of the Strait of Gibraltar as a gene flow barrier in terrestrial arthropods: a case study with the scorpion Buthus occitanus as model organism.

    Science.gov (United States)

    Gantenbein, Benjamin; Largiadèr, Carlo R

    2003-07-01

    The phylogenetic relationship between Buthus occitanus populations across the Strait of Gibraltar was investigated using nuclear 18S/ITS-1 DNA sequences and mitochondrial 16S and COI DNA sequences. All analyses showed that the European samples are highly separated from North African samples, and also suggest the existence of three main groups within this species complex, i.e., an European, an Atlas (=Moroccan samples) and a Tell-Atlas group (=Tunisian samples). The European clade was subdivided into three distinct subclades. The application of a previous calibration of the molecular clock of another buthid species suggested that most of the detected mitochondrial DNA lineages including the European lineages are about three times older than the re-opening of the Gibraltar Strait, and consequently, that other and older vicariant events are responsible for the observed phylogeographic structure of this species complex. Concerning the Moroccan samples, a discordance between nuclear and mitochondrial gene markers was observed. The 18S/ITS-1 gene tree could not resolve the phylogenetic relationships among the Moroccan B. occitanus subspecies and the closely related species B. atlantis, whereas mitochondrial genes suggested the co-existence of several old phylogenetic lineages in Morocco. We hypothesized that this difference may be explained by male-biased gene flow and gene conversion at the tandemly repeated 18S/ITS-1 gene regions.

  6. Sequence diversity patterns suggesting balancing selection in partially sex-linked genes of the plant Silene latifolia are not generated by demographic history or gene flow.

    Science.gov (United States)

    Guirao-Rico, Sara; Sánchez-Gracia, Alejandro; Charlesworth, Deborah

    2017-03-01

    DNA sequence diversity in genes in the partially sex-linked pseudoautosomal region (PAR) of the sex chromosomes of the plant Silene latifolia is higher than expected from within-species diversity of other genes. This could be the footprint of sexually antagonistic (SA) alleles that are maintained by balancing selection in a PAR gene (or genes) and affect polymorphism in linked genome regions. SA selection is predicted to occur during sex chromosome evolution, but it is important to test whether the unexpectedly high sequence polymorphism could be explained without it, purely by the combined effects of partial linkage with the sex-determining region and the population's demographic history, including possible introgression from Silene dioica. To test this, we applied approximate Bayesian computation-based model choice to autosomal sequence diversity data, to find the most plausible scenario for the recent history of S. latifolia and then to estimate the posterior density of the most relevant parameters. We then used these densities to simulate variation to be expected at PAR genes. We conclude that an excess of variants at high frequencies at PAR genes should arise in S. latifolia populations only for genes with strong associations with fully sex-linked genes, which requires closer linkage with the fully sex-linked region than that estimated for the PAR genes where apparent deviations from neutrality were observed. These results support the need to invoke selection to explain the S. latifolia PAR gene diversity, and encourage further work to test the possibility of balancing selection due to sexual antagonism. © 2016 John Wiley & Sons Ltd.

  7. A meta-analysis of nonrandomized effectiveness studies on outpatient cognitive behavioral therapy for adult anxiety disorders.

    Science.gov (United States)

    Hans, Eva; Hiller, Wolfgang

    2013-12-01

    The primary aim of this study was to assess the overall effectiveness of individual and group outpatient cognitive behavioral therapy (CBT) for adults with a primary anxiety disorder in routine clinical practice. We conducted a random effects meta-analysis of 71 nonrandomized effectiveness studies on outpatient individual and group CBT for adult anxiety disorders. Standardized mean gain effect sizes pre- to posttreatment, and posttreatment to follow-up are reported for disorder-specific symptoms, depression, and general anxiety. The mean dropout from CBT is reported. Outpatient CBT was effective in reducing disorder-specific symptoms in completer (d=0.90-1.91) and intention-to-treat samples (d=0.67-1.45). Moderate to large (d=0.54-1.09) and small to large effect sizes (d=0.42-0.97) were found for depressive and general anxiety symptoms posttreatment. Across all anxiety disorders, the weighted mean dropout rate was 15.06%. Posttreatment gains for disorder-specific anxiety were maintained 12months after completion of therapy. CBT for adult anxiety disorders is very effective and widely accepted in routine practice settings. However, the methodological and reporting quality of nonrandomized effectiveness studies must be improved. © 2013.

  8. Discovering non-random segregation of sister chromatids: The naïve treatment of a premature discovery

    Directory of Open Access Journals (Sweden)

    Karl G. Lark

    2013-02-01

    Full Text Available The discovery of non-random chromosome segregation is discussed from the perspective of what was known in1965 and1966. The distinction between daughter, parent or grandparent strands of DNA was developed in a bacterial system and led to the discovery that multiple copies of DNA elements of bacteria are not distributed randomly with respect to the age of the template strand. Experiments with higher eukaryotic cells demonstrated that during mitosis Mendel’s laws were violated; and the initial serendipitous choice of eukaryotic cell system led to the striking example of non-random segregation of parent and grand-parent DNA template strands in primary cultures of cells derived from mouse embryos. Attempts to extrapolate these findings to established TC lines demonstrated that the property could be lost. Experiments using plant root tips demonstrated that the phenomenon exists in plants and that it was, at some level, under genetic control. Despite publication in major journals and symposia (Lark et al. (1966a; Lark (1967a; 1967b; 1969, 1969a; 1969b the potential implications of these findings were ignored for several decades. Here we explore possible reasons for the pre-maturity (Stent, 1972 of this discovery.

  9. Cell-type-specific Jumonji histone demethylase gene expression in the healthy rat CNS: detection by a novel flow cytometry method

    Directory of Open Access Journals (Sweden)

    Stephanie M.C. Smith

    2014-05-01

    Full Text Available Our understanding of how histone demethylation contributes to the regulation of basal gene expression in the brain is largely unknown in any injury model, and especially in the healthy adult brain. Although Jumonji genes are often regulated transcriptionally, cell-specific gene expression of Jumonji histone demethylases in the brain remains poorly understood. Thus, in the present study we profiled the mRNA levels of 26 Jumonji genes in microglia (CD11b+, neurons (NeuN+ and astrocytes (GFAP+ from the healthy adult rat brain. We optimized a method combining a mZBF (modified zinc-based fixative and FCM (flow cytometry to simultaneously sort cells from non-transgenic animals. We evaluated cell-surface, intracellular and nuclear proteins, including histones, as well as messenger- and micro-RNAs in different cell types simultaneously from a single-sorted sample. We found that 12 Jumonji genes were differentially expressed between adult microglia, neurons and astrocytes. While JMJD2D was neuron-restricted, PHF8 and JMJD1C were expressed in all three cell types although the expression was highest in neurons. JMJD3 and JMJD5 were expressed in all cell types, but were highly enriched in microglia; astrocytes had the lowest expression of UTX and JHDM1D. Levels of global H3K27 (H3 lysine 27 methylation varied among cell types and appeared to be lowest in microglia, indicating that differences in basal gene expression of specific Jumonji histone demethylases may contribute to cell-specific gene expression in the CNS (central nervous system. This multiparametric technique will be valuable for simultaneously assaying chromatin modifications and gene regulation in the adult CNS.

  10. Informal “Seed” Systems and the Management of Gene Flow in Traditional Agroecosystems: The Case of Cassava in Cauca, Colombia

    Science.gov (United States)

    Dyer, George A.; González, Carolina; Lopera, Diana Carolina

    2011-01-01

    Our ability to manage gene flow within traditional agroecosystems and their repercussions requires understanding the biology of crops, including farming practices' role in crop ecology. That these practices' effects on crop population genetics have not been quantified bespeaks lack of an appropriate analytical framework. We use a model that construes seed-management practices as part of a crop's demography to describe the dynamics of cassava (Manihot esculenta Crantz) in Cauca, Colombia. We quantify several management practices for cassava—the first estimates of their kind for a vegetatively-propagated crop—describe their demographic repercussions, and compare them to those of maize, a sexually-reproduced grain crop. We discuss the implications for gene flow, the conservation of cassava diversity, and the biosafety of vegetatively-propagated crops in centers of diversity. Cassava populations are surprisingly open and dynamic: farmers exchange germplasm across localities, particularly improved varieties, and distribute it among neighbors at extremely high rates vis-à-vis maize. This implies that a large portion of cassava populations consists of non-local germplasm, often grown in mixed stands with local varieties. Gene flow from this germplasm into local seed banks and gene pools via pollen has been documented, but its extent remains uncertain. In sum, cassava's biology and vegetative propagation might facilitate pre-release confinement of genetically-modified varieties, as expected, but simultaneously contribute to their diffusion across traditional agroecosystems if released. Genetically-modified cassava is unlikely to displace landraces or compromise their diversity; but rapid diffusion of improved germplasm and subsequent incorporation into cassava landraces, seed banks or wild populations could obstruct the tracking and eradication of deleterious transgenes. Attempts to regulate traditional farming practices to reduce the risks could compromise cassava

  11. Information and information flow an introduction

    CERN Document Server

    Bremer, Manuel

    2004-01-01

    This book is conceived as an introductory text into the theory of syntactic and semantic information, and information flow. Syntactic information theory is concerned with the information contained in the very fact that some signal has a non-random structure. Semantic information theory is concerned with the meaning or information content of messages and the like. The theory of information flow is concerned with deriving some piece of information from another. The main part will take us to situation semantics as a foundation of modern approaches in information theory. We give a brief overview o

  12. Current versus historical population sizes in vertebrate species with high gene flow: a comparison based on mitochondrial DNA lineages and inbreeding theory for neutral mutations.

    Science.gov (United States)

    Avise, J C; Ball, R M; Arnold, J

    1988-07-01

    Using inbreeding theory as applied to neutral alleles inherited maternally, we generate expected probability distributions of times to identity by descent for random pairs of mitochondrial genotypes within a population or within an entire species characterized by high gene flow. For comparisons with these expectations, empirical distributions of times to most recent common ancestry were calculated (by conventional mtDNA clock calibrations) from mtDNA haplotype distances observed within each of three vertebrate species--American eels, hardhead catfish, and redwinged blackbirds. These species were chosen for analysis because census population size in each is currently large and because both genetic and life-history data are consistent with the postulate that historical gene flow within these species has been high. The observed molecular distances among mtDNA lineages were two to three orders of magnitude lower than predicted from census sizes of breeding females, suggesting that rate of mtDNA evolution is decelerated in these species and/or that long-term effective population size is vastly smaller than present-day population size. Several considerations point to the latter possibility as most likely. The genetic structure of any species is greatly influenced by historical demography; even for species that are currently abundant, mtDNA gene lineages appear to have been channeled through fairly small numbers of ancestors.

  13. Effect of host plant chemistry on genetic differentiation and reduction of gene flow among Anastrepha fraterculus (Diptera: Tephritidae) populations exploiting sympatric, synchronic hosts.

    Science.gov (United States)

    Oroño, Luis; Paulin, Laura; Alberti, Andrea C; Hilal, Mirna; Ovruski, Sergio; Vilardi, Juan C; Rull, Juan; Aluja, Martin

    2013-08-01

    Herbivore host specialization includes changes in behavior, driven by locally induced adaptations to specific plants. These adaptations often result in sexual isolation that can be gauged through detection of reduced gene flow between host associated populations. Hypothetically, reduced gene flow can be mediated both by differential response to specific plant kairomones and by the influence of larval diet on some adult traits such as pheromone composition. These hypotheses could serve as a model to explain rapid radiation of phytophagous tephritid fruit flies, a group that includes several complexes of cryptic species. The South American Fruit Fly Anastrepha fraterculus (Wiedemann) is a complex of at least seven cryptic species among which pheromone mediated sexual isolation resulted in rapid differentiation. Cryptic species also exhibit differences in host affiliation. In search of a model explaining rapid radiation in this group, we studied host plant chemical composition and genetic structure of three host associated sympatric populations of A. fraterculus. Chemical composition among host plant fruit varied widely both for nutrient and potentially toxic secondary metabolite content. Adaptation to plant chemistry appears to have produced population differentiation. We found host mediated differentiation to be stronger between populations exploiting sympatric synchronic hosts differing in chemical composition, than between populations that exploit hosts that fruit in succession. Gene flow among such host associated populations was extremely low. We propose as a working hypothesis for future research, that for those differences to persist over time, isolating mechanisms such as male produced sex pheromones and female preferences resulting from adaptation to different larval diets should evolve.

  14. From glacial refugia to modern populations: new assemblages of organelle genomes generated by differential cytoplasmic gene flow in transcontinental black spruce.

    Science.gov (United States)

    Gérardi, Sébastien; Jaramillo-Correa, Juan P; Beaulieu, Jean; Bousquet, Jean

    2010-12-01

    Assessing species' range-wide cytoplasmic diversity provides valuable insights regarding their dispersal and adaptive potential in a changing environment. Transcontinental chloroplast (cpDNA) and mitochondrial DNA (mtDNA) population structures were compared to identify putative ancestral and new cytoplasmic genome assemblages in black spruce (Picea mariana), a North American boreal conifer. Mean within-population diversity and allelic richness for cpSSR markers were 0.80 and 4.21, respectively, and diminished westward. Population differentiation based on G(ST) was lower for cpDNA than for mtDNA (G(ST) =0.104 and 0.645, respectively) but appeared comparable when estimated using Jost differentiation index (D=0.459 and 0.537, respectively). Further analyses resulted in the delineation of at least three genetically distinct cpDNA lineages partially congruent with those inferred from mtDNA data, which roughly corresponded to western, central and eastern Canada. Additionally, the patterns of variation in Alaska for both cpDNA and mtDNA markers suggested that black spruce survived the last glacial maximum in this northern region. The range-wide comparison of the geographic extent of cytoplasmic DNA lineages revealed that extensive pollen gene flow between ancestral lineages occurred preferentially from west to east during the postglacial expansion of the species, while seed-mediated gene flow remained geographically restricted. This differential gene flow promoted intraspecific cytoplasmic capture that generated new assemblages of cpDNA and mtDNA genomes during the Holocene. Hence, black spruce postglacial colonization unexpectedly resulted in an increase in genetic diversity with possible adaptive consequences. © 2010 Blackwell Publishing Ltd.

  15. Role of selection and gene flow in population differentiation at the edge vs. interior of the species range differing in climatic conditions.

    Science.gov (United States)

    Volis, S; Ormanbekova, D; Shulgina, I

    2016-04-01

    Evaluating the relative importance of neutral and adaptive processes as determinants of population differentiation across environments is a central theme of evolutionary biology. We applied the QST-FST comparison flanked by a direct test for local adaptation to infer the role of climate-driven selection and gene flow in population differentiation of an annual grass Avena sterilis in two distinct parts of the species range, edge and interior, which represent two globally different climates, desert and Mediterranean. In a multiyear reciprocal transplant experiment, the plants of desert and Mediterranean origin demonstrated home advantage, and population differentiation in several phenotypic traits related to reproduction exceeded neutral predictions, as determined by comparisons of QST values with theoretical FST distributions. Thus, variation in these traits likely resulted from local adaptation to desert and Mediterranean environments. The two separate common garden experiments conducted with different experimental design revealed that two population comparisons, in contrast to multi-population comparisons, are likely to detect population differences in virtually every trait, but many of these differences reflect effects of local rather than regional environment. We detected a general reduction in neutral (SSR) genetic variation but not in adaptive quantitative trait variation in peripheral desert as compared with Mediterranean core populations. On the other hand, the molecular data indicated intensive gene flow from the Mediterranean core towards desert periphery. Although species range position in our study (edge vs. interior) was confounded with climate (desert vs. Mediterranean), the results suggest that the gene flow from the species core does not have negative consequences for either performance of the peripheral plants or their adaptive potential.

  16. Revolution of S-stars and oscillation of solar and terrestrial observables: nonrandom coincidence of periods

    CERN Document Server

    Rusov, V D; Eingorn, M V

    2015-01-01

    A striking coincidence of revolution periods of S-stars orbiting a supermassive black hole at the Galactic Center of the Milky Way and oscillation periods of such solar and terrestrial observables as the sunspot number, the geomagnetic field Y-component and the global temperature is established on basis of the corresponding experimental data. Rejecting randomness of this discovered coincidence, we put forward a hypothesis that modulation of dark matter flows in the Milky Way by the S-stars is responsible for such a frequency transfer from the Galactic Center to the Solar System.

  17. Genetic diversity and gene flow of humans, Plasmodium falciparum, and Anopheles farauti s.s. of Vanuatu: inferred malaria dispersal and implications for malaria control.

    Science.gov (United States)

    Lum, J K; Kaneko, A; Taleo, G; Amos, M; Reiff, D M

    2007-08-01

    A comparison of the patterns of gene flow within and between islands and the genetic diversities of the three species required for malaria transmission (humans, Plasmodium falciparum, and Anopheles farauti s.s.) within the model island system of Vanuatu, shows that the active dispersal of An. farauti s.s. is responsible for within island movement of parasites. In contrast, since both P. falciparum and An. farauti s.s. populations are largely restricted to islands, movement of parasites between islands is likely due to human transport. Thus, control of vectors is crucial for controlling malaria within islands, while control of human movement is essential to control malaria transmission across the archipelago.

  18. Determining gene flow and the influence of selection across the equatorial barrier of the East Pacific Rise in the tube-dwelling polychaete Alvinella pompejana

    Directory of Open Access Journals (Sweden)

    Plouviez Sophie

    2010-07-01

    Full Text Available Abstract Background Comparative phylogeography recently performed on the mitochondrial cytochrome oxidase I (mtCOI gene from seven deep-sea vent species suggested that the East Pacific Rise fauna has undergone a vicariant event with the emergence of a north/south physical barrier at the Equator 1-2 Mya. Within this specialised fauna, the tube-dwelling polychaete Alvinella pompejana showed reciprocal monophyly at mtCOI on each side of the Equator (9°50'N/7°25'S, suggesting potential, ongoing allopatric speciation. However, the development of a barrier to gene flow is a long and complex process. Secondary contact between previously isolated populations can occur when physical isolation has not persisted long enough to result in reproductive isolation between genetically divergent lineages, potentially leading to hybridisation and subsequent allelic introgression. The present study evaluates the strength of the equatorial barrier to gene flow and tests for potential secondary contact zones between A. pompejana populations by comparing the mtCOI gene with nuclear genes. Results Allozyme frequencies and the analysis of nucleotide polymorphisms at three nuclear loci confirmed the north/south genetic differentiation of Alvinella pompejana populations along the East Pacific Rise. Migration was oriented north-to-south with a moderate allelic introgression between the two geographic groups over a narrow geographic range just south of the barrier. Multilocus analysis also indicated that southern populations have undergone demographic expansion as previously suggested by a multispecies approach. A strong shift in allozyme frequencies together with a high level of divergence between alleles and a low number of 'hybrid' individuals were observed between the northern and southern groups using the phosphoglucomutase gene. In contrast, the S-adenosylhomocysteine hydrolase gene exhibited reduced diversity and a lack of population differentiation possibly due to

  19. Pollen-mediated gene flow in a highly fragmented landscape: consequences for defining a conservation strategy of the relict Laperrine's olive.

    Science.gov (United States)

    Besnard, Guillaume; Baali-Cherif, Djamel; Bettinelli-Riccardi, Sandra; Parietti, Davis; Bouguedoura, Nadia

    2009-07-01

    In the present central Saharan conditions, the Laperrine's olive regeneration has never been observed and its populations are locally threatened. The production of plants originating from seeds was proposed as a multiplication strategy. In order to determine the impact of sexual reproduction, seeds issued from ten mothers (sampled from four locations in the Hoggar, Algeria) were genotyped using microsatellites. Compared to the initial population, a significant lost of allelic richness was revealed, indicating that our seed sampling was not representative of the local gene diversity. Paternity analyses allowed measurement of the effective pollen-mediated gene flow within patches. Preferential mating between some genotypes was revealed. A trend for a higher multipaternity on seeds collected on trees from relatively large patches was also observed. Lastly, seedlings issued from trees of small patches displayed low growth performance. The implications of our observations in the development of an efficient conservation strategy by seeds are discussed.

  20. Regulation of pepc gene expression in Anabaena sp. PCC 7120 and its effects on cyclic electron flow around photosystem I and tolerances to environmental stresses

    Institute of Scientific and Technical Information of China (English)

    Xiao-Hui Jia; Peng-Peng Zhang; Ding-Ji Shi; Hua-Ling Mi; Jia-Cheng Zhu; Xi-Wen Huang; Pei-Min He

    2015-01-01

    Since pepc gene encoding phosphoenolpyruvate carboxylase (PEPCase) has been cloned from Anabaena sp. PCC 7120 and other cyanobacteria, the effects of pepc gene expression on photosynthesis have not been reported yet. In this study, we constructed mutants containing either upregu-lated (forward) or downregulated (reverse) pepc gene in Anabaena sp. PCC 7120. Results from real‐time quantitative polymerase chain reaction (RT‐qPCR), Western blot and enzymatic analysis showed that PEPCase activity was signifi-cantly reduced in the reverse mutant compared with the wild type, and that of the forward mutant was obviously increased. Interestingly, the net photosynthesis in both the reverse mutant and the forward mutant were higher than that of the wild type, but dark respiration was decreased only in the reverse mutant. The absorbance changes of P700 upon saturation pulse showed the photosystem I (PSI) activity was inhibited, as reflected by Y(I), and Y(NA) was elevated, and dark reduction of P700þ was stimulated, indicating enhanced cyclic electron flow (CEF) around PSI in the reverse mutant. Additional y, the reverse mutant photosynthesis was higher than that of the wild type in low temperature, low and high pH, and high salinity, and this implies increased tolerance in the reverse mutant through downregulated pepc gene.

  1. Genetic studies of the Macushi and Wapishana Indians. II. Data on 12 genetic polymorphisms of the red cell and serum proteins: gene flow between the tribes

    Energy Technology Data Exchange (ETDEWEB)

    Neel, J.V. (Univ. of Michigan, Ann Arbor); Gershowitz, H.; Spielman, R.S.; Migliazza, E.C.; Salzano, F.M.; Oliver, W.J.

    1977-01-01

    Blood samples from 509 Macushi (3 villages) and 623 Wapishana (11 villages) of Northern Brasil and Southern Guyana have been analyzed with respect to the phenotype and gene frequencies at the following 12 polymorphic loci: ABO, Kell-Cellano, MNSs, Rh, P, Duffy, Kidd, Diego, Lewis, Group-specific component, and the immunoglobulin allotypes for the Gm and Inv systems. The data suggest that 5 to 6% of the Wapishana gene pool is derived from non-Indians but only 1 to 2% of the Macushi. Inter- and intratribal genetic distances between villages are calculated for these data in an effort to understand gene flow between the tribes and to account for the unusual distribution of a newly-discovered genetic polymorphism of erythrocyte esterase A thus far limited to these 2 tribes. The data are puzzling and consistent with the possibility that both the Carib-speaking Macushi and the Arawak-speaking Wapishana have derived the esterase A allele in question from some third group now extinct or thus far undiscovered. Intertribal genetic distances based on gene frequencies at 6 loci are derived for 20 Amerindian tribes (including these 2); the ''central'' position of these 2 tribes can in part be explained by the active migration matrix connecting them.

  2. Regulation of pepc gene expression in Anabaena sp. PCC 7120 and its effects on cyclic electron flow around photosystem I and tolerances to environmental stresses.

    Science.gov (United States)

    Jia, Xiao-Hui; Zhang, Peng-Peng; Shi, Ding-Ji; Mi, Hua-Ling; Zhu, Jia-Cheng; Huang, Xi-Wen; He, Pei-Min

    2015-05-01

    Since pepc gene encoding phosphoenolpyruvate carboxylase (PEPCase) has been cloned from Anabaena sp. PCC 7120 and other cyanobacteria, the effects of pepc gene expression on photosynthesis have not been reported yet. In this study, we constructed mutants containing either upregulated (forward) or downregulated (reverse) pepc gene in Anabaena sp. PCC 7120. Results from real-time quantitative polymerase chain reaction (RT-qPCR), Western blot and enzymatic analysis showed that PEPCase activity was significantly reduced in the reverse mutant compared with the wild type, and that of the forward mutant was obviously increased. Interestingly, the net photosynthesis in both the reverse mutant and the forward mutant were higher than that of the wild type, but dark respiration was decreased only in the reverse mutant. The absorbance changes of P700 upon saturation pulse showed the photosystem I (PSI) activity was inhibited, as reflected by Y(I), and Y(NA) was elevated, and dark reduction of P700(+) was stimulated, indicating enhanced cyclic electron flow (CEF) around PSI in the reverse mutant. Additionally, the reverse mutant photosynthesis was higher than that of the wild type in low temperature, low and high pH, and high salinity, and this implies increased tolerance in the reverse mutant through downregulated pepc gene.

  3. Issues Relating to Study Design and Risk of Bias When Including Non-Randomized Studies in Systematic Reviews on the Effects of Interventions

    Science.gov (United States)

    Higgins, Julian P. T.; Ramsay, Craig; Reeves, Barnaby C.; Deeks, Jonathan J.; Shea, Beverley; Valentine, Jeffrey C.; Tugwell, Peter; Wells, George

    2013-01-01

    Non-randomized studies may provide valuable evidence on the effects of interventions. They are the main source of evidence on the intended effects of some types of interventions and often provide the only evidence about the effects of interventions on long-term outcomes, rare events or adverse effects. Therefore, systematic reviews on the effects…

  4. Issues Relating to Confounding and Meta-analysis When Including Non-Randomized Studies in Systematic Reviews on the Effects of Interventions

    Science.gov (United States)

    Valentine, Jeffrey C.; Thompson, Simon G.

    2013-01-01

    Background: Confounding caused by selection bias is often a key difference between non-randomized studies (NRS) and randomized controlled trials (RCTs) of interventions. Key methodological issues: In this third paper of the series, we consider issues relating to the inclusion of NRS in systematic reviews on the effects of interventions. We discuss…

  5. Evaluation of the Prevention and Reactivation Care Program (PReCaP) for the hospitalized elderly: A prospective nonrandomized controlled trial

    NARCIS (Netherlands)

    K.J.E. Asmus-Szepesi (Kirsten); L.E. Flinterman (Linda); M.A. Koopmanschap (Marc); A.P. Nieboer (Anna); T.J.E.M. Bakker (Ton); J.P. Mackenbach (Johan); E.W. Steyerberg (Ewout)

    2015-01-01

    textabstractBackground: The hospitalized elderly are at risk of functional decline. We evaluated the effects and care costs of a specialized geriatric rehabilitation program aimed at preventing functional decline among at-risk hospitalized elderly. Methods: The prospective nonrandomized controlled

  6. Strait of Gibraltar: an effective gene-flow barrier for wind-pollinated Carex helodes (Cyperaceae) as revealed by DNA sequences, AFLP, and cytogenetic variation.

    Science.gov (United States)

    Escudero, Marcial; Vargas, Pablo; Valcárcel, Virginia; Luceño, Modesto

    2008-06-01

    The Strait of Gibraltar is the most important barrier disconnecting the landmasses of Europe and Africa on the western Mediterranean extreme. Carex helodes is a wind-pollinated species endemic to the western Mediterranean. Because molecular and cytogenetic data allow the inference of its evolutionary history, we analyzed variations in chromosome number, including meiotic chromosome behavior, amplified fragment length polymorphism (AFLP) fingerprints, and nucleotide substitutions in plastid and nuclear DNA sequences. Cytogeographic results showed that the African populations have stabilized at a single chromosome number of 2n = 74, whereas the most frequent cytotype in Iberia is 2n = 72. Phylogenetic reconstructions of 17 sequences from nine closely related species revealed that C. helodes is monophyletic and that the Moroccan populations are embedded in the Iberian lineages. The haplotype network is also consistent with a European origin of the northern African haplotype. AFLP analysis also revealed hierarchical levels of genetic variation compatible with a founder effect process responsible for the African populations. All sources of evidence support the hypothesis that the Strait of Gibraltar has been an effective gene-flow barrier, generating two isolated evolutionary lineages after their dispersal. Recent connections between the two lineages appear unlikely, whereas active gene flow occurs among populations within the two lineages.

  7. The walk is never random: subtle landscape effects shape gene flow in a continuous white-tailed deer population in the Midwestern United States.

    Science.gov (United States)

    Robinson, Stacie J; Samuel, Michael D; Lopez, Davin L; Shelton, Paul

    2012-09-01

    One of the pervasive challenges in landscape genetics is detecting gene flow patterns within continuous populations of highly mobile wildlife. Understanding population genetic structure within a continuous population can give insights into social structure, movement across the landscape and contact between populations, which influence ecological interactions, reproductive dynamics or pathogen transmission. We investigated the genetic structure of a large population of deer spanning the area of Wisconsin and Illinois, USA, affected by chronic wasting disease. We combined multiscale investigation, landscape genetic techniques and spatial statistical modelling to address the complex questions of landscape factors influencing population structure. We sampled over 2000 deer and used spatial autocorrelation and a spatial principal components analysis to describe the population genetic structure. We evaluated landscape effects on this pattern using a spatial autoregressive model within a model selection framework to test alternative hypotheses about gene flow. We found high levels of genetic connectivity, with gradients of variation across the large continuous population of white-tailed deer. At the fine scale, spatial clustering of related animals was correlated with the amount and arrangement of forested habitat. At the broader scale, impediments to dispersal were important to shaping genetic connectivity within the population. We found significant barrier effects of individual state and interstate highways and rivers. Our results offer an important understanding of deer biology and movement that will help inform the management of this species in an area where overabundance and disease spread are primary concerns.

  8. Ecological differentiation, lack of hybrids involving diploids, and asymmetric gene flow between polyploids in narrow contact zones of Senecio carniolicus (syn. Jacobaea carniolica, Asteraceae).

    Science.gov (United States)

    Hülber, Karl; Sonnleitner, Michaela; Suda, Jan; Krejčíková, Jana; Schönswetter, Peter; Schneeweiss, Gerald M; Winkler, Manuela

    2015-03-01

    Areas of immediate contact of different cytotypes offer a unique opportunity to study evolutionary dynamics within heteroploid species and to assess isolation mechanisms governing coexistence of cytotypes of different ploidy. The degree of reproductive isolation of cytotypes, that is, the frequency of heteroploid crosses and subsequent formation of viable and (partly) fertile hybrids, plays a crucial role for the long-term integrity of lineages in contact zones. Here, we assessed fine-scale distribution, spatial clustering, and ecological niches as well as patterns of gene flow in parental and hybrid cytotypes in zones of immediate contact of di-, tetra-, and hexaploid Senecio carniolicus (Asteraceae) in the Eastern Alps. Cytotypes were spatially separated also at the investigated microscale; the strongest spatial separation was observed for the fully interfertile tetra- and hexaploids. The three main cytotypes showed highly significant niche differences, which were, however, weaker than across their entire distribution ranges in the Eastern Alps. Individuals with intermediate ploidy levels were found neither in the diploid/tetraploid nor in the diploid/hexaploid contact zones indicating strong reproductive barriers. In contrast, pentaploid individuals were frequent in the tetraploid/hexaploid contact zone, albeit limited to a narrow strip in the immediate contact zone of their parental cytotypes. AFLP fingerprinting data revealed introgressive gene flow mediated by pentaploid hybrids from tetra- to hexaploid individuals, but not vice versa. The ecological niche of pentaploids differed significantly from that of tetraploids but not from hexaploids.

  9. Merging pedigree databases to describe and compare mating practices and gene flow between pedigree dogs in France, Sweden and the UK.

    Science.gov (United States)

    Wang, S; Leroy, G; Malm, S; Lewis, T; Strandberg, E; Fikse, W F

    2017-04-01

    Merging pedigree databases across countries may improve the ability of kennel organizations to monitor genetic variability and health-related issues of pedigree dogs. We used data provided by the Société Centrale Canine (France), Svenska Kennelklubben (Sweden) and the Kennel Club (UK) to study the feasibility of merging pedigree databases across countries and describe breeding practices and international gene flow within the following four breeds: Bullmastiff (BMA), English setter (ESE), Bernese mountain dog (BMD) and Labrador retriever (LBR). After merging the databases, genealogical parameters and founder contributions were calculated according to the birth period, breed and registration country of the dogs. Throughout the investigated period, mating between close relatives, measured as the proportion of inbred individuals (considering only two generations of pedigree), decreased or remained stable, with the exception of LBR in France. Gene flow between countries became more frequent, and the origins of populations within countries became more diverse over time. In conclusion, the potential to reduce inbreeding within purebred dog populations through exchanging breeding animals across countries was confirmed by an improved effective population size when merging populations from different countries. © 2016 Blackwell Verlag GmbH.

  10. Counterselection of prokaryotic ribosomal RNA during reverse transcription using non-random hexameric oligonucleotides.

    Science.gov (United States)

    Gonzalez, J M; Robb, F T

    2007-12-01

    Ribosomal RNA (rRNA) is the major component in total RNA extracts, interfering with the synthesis of cDNA corresponding to messenger RNA (mRNA). In this study, we present a novel strategy for selectively discriminating against rRNA and favoring mRNA from prokaryotes during synthesis of cDNA by reverse transcriptase. Our technique is based on the fact that rRNA sequences, in many species, are G+C rich relative to the genome at large, and highly conserved among prokaryotes. The sequence TTTT is therefore rarely found in rRNA sequences. However, TTTT priming sites are found at a much higher frequency in protein-encoding gene sequences. We designed specific hexamers (HD/DHTTTT) to prime reverse transcription reactions resulting in a selective synthesis of cDNA corresponding to mRNA from prokaryotic total RNA extractions.

  11. Rapid detection of BCR-ABL fusion genes using a novel combined LUX primer, in-cell RT-PCR and flow cytometric method.

    Science.gov (United States)

    Shi, Yan; Li, Li-Zhen; Sun, Jian-Zhi; Zhang, Ti; Peng, Jun; Xu, Cong-Gao

    2008-01-01

    Currently, quantitative and semiquantitative assays for minimal residual disease detection include fluorescence in situ hybridisation, multiparameter flow cytometric immunophenotyping and real-time quantitative polymerase chain reaction (RQ-PCR). We have developed a new approach to detect hybrid breakpoint cluster region and Abelson proto-oncogene (BCR-ABL) transcripts inside suspension cells using in situ RT-PCR and light upon extension (LUX) primer, followed by rapid quantitative analysis with flow cytometry. After cellular permeabilization and fixation of single cell suspension, the neoplastic mRNA was reverse transcribed and amplified by PCR with LUX primer. The results demonstrated that a strong positive yellow-green signal was observed in 99-100% cells of K562 cell line, only the red nucleus was detected in NB4 cell line and normal controls. The technique has been utilised to study 12 patients with chronic myeloid leukemia, and the results were compared with those of BCR-ABL fusion mRNA by RT-PCR and BCR-ABL fusion gene of the interphase cells by fluorescence in situ hybridization (FISH). In the five diagnosed patients, 90-98% cells were strongly positive. Four patients, including three patients treated with interferon-alpha and hydroxyurea and one patient treated with imatinib mesylate, had 26-82.5% positive cells. Three patients treated with imatinib mesylate were negative. The in situ RT-PCR results demonstrated complete concordance with the results of I-FISH and RT-PCR. A fluorescence signal was detectable at 1/10(4) cells and became negative below this threshold with flow cytometry. The results of the present study suggest that (1) LUX primers can be used to efficiently detect BCR-ABL fusion mRNA by in-cell RT-PCR; (2) the novel technique is a specific and sensitive way of detecting fusion gene with potential clinical usefulness.

  12. STUDY OF GENE FLOW FROM GM COTTON (Gossypium hirsutum VARIETIES IN “EL ESPINAL” (TOLIMA, COLOMBIA

    Directory of Open Access Journals (Sweden)

    LEIDY YANIRA RACHE CARDENAL

    2013-01-01

    Full Text Available En el 2009 se plantaron 4088 hectáreas de algodón genéticamente modificado en el departamento de Tolima (Colombia, sin embargo, hay ciertas incertidumbres acerca de las medidas de contención necesarias para impedir el movimiento de polen y semillas desde los campos GM regulados, hacia los campos adyacentes de cultivos convencionales. En este estudio se evaluó el flujo de genes mediado por polen y semillas desde variedades GM hacia variedades convencionales o individuos ferales, en el cultivo del algodón. Para detectar el flujo de genes se utilizaron ImmunostripTM, PCR y ELISA. Cincuenta y seis refugios, 27 campos con algodón convencional y cuatro individuos ferales de la empresa “Remolinos S.A.” localizada en El Espinal (Tolima fueron analizados en el primer semestre de 2010. Los resultados indicaron presencia de plantas GM en 45 refugios (80,4 % y 26 campos de algodón convencional (96 %, además de un flujo génico mediado por polen en un campo de algodón convencional y nueve refugios. En todos los campos cultivados con algodón convencional se evidenció flujo de genes desde algodón GM. Solo en dos refugios y en dos individuos ferales no se evidenció flujo de genes desde algodón GM.

  13. Bacterial characterization of Beijing drinking water by flow cytometry and MiSeq sequencing of the 16S rRNA gene.

    Science.gov (United States)

    Liu, Tingting; Kong, Weiwen; Chen, Nan; Zhu, Jing; Wang, Jingqi; He, Xiaoqing; Jin, Yi

    2016-02-01

    Flow cytometry (FCM) and 16S rRNA gene sequencing data are commonly used to monitor and characterize microbial differences in drinking water distribution systems. In this study, to assess microbial differences in drinking water distribution systems, 12 water samples from different sources water (groundwater, GW; surface water, SW) were analyzed by FCM, heterotrophic plate count (HPC), and 16S rRNA gene sequencing. FCM intact cell concentrations varied from 2.2 × 10(3) cells/mL to 1.6 × 10(4) cells/mL in the network. Characteristics of each water sample were also observed by FCM fluorescence fingerprint analysis. 16S rRNA gene sequencing showed that Proteobacteria (76.9-42.3%) or Cyanobacteria (42.0-3.1%) was most abundant among samples. Proteobacteria were abundant in samples containing chlorine, indicating resistance to disinfection. Interestingly, Mycobacterium, Corynebacterium, and Pseudomonas, were detected in drinking water distribution systems. There was no evidence that these microorganisms represented a health concern through water consumption by the general population. However, they provided a health risk for special crowd, such as the elderly or infants, patients with burns and immune-compromised people exposed by drinking. The combined use of FCM to detect total bacteria concentrations and sequencing to determine the relative abundance of pathogenic bacteria resulted in the quantitative evaluation of drinking water distribution systems. Knowledge regarding the concentration of opportunistic pathogenic bacteria will be particularly useful for epidemiological studies.

  14. Fasciola hepatica demonstrates high levels of genetic diversity, a lack of population structure and high gene flow: possible implications for drug resistance.

    Science.gov (United States)

    Beesley, Nicola J; Williams, Diana J L; Paterson, Steve; Hodgkinson, Jane

    2017-01-01

    Fasciola hepatica, the liver fluke, is a trematode parasite of considerable economic importance to the livestock industry and is a re-emerging zoonosis that poses a risk to human health in F. hepatica-endemic areas worldwide. Drug resistance is a substantial threat to the current and future control of F. hepatica, yet little is known about how the biology of the parasite influences the development and spread of resistance. Given that F. hepatica can self-fertilise and therefore inbreed, there is the potential for greater population differentiation and an increased likelihood of recessive alleles, such as drug resistance genes, coming together. This could be compounded by clonal expansion within the snail intermediate host and aggregation of parasites of the same genotype on pasture. Alternatively, widespread movement of animals that typically occurs in the UK could promote high levels of gene flow and prevent population differentiation. We identified clonal parasites with identical multilocus genotypes in 61% of hosts. Despite this, 84% of 1579 adult parasites had unique multilocus genotypes, which supports high levels of genotypic diversity within F. hepatica populations. Our analyses indicate a selfing rate no greater than 2%, suggesting that this diversity is in part due to the propensity for F. hepatica to cross-fertilise. Finally, although we identified high genetic diversity within a given host, there was little evidence for differentiation between populations from different hosts, indicating a single panmictic population. This implies that, once those emerge, anthelmintic resistance genes have the potential to spread rapidly through liver fluke populations.

  15. Nonrandom spatial clustering of spontaneous anterior fossa cerebrospinal fluid fistulas and predilection for the posterior cribriform plate.

    Science.gov (United States)

    Murray, Richard D; Friedlander, Rachel; Hanz, Samuel; Singh, Harminder; Anand, Vijay K; Schwartz, Theodore H

    2017-05-01

    OBJECTIVE The anterior skull base is a common site for the spontaneous development of meningoceles, encephaloceles, and meningoencephaloceles that can lead to cerebrospinal fluid (CSF) fistula formation, particularly in association with idiopathic intracranial hypertension. In some circumstances the lesions are difficult to localize. Whether all sites in the anterior skull base are equally prone to fistula formation or whether they are distributed randomly throughout the anterior skull base is unknown, although the anterior cribriform plate has been proposed as the most frequent location. The purpose of this study was to identify sites of predilection in order to provide assistance for clinicians in finding occult leaks and increase the understanding of the etiology of this pathology. METHODS The authors performed a retrospective review of a prospectively acquired surgical database of all endonasal endoscopic surgeries performed at Weill Cornell Medical College by the senior authors. Spontaneous CSF fistulas of the anterior skull base were identified. The anatomical sites of the defects were located on radiographic images and normalized to a theoretical 4 × 2 grid representing the anterior midline skull base. Data from the left and right skull base were combined to increase statistical power. This grid was then used to analyze the distribution of defects. Frequency analysis was performed by means of a chi-square test, with a subsequent Monte Carlo simulation to further strengthen the statistical support of the conclusions. RESULTS Nineteen cases of spontaneous CSF fistulas were identified. Frequency analysis using chi-square indicated a nonrandom distribution of sites (p = 0.035). Monte Carlo simulation supported this conclusion (p = 0.034). Seventy-four percent of cases occurred in the cribriform plate (p = 0.086). Moreover, 37% of all defects occurred in the posterior third of the cribriform plate. CONCLUSIONS Anterior skull base spontaneous CSF leaks are

  16. Apparent Variation in Neanderthal Admixture among African Populations is Consistent with Gene Flow from Non-African Populations

    OpenAIRE

    Wang, Shuoguo; Lachance, Joseph; Tishkoff, Sarah A.; Hey, Jody; Xing, Jinchuan

    2013-01-01

    Recent studies have found evidence of introgression from Neanderthals into modern humans outside of sub-Saharan Africa. Given the geographic range of Neanderthals, the findings have been interpreted as evidence of gene exchange between Neanderthals and modern humans descended from the Out-of-Africa (OOA) migration. Here, we examine an alternative interpretation in which the introgression occurred earlier within Africa, between ancestors or relatives of Neanderthals and a subset of African mod...

  17. Can functional gene abundance predict N-fluxes? Examples from a well-studied hydrological flow path in a forested watershed in SW China

    Science.gov (United States)

    Liu, Binbin; Muzammil, Bushra; Dörsch, Peter; Zhu, Jing; Mulder, Jan; Frostegård, Åsa

    2014-05-01

    Edaphic, climatic and management factors shape soil microbial communities taxonomically and functionally, resulting in spatial separation of nitrogen (N) oxidation and reduction processes along hydrological flowpaths. In a recent study, we investigated N-cycling processes and N2O emissions along a mesic hillslope (HS) and a hydrologically connected groundwater discharge zone (GDZ) in a forested headwater catchment dominated by acid soils (pH 4.0 - 4.5) in subtropical China (Chongqing). The watershed receives 50 kg N ha-1 a-1 through atmogenic deposition (2/3 as ammonium), most of which is removed before discharge. Surprisingly, N2O emissions were found to be greatest on the well-drained HS, whereas a drop of NO3- concentrations along the flow path indicated that N removal was highest in the moist GDZ. Nitrification was assumed to be none-limiting as the total flux of NO3- leaving the hill slope soils roughly equalled the input of NH4+. To understand watershed N-cycling and removal in more detail, we studied the abundance of functional genes involved in ammonium oxidation (amoA of AOB and AOA), nitrite oxidation (nxrB) and denitrification (nirK, nirS, nosZ) in top soils from 8 locations along the flow path spanning from the hilltop to the outlet of the GDZ. 16S rRNA gene abundance was assessed as a general marker for bacterial abundance. All genes showed highest abundance per gram soil in the heavily disturbed GDZ (formerly cultivated terraces), despite lower soil organic carbon content (1-4% w/w as opposed to 10-20% w/w in HS topsoil) and periodically stagnant conditions due to high water tables after monsoonal rainfalls. Ratios of nosZ/nirS+nirK, commonly used to predict denitrification product stoichiometry (N2O/N2), yielded counterintuitive results with higher values for HS than for GDZ. However, comparing nir gene with 16S rRNA gene abundance revealed that denitrifiers accounted for up to 10% of the bacterial community in the GDZ soils whereas this value was

  18. Nonrandomized Trial of Feasibility and Acceptability of Strategies for Promotion of Soapy Water as a Handwashing Agent in Rural Bangladesh.

    Science.gov (United States)

    Ashraf, Sania; Nizame, Fosiul A; Islam, Mahfuza; Dutta, Notan C; Yeasmin, Dalia; Akhter, Sadika; Abedin, Jaynal; Winch, Peter J; Ram, Pavani K; Unicomb, Leanne; Leontsini, Elli; Luby, Stephen P

    2017-02-08

    We conducted a nonrandomized trial of strategies to promote soapy water for handwashing in rural Bangladesh and measured uptake. We enrolled households with children promotion of soapy water (N = 120), soapy water promotion plus handwashing stations (N = 103), and soapy water promotion, stations plus detergent refills (N = 90); we also enrolled control households (N = 72). Our handwashing stations included tap-fitted buckets and soapy water bottles. Community promoters visited households and held community meetings to demonstrate soapy water preparation and promote handwashing at key times. Field workers measured uptake 4 months later. In-depth interviews and focus group discussions assessed factors associated with uptake. More households had soapy water at the handwashing place in progressively intensive arms: 18% (promotion), 60% (promotion plus station), and 71% (promotion, station with refills). Compared with the promotion-only arm, more households that received stations had soapy water at the primary handwashing station (44%, P ≤ 0.001; 71%, P < 0.001 with station plus detergent refill). Qualitative findings highlighted several dimensions that affected use: contextual (shared courtyard), psychosocial (perceived value), and technology dimensions (ease of use, convenience). Soapy water may increase habitual handwashing by addressing barriers of cost and availability of handwashing agents near water sources. Further research should inform optimal strategies to scale-up soapy water as a handwashing agent to study health impact.

  19. Randomly and Non-Randomly Missing Renal Function Data in the Strong Heart Study: A Comparison of Imputation Methods.

    Science.gov (United States)

    Shara, Nawar; Yassin, Sayf A; Valaitis, Eduardas; Wang, Hong; Howard, Barbara V; Wang, Wenyu; Lee, Elisa T; Umans, Jason G

    2015-01-01

    Kidney and cardiovascular disease are widespread among populations with high prevalence of diabetes, such as American Indians participating in the Strong Heart Study (SHS). Studying these conditions simultaneously in longitudinal studies is challenging, because the morbidity and mortality associated with these diseases result in missing data, and these data are likely not missing at random. When such data are merely excluded, study findings may be compromised. In this article, a subset of 2264 participants with complete renal function data from Strong Heart Exams 1 (1989-1991), 2 (1993-1995), and 3 (1998-1999) was used to examine the performance of five methods used to impute missing data: listwise deletion, mean of serial measures, adjacent value, multiple imputation, and pattern-mixture. Three missing at random models and one non-missing at random model were used to compare the performance of the imputation techniques on randomly and non-randomly missing data. The pattern-mixture method was found to perform best for imputing renal function data that were not missing at random. Determining whether data are missing at random or not can help in choosing the imputation method that will provide the most accurate results.

  20. Nonrandomized Trial of Feasibility and Acceptability of Strategies for Promotion of Soapy Water as a Handwashing Agent in Rural Bangladesh

    Science.gov (United States)

    Ashraf, Sania; Nizame, Fosiul A.; Islam, Mahfuza; Dutta, Notan C.; Yeasmin, Dalia; Akhter, Sadika; Abedin, Jaynal; Winch, Peter J.; Ram, Pavani K.; Unicomb, Leanne; Leontsini, Elli; Luby, Stephen P.

    2017-01-01

    We conducted a nonrandomized trial of strategies to promote soapy water for handwashing in rural Bangladesh and measured uptake. We enrolled households with children promotion of soapy water (N = 120), soapy water promotion plus handwashing stations (N = 103), and soapy water promotion, stations plus detergent refills (N = 90); we also enrolled control households (N = 72). Our handwashing stations included tap-fitted buckets and soapy water bottles. Community promoters visited households and held community meetings to demonstrate soapy water preparation and promote handwashing at key times. Field workers measured uptake 4 months later. In-depth interviews and focus group discussions assessed factors associated with uptake. More households had soapy water at the handwashing place in progressively intensive arms: 18% (promotion), 60% (promotion plus station), and 71% (promotion, station with refills). Compared with the promotion-only arm, more households that received stations had soapy water at the primary handwashing station (44%, P ≤ 0.001; 71%, P strategies to scale-up soapy water as a handwashing agent to study health impact. PMID:28025233

  1. Randomly and Non-Randomly Missing Renal Function Data in the Strong Heart Study: A Comparison of Imputation Methods.

    Directory of Open Access Journals (Sweden)

    Nawar Shara

    Full Text Available Kidney and cardiovascular disease are widespread among populations with high prevalence of diabetes, such as American Indians participating in the Strong Heart Study (SHS. Studying these conditions simultaneously in longitudinal studies is challenging, because the morbidity and mortality associated with these diseases result in missing data, and these data are likely not missing at random. When such data are merely excluded, study findings may be compromised. In this article, a subset of 2264 participants with complete renal function data from Strong Heart Exams 1 (1989-1991, 2 (1993-1995, and 3 (1998-1999 was used to examine the performance of five methods used to impute missing data: listwise deletion, mean of serial measures, adjacent value, multiple imputation, and pattern-mixture. Three missing at random models and one non-missing at random model were used to compare the performance of the imputation techniques on randomly and non-randomly missing data. The pattern-mixture method was found to perform best for imputing renal function data that were not missing at random. Determining whether data are missing at random or not can help in choosing the imputation method that will provide the most accurate results.

  2. Composition, richness and nonrandom assembly of culturable bacterial-microfungal communities in floral nectar of Mediterranean plants.

    Science.gov (United States)

    Alvarez-Pérez, Sergio; Herrera, Carlos M

    2013-03-01

    The recent upsurge of interest in the role of floral nectar as a habitat for microorganisms has led to some detailed analyses of nectarivorous yeasts. In contrast, very little is known on the occurrence and diversity of nectar-dwelling bacteria, and bacterial-fungal interactions within nectar remain unexplored. In this work, we studied both the culturable bacteria and microfungi found in the floral nectar of wild Mediterranean plants. In general, bacteria and yeasts were found coexisting in nectar more often than would be expected by chance, and such positive association persisted after accounting for phylogenetic nonindependence of the plant species surveyed. Metschnikowia species were confirmed as the main fungal components of nectar communities, and Acinetobacter was identified as the main bacterial taxa. Finally, individual Operational Taxonomic Units (OTUs) were found to co-occur less frequently than predicted by random expectations. There existed, however, some pairwise associations between OTUs that seemed to account for the general pattern of positive bacteria-yeasts coexistence. We conclude that the culturable communities of nectar microorganisms associated with wild Mediterranean plants are nonrandom assemblages of bacterial and yeast species. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

  3. Non-random distribution of amino acids in the transmembrane segments of human type I single span membrane proteins.

    Science.gov (United States)

    Landolt-Marticorena, C; Williams, K A; Deber, C M; Reithmeier, R A

    1993-02-05

    The distribution of amino acids in the transmembrane segments and flanking regions of 115 human type I single span (amino terminus extracellular and carboxyl terminus cytosolic) plasma membrane proteins was found to be non-random. In this sample, Ile was preferentially localized to the amino-terminal region of the hydrophobic transmembrane segments, followed by Val, while Leu predominated in the carboxyl-terminal half of the segment. Although Gly residues were preferentially located in the transmembrane segment, this residue was excluded from the carboxyl-terminal and adjacent boundary regions. Aromatic residues (Tyr, Trp and Phe) occurred preferentially at the cytoplasmic boundary, with Trp also favored at the extracellular boundary. The extracellular flanking sequence amino-terminal to the transmembrane segment was enriched in residues predicted to initiate helix formation (Pro, Asn and Ser), while Arg and Lys were enriched in the cytoplasmic flank where they may function as topological determinants. The positional preferences of these particular amino acids within the transmembrane segment and flanking regions suggests that, in addition to lipid-protein interactions, these residues may participate in specific protein-protein interactions. A consensus sequence motif for type I membrane proteins is proposed and its role in the biosynthesis, folding, assembly and function of these segments is discussed.

  4. Eclipse period of R1 plasmids during downshift from elevated copy number: Nonrandom selection of copies for replication.

    Science.gov (United States)

    Olsson, Jan A; Berg, Otto; Nordström, Kurt; Dasgupta, Santanu

    2012-03-01

    The classical Meselson-Stahl density-shift method was used to study replication of pOU71, a runaway-replication derivative of plasmid R1 in Escherichia coli. The miniplasmid maintained the normal low copy number of R1 during steady growth at 30°C, but as growth temperatures were raised above 34°C, the copy number of the plasmid increased to higher levels, and at 42°C, it replicated without control in a runaway replication mode with lethal consequences for the host. The eclipse periods (minimum time between successive replication of the same DNA) of the plasmid shortened with rising copy numbers at increasing growth temperatures (Olsson et al., 2003). In this work, eclipse periods were measured during downshifts in copy number of pOU71 after it had replicated at 39 and 42°C, resulting in 7- and 50-fold higher than normal plasmid copy number per cell, respectively. Eclipse periods for plasmid replication, measured during copy number downshift, suggested that plasmid R1, normally selected randomly for replication, showed a bias such that a newly replicated DNA had a higher probability of replication compared to the bulk of the R1 population. However, even the unexpected nonrandom replication followed the copy number kinetics such that every generation, the plasmids underwent the normal inherited number of replication, n, independent of the actual number of plasmid copies in a newborn cell.

  5. Does balneotherapy with low radon concentration in water influence the endocrine system? A controlled non-randomized pilot study.

    Science.gov (United States)

    Nagy, Katalin; Berhés, István; Kovács, Tibor; Kávási, Norbert; Somlai, János; Bender, Tamás

    2009-08-01

    Radon bath is a well-established modality of balneotherapy for the management of degenerative musculoskeletal disorders. The present study was conducted to ascertain whether baths of relatively low (80 Bq/l) radon concentration have any influence on the functioning of the endocrine system. In the study, a non-randomized pilot study, 27 patients with degenerative musculoskeletal disorders received 30-min radon baths (of 31-32 degrees C temperature and 80 Bq/l average radon concentration) daily, for 15 days. Twenty-five patients with matching pathologies were subjected to balneotherapy according to the same protocol, using thermal water with negligible radon content (6 Bq/l). Serum thyroid stimulating hormone, prolactin, cortisol, adrenocorticotropic hormone, and dehydroepiandrosterone levels were measured before and after a balneotherapy course of 15 sessions. Comparison of the accumulated data using the Wilcoxon test did not reveal any significant difference between pre- and post-treatment values or between the two patient groups. It is noted that while the beneficial effects of balneotherapy with radon-containing water on degenerative disorders is widely known, only few data have been published in the literature on its effect on endocrine functions. The present study failed to demonstrate any substantial effect of thermal water with relatively low radon content on the functioning of the endocrine system.

  6. Botulinum toxin injection versus lateral internal sphincterotomy in the treatment of chronic anal fissure: a non-randomized controlled trial

    Directory of Open Access Journals (Sweden)

    Ulusoy Nefise B

    2004-03-01

    Full Text Available Abstract Background Although lateral internal sphincterotomy is the gold-standard treatment for chronic anal fissure, intrasphincteric injection of botulinum toxin seems to be a reliable new option. The aim of this non-randomized study is to compare the effect of lateral internal sphincterotomy and botulinum toxin injection treatments on the outcome and reduction of anal sphincter pressures in patients with chronic anal fissure. Methods Patients with chronic anal fissure were treated with either botulinum toxin injection or lateral internal sphincterotomy by their own choice. Maximal resting pressure and maximal squeeze pressure measurements were performed before and 2 weeks after treatments by anal manometry. Patients were followed for fissure relapse during 14 months. Results Twenty-one consecutive outpatients with posterior chronic anal fissure were enrolled. Eleven patients underwent surgery and ten patients received botulinum toxin injection treatment. Before the treatment, anal pressures were found to be similar in both groups. After the treatment, the maximal resting pressures were reduced from 104 ± 22 mmHg to 86 ± 15 mmHg in the surgery group (p 0.05 in the surgery group, and from 117 ± 62 mmHg to 76 ± 34 (p 0.05. There were no relapses during the 14 months of follow up. Conclusion Lateral internal sphincterotomy and botulinum toxin injection treatments both seem to be equally effective in the treatment of chronic anal fissure.

  7. Rapid identification of Candida spp. frequently involved in invasive mycoses by using flow-through hybridization and Gene Chip (FHGC) technology.

    Science.gov (United States)

    Li, Chen; Ding, Xiurong; Liu, Zhizhong; Zhu, Juanjuan

    2017-01-01

    The incidence of invasive fungal infections in immunocompromised patients has increased in recent decades. Rapid and accurate identification of these pathogenic fungi is crucial for initiating a timely, safe, and effective antifungal therapy. Here we developed a microarray based on flow-through hybridization gene chip technology. The microarray was tested for its specificity using a panel of reference and blinded clinical isolates. The results proved that this microarray was highly discriminative, leading to the unequivocal identification of each species, including Candida famata and the highly related species Candida parapsilosis, Candida orthopsilosis, and Candida metapsilosis. This new system represents a reliable method that is of potential use in clinical laboratories for the simultaneous detection and identification of the most common pathogenic fungi. Copyright © 2016 Elsevier B.V. All rights reserved.

  8. No evidence of contemporary interploidy gene flow between the closely related European woodland violets Viola reichenbachiana and V. riviniana (sect. Viola, Violaceae).

    Science.gov (United States)

    Migdałek, G; Nowak, J; Saługa, M; Cieślak, E; Szczepaniak, M; Ronikier, M; Marcussen, T; Słomka, A; Kuta, E

    2017-07-01

    Viola reichenbachiana (2n = 4x = 20) and V. riviniana (2n = 8x = 40) are closely related species widely distributed in Europe, often sharing the same habitat throughout their overlapping ranges. It has been suggested in numerous studies that their high intraspecific morphological variability and plasticity might have been further increased by interspecific hybridisation in contact zones, given the sympatry of the species and the incomplete sterility of their hybrid. The aims of this study were to: (i) confirm that V. reichenbachiana and V. riviniana have one 4x genome in common, and (ii) determine the impact of hybridisation and introgression on genetic variation of these two species in selected European populations. For our study, we used 31 Viola populations from four European countries, which were analysed using AFLP and sequencing of a variable plastid intergenic spacer, trnH-psbA. Our analysis revealed that V. reichenbachiana exhibited larger haplotype diversity, having three species-specific haplotypes versus one in V. riviniana. The relationships among haplotypes suggest transfer of common haplotypes into V. riviniana from both V. reichenbachiana and hypothetically the other, now extinct, parental species. AFLP analysis showed low overall genetic diversity of both species, with V. riviniana showing higher among-population diversity. None of the morphologically designated hybrid populations had additive AFLP polymorphisms that would have indicated recent hybridisation. Also, kinship coefficients between both species did not indicate gene flow. V. riviniana showed significant population subdivision and significant isolation by distance, in contrast to V. reichenbachiana. The results indicate lack of gene flow between species, high influence of selfing on genetic variability, as well as probably only localised introgression toward V. riviniana. © 2017 German Botanical Society and The Royal Botanical Society of the Netherlands.

  9. Ancient female philopatry, asymmetric male gene flow, and synchronous population expansion support the influence of climatic oscillations on the evolution of South American sea lion (Otaria flavescens)

    Science.gov (United States)

    Gehara, Marcelo C. M.; Fraga, Lúcia D.; Lopes, Fernando; Túnez, Juan Ignacio; Cassini, Marcelo H.; Majluf, Patricia; Cárdenas-Alayza, Susana; Pavés, Héctor J.; Crespo, Enrique Alberto; García, Nestor; Loizaga de Castro, Rocío; Hoelzel, A. Rus; Sepúlveda, Maritza; Olavarría, Carlos; Valiati, Victor Hugo; Quiñones, Renato; Pérez-Alvarez, Maria Jose; Ott, Paulo Henrique

    2017-01-01

    The South American sea lion (Otaria flavescens) is widely distributed along the southern Atlantic and Pacific coasts of South America with a history of significant commercial exploitation. We aimed to evaluate the population genetic structure and the evolutionary history of South American sea lion along its distribution by analyses of mitochondrial DNA (mtDNA) and 10 nuclear microsatellites loci. We analyzed 147 sequences of mtDNA control region and genotyped 111 individuals of South American sea lion for 10 microsatellite loci, representing six populations (Peru, Northern Chile, Southern Chile, Uruguay (Brazil), Argentina and Falkland (Malvinas) Islands) and covering the entire distribution of the species. The mtDNA phylogeny shows that haplotypes from the two oceans comprise two very divergent clades as observed in previous studies, suggesting a long period (>1 million years) of low inter-oceanic female gene flow. Bayesian analysis of bi-parental genetic diversity supports significant (but less pronounced than mitochondrial) genetic structure between Pacific and Atlantic populations, although also suggested some inter-oceanic gene flow mediated by males. Higher male migration rates were found in the intra-oceanic population comparisons, supporting very high female philopatry in the species. Demographic analyses showed that populations from both oceans went through a large population expansion ~10,000 years ago, suggesting a very similar influence of historical environmental factors, such as the last glacial cycle, on both regions. Our results support the proposition that the Pacific and Atlantic populations of the South American sea lion should be considered distinct evolutionarily significant units, with at least two managements units in each ocean. PMID:28654647

  10. Full life-cycle assessment of gene flow consistent with fitness differences in transgenic and wild-type Japanese medaka fish (Oryzias latipes).

    Science.gov (United States)

    Pennington, Kelly M; Kapuscinski, Anne R; Morton, Michael S; Cooper, Anne M; Miller, Loren M

    2010-01-01

    Transgenic fish in development for aquaculture could escape from farms and interbreed with wild relatives in the nearby environment. Predicting whether escapes would result in transgene introgression is a major challenge in assessing environmental risks of transgenic fish. Previous studies have simulated gene flow from transgenic fish using mathematical modeling of fitness traits to predict the relative selective value of transgenic genotypes. Here, we present the first study of gene flow over the full life cycle in openly-breeding populations of transgenic animals, along with measurement of fitness traits. We conducted two invasion experiments in which we released two lines of growth-enhanced transgenic fish (T67 and T400), Japanese medaka (Oryzias latipes), into populations of wild-type (W) medaka in structured mesocosms. After several generations, the frequency of transgenic fish varied across replicates in the first invasion experiment (6 months), but the frequency of transgenic fish decreased in the second experiment (19 months). We also measured selected fitness traits in transgenic and wild-type medaka because these traits could be used to predict the relative selective value of a genotype. We found that: T400 males were more fertile than W males; offspring of W females lived longer than those with transgenic mothers; and W and T67 females reached sexual maturity sooner than T400 females. In contrast with other research that reported larger transgenic males had a mating advantage, we found that W males obtained more matings with females than T males; genetic background effects may account for our differing results as we compared W and T fish derived from different strains. The decreasing frequency of transgenic fish in the second invasion experiment suggests that transgenic fish had a selective disadvantage in the experimental environment. Our finding of transgenic advantage of some fitness traits and wild-type advantage in others is consistent with our

  11. CHO-S antibody titers >1 gram/liter using flow electroporation-mediated transient gene expression followed by rapid migration to high-yield stable cell lines.

    Science.gov (United States)

    Steger, Krista; Brady, James; Wang, Weili; Duskin, Meg; Donato, Karen; Peshwa, Madhusudan

    2015-04-01

    In recent years, researchers have turned to transient gene expression (TGE) as an alternative to CHO stable cell line generation for early-stage antibody development. Despite advances in transfection methods and culture optimization, the majority of CHO-based TGE systems produce insufficient antibody titers for extensive use within biotherapeutic development pipelines. Flow electroporation using the MaxCyte STX Scalable Transfection System is a highly efficient, scalable means of CHO-based TGE for gram-level production of antibodies without the need for specialized expression vectors or genetically engineered CHO cell lines. CHO cell flow electroporation is easily scaled from milligram to multigram quantities without protocol reoptimization while maintaining transfection performance and antibody productivity. In this article, data are presented that demonstrate the reproducibility, scalability, and antibody production capabilities of CHO-based TGE using the MaxCyte STX. Data show optimization of posttransfection parameters such as cell density, media composition, and feed strategy that result in secreted antibody titers >1 g/L and production of multiple grams of antibody within 2 weeks of a single CHO-S cell transfection. In addition, data are presented to demonstrate the application of scalable electroporation for the rapid generation of high-yield stable CHO cell lines to bridge the gap between early- and late-stage antibody development activities.

  12. The flow cytometry-defined light chain cytoplasmic immunoglobulin index and an associated 12-gene expression signature are independent prognostic factors in multiple myeloma.

    Science.gov (United States)

    Papanikolaou, X; Alapat, D; Rosenthal, A; Stein, C; Epstein, J; Owens, R; Yaccoby, S; Johnson, S; Bailey, C; Heuck, C; Tian, E; Joiner, A; van Rhee, F; Khan, R; Zangari, M; Jethava, Y; Waheed, S; Davies, F; Morgan, G; Barlogie, B

    2015-08-01

    As part of Total Therapy (TT) 3b, baseline marrow aspirates were subjected to two-color flow cytometry of nuclear DNA content and cytoplasmic immunoglobulin (DNA/CIG) as well as plasma cell gene expression profiling (GEP). DNA/CIG-derived parameters, GEP and standard clinical variables were examined for their effects on overall survival (OS) and progression-free survival (PFS). Among DNA/CIG parameters, the percentage of the light chain-restricted (LCR) cells and their cytoplasmic immunoglobulin index (CIg) were linked to poor outcome. In the absence of GEP data, low CIg CIg survived the model along with GEP70-defined high risk and low albumin. Low CIg was linked to beta-2-microglobulin >5.5 mg/l, a percentage of LCR cells exceeding 50%, C-reactive protein ⩾8 mg/l and GEP-derived high centrosome index. Further analysis revealed an association of low CIg with 12 gene probes implicated in cell cycle regulation, differentiation and drug transportation from which a risk score was developed in TT3b that held prognostic significance also in TT3a, TT2 and HOVON trials, thus validating its general applicability. Low CIg is a powerful new prognostic variable and has identified potentially drug-able targets.

  13. Fluxo gênico em soja na Região Oeste do Paraná Soybean gene flow in the Western Region of Paraná

    Directory of Open Access Journals (Sweden)

    Ivan Schuster

    2007-04-01

    Full Text Available Este trabalho teve o objetivo de avaliar o fluxo gênico em soja, na Região Oeste do Paraná. Foram semeados cinco círculos concêntricos, com a cultivar CD 219RR, que contém o gene CP4 EPSPS. Os círculos foram espaçados em 50 cm, com círculo interno de diâmetro de 50 cm. Externamente a estes, foi semeada a cultivar CD 211 (convencional, também em cinco círculos concêntricos, espaçados em 1 m. As plantas da cultivar CD 211 foram colhidas e trilhadas individualmente, e as sementes semeadas novamente no campo. Após a emergência, foram obtidas 151.772 plântulas, as quais, com 15 dias, foram pulverizadas com 900 g ha-1 de i.a. de glifosato. Após uma semana, plantas sobreviventes foram submetidas à análise de PCR, para verificar a presença do gene CP4 EPSPS. A taxa de fecundação cruzada foi de 0,61, 0,29, 0,23, 0,22 e 0,23% respectivamente a 1, 2, 3, 4 e 5 m de distância das plantas geneticamente modificadas.The objective of this work was to evaluate soybean gene flow in the Western Region of Paraná. Five concentric circles were sowed with the CD 219RR cultivar, which contains the CP4 EPSPS gene. The circles were spaced in 50 cm and the central circle had 50 cm in diameter. Externally to the CD 219RR circles, five concentric circles were sowed with CD 211 cultivar, a no genetically modified soybean, spaced of 1 m. The CD 211 plants were harvested and threshed separately and the seeds were sowed again. After the emergency, 151,772 seedlings were obtained, which with 15 days were sprayed with 900 g ha-1 a.i. of glyphosate. After one week, the surviving plants were analysed by PCR to verify the CP4 EPSPS gene presence. The cross-pollinating rate was 0.61, 0.29, 0.23, 0.22 and 0.23% in 1, 2, 3, 4 and 5 m distance of the genetically modified plants, respectively.

  14. High gene flow and genetic diversity in three economically important Zanthoxylum Spp. of Upper Brahmaputra Valley Zone of NE India using molecular markers

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    K. Medhi

    2014-12-01

    Full Text Available The genetic diversity in Zanthoxylum species viz. Zanthoxylum nitidum, Zanthoxylum oxyphyllum and Zanthoxylum rhesta collected from the Upper Brahmaputra Valley Zone of Assam (NE India was amplified using 13 random amplified polymorphic DNA (RAPD markers and 9 inter-simple sequence repeat (ISSR markers. RAPD markers were able to detect 81.82% polymorphism whereas ISSR detected 98.02% polymorphism. The genetic similarities were analyzed from the dendrogram constructed by RAPD and ISSR fingerprinting methods which divided the 3 species of Zanthoxylum into 3 clear different clusters. The principle component analysis (PCA was carried out to confirm the clustering pattern of RAPD and ISSR analysis. Analysis of molecular variance (AMOVA revealed the presence of significant variability between different Zanthoxylum species and within the species by both RAPD and ISSR markers. Z. nitidum was found to be sharing a high degree of variation with the other two Zanthoxylum species under study. The Nei's gene diversity (h, Shannon's information index (I, observed number of alleles (na and effective number of alleles (ne were also found to be higher in ISSR markers (0.3526, 0.5230, 1.9802 and 1.6145 than in RAPD markers (0.3144, 0.4610, 1.8182 and 1.5571. The values for total genotype diversity for among population (HT, within population diversity (Hs and gene flow (Nm were more in ISSR (0.3491, 0.2644 and 1.5610 than RAPD (0.3128, 0.2264 and 1.3087 but the mean coefficient of gene differentiation (GST was more in RAPD (0.2764 than ISSR (0.2426. A comparison of this two finger printing methods was done by calculating MR, EMI and MI. The correlation coefficient between data matrices of RAPD and ISSR based on Mantel test was found to be significant (r = 0.65612.

  15. A prospective, non-randomized study of home use of mifepristone for medical abortion in the U.S.

    Science.gov (United States)

    Chong, Erica; Frye, Laura J; Castle, Jen; Dean, Gillian; Kuehl, Laurel; Winikoff, Beverly

    2015-09-01

    To determine the acceptability of taking mifepristone at home for early medical abortion in the United States. This prospective, non-randomized, open-label study at six Planned Parenthood centers gave women with pregnancies up to 63 days' gestation seeking medical abortion the choice of taking mifepristone in the center or at home. Participants were interviewed at a follow-up visit 1-2 weeks after mifepristone administration to assess their experience with the option they selected. Four-hundred women were enrolled between April 2013 and June 2014 of which 32% (n=128) chose to take mifepristone at home. Abortion success rates did not differ between home and center users (96% and 97%). Among home users, 82% reported taking the mifepristone at the time they planned with their provider and no participant took it after 63 days' gestation. The most common reason cited for selecting home use was scheduling flexibility and significantly more home users took misoprostol on the weekend (50% vs. 36%, p=.02). Home users were more likely than center users to report missing no days of work due to the abortion (47% vs. 28%, p=.08). Ninety-nine percent of home users reported that they would take mifepristone at home again and 96% would recommend home use to a friend. Offering this option did not increase the service delivery burden on study providers, who would recommend home use in the future for most participants. Home use of mifepristone is a highly acceptable practice for which there is current demand, and it should be offered as part of routine medical abortion services. Offering the option of home use of mifepristone to medical abortion patients can provide women and clinics with more flexibility while maintaining a safe, effective and acceptable service. These results provide support for telemedicine or pharmacy distribution. Copyright © 2015 Elsevier Inc. All rights reserved.

  16. Cortical Microtubule Arrays Are Initiated from a Nonrandom Prepattern Driven by Atypical Microtubule Initiation1[W][OA

    Science.gov (United States)

    Lindeboom, Jelmer J.; Lioutas, Antonios; Deinum, Eva E.; Tindemans, Simon H.; Ehrhardt, David W.; Emons, Anne Mie C.; Vos, Jan W.; Mulder, Bela M.

    2013-01-01

    The ordered arrangement of cortical microtubules in growing plant cells is essential for anisotropic cell expansion and, hence, for plant morphogenesis. These arrays are dismantled when the microtubule cytoskeleton is rearranged during mitosis and reassembled following completion of cytokinesis. The reassembly of the cortical array has often been considered as initiating from a state of randomness, from which order arises at least partly through self-organizing mechanisms. However, some studies have shown evidence for ordering at early stages of array assembly. To investigate how cortical arrays are initiated in higher plant cells, we performed live-cell imaging studies of cortical array assembly in tobacco (Nicotiana tabacum) Bright Yellow-2 cells after cytokinesis and drug-induced disassembly. We found that cortical arrays in both cases did not initiate randomly but with a significant overrepresentation of microtubules at diagonal angles with respect to the cell axis, which coincides with the predominant orientation of the microtubules before their disappearance from the cell cortex in preprophase. In Arabidopsis (Arabidopsis thaliana) root cells, recovery from drug-induced disassembly was also nonrandom and correlated with the organization of the previous array, although no diagonal bias was observed in these cells. Surprisingly, during initiation, only about one-half of the new microtubules were nucleated from locations marked by green fluorescent protein-γ-tubulin complex protein2-tagged γ-nucleation complexes (γ-tubulin ring complex), therefore indicating that a large proportion of early polymers was initiated by a noncanonical mechanism not involving γ-tubulin ring complex. Simulation studies indicate that the high rate of noncanonical initiation of new microtubules has the potential to accelerate the rate of array repopulation. PMID:23300168

  17. Telomere disruption results in non-random formation of de novo dicentric chromosomes involving acrocentric human chromosomes.

    Science.gov (United States)

    Stimpson, Kaitlin M; Song, Ihn Young; Jauch, Anna; Holtgreve-Grez, Heidi; Hayden, Karen E; Bridger, Joanna M; Sullivan, Beth A

    2010-08-12

    Genome rearrangement often produces chromosomes with two centromeres (dicentrics) that are inherently unstable because of bridge formation and breakage during cell division. However, mammalian dicentrics, and particularly those in humans, can be quite stable, usually because one centromere is functionally silenced. Molecular mechanisms of centromere inactivation are poorly understood since there are few systems to experimentally create dicentric human chromosomes. Here, we describe a human cell culture model that enriches for de novo dicentrics. We demonstrate that transient disruption of human telomere structure non-randomly produces dicentric fusions involving acrocentric chromosomes. The induced dicentrics vary in structure near fusion breakpoints and like naturally-occurring dicentrics, exhibit various inter-centromeric distances. Many functional dicentrics persist for months after formation. Even those with distantly spaced centromeres remain functionally dicentric for 20 cell generations. Other dicentrics within the population reflect centromere inactivation. In some cases, centromere inactivation occurs by an apparently epigenetic mechanism. In other dicentrics, the size of the alpha-satellite DNA array associated with CENP-A is reduced compared to the same array before dicentric formation. Extra-chromosomal fragments that contained CENP-A often appear in the same cells as dicentrics. Some of these fragments are derived from the same alpha-satellite DNA array as inactivated centromeres. Our results indicate that dicentric human chromosomes undergo alternative fates after formation. Many retain two active centromeres and are stable through multiple cell divisions. Others undergo centromere inactivation. This event occurs within a broad temporal window and can involve deletion of chromatin that marks the locus as a site for CENP-A maintenance/replenishment.

  18. Telomere disruption results in non-random formation of de novo dicentric chromosomes involving acrocentric human chromosomes.

    Directory of Open Access Journals (Sweden)

    Kaitlin M Stimpson

    2010-08-01

    Full Text Available Genome rearrangement often produces chromosomes with two centromeres (dicentrics that are inherently unstable because of bridge formation and breakage during cell division. However, mammalian dicentrics, and particularly those in humans, can be quite stable, usually because one centromere is functionally silenced. Molecular mechanisms of centromere inactivation are poorly understood since there are few systems to experimentally create dicentric human chromosomes. Here, we describe a human cell culture model that enriches for de novo dicentrics. We demonstrate that transient disruption of human telomere structure non-randomly produces dicentric fusions involving acrocentric chromosomes. The induced dicentrics vary in structure near fusion breakpoints and like naturally-occurring dicentrics, exhibit various inter-centromeric distances. Many functional dicentrics persist for months after formation. Even those with distantly spaced centromeres remain functionally dicentric for 20 cell generations. Other dicentrics within the population reflect centromere inactivation. In some cases, centromere inactivation occurs by an apparently epigenetic mechanism. In other dicentrics, the size of the alpha-satellite DNA array associated with CENP-A is reduced compared to the same array before dicentric formation. Extra-chromosomal fragments that contained CENP-A often appear in the same cells as dicentrics. Some of these fragments are derived from the same alpha-satellite DNA array as inactivated centromeres. Our results indicate that dicentric human chromosomes undergo alternative fates after formation. Many retain two active centromeres and are stable through multiple cell divisions. Others undergo centromere inactivation. This event occurs within a broad temporal window and can involve deletion of chromatin that marks the locus as a site for CENP-A maintenance/replenishment.

  19. Effectiveness of a mindfulness-based intervention on oncology nurses' burnout and compassion fatigue symptoms: A non-randomized study.

    Science.gov (United States)

    Duarte, Joana; Pinto-Gouveia, José

    2016-12-01

    Job stress and burnout are highly frequent in healthcare professionals, and prevalence in nurses can be as high as 40%. Mindfulness-based interventions have been shown to be effective in reducing stress and increasing well-being in a wide range of populations and contexts. However, controlled studies with healthcare professionals, and especially nurses, are scarce. The aim of this study was to explore the effectiveness of an on-site, abbreviated mindfulness-based intervention for nurses, using a nonrandomized, wait-list comparison design. The effectiveness of the intervention was measured through several validated self-report measures that participants completed before and after the intervention, assessing burnout, compassion fatigue, psychological symptoms, mindfulness, self-compassion, experiential avoidances, rumination, and satisfaction with life. A sample of 94 oncology nurses agreed to participate in the study and self-selected into an experimental (n=45) and comparison condition (n=48). Complete data was obtained for 48 of the initial 94 participants, mainly due to poor follow-up data rather than high drop-out rate. Statistical analyses included a series of 2×2 ANOVAs and ANCOVAs. Results indicated that nurses in the intervention reported significant decreases in compassion fatigue, burnout, stress, experiential avoidance, and increases in satisfaction with life, mindfulness and self-compassion, with medium to large effect sizes. Nurses in the comparison group didn't present significant changes in these variables. Results also pointed to a high degree of acceptability of the intervention. This study provides preliminary evidence that mindfulness-based interventions may be efficacious in reducing oncology nurses' psychological symptoms and improving their overall well-being, and thus may be worthy of further study in this population. Copyright © 2016 Elsevier Ltd. All rights reserved.

  20. Comparative Evaluation of Liposomal Albendazole and Tablet-Albendazole Against Hepatic Cystic Echinococcosis: A Non-Randomized Clinical Trial.

    Science.gov (United States)

    Li, Haitao; Song, Tao; Shao, Yingmei; Aili, Tuergan; Ahan, Ayifuhan; Wen, Hao

    2016-01-01

    In this study, we aimed to compare the clinical efficacy of liposomal albendazole (L-ABZ) and tablet-albendazole (T-ABZ) for the treatment of human hepatic cystic echinococcosis (CE). Sixty patients with single cyst (CE1) or daughter cyst (CE2) were included in this study and were nonrandomly divided into the L-ABZ group (n = 30, 10  mg/kg per day, p.o., b.i.d.) and T-ABZ group (n = 30, 12-20 mg/kg per day, p.o., b.i.d.), respectively. The treatment duration lasted for 6 months, during which dynamic follow-up was carried out to evaluate the clinical efficacy through calculating the total effective rates (TERs). Measurement data and numerous data were analyzed by the chi-square test. Two-sided tests were performed for all the statistical tests. In our study, 2 patients were lost in the follow-up in the L-ABZ group. One patient was lost in the follow-up in the T-ABZ group, and 1 patient was withdrawal from the study due to receiving surgery. Significant difference was identified in the 3-month TERs of L-ABZ group and T-ABZ group (33.3% vs 76.7%, P  0.05). Based on our study, both T-ABZ and L-ABZ are effective for treating human CE. The TER in the L-ABZ group is superior to that of T-ABZ.

  1. Effectiveness and Safety of Acupuncture for Poststroke Dysphagia: Study Protocol for a Pragmatic Multicenter Nonrandomized Controlled Trial

    Science.gov (United States)

    Guo, Yuan Qi

    2017-01-01

    Background. Dysphagia is one of the most common complications of stroke. Acupuncture is widely employed to treat poststroke dysphagia in East Asia. No evidence is established to support such treatment approach. This proposed study aims to evaluate the effectiveness and safety of acupuncture for the treatment of poststroke dysphagia. Methods and Design. This is a multicenter, pragmatic, single-blinded, nonrandomized controlled clinical trial. A total of 140 eligible patients will be enrolled in the study. Subjects who are eligible in study but refuse to have acupuncture treatment will be put on the no-acupuncture control arm. Both groups of patients will receive standard routine care, while the patients of intervention group will receive add-on standardized acupuncture treatment. Each participant in intervention group will receive a total of 24 sessions of acupuncture treatment (three times per week). The primary outcome measure is the Royal Brisbane Hospital Outcome Measure for Swallowing (RBHOMS). Secondary outcome measures include functional oral intake scale, swallow quality-of-life questionnaire in Chinese version, BMI of the participant, and adverse events. All outcome measures will be assessed at baseline, at the end of acupuncture treatment (month 2), and at two months after treatment (month 4). Ethics and Dissemination. The ethics approval of clinical research study was granted by the Research Ethics Committee of both New Territories East and West Cluster of Hong Kong. Written informed consent will be obtained from all participants and the study will be undertaken according to the ICH-GCP Guidelines. Trial Registration. This trial is registered with chictr.org (registration number: ChiCTR-TRC-12002621 and registration date: 2012-10-26). PMID:28246537

  2. Apparent variation in Neanderthal admixture among African populations is consistent with gene flow from Non-African populations.

    Science.gov (United States)

    Wang, Shuoguo; Lachance, Joseph; Tishkoff, Sarah A; Hey, Jody; Xing, Jinchuan

    2013-01-01

    Recent studies have found evidence of introgression from Neanderthals into modern humans outside of sub-Saharan Africa. Given the geographic range of Neanderthals, the findings have been interpreted as evidence of gene exchange between Neanderthals and modern humans descended from the Out-of-Africa (OOA) migration. Here, we examine an alternative interpretation in which the introgression occurred earlier within Africa, between ancestors or relatives of Neanderthals and a subset of African modern humans who were the ancestors of those involved in the OOA migration. Under the alternative model, if the population structure among present-day Africans predates the OOA migration, we might find some African populations show a signal of Neanderthal introgression whereas others do not. To test this alternative model, we compiled a whole-genome data set including 38 sub-Saharan Africans from eight populations and 25 non-African individuals from five populations. We assessed differences in the amount of Neanderthal-like single-nucleotide polymorphism alleles among these populations and observed up to 1.5% difference in the number of Neanderthal-like alleles among African populations. Further analyses suggest that these differences are likely due to recent non-African admixture in these populations. After accounting for recent non-African admixture, our results do not support the alternative model of older (e.g., >100 kya) admixture between modern humans and Neanderthal-like hominids within Africa.

  3. Behavioural determinants of gene flow in malaria vector populations: Anopheles gambiae males select large females as mates

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    Yan G

    2002-08-01

    Full Text Available Abstract Background Plasmodium-refractory mosquitoes are being rapidly developed for malaria control but will only succeed if they can successfully compete for mates when released into the wild. Pre-copulatory behavioural traits maintain genetic population structure in wild mosquito populations and mating barriers have foiled previous attempts to control malaria vectors through sterile male release. Methods Varying numbers of virgin male and female Anopheles gambiae Giles, from two strains of different innate sizes, were allowed to mate under standardized conditions in laboratory cages, following which, the insemination status, oviposition success and egg batch size of each female was assessed. The influence of male and female numbers, strain combination and female size were determined using logistic regression, correlation analysis and a simple mechanistic model of male competition for females. Results Male An. gambiae select females on the basis of size because of much greater fecundity among large females. Even under conditions where large numbers of males must compete for a smaller number of females, the largest females are more likely to become inseminated, to successfully oviposit and to produce large egg batches. Conclusions Sexual selection, on the basis of size, could either promote or limit the spread of malaria-refractory genes into wild populations and needs to be considered in the continued development and eventual release of transgenic vectors. Fundamental studies of behavioural ecology in malaria vectors such as An. gambiae can have important implications for malaria control and should be prioritised for more extensive investigation in the future.

  4. Restricted gene flow in the Caribbean staghorn coral Acropora cervicornis: implications for the recovery of endangered reefs.

    Science.gov (United States)

    Vollmer, Steven V; Palumbi, Stephen R

    2007-01-01

    Coral reef conservation requires information about the distance over which healthy reefs can rescue damaged reefs through input of coral larvae. This information is desperately needed in the Caribbean where the 2 dominant shallow water corals Acropora cervicornis and Acropora palmata have suffered unprecedented declines. Here we compare the population genetic structure in the staghorn coral A. cervicornis across the greater Caribbean using DNA sequence data from 1 mitochondrial and 3 nuclear genes. Data from 160 individuals from 22 populations and 9 regions show that A. cervicornis exhibits significant population genetic structure across the greater Caribbean in both the mitochondrial (Phi(st) = 0.130) and nuclear data (Phi(st) = 0.067). The highest population structure was observed in the species' own, native mtDNA haplotypes (Phi(st) = 0.235). Introgressed alleles from A. palmata tempered higher population structure in A. cervicornis over regional scales but in some cases generated highly localized "introgression hot spots" and fine-scale genetic structure among reefs separated by as few as 2 km. These data show that larval dispersal over moderate or long distances (>500 km) is limited for this threatened species and in some cases locally limited as well. Thus, the endangered Caribbean staghorn corals require local source populations for their recovery and targeted conservation efforts over spatial scales much smaller than the hundreds to thousands of kilometers usually proposed for marine reserves.

  5. The constrained maximal expression level owing to haploidy shapes gene content on the mammalian X chromosome

    DEFF Research Database (Denmark)

    Hurst, Laurence D.; Ghanbarian, Avazeh T.; Forrest, Alistair R R

    2015-01-01

    X chromosomes are unusual in many regards, not least of which is their nonrandom gene content. The causes of this bias are commonly discussed in the context of sexual antagonism and the avoidance of activity in the male germline. Here, we examine the notion that, at least in some taxa, functional...

  6. The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome

    NARCIS (Netherlands)

    Hurst, Laurence D; Ghanbarian, Avazeh T; Forrest, Alistair R R; Clevers, JC; Huminiecki, Lukasz

    2015-01-01

    X chromosomes are unusual in many regards, not least of which is their nonrandom gene content. The causes of this bias are commonly discussed in the context of sexual antagonism and the avoidance of activity in the male germline. Here, we examine the notion that, at least in some taxa, functionally

  7. Ancient DNA reveals prehistoric gene-flow from siberia in the complex human population history of North East Europe.

    Science.gov (United States)

    Der Sarkissian, Clio; Balanovsky, Oleg; Brandt, Guido; Khartanovich, Valery; Buzhilova, Alexandra; Koshel, Sergey; Zaporozhchenko, Valery; Gronenborn, Detlef; Moiseyev, Vyacheslav; Kolpakov, Eugen; Shumkin, Vladimir; Alt, Kurt W; Balanovska, Elena; Cooper, Alan; Haak, Wolfgang

    2013-01-01

    North East Europe harbors a high diversity of cultures and languages, suggesting a complex genetic history. Archaeological, anthropological, and genetic research has revealed a series of influences from Western and Eastern Eurasia in the past. While genetic data from modern-day populations is commonly used to make inferences about their origins and past migrations, ancient DNA provides a powerful test of such hypotheses by giving a snapshot of the past genetic diversity. In order to better understand the dynamics that have shaped the gene pool of North East Europeans, we generated and analyzed 34 mitochondrial genotypes from the skeletal remains of three archaeological sites in northwest Russia. These sites were dated to the Mesolithic and the Early Metal Age (7,500 and 3,500 uncalibrated years Before Present). We applied a suite of population genetic analyses (principal component analysis, genetic distance mapping, haplotype sharing analyses) and compared past demographic models through coalescent simulations using Bayesian Serial SimCoal and Approximate Bayesian Computation. Comparisons of genetic data from ancient and modern-day populations revealed significant changes in the mitochondrial makeup of North East Europeans through time. Mesolithic foragers showed high frequencies and diversity of haplogroups U (U2e, U4, U5a), a pattern observed previously in European hunter-gatherers from Iberia to Scandinavia. In contrast, the presence of mitochondrial DNA haplogroups C, D, and Z in Early Metal Age individuals suggested discontinuity with Mesolithic hunter-gatherers and genetic influx from central/eastern Siberia. We identified remarkable genetic dissimilarities between prehistoric and modern-day North East Europeans/Saami, which suggests an important role of post-Mesolithic migrations from Western Europe and subsequent population replacement/extinctions. This work demonstrates how ancient DNA can improve our understanding of human population movements across

  8. Ancient DNA reveals prehistoric gene-flow from siberia in the complex human population history of North East Europe.

    Directory of Open Access Journals (Sweden)

    Clio Der Sarkissian

    Full Text Available North East Europe harbors a high diversity of cultures and languages, suggesting a complex genetic history. Archaeological, anthropological, and genetic research has revealed a series of influences from Western and Eastern Eurasia in the past. While genetic data from modern-day populations is commonly used to make inferences about their origins and past migrations, ancient DNA provides a powerful test of such hypotheses by giving a snapshot of the past genetic diversity. In order to better understand the dynamics that have shaped the gene pool of North East Europeans, we generated and analyzed 34 mitochondrial genotypes from the skeletal remains of three archaeological sites in northwest Russia. These sites were dated to the Mesolithic and the Early Metal Age (7,500 and 3,500 uncalibrated years Before Present. We applied a suite of population genetic analyses (principal component analysis, genetic distance mapping, haplotype sharing analyses and compared past demographic models through coalescent simulations using Bayesian Serial SimCoal and Approximate Bayesian Computation. Comparisons of genetic data from ancient and modern-day populations revealed significant changes in the mitochondrial makeup of North East Europeans through time. Mesolithic foragers showed high frequencies and diversity of haplogroups U (U2e, U4, U5a, a pattern observed previously in European hunter-gatherers from Iberia to Scandinavia. In contrast, the presence of mitochondrial DNA haplogroups C, D, and Z in Early Metal Age individuals suggested discontinuity with Mesolithic hunter-gatherers and genetic influx from central/eastern Siberia. We identified remarkable genetic dissimilarities between prehistoric and modern-day North East Europeans/Saami, which suggests an important role of post-Mesolithic migrations from Western Europe and subsequent population replacement/extinctions. This work demonstrates how ancient DNA can improve our understanding of human population

  9. Pollen-Mediated Gene Flow in Maize: Implications for Isolation Requirements and Coexistence in Mexico, the Center of Origin of Maize.

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    Baltazar M Baltazar

    Full Text Available Mexico, the center of origin of maize (Zea mays L., has taken actions to preserve the identity and diversity of maize landraces and wild relatives. Historically, spatial isolation has been used in seed production to maintain seed purity. Spatial isolation can also be a key component for a strategy to minimize pollen-mediated gene flow in Mexico between transgenic maize and sexually compatible plants of maize conventional hybrids, landraces, and wild relatives. The objective of this research was to generate field maize-to-maize outcrossing data to help guide coexistence discussions in Mexico. In this study, outcrossing rates were determined and modeled from eight locations in six northern states, which represent the most economically important areas for the cultivation of hybrid maize in Mexico. At each site, pollen source plots were planted with a yellow-kernel maize hybrid and surrounded by plots with a white-kernel conventional maize hybrid (pollen recipient of the same maturity. Outcrossing rates were then quantified by assessing the number of yellow kernels harvested from white-kernel hybrid plots. The highest outcrossing values were observed near the pollen source (12.9% at 1 m distance. The outcrossing levels declined sharply to 4.6, 2.7, 1.4, 1.0, 0.9, 0.5, and 0.5% as the distance from the pollen source increased to 2, 4, 8, 12, 16, 20, and 25 m, respectively. At distances beyond 20 m outcrossing values at all locations were below 1%. These trends are consistent with studies conducted in other world regions. The results suggest that coexistence measures that have been implemented in other geographies, such as spatial isolation, would be successful in Mexico to minimize transgenic maize pollen flow to conventional maize hybrids, landraces and wild relatives.

  10. Pollen-Mediated Gene Flow in Maize: Implications for Isolation Requirements and Coexistence in Mexico, the Center of Origin of Maize.

    Science.gov (United States)

    Baltazar, Baltazar M; Castro Espinoza, Luciano; Espinoza Banda, Armando; de la Fuente Martínez, Juan Manuel; Garzón Tiznado, José Antonio; González García, Juvencio; Gutiérrez, Marco Antonio; Guzmán Rodríguez, José Luis; Heredia Díaz, Oscar; Horak, Michael J; Madueño Martínez, Jesús Ignacio; Schapaugh, Adam W; Stojšin, Duška; Uribe Montes, Hugo Raúl; Zavala García, Francisco

    2015-01-01

    Mexico, the center of origin of maize (Zea mays L.), has taken actions to preserve the identity and diversity of maize landraces and wild relatives. Historically, spatial isolation has been used in seed production to maintain seed purity. Spatial isolation can also be a key component for a strategy to minimize pollen-mediated gene flow in Mexico between transgenic maize and sexually compatible plants of maize conventional hybrids, landraces, and wild relatives. The objective of this research was to generate field maize-to-maize outcrossing data to help guide coexistence discussions in Mexico. In this study, outcrossing rates were determined and modeled from eight locations in six northern states, which represent the most economically important areas for the cultivation of hybrid maize in Mexico. At each site, pollen source plots were planted with a yellow-kernel maize hybrid and surrounded by plots with a white-kernel conventional maize hybrid (pollen recipient) of the same maturity. Outcrossing rates were then quantified by assessing the number of yellow kernels harvested from white-kernel hybrid plots. The highest outcrossing values were observed near the pollen source (12.9% at 1 m distance). The outcrossing levels declined sharply to 4.6, 2.7, 1.4, 1.0, 0.9, 0.5, and 0.5% as the distance from the pollen source increased to 2, 4, 8, 12, 16, 20, and 25 m, respectively. At distances beyond 20 m outcrossing values at all locations were below 1%. These trends are consistent with studies conducted in other world regions. The results suggest that coexistence measures that have been implemented in other geographies, such as spatial isolation, would be successful in Mexico to minimize transgenic maize pollen flow to conventional maize hybrids, landraces and wild relatives.

  11. Landscape management and domestication of Stenocereus pruinosus (Cactaceae in the Tehuacán Valley: human guided selection and gene flow

    Directory of Open Access Journals (Sweden)

    Parra Fabiola

    2012-08-01

    Full Text Available Abstract Background Use of plant resources and ecosystems practiced by indigenous peoples of Mesoamerica commonly involves domestication of plant populations and landscapes. Our study analyzed interactions of coexisting wild and managed populations of the pitaya Stenocereus pruinosus, a columnar cactus used for its edible fruit occurring in natural forests, silviculturally managed in milpa agroforestry systems, and agriculturally managed in homegardens of the Tehuacán Valley, Mexico. We aimed at analyzing criteria of artificial selection and their consequences on phenotypic diversity and differentiation, as well as documenting management of propagules at landscape level and their possible contribution to gene flow among populations. Methods Semi-structured interviews were conducted to 83 households of the region to document perception of variation, criteria of artificial selection, and patterns of moving propagules among wild and managed populations. Morphological variation of trees from nine wild, silviculturally and agriculturally managed populations was analyzed for 37 characters through univariate and multivariate statistical methods. In addition, indexes of morphological diversity (MD per population and phenotypic differentiation (PD among populations were calculated using character states and frequencies. Results People recognized 15 pitaya varieties based on their pulp color, fruit size, form, flavor, and thorniness. On average, in wild populations we recorded one variety per population, in silviculturally managed populations 1.58 ± 0.77 varieties per parcel, and in agriculturally managed populations 2.19 ± 1.12 varieties per homegarden. Farmers select in favor of sweet flavor (71% of households interviewed and pulp color (46% mainly red, orange and yellow. Artificial selection is practiced in homegardens and 65% of people interviewed also do it in agroforestry systems. People obtain fruit and branches from different population

  12. Progressive colonization and restricted gene flow shape island-dependent population structure in Galápagos marine iguanas (Amblyrhynchus cristatus

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    Snell Howard L

    2009-12-01

    Full Text Available Abstract Background Marine iguanas (Amblyrhynchus cristatus inhabit the coastlines of large and small islands throughout the Galápagos archipelago, providing a rich system to study the spatial and temporal factors influencing the phylogeographic distribution and population structure of a species. Here, we analyze the microevolution of marine iguanas using the complete mitochondrial control region (CR as well as 13 microsatellite loci representing more than 1200 individuals from 13 islands. Results CR data show that marine iguanas occupy three general clades: one that is widely distributed across the northern archipelago, and likely spread from east to west by way of the South Equatorial current, a second that is found mostly on the older eastern and central islands, and a third that is limited to the younger northern and western islands. Generally, the CR haplotype distribution pattern supports the colonization of the archipelago from the older, eastern islands to the younger, western islands. However, there are also signatures of recurrent, historical gene flow between islands after population establishment. Bayesian cluster analysis of microsatellite genotypes indicates the existence of twenty distinct genetic clusters generally following a one-cluster-per-island pattern. However, two well-differentiated clusters were found on the easternmost island of San Cristóbal, while nine distinct and highly intermixed clusters were found on youngest, westernmost islands of Isabela and Fernandina. High mtDNA and microsatellite genetic diversity were observed for populations on Isabela and Fernandina that may be the result of a recent population expansion and founder events from multiple sources. Conclusions While a past genetic study based on pure FST analysis suggested that marine iguana populations display high levels of nuclear (but not mitochondrial gene flow due to male-biased dispersal, the results of our sex-biased dispersal tests and the

  13. Genotoxicity of doxorubicin in F344 rats by combining the comet assay, flow-cytometric peripheral blood micronucleus test, and pathway-focused gene expression profiling.

    Science.gov (United States)

    Manjanatha, Mugimane G; Bishop, Michelle E; Pearce, Mason G; Kulkarni, Rohan; Lyn-Cook, Lascelles E; Ding, Wei

    2014-01-01

    Doxorubicin (DOX) is an antineoplastic drug effective against many human malignancies. DOX's clinical efficacy is greatly limited because of severe cardiotoxicity. To evaluate if DOX is genotoxic in the heart, ~7-week-old, male F344 rats were administered intravenously 1, 2, and 3 mg/kg bw DOX at 0, 24, 48, and 69 hr and the Comet assays in heart, liver, kidney, and testis and micronucleus (MN) assay in the peripheral blood (PB) erythrocytes using flow cytometry were conducted. Rats were euthanized at 72 hr and PB was removed for the MN assay and single cells were isolated from multiple tissues for the Comet assays. None of the doses of DOX induced a significant DNA damage in any of the tissues examined by the alkaline Comet assay. Contrastingly, the glycosylase enzymes-modified Comet assay showed a significant dose dependent increase in the oxidative DNA damage in the cardiac tissue (P ≤ 0.05). In the liver, only the top dose induced significant increase in the oxidative DNA damage (P ≤ 0.05). The histopathology showed no severe cardiotoxicity but non-neoplastic lesions were present in both untreated and treated samples. A severe toxicity likely occurred in the bone marrow because no viable reticulocytes could be screened for the MN assay. Gene expression profiling of the heart tissues showed a significant alteration in the expression of 11 DNA damage and repair genes. These results suggest that DOX is genotoxic in the heart and the DNA damage may be induced primarily via the production of reactive oxygen species.

  14. Improvement of functional constipation with kiwifruit intake in a Mediterranean patient population: An open, non-randomized pilot study

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    Oriol Cunillera

    2015-07-01

    Full Text Available Introduction: Kiwifruit consumption has shown to improve functional constipation in healthy elderly population, according to studies in New Zealand and China. The aim of this study was to evaluate the effect of kiwifruit intake on functional constipation in a Mediterranean patient population characterized by its distinctive nutritional habits.Material and Methods: An open, non-controlled and non-randomized longitudinal study was conducted in 46 patients with constipation (Rome III criteria. Patients monitored for five weeks: weeks 1 and 2 no kiwifruit and weeks 3-5 three kiwifruit per day (Green kiwifruit, Actinidia deliciosa var Hayward. Bristol Scale, volume of stools, and ease of defecation was self- reported daily. The evolution of the categorical variables was tested using the Bhapkar test; functional data methodology was used for continuous variables, and Generalized Estimating Equation (GEE models were adjusted.Results: The percentage of patients with ≥3 stools per week increased from 82.61% (95% CI: 69–91.2 at week 1 to 97.78% (95% CI: 87.4–99.9 at week 2 of kiwifruit intake, with 76.09% (95% CI: 61.9–86.2 responding during the first week. The reporting of stable ideal stools increased from 17.39% (95% CI: 8.8–31 at week 2 to 33.33% (95% CI: 21.3–48 at week 5. According to GEE models, the number of depositions increased significantly (p-values<0.001 in 0.398 daily units at week 1 the first week of intake, up to 0.593 daily units at week 5; significant improvements on facility in evacuation and volume of evacuation were found from the firstweek of intake (all p-values<0.001.Conclusions: The intake of three kiwifruits per day significantly improves the quality of evacuation (number of depositions, volume, consistency and ease in a Mediterranean patient population suffering from functional constipation.

  15. Neurotransmitter changes in patients with Parkinson's disease detected by encephalofluctuography technology A non-randomized control study

    Institute of Scientific and Technical Information of China (English)

    Yan Han; Zhenfu Wang; Yang Yang; Xianhong Chen; Hong Sun

    2008-01-01

    BACKGROUND: Encephalofluctuograph Technology (ET) is an advanced and non-traumatic analytical method of brain function. ET can acquire super-slow waves from electroencephalic signals. Studies have shown that these particular spectra can reflect neurochemical processes in the brain. OBJECTIVE: To verify neurotransmitter changes in the brains Parkinson's disease (PD) patients through the use of ET. DESIGN, TIME AND SETTING: A non-randomized concurrent control experiment was performed at the Department of Neurology in Southern Building, General Hospital of Chinese PLA from August to December 2007. PARTICIPANTS: Sixty-one outpatients with PD were selected from the General Hospital of Chinese PLA from August 2007 to December 2007. In addition, 48 healthy subjects were selected as normal controls. METHODS: All patients underwent assessment of the sub scale Ⅱ,Ⅲ, and V of the Unified Parkinson's Disease Rating Scale (UPDRS), in which part Ⅱ was used to inform activity of daily living, part Ⅲ reflected athletic ability, and part Ⅴ was the Hoehn & Yahr grade for symptoms evaluation. Correlation analysis was performed between dopamine levels and UPDRS assessment. Neurotransmitter changes were observed forty-eight prior to and 1.5 hours after medicating with Benserazide. The S1, S2, S4, S5,S7, and S11 spectras respectively reflect gamma-aminobutyric acid (GABA), glutamic acid (Glu), 5-hydroxytryptamine (5-HT), acetylcholine (ACh), norepinephrine, and dopamine. MAIN OUTCOME MEASURES: Neurotransmitter changes in the brains of all subjects, and correlations between dopamine concentrations and UPDRS assessmen