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Sample records for dna divergent paralogues

  1. Divergent paralogues of ribosomal DNA in eucalypts (Myrtaceae).

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    Bayly, Michael J; Ladiges, Pauline Y

    2007-07-01

    The presence of divergent paralogues of nuclear ribosomal DNA, from the 18S-5.8S-26S cistron, is reported in members of Eucalyptus subg. Eucalyptus. These paralogues, which include non-functional pseudogenes, probably diverged prior to the differentiation of species groups in subg. Eucalyptus. When compared with presumably functional sequences, the pseudogenes show greater sequence variation between species, particularly in the 5.8S gene. They are also characterised by reduced GC content, associated with a reduced number of CpG and CpNpG methylation sites, and an increase in the inferred number of methylation-induced substitutions. Some pseudogenes also lack motifs that are usually conserved in plants, both in ITS1 and the 5.8S gene. Two main lineages of pseudogenes are identified, one isolated from a group of western Australian species, one from a group of eastern Australian species. It is not clear whether these two lineages of pseudogenes are orthologous, or represent independent divergences from functional sequence types. The presence of divergent rDNA paralogues highlights the need for caution when interpreting eucalypt phylogenies based on ITS sequences.

  2. Interactions among Trypanosoma brucei RAD51 paralogues in DNA repair and antigenic variation.

    Science.gov (United States)

    Dobson, Rachel; Stockdale, Christopher; Lapsley, Craig; Wilkes, Jonathan; McCulloch, Richard

    2011-07-01

    Homologous recombination in Trypanosoma brucei is used for moving variant surface glycoprotein (VSG) genes into expression sites during immune evasion by antigenic variation. A major route for such VSG switching is gene conversion reactions in which RAD51, a universally conserved recombinase, catalyses homology-directed strand exchange. In any eukaryote, RAD51-directed strand exchange in vivo is mediated by further factors, including RAD51-related proteins termed Rad51 paralogues. These appear to be ubiquitously conserved, although their detailed roles in recombination remain unclear. In T. brucei, four putative RAD51 paralogue genes have been identified by sequence homology. Here we show that all four RAD51 paralogues act in DNA repair, recombination and RAD51 subnuclear dynamics, though not equivalently, while mutation of only one RAD51 paralogue gene significantly impedes VSG switching. We also show that the T. brucei RAD51 paralogues interact, and that the complexes they form may explain the distinct phenotypes of the mutants as well as observed expression interdependency. Finally, we document the Rad51 paralogues that are encoded by a wide range of protists, demonstrating that the Rad51 paralogue repertoire in T. brucei is unusually large among microbial eukaryotes and that one member of the protein family corresponds with a key, conserved eukaryotic Rad51 paralogue. © 2011 Blackwell Publishing Ltd.

  3. Nucleosomes shape DNA polymorphism and divergence.

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    Sasha A Langley

    2014-07-01

    Full Text Available An estimated 80% of genomic DNA in eukaryotes is packaged as nucleosomes, which, together with the remaining interstitial linker regions, generate higher order chromatin structures [1]. Nucleosome sequences isolated from diverse organisms exhibit ∼10 bp periodic variations in AA, TT and GC dinucleotide frequencies. These sequence elements generate intrinsically curved DNA and help establish the histone-DNA interface. We investigated an important unanswered question concerning the interplay between chromatin organization and genome evolution: do the DNA sequence preferences inherent to the highly conserved histone core exert detectable natural selection on genomic divergence and polymorphism? To address this hypothesis, we isolated nucleosomal DNA sequences from Drosophila melanogaster embryos and examined the underlying genomic variation within and between species. We found that divergence along the D. melanogaster lineage is periodic across nucleosome regions with base changes following preferred nucleotides, providing new evidence for systematic evolutionary forces in the generation and maintenance of nucleosome-associated dinucleotide periodicities. Further, Single Nucleotide Polymorphism (SNP frequency spectra show striking periodicities across nucleosomal regions, paralleling divergence patterns. Preferred alleles occur at higher frequencies in natural populations, consistent with a central role for natural selection. These patterns are stronger for nucleosomes in introns than in intergenic regions, suggesting selection is stronger in transcribed regions where nucleosomes undergo more displacement, remodeling and functional modification. In addition, we observe a large-scale (∼180 bp periodic enrichment of AA/TT dinucleotides associated with nucleosome occupancy, while GC dinucleotide frequency peaks in linker regions. Divergence and polymorphism data also support a role for natural selection in the generation and maintenance of these

  4. Ureaplasma antigenic variation beyond MBA phase variation: DNA inversions generating chimeric structures and switching in expression of the MBA N-terminal paralogue UU172.

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    Zimmerman, Carl-Ulrich R; Rosengarten, Renate; Spergser, Joachim

    2011-02-01

    Phase variation of the major ureaplasma surface membrane protein, the multiple-banded antigen (MBA), with its counterpart, the UU376 protein, was recently discussed as a result of DNA inversion occurring at specific inverted repeats. Two similar inverted repeats to the ones within the mba locus were found in the genome of Ureaplasma parvum serovar 3; one within the MBA N-terminal paralogue UU172 and another in the adjacent intergenic spacer region. In this report, we demonstrate on both genomic and protein level that DNA inversion at these inverted repeats leads to alternating expression between UU172 and the neighbouring conserved hypothetical ORF UU171. Sequence analysis of this phase-variable 'UU172 element' from both U. parvum and U. urealyticum strains revealed that it is highly conserved among both species and that it also includes the orthologue of UU144. A third inverted repeat region in UU144 is proposed to serve as an additional potential inversion site from which chimeric genes can evolve. Our results indicate that site-specific recombination events in the genome of U. parvum serovar 3 are dynamic and frequent, leading to a broad spectrum of antigenic variation by which the organism may evade host immune responses. © 2010 Blackwell Publishing Ltd.

  5. Evolution and regulation of cellular periodic processes: a role for paralogues

    DEFF Research Database (Denmark)

    Trachana, Kalliopi; Jensen, Lars Juhl; Bork, Peer

    2010-01-01

    paralogues. Thus, diverged temporal expression of paralogues seems to facilitate cellular orchestration under different periodic stimuli. Lineage-specific functional repertoires of periodic-associated paralogues imply that this mode of regulation might have evolved independently in several organisms....... performed the first systematic comparison in three organisms (Homo sapiens, Arabidopsis thaliana and Saccharomyces cerevisiae) by using public microarray data. We observed that although diurnal-regulated and ultradian-regulated genes are not generally cell-cycle-regulated, they tend to have cell-cycle-regulated...

  6. Divergence of gene body DNA methylation and evolution of plant duplicate genes.

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    Jun Wang

    Full Text Available It has been shown that gene body DNA methylation is associated with gene expression. However, whether and how deviation of gene body DNA methylation between duplicate genes can influence their divergence remains largely unexplored. Here, we aim to elucidate the potential role of gene body DNA methylation in the fate of duplicate genes. We identified paralogous gene pairs from Arabidopsis and rice (Oryza sativa ssp. japonica genomes and reprocessed their single-base resolution methylome data. We show that methylation in paralogous genes nonlinearly correlates with several gene properties including exon number/gene length, expression level and mutation rate. Further, we demonstrated that divergence of methylation level and pattern in paralogs indeed positively correlate with their sequence and expression divergences. This result held even after controlling for other confounding factors known to influence the divergence of paralogs. We observed that methylation level divergence might be more relevant to the expression divergence of paralogs than methylation pattern divergence. Finally, we explored the mechanisms that might give rise to the divergence of gene body methylation in paralogs. We found that exonic methylation divergence more closely correlates with expression divergence than intronic methylation divergence. We show that genomic environments (e.g., flanked by transposable elements and repetitive sequences of paralogs generated by various duplication mechanisms are associated with the methylation divergence of paralogs. Overall, our results suggest that the changes in gene body DNA methylation could provide another avenue for duplicate genes to develop differential expression patterns and undergo different evolutionary fates in plant genomes.

  7. Protein-protein interactions in paralogues: Electrostatics modulates specificity on a conserved steric scaffold.

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    Ivanov, Stefan M; Cawley, Andrew; Huber, Roland G; Bond, Peter J; Warwicker, Jim

    2017-01-01

    An improved knowledge of protein-protein interactions is essential for better understanding of metabolic and signaling networks, and cellular function. Progress tends to be based on structure determination and predictions using known structures, along with computational methods based on evolutionary information or detailed atomistic descriptions. We hypothesized that for the case of interactions across a common interface, between proteins from a pair of paralogue families or within a family of paralogues, a relatively simple interface description could distinguish between binding and non-binding pairs. Using binding data for several systems, and large-scale comparative modeling based on known template complex structures, it is found that charge-charge interactions (for groups bearing net charge) are generally a better discriminant than buried non-polar surface. This is particularly the case for paralogue families that are less divergent, with more reliable comparative modeling. We suggest that electrostatic interactions are major determinants of specificity in such systems, an observation that could be used to predict binding partners.

  8. Protein-protein interactions in paralogues: Electrostatics modulates specificity on a conserved steric scaffold.

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    Stefan M Ivanov

    Full Text Available An improved knowledge of protein-protein interactions is essential for better understanding of metabolic and signaling networks, and cellular function. Progress tends to be based on structure determination and predictions using known structures, along with computational methods based on evolutionary information or detailed atomistic descriptions. We hypothesized that for the case of interactions across a common interface, between proteins from a pair of paralogue families or within a family of paralogues, a relatively simple interface description could distinguish between binding and non-binding pairs. Using binding data for several systems, and large-scale comparative modeling based on known template complex structures, it is found that charge-charge interactions (for groups bearing net charge are generally a better discriminant than buried non-polar surface. This is particularly the case for paralogue families that are less divergent, with more reliable comparative modeling. We suggest that electrostatic interactions are major determinants of specificity in such systems, an observation that could be used to predict binding partners.

  9. DNA barcoding of recently diverged species: relative performance of matching methods.

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    Robin van Velzen

    Full Text Available Recently diverged species are challenging for identification, yet they are frequently of special interest scientifically as well as from a regulatory perspective. DNA barcoding has proven instrumental in species identification, especially in insects and vertebrates, but for the identification of recently diverged species it has been reported to be problematic in some cases. Problems are mostly due to incomplete lineage sorting or simply lack of a 'barcode gap' and probably related to large effective population size and/or low mutation rate. Our objective was to compare six methods in their ability to correctly identify recently diverged species with DNA barcodes: neighbor joining and parsimony (both tree-based, nearest neighbor and BLAST (similarity-based, and the diagnostic methods DNA-BAR, and BLOG. We analyzed simulated data assuming three different effective population sizes as well as three selected empirical data sets from published studies. Results show, as expected, that success rates are significantly lower for recently diverged species (∼75% than for older species (∼97% (P<0.00001. Similarity-based and diagnostic methods significantly outperform tree-based methods, when applied to simulated DNA barcode data (P<0.00001. The diagnostic method BLOG had highest correct query identification rate based on simulated (86.2% as well as empirical data (93.1%, indicating that it is a consistently better method overall. Another advantage of BLOG is that it offers species-level information that can be used outside the realm of DNA barcoding, for instance in species description or molecular detection assays. Even though we can confirm that identification success based on DNA barcoding is generally high in our data, recently diverged species remain difficult to identify. Nevertheless, our results contribute to improved solutions for their accurate identification.

  10. Transformation-associated recombination between diverged and homologous DNA repeats is induced by strand breaks

    Energy Technology Data Exchange (ETDEWEB)

    Larionov, V.; Kouprina, N. [National Inst. of Environmental Health Sciences, Research Triangle Park, NC (United States)]|[Institute of Cytology, St. Petersburg, (Russian Federation); Edlarov, M. [National Inst. of Environmental Health Sciences, Research Triangle Park, NC (United States)]|[Center of Bioengineering, Moscow, (Russian Federation); Perkins, E.; Porter, G.; Resnick, M.A. [National Inst. of Environmental Health Sciences, Research Triangle Park, NC (United States)

    1993-12-31

    Rearrangement and deletion within plasmid DNA is commonly observed during transformation. We have examined the mechanisms of transformation-associated recombination in the yeast Saccharomyces cerevisiae using a plasmid system which allowed the effects of physical state and/or extent of homology on recombination to be studied. The plasmid contains homologous or diverged (19%) DNA repeats separated by a genetically detectable color marker. Recombination during transformation for covalently closed circular plasmids was over 100-fold more frequent than during mitotic growth. The frequency of recombination is partly dependent on the method of transformation in that procedures involving lithium acetate or spheroplasting yield higher frequencies than electroporation. When present in the repeats, unique single-strand breaks that are ligatable, as well as double-strand breaks, lead to high levels of recombination between diverged and identical repeats. The transformation-associated recombination between repeat DNA`s is under the influence of the RADS2, RADI and the RNCI genes,

  11. Extent and divergence of heteroplasmy of the DNA barcoding region in Anapodisma miramae (Orthoptera: Acrididae).

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    Kang, Ah Rang; Kim, Min Jee; Park, In Ah; Kim, Kee Young; Kim, Iksoo

    2016-09-01

    A partial sequence of the mitochondrial cytochrome oxidase subunit I (COI) gene is widely used as a molecular marker for species identification in animals, also termed a DNA barcode. However, the presence of more than one sequence type in a single individual, also known as heteroplasmy, is one of the shortcomings of barcode identification. In this study, we examined the extent and divergence of COI heteroplasmy, including nuclear-encoded mitochondrial pseudogenes (NUMTs), at the genomic-DNA level from 13 insect species including orthopteran Anapodisma miramae, and a long fragment of mitochondrial DNA and cDNA from A. miramae as templates. When multiple numbers of clones originated from genomic DNA were sequenced, heteroplasmy was prevalent in all species and NUMTs were observed in five species. Long fragment DNA (∼13.5 kb) also is a source of heteroplasmic amplification, but the divergent haplotypes and NUMTs obtained from genomic DNA were not detected in A. miramae. On the other hand, cDNA was relatively heteroplasmy-free. Consistently, one dominant haplotype was always obtained from the genomic DNA-origin clones in all species and also from the long fragment- and cDNA-origin clones in the two tested individuals of A. miramae. Furthermore, the dominant haplotype was identical in sequence, regardless of the DNA source in A. miramae. Thus, one possible solution to avoid the barcoding problem in relationship to heteroplasmy could be the acquisition of multiple numbers of barcoding sequences to determine a dominant haplotype that can be assigned as barcoding sequence for a given species.

  12. Single-stranded DNA cleavage by divergent CRISPR-Cas9 enzymes

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    Ma, Enbo; Harrington, Lucas B.; O’Connell, Mitchell R.; Zhou, Kaihong; Doudna, Jennifer A.

    2015-01-01

    Summary Double-stranded DNA (dsDNA) cleavage by Cas9 is a hallmark of type II CRISPR-Cas immune systems. Cas9–guide RNA complexes recognize 20-base-pair sequences in DNA and generate a site-specific double-strand break, a robust activity harnessed for genome editing. DNA recognition by all studied Cas9 enzymes requires a protospacer adjacent motif (PAM) next to the target site. We show that Cas9 enzymes from evolutionarily divergent bacteria can recognize and cleave single-stranded DNA (ssDNA) by an RNA-guided, PAM-independent recognition mechanism. Comparative analysis shows that in contrast to the type II-A S. pyogenes Cas9 that is widely used for genome engineering, the smaller type II-C Cas9 proteins have limited dsDNA binding and unwinding activity and promiscuous guide-RNA specificity. These results indicate that inefficiency of type II-C Cas9 enzymes for genome editing results from a limited ability to cleave dsDNA, and suggest that ssDNA cleavage was an ancestral function of the Cas9 enzyme family. PMID:26545076

  13. Transformation-associated recombination between diverged and homologous DNA repeats is induced by strand breaks

    Energy Technology Data Exchange (ETDEWEB)

    Larionov, V.; Kouprina, N. [National Institute of Environmental Health Sciences (NIH), Research Triangle Park, NC (United States)]|[Institute of Cytology, St. Petersburg (Russian Federation); Eldarov, M. [National Institute of Environmental Health Sciences (NIH), Research Triangle Park, NC (United States)]|[Center for Bioengineering, Moscow (Russian Federation); Perkins, E.; Porter, G.; Resnick, M.A. [National Institute of Environmental Health Sciences (NIH), Research Triangle Park, NC (United States)

    1994-10-01

    Rearrangement and deletion within plasmid DNA is commonly observed during transformation. We have examined the mechanisms of transformation-associated recombination in the yeast Saccharomyces cerevisiae using a plasmid system which allowed the effects of physical state and/or extent of homology on recombination to be studied. The plasmid contains homologous or diverged (19%) DNA repeats separated by a genetically detectable color marker. Recombination during transformation for covalently closed circular plasmids was over 100-fold more frequent than during mitotic-growth. The frequency of recombination is partly dependent on the method of transformation In that procedures involving lithium acetate or spheroplasting yield higher frequencies than electroporation. When present in the repeats, unique single-strand breaks that are ligatable, as well as double-strand breaks, lead to high levels of recombination between diverged and identical repeats. The transformation-associated recombination between repeat DNA`s is under the influence of the RAD52, RAD1 and the RNC1 genes.

  14. Two Plastid DNA Lineages—Rapa/Oleracea and Nigra—within the Tribe Brassiceae Can Be Best Explained by Reciprocal Crosses at Hexaploidy: Evidence from Divergence Times of the Plastid Genomes and R-Block Genes of the A and B Genomes of Brassica juncea

    Science.gov (United States)

    Gupta, Vibha; Paritosh, Kumar; Pradhan, Akshay K.; Pental, Deepak

    2014-01-01

    Brassica species (tribe Brassiceae) belonging to U's triangle—B. rapa (AA), B. nigra (BB), B. oleracea (CC), B. juncea (AABB), B. napus (AACC) and B. carinata (BBCC)—originated via two polyploidization rounds: a U event producing the three allopolyploids, and a more ancient b genome-triplication event giving rise to the A-, B-, and C-genome diploid species. Molecular mapping studies, in situ hybridization, and genome sequencing of B. rapa support the genome triplication origin of tribe Brassiceae, and suggest that these three diploid species diversified from a common hexaploid ancestor. Analysis of plastid DNA has revealed two distinct lineages—Rapa/Oleracea and Nigra—that conflict with hexaploidization as a single event defining the tribe Brassiceae. We analysed an R-block region of A. thaliana present in six copies in B. juncea (AABB), three copies each on A- and B-genomes to study gene fractionation pattern and synonymous base substitution rates (Ks values). Divergence time of paralogues within the A and B genomes and homoeologues between the A and B genomes was estimated. Homoeologous R blocks of the A and B genomes exhibited high gene collinearity and a conserved gene fractionation pattern. The three progenitors of diploid Brassicas were estimated to have diverged approximately 12 mya. Divergence of B. rapa and B. nigra, calculated from plastid gene sequences, was estimated to have occurred approximately 12 mya, coinciding with the divergence of the three genomes participating in the b event. Divergence of B. juncea A and B genome homoeologues was estimated to have taken place around 7 mya. Based on divergence time estimates and the presence of distinct plastid lineages in tribe Brassiceae, it is concluded that at least two independent triplication events involving reciprocal crosses at the time of the b event have given rise to Rapa/Oleracea and Nigra lineages. PMID:24691069

  15. Chloroplast DNA Structural Variation, Phylogeny, and Age of Divergence among Diploid Cotton Species

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    Li, Pengbo; Liu, Fang; Wang, Yumei; Xu, Qin; Shang, Mingzhao; Zhou, Zhongli; Cai, Xiaoyan; Wang, Xingxing; Wendel, Jonathan F.; Wang, Kunbo

    2016-01-01

    The cotton genus (Gossypium spp.) contains 8 monophyletic diploid genome groups (A, B, C, D, E, F, G, K) and a single allotetraploid clade (AD). To gain insight into the phylogeny of Gossypium and molecular evolution of the chloroplast genome in this group, we performed a comparative analysis of 19 Gossypium chloroplast genomes, six reported here for the first time. Nucleotide distance in non-coding regions was about three times that of coding regions. As expected, distances were smaller within than among genome groups. Phylogenetic topologies based on nucleotide and indel data support for the resolution of the 8 genome groups into 6 clades. Phylogenetic analysis of indel distribution among the 19 genomes demonstrates contrasting evolutionary dynamics in different clades, with a parallel genome downsizing in two genome groups and a biased accumulation of insertions in the clade containing the cultivated cottons leading to large (for Gossypium) chloroplast genomes. Divergence time estimates derived from the cpDNA sequence suggest that the major diploid clades had diverged approximately 10 to 11 million years ago. The complete nucleotide sequences of 6 cpDNA genomes are provided, offering a resource for cytonuclear studies in Gossypium. PMID:27309527

  16. Ancient DNA evidence for the loss of a highly divergent brown bear clade during historical times.

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    Calvignac, Sebastien; Hughes, Sandrine; Tougard, Christelle; Michaux, Jacques; Thevenot, Michel; Philippe, Michel; Hamdine, Watik; Hänni, Catherine

    2008-04-01

    The genetic diversity of present-day brown bears (Ursus arctos) has been extensively studied over the years and appears to be geographically structured into five main clades. The question of the past diversity of the species has been recently addressed by ancient DNA studies that concluded to a relative genetic stability over the last 35,000 years. However, the post-last glacial maximum genetic diversity of the species still remains poorly documented, notably in the Old World. Here, we analyse Atlas brown bears, which became extinct during the Holocene period. A divergent brown bear mitochondrial DNA lineage not present in any of the previously studied modern or ancient bear samples was uncovered, suggesting that the diversity of U. arctos was larger in the past than it is now. Specifically, a significant portion (with respect to sequence divergence) of the intraspecific diversity of the brown bear was lost with the extinction of the Atlas brown bear after the Pleistocene/Holocene transition.

  17. A novel, highly divergent ssDNA virus identified in Brazil infecting apple, pear and grapevine.

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    Basso, Marcos Fernando; da Silva, José Cleydson Ferreira; Fajardo, Thor Vinícius Martins; Fontes, Elizabeth Pacheco Batista; Zerbini, Francisco Murilo

    2015-12-02

    Fruit trees of temperate and tropical climates are of great economical importance worldwide and several viruses have been reported affecting their productivity and longevity. Fruit trees of different Brazilian regions displaying virus-like symptoms were evaluated for infection by circular DNA viruses. Seventy-four fruit trees were sampled and a novel, highly divergent, monopartite circular ssDNA virus was cloned from apple, pear and grapevine trees. Forty-five complete viral genomes were sequenced, with a size of approx. 3.4 kb and organized into five ORFs. Deduced amino acid sequences showed identities in the range of 38% with unclassified circular ssDNA viruses, nanoviruses and alphasatellites (putative Replication-associated protein, Rep), and begomo-, curto- and mastreviruses (putative coat protein, CP, and movement protein, MP). A large intergenic region contains a short palindromic sequence capable of forming a hairpin-like structure with the loop sequence TAGTATTAC, identical to the conserved nonanucleotide of circoviruses, nanoviruses and alphasatellites. Recombination events were not detected and phylogenetic analysis showed a relationship with circo-, nano- and geminiviruses. PCR confirmed the presence of this novel ssDNA virus in field plants. Infectivity tests using the cloned viral genome confirmed its ability to infect apple and pear tree seedlings, but not Nicotiana benthamiana. The name "Temperate fruit decay-associated virus" (TFDaV) is proposed for this novel virus. Copyright © 2015 Elsevier B.V. All rights reserved.

  18. Hosts, distribution and genetic divergence (16S rDNA) of Amblyomma dubitatum (Acari: Ixodidae).

    Science.gov (United States)

    Nava, Santiago; Venzal, José M; Labruna, Marcelo B; Mastropaolo, Mariano; González, Enrique M; Mangold, Atilio J; Guglielmone, Alberto A

    2010-08-01

    We supply information about hosts and distribution of Amblyomma dubitatum. In addition, we carry out an analysis of genetic divergence among specimens of A. dubitatum from different localities and with respect to other Neotropical Amblyomma species, using sequences of 16S rDNA gene. Although specimens of A. dubitatum were collected on several mammal species as cattle horse, Tapirus terrestris, Mazama gouazoubira, Tayassu pecari, Sus scrofa, Cerdocyon thous, Myocastor coypus, Allouata caraya, Glossophaga soricina and man, most records of immature and adult stages of A. dubitatum were made on Hydrochoerus hydrochaeris, making this rodent the principal host for all parasitic stages of this ticks. Cricetidae rodents (Lundomys molitor, Scapteromys tumidus), opossums (Didelphis albiventris) and vizcacha (Lagostomus maximus) also were recorded as hosts for immature stages. All findings of A. dubitatum correspond to localities of Argentina, Brazil, Paraguay and Uruguay, and they were concentrated in the Biogeographical provinces of Pampa, Chaco, Cerrado, Brazilian Atlantic Forest, Parana Forest and Araucaria angustifolia Forest. The distribution of A. dubitatum is narrower than that of its principal host, therefore environmental variables rather than hosts determine the distributional ranges of this tick. The intraspecific genetic divergence among 16S rDNA sequences of A. dubitatum ticks collected in different localities from Argentina, Brazil and Uruguay was in all cases lower than 0.8%, whereas the differences with the remaining Amblyomma species included in the analysis were always bigger than 6.8%. Thus, the taxonomic status of A. dubitatum along its distribution appears to be certain at the specific level.

  19. Next-generation sequencing reveals recent horizontal transfer of a DNA transposon between divergent mosquitoes.

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    Yupu Diao

    2011-02-01

    Full Text Available Horizontal transfer of genetic material between complex organisms often involves transposable elements (TEs. For example, a DNA transposon mariner has been shown to undergo horizontal transfer between different orders of insects and between different phyla of animals. Here we report the discovery and characterization of an ITmD37D transposon, MJ1, in Anopheles sinensis. We show that some MJ1 elements in Aedes aegypti and An. sinensis contain intact open reading frames and share nearly 99% nucleotide identity over the entire transposon, which is unexpectedly high given that these two genera had diverged 145-200 million years ago. Chromosomal hybridization and TE-display showed that MJ1 copy number is low in An. sinensis. Among 24 mosquito species surveyed, MJ1 is only found in Ae. aegypti and the hyrcanus group of anopheline mosquitoes to which An. sinensis belongs. Phylogenetic analysis is consistent with horizontal transfer and provides the basis for inference of its timing and direction. Although report of horizontal transfer of DNA transposons between higher eukaryotes is accumulating, our analysis is one of a small number of cases in which horizontal transfer of nearly identical TEs among highly divergent species has been thoroughly investigated and strongly supported. Horizontal transfer involving mosquitoes is of particular interest because there are ongoing investigations of the possibility of spreading pathogen-resistant genes into mosquito populations to control malaria and other infectious diseases. The initial indication of horizontal transfer of MJ1 came from comparisons between a 0.4x coverage An. sinensis 454 sequence database and available TEs in mosquito genomes. Therefore we have shown that it is feasible to use low coverage sequencing to systematically uncover horizontal transfer events. Expanding such efforts across a wide range of species will generate novel insights into the relative frequency of horizontal transfer of

  20. Mechanistically Distinct Pathways of Divergent Regulatory DNA Creation Contribute to Evolution of Human-Specific Genomic Regulatory Networks Driving Phenotypic Divergence of Homo sapiens.

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    Glinsky, Gennadi V

    2016-09-19

    Thousands of candidate human-specific regulatory sequences (HSRS) have been identified, supporting the hypothesis that unique to human phenotypes result from human-specific alterations of genomic regulatory networks. Collectively, a compendium of multiple diverse families of HSRS that are functionally and structurally divergent from Great Apes could be defined as the backbone of human-specific genomic regulatory networks. Here, the conservation patterns analysis of 18,364 candidate HSRS was carried out requiring that 100% of bases must remap during the alignments of human, chimpanzee, and bonobo sequences. A total of 5,535 candidate HSRS were identified that are: (i) highly conserved in Great Apes; (ii) evolved by the exaptation of highly conserved ancestral DNA; (iii) defined by either the acceleration of mutation rates on the human lineage or the functional divergence from non-human primates. The exaptation of highly conserved ancestral DNA pathway seems mechanistically distinct from the evolution of regulatory DNA segments driven by the species-specific expansion of transposable elements. Genome-wide proximity placement analysis of HSRS revealed that a small fraction of topologically associating domains (TADs) contain more than half of HSRS from four distinct families. TADs that are enriched for HSRS and termed rapidly evolving in humans TADs (revTADs) comprise 0.8-10.3% of 3,127 TADs in the hESC genome. RevTADs manifest distinct correlation patterns between placements of human accelerated regions, human-specific transcription factor-binding sites, and recombination rates. There is a significant enrichment within revTAD boundaries of hESC-enhancers, primate-specific CTCF-binding sites, human-specific RNAPII-binding sites, hCONDELs, and H3K4me3 peaks with human-specific enrichment at TSS in prefrontal cortex neurons (P Homo sapiens is driven by the evolution of human-specific genomic regulatory networks via at least two mechanistically distinct pathways of

  1. Independent specialisation of myosin II paralogues in muscle vs. non-muscle functions during early animal evolution: a ctenophore perspective.

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    Dayraud, Cyrielle; Alié, Alexandre; Jager, Muriel; Chang, Patrick; Le Guyader, Hervé; Manuel, Michaël; Quéinnec, Eric

    2012-07-02

    Myosin II (or Myosin Heavy Chain II, MHCII) is a family of molecular motors involved in the contractile activity of animal muscle cells but also in various other cellular processes in non-muscle cells. Previous phylogenetic analyses of bilaterian MHCII genes identified two main clades associated respectively with smooth/non-muscle cells (MHCIIa) and striated muscle cells (MHCIIb). Muscle cells are generally thought to have originated only once in ancient animal history, and decisive insights about their early evolution are expected to come from expression studies of Myosin II genes in the two non-bilaterian phyla that possess muscles, the Cnidaria and Ctenophora. We have uncovered three MHCII paralogues in the ctenophore species Pleurobrachia pileus. Phylogenetic analyses indicate that the MHCIIa / MHCIIb duplication is more ancient than the divergence between extant metazoan lineages. The ctenophore MHCIIa gene (PpiMHCIIa) has an expression pattern akin to that of "stem cell markers" (Piwi, Vasa…) and is expressed in proliferating cells. We identified two MHCIIb genes that originated from a ctenophore-specific duplication. PpiMHCIIb1 represents the exclusively muscular form of myosin II in ctenophore, while PpiMHCIIb2 is expressed in non-muscle cells of various types. In parallel, our phalloidin staining and TEM observations highlight the structural complexity of ctenophore musculature and emphasize the experimental interest of the ctenophore tentacle root, in which myogenesis is spatially ordered and strikingly similar to striated muscle formation in vertebrates. MHCIIa expression in putative stem cells/proliferating cells probably represents an ancestral trait, while specific involvement of some MHCIIa genes in smooth muscle fibres is a uniquely derived feature of the vertebrates. That one ctenophore MHCIIb paralogue (PpiMHCIIb2) has retained MHCIIa-like expression features furthermore suggests that muscular expression of the other paralogue, PpiMHCIIb1, was

  2. Independent specialisation of myosin II paralogues in muscle vs. non-muscle functions during early animal evolution: a ctenophore perspective

    Science.gov (United States)

    2012-01-01

    Background Myosin II (or Myosin Heavy Chain II, MHCII) is a family of molecular motors involved in the contractile activity of animal muscle cells but also in various other cellular processes in non-muscle cells. Previous phylogenetic analyses of bilaterian MHCII genes identified two main clades associated respectively with smooth/non-muscle cells (MHCIIa) and striated muscle cells (MHCIIb). Muscle cells are generally thought to have originated only once in ancient animal history, and decisive insights about their early evolution are expected to come from expression studies of Myosin II genes in the two non-bilaterian phyla that possess muscles, the Cnidaria and Ctenophora. Results We have uncovered three MHCII paralogues in the ctenophore species Pleurobrachia pileus. Phylogenetic analyses indicate that the MHCIIa / MHCIIb duplication is more ancient than the divergence between extant metazoan lineages. The ctenophore MHCIIa gene (PpiMHCIIa) has an expression pattern akin to that of "stem cell markers" (Piwi, Vasa…) and is expressed in proliferating cells. We identified two MHCIIb genes that originated from a ctenophore-specific duplication. PpiMHCIIb1 represents the exclusively muscular form of myosin II in ctenophore, while PpiMHCIIb2 is expressed in non-muscle cells of various types. In parallel, our phalloidin staining and TEM observations highlight the structural complexity of ctenophore musculature and emphasize the experimental interest of the ctenophore tentacle root, in which myogenesis is spatially ordered and strikingly similar to striated muscle formation in vertebrates. Conclusion MHCIIa expression in putative stem cells/proliferating cells probably represents an ancestral trait, while specific involvement of some MHCIIa genes in smooth muscle fibres is a uniquely derived feature of the vertebrates. That one ctenophore MHCIIb paralogue (PpiMHCIIb2) has retained MHCIIa-like expression features furthermore suggests that muscular expression of the

  3. Independent specialisation of myosin II paralogues in muscle vs. non-muscle functions during early animal evolution: a ctenophore perspective

    Directory of Open Access Journals (Sweden)

    Dayraud Cyrielle

    2012-07-01

    Full Text Available Abstract Background Myosin II (or Myosin Heavy Chain II, MHCII is a family of molecular motors involved in the contractile activity of animal muscle cells but also in various other cellular processes in non-muscle cells. Previous phylogenetic analyses of bilaterian MHCII genes identified two main clades associated respectively with smooth/non-muscle cells (MHCIIa and striated muscle cells (MHCIIb. Muscle cells are generally thought to have originated only once in ancient animal history, and decisive insights about their early evolution are expected to come from expression studies of Myosin II genes in the two non-bilaterian phyla that possess muscles, the Cnidaria and Ctenophora. Results We have uncovered three MHCII paralogues in the ctenophore species Pleurobrachia pileus. Phylogenetic analyses indicate that the MHCIIa / MHCIIb duplication is more ancient than the divergence between extant metazoan lineages. The ctenophore MHCIIa gene (PpiMHCIIa has an expression pattern akin to that of "stem cell markers" (Piwi, Vasa… and is expressed in proliferating cells. We identified two MHCIIb genes that originated from a ctenophore-specific duplication. PpiMHCIIb1 represents the exclusively muscular form of myosin II in ctenophore, while PpiMHCIIb2 is expressed in non-muscle cells of various types. In parallel, our phalloidin staining and TEM observations highlight the structural complexity of ctenophore musculature and emphasize the experimental interest of the ctenophore tentacle root, in which myogenesis is spatially ordered and strikingly similar to striated muscle formation in vertebrates. Conclusion MHCIIa expression in putative stem cells/proliferating cells probably represents an ancestral trait, while specific involvement of some MHCIIa genes in smooth muscle fibres is a uniquely derived feature of the vertebrates. That one ctenophore MHCIIb paralogue (PpiMHCIIb2 has retained MHCIIa-like expression features furthermore suggests that muscular

  4. Initiation of mtDNA transcription is followed by pausing, and diverges across human cell types and during evolution.

    Science.gov (United States)

    Blumberg, Amit; Rice, Edward J; Kundaje, Anshul; Danko, Charles G; Mishmar, Dan

    2017-03-01

    Mitochondrial DNA (mtDNA) genes are long known to be cotranscribed in polycistrones, yet it remains impossible to study nascent mtDNA transcripts quantitatively in vivo using existing tools. To this end, we used deep sequencing (GRO-seq and PRO-seq) and analyzed nascent mtDNA-encoded RNA transcripts in diverse human cell lines and metazoan organisms. Surprisingly, accurate detection of human mtDNA transcription initiation sites (TISs) in the heavy and light strands revealed a novel conserved transcription pausing site near the light-strand TIS. This pausing site correlated with the presence of a bacterial pausing sequence motif, with reduced SNP density, and with a DNase footprinting signal in all tested cells. Its location within conserved sequence block 3 (CSBIII), just upstream of the known transcription-replication transition point, suggests involvement in such transition. Analysis of nonhuman organisms enabled de novo mtDNA sequence assembly, as well as detection of previously unknown mtDNA TIS, pausing, and transcription termination sites with unprecedented accuracy. Whereas mammals ( Pan troglodytes , Macaca mulatta , Rattus norvegicus , and Mus musculus ) showed a human-like mtDNA transcription pattern, the invertebrate pattern ( Drosophila melanogaster and Caenorhabditis elegans ) profoundly diverged. Our approach paves the path toward in vivo, quantitative, reference sequence-free analysis of mtDNA transcription in all eukaryotes. © 2017 Blumberg et al.; Published by Cold Spring Harbor Laboratory Press.

  5. Four CISH paralogues are present in rainbow trout Oncorhynchus mykiss: differential expression and modulation during immune responses and development.

    Science.gov (United States)

    Maehr, Tanja; Vecino, Jose L González; Wadsworth, Simon; Wang, Tiehui; Secombes, Christopher J

    2014-11-01

    Suppressor of cytokine signalling (SOCS) family members are crucial in the control and attenuation of cytokine induced responses via activation of the JAK/STAT, TLR and NF-kB signalling pathways. SOCS proteins orchestrate the termination of many types of immune responses and are often the targets of microbial pathogens exploiting SOCS mechanisms to evade the host's immune response. Through whole and lineage specific genome duplication events, the teleost cytokine/SOCS network is complex. Not only are the orthologues of all mammalian SOCS members present, namely cytokine inducible Src homology 2 (SH2)-containing protein (CISH) and SOCS-1 to -7, but multiple gene copies exist that may potentially become functionally divergent. In this paper we focus on the CISH genes in rainbow trout (Oncorhynchus mykiss), and have cloned two further paralogues, CISHa2 and CISHb2, additional to the known CISHa1 and CISHb1 genes. We present for the first time a comparative expression analysis of these four paralogues, to establish whether subfunctionalisation is apparent. In vivo examination of gene expression revealed a higher constitutive expression level of CISHa paralogues compared to CISHb expression in adult trout tissues. All CISHs were relatively highly abundant in immune tissues but CISHa2 and CISHb2 had highest expression in the heart and muscle. An inverse picture of CISH abundance during trout ontogeny was seen, and further hints at differential roles of the four genes in immune regulation and development. Stimulation of head kidney (HK) leukocytes with trout recombinant interleukin (rIL)-15 and rIL-21 had a major effect on CISHa2 and to a lesser extent CISHa1 expression. In HK macrophages rIL-1β, phytohemagglutinin, and phorbol 12-myristate 13-acetate also had a strong impact on CISHa2 expression. Yersinia ruckeri infection caused a temporally and spatially differential onset of CISH expression that may be viewed in the context of pathogen evasion strategies. These data

  6. Accurate, high-throughput typing of copy number variation using paralogue ratios from dispersed repeats.

    Science.gov (United States)

    Armour, John A L; Palla, Raquel; Zeeuwen, Patrick L J M; den Heijer, Martin; Schalkwijk, Joost; Hollox, Edward J

    2007-01-01

    Recent work has demonstrated an unexpected prevalence of copy number variation in the human genome, and has highlighted the part this variation may play in predisposition to common phenotypes. Some important genes vary in number over a high range (e.g. DEFB4, which commonly varies between two and seven copies), and have posed formidable technical challenges for accurate copy number typing, so that there are no simple, cheap, high-throughput approaches suitable for large-scale screening. We have developed a simple comparative PCR method based on dispersed repeat sequences, using a single pair of precisely designed primers to amplify products simultaneously from both test and reference loci, which are subsequently distinguished and quantified via internal sequence differences. We have validated the method for the measurement of copy number at DEFB4 by comparison of results from >800 DNA samples with copy number measurements by MAPH/REDVR, MLPA and array-CGH. The new Paralogue Ratio Test (PRT) method can require as little as 10 ng genomic DNA, appears to be comparable in accuracy to the other methods, and for the first time provides a rapid, simple and inexpensive method for copy number analysis, suitable for application to typing thousands of samples in large case-control association studies.

  7. DNA Barcoding: Amplification and sequence analysis of rbcl and matK genome regions in three divergent plant species

    Directory of Open Access Journals (Sweden)

    Javed Iqbal Wattoo

    2016-11-01

    Full Text Available Background: DNA barcoding is a novel method of species identification based on nucleotide diversity of conserved sequences. The establishment and refining of plant DNA barcoding systems is more challenging due to high genetic diversity among different species. Therefore, targeting the conserved nuclear transcribed regions would be more reliable for plant scientists to reveal genetic diversity, species discrimination and phylogeny. Methods: In this study, we amplified and sequenced the chloroplast DNA regions (matk+rbcl of Solanum nigrum, Euphorbia helioscopia and Dalbergia sissoo to study the functional annotation, homology modeling and sequence analysis to allow a more efficient utilization of these sequences among different plant species. These three species represent three families; Solanaceae, Euphorbiaceae and Fabaceae respectively. Biological sequence homology and divergence of amplified sequences was studied using Basic Local Alignment Tool (BLAST. Results: Both primers (matk+rbcl showed good amplification in three species. The sequenced regions reveled conserved genome information for future identification of different medicinal plants belonging to these species. The amplified conserved barcodes revealed different levels of biological homology after sequence analysis. The results clearly showed that the use of these conserved DNA sequences as barcode primers would be an accurate way for species identification and discrimination. Conclusion: The amplification and sequencing of conserved genome regions identified a novel sequence of matK in native species of Solanum nigrum. The findings of the study would be applicable in medicinal industry to establish DNA based identification of different medicinal plant species to monitor adulteration.

  8. Two divergent leptin paralogues in zebrafish (Danio rerio) that originate early in teleostean evolution.

    NARCIS (Netherlands)

    Gorissen, M.H.A.G.; Bernier, N.J.; Nabuurs, S.B.; Flik, G.; Huising, M.O.

    2009-01-01

    We describe duplicate leptin genes in zebrafish (Danio rerio) that share merely 24% amino acid identity with each other and only 18% with human leptin. We were also able to retrieve a second leptin gene in medaka (Oryzias latipes). The presence of duplicate leptin genes in these two distantly

  9. Allopatry as a Gordian Knot for Taxonomists: Patterns of DNA Barcode Divergence in Arctic-Alpine Lepidoptera

    Science.gov (United States)

    Mutanen, Marko; Hausmann, Axel; Hebert, Paul D. N.; Landry, Jean-François; de Waard, Jeremy R.; Huemer, Peter

    2012-01-01

    Many cold adapted species occur in both montane settings and in the subarctic. Their disjunct distributions create taxonomic complexity because there is no standardized method to establish whether their allopatric populations represent single or different species. This study employs DNA barcoding to gain new perspectives on the levels and patterns of sequence divergence among populations of 122 arctic-alpine species of Lepidoptera from the Alps, Fennoscandia and North America. It reveals intraspecific variability in the barcode region ranging from 0.00–10.08%. Eleven supposedly different species pairs or groups show close genetic similarity, suggesting possible synonymy in many cases. However, a total of 33 species show evidence of cryptic diversity as evidenced by the presence of lineages with over 2% maximum barcode divergence in Europe, in North America or between the two continents. Our study also reveals cases where taxonomic names have been used inconsistently between regions and exposes misidentifications. Overall, DNA barcodes have great potential to both increase taxonomic resolution and to make decisions concerning the taxonomic status of allopatric populations more objective. PMID:23071761

  10. Refugial isolation and divergence in the Narrowheaded Gartersnake species complex (Thamnophis rufipunctatus) as revealed by multilocus DNA sequence data.

    Science.gov (United States)

    Wood, Dustin A; Vandergast, A G; Lemos Espinal, J A; Fisher, R N; Holycross, A T

    2011-09-01

    Glacial-interglacial cycles of the Pleistocene are hypothesized as one of the foremost contributors to biological diversification. This is especially true for cold-adapted montane species, where range shifts have had a pronounced effect on population-level divergence. Gartersnakes of the Thamnophis rufipunctatus species complex are restricted to cold headwater streams in the highlands of the Sierra Madre Occidental and southwestern USA. We used coalescent and multilocus phylogenetic approaches to test whether genetic diversification of this montane-restricted species complex is consistent with two prevailing models of range fluctuation for species affected by Pleistocene climate changes. Our concatenated nuDNA and multilocus species analyses recovered evidence for the persistence of multiple lineages that are restricted geographically, despite a mtDNA signature consistent with either more recent connectivity (and introgression) or recent expansion (and incomplete lineage sorting). Divergence times estimated using a relaxed molecular clock and fossil calibrations fall within the Late Pleistocene, and zero gene flow scenarios among current geographically isolated lineages could not be rejected. These results suggest that increased climate shifts in the Late Pleistocene have driven diversification and current range retraction patterns and that the differences between markers reflect the stochasticity of gene lineages (i.e. ancestral polymorphism) rather than gene flow and introgression. These results have important implications for the conservation of T. rufipunctatus (sensu novo), which is restricted to two drainage systems in the southwestern US and has undergone a recent and dramatic decline. © 2011 Blackwell Publishing Ltd.

  11. DNA barcoding of bark and ambrosia beetles reveals excessive NUMTs and consistent east-west divergence across Palearctic forests.

    Science.gov (United States)

    Jordal, Bjarte H; Kambestad, Marius

    2014-01-01

    A comprehensive DNA barcoding library is very useful for rapid identification and detection of invasive pest species. We tested the performance of species identification in the economically most damaging group of wood-boring insects - the bark and ambrosia beetles - with particular focus on broad geographical sampling across the boreal Palearctic forests. Neighbour-joining and Bayesian analyses of cytochrome oxidase I (COI) sequences from 151 species in 40 genera revealed high congruence between morphology-based identification and sequence clusters. Inconsistencies with morphological identifications included the discovery of a likely cryptic Nearctic species of Dryocoetes autographus, the possible hybrid origin of shared mitochondrial haplotypes in Pityophthorus micrographus and P. pityographus, and a possible paraphyletic Xyleborinus saxeseni. The first record of Orthotomicus suturalis in North America was confirmed by DNA barcoding. The mitochondrial data also revealed consistent divergence across the Palearctic or Holarctic, confirmed in part by data from the large ribosomal subunit (28S). Some populations had considerable variation in the mitochondrial barcoding marker, but were invariant in the nuclear ribosomal marker. These findings must be viewed in light of the high number of nuclear insertions of mitochondrial DNA (NUMTs) detected in eight bark beetle species, suggesting the possible presence of additional cryptic NUMTs. The occurrence of paralogous COI copies, hybridization or cryptic speciation demands a stronger focus on data quality assessment in the construction of DNA barcoding databases. © 2013 John Wiley & Sons Ltd.

  12. Integrating phylogeographic patterns of microsatellite and mtDNA divergence to infer the evolutionary history of chamois (genus Rupicapra).

    Science.gov (United States)

    Rodríguez, Fernando; Pérez, Trinidad; Hammer, Sabine E; Albornoz, Jesús; Domínguez, Ana

    2010-07-22

    The chamois, distributed over most of the medium to high altitude mountain ranges of southern Eurasia, provides an excellent model for exploring the effects of historical and evolutionary events on diversification. Populations have been grouped into two species, Rupicapra pyrenaica from southwestern Europe and R. rupicapra from eastern Europe. However, a previous study of cytochrome b revealed that the two proposed species were non-monophyletic. The reconstruction of phylogenetic relationships between animal species often depends on the markers studied. To further elucidate the evolutionary history of chamois, we extended earlier studies by analysing DNA sequences of four mitochondrial regions (ND1, 12S, tRNApro and Control Region) and microsatellites (20 loci) to include all subspecies and cover its entire distribution range. We found discordant microsatellite (musat) and mitochondrial (mt) DNA phylogenies. Mitochondrial phylogenies form three clades, West, Central and East (mtW, mtC and mtE), at variance with taxonomic classification. Our divergence age estimates indicate an initial separation into branches mtW-mtC and mtE 1.7 million years ago (mya), in the late Pliocene-early Pleistocene, quickly followed by the split of clades mtW and mtC. Clade mtW contains haplotypes from the Iberian peninsula and the western Alps, Clade mtC includes haplotypes from the Apennines and the Massif of Chartreuse and Clade mtE comprises populations to the east of the Alps. Divergence among populations within these three major clades is recent (< 0.5 mya). New microsatellite multilocus genotypes added to previously published data revealed differences between every pair of subspecies, forming three well defined groups (musatW, musatC and musatE) also with a strong geographic signature. Grouping does not correspond with the mitochondrial lineages but is closer to morphology and taxonomic classification. Recent drastic reductions in population size can be noted for the subspecies

  13. Integrating phylogeographic patterns of microsatellite and mtDNA divergence to infer the evolutionary history of chamois (genus Rupicapra

    Directory of Open Access Journals (Sweden)

    Albornoz Jesús

    2010-07-01

    Full Text Available Abstract Background The chamois, distributed over most of the medium to high altitude mountain ranges of southern Eurasia, provides an excellent model for exploring the effects of historical and evolutionary events on diversification. Populations have been grouped into two species, Rupicapra pyrenaica from southwestern Europe and R. rupicapra from eastern Europe. However, a previous study of cytochrome b revealed that the two proposed species were non-monophyletic. The reconstruction of phylogenetic relationships between animal species often depends on the markers studied. To further elucidate the evolutionary history of chamois, we extended earlier studies by analysing DNA sequences of four mitochondrial regions (ND1, 12S, tRNApro and Control Region and microsatellites (20 loci to include all subspecies and cover its entire distribution range. Results We found discordant microsatellite (μsat and mitochondrial (mt DNA phylogenies. Mitochondrial phylogenies form three clades, West, Central and East (mtW, mtC and mtE, at variance with taxonomic classification. Our divergence age estimates indicate an initial separation into branches mtW-mtC and mtE 1.7 million years ago (mya, in the late Pliocene-early Pleistocene, quickly followed by the split of clades mtW and mtC. Clade mtW contains haplotypes from the Iberian peninsula and the western Alps, Clade mtC includes haplotypes from the Apennines and the Massif of Chartreuse and Clade mtE comprises populations to the east of the Alps. Divergence among populations within these three major clades is recent (ornata as an extremely low diversity. Conclusions The phylogeographic patterns for mtDNA and microsatellites suggest an evolutionary history with limited range contractions and expansions during the Quaternary period and reflect a major effect of the Alpine barrier on west-east differentiation. The contrasting phylogenies for mtDNA and microsatellites indicate events of hybridization among highly

  14. Structural Mechanisms of Inactivation in Scabies Mite Serine Protease Paralogues

    Energy Technology Data Exchange (ETDEWEB)

    Fischer, Katja; Langendorf, Christopher G.; Irving, James A.; Reynolds, Simone; Willis, Charlene; Beckham, Simone; Law, Ruby H.P.; Yang, Sundy; Bashtannyk-Puhalovich, Tanya A.; McGowan, Sheena; Whisstock, James C.; Pike, Robert N.; Kemp, David J.; Buckle, Ashley M.; (Monash); (Queensland Inst. of Med. Rsrch.)

    2009-08-07

    The scabies mite (Sarcoptes scabiei) is a parasite responsible for major morbidity in disadvantaged communities and immuno-compromised patients worldwide. In addition to the physical discomfort caused by the disease, scabies infestations facilitate infection by Streptococcal species via skin lesions, resulting in a high prevalence of rheumatic fever/heart disease in affected communities. The scabies mite produces 33 proteins that are closely related to those in the dust mite group 3 allergen and belong to the S1-like protease family (chymotrypsin-like). However, all but one of these molecules contain mutations in the conserved active-site catalytic triad that are predicted to render them catalytically inactive. These molecules are thus termed scabies mite inactivated protease paralogues (SMIPPs). The precise function of SMIPPs is unclear; however, it has been suggested that these proteins might function by binding and protecting target substrates from cleavage by host immune proteases, thus preventing the host from mounting an effective immune challenge. In order to begin to understand the structural basis for SMIPP function, we solved the crystal structures of SMIPP-S-I1 and SMIPP-S-D1 at 1.85 {angstrom} and 2.0 {angstrom} resolution, respectively. Both structures adopt the characteristic serine protease fold, albeit with large structural variations over much of the molecule. In both structures, mutations in the catalytic triad together with occlusion of the S1 subsite by a conserved Tyr200 residue is predicted to block substrate ingress. Accordingly, we show that both proteases lack catalytic function. Attempts to restore function (via site-directed mutagenesis of catalytic residues as well as Tyr200) were unsuccessful. Taken together, these data suggest that SMIPPs have lost the ability to bind substrates in a classical 'canonical' fashion, and instead have evolved alternative functions in the lifecycle of the scabies mite.

  15. Divergent evolutionary histories of DNA markers in a Hawaiian population of the coral Montipora capitata

    OpenAIRE

    Putnam, Hollie M.; Adams, Diane K.; Zelzion, Ehud; Wagner, Nicole E.; Qiu, Huan; Mass, Tali; Falkowski, Paul G.; Gates, Ruth D.; Bhattacharya, Debashish

    2017-01-01

    We investigated intra- and inter-colony sequence variation in a population of the dominant Hawaiian coral Montipora capitata by analyzing marker gene and genomic data. Ribosomal ITS1 regions showed evidence of a reticulate history among the colonies, suggesting incomplete rDNA repeat homogenization. Analysis of the mitochondrial genome identified a major (M. capitata) and a minor (M. flabellata) haplotype in single polyp-derived sperm bundle DNA with some colonies containing 2–3 different mtD...

  16. Evaluation of evolutionary divergence in the genus Naegleria by analysis of ribosomal DNA plasmid restriction patterns.

    Science.gov (United States)

    Clark, C G; Cross, G A; De Jonckheere, J F

    1989-05-15

    Ribosomal DNA (rDNA) plasmid restriction maps of 10 strains and rDNA hybridisation patterns of 61 additional strains have been used to assess inter- and intra-specific diversity and phylogenetic relationships in the genus Naegleria. The results obtained by this method largely confirm those of previous studies based on a variety of other criteria. They indicate that very little variation exists within the pathogenic species Naegleria fowleri despite its worldwide distribution and that it is closely related to the nonpathogenic Naegleria lovaniensis. Naegleria gruberi is most likely a polyphyletic grouping and care should be taken when using one strain as a reference point for this species. In addition, the two subspecies of the pathogenic Naegleria australiensis arose separately from within the range of variability encompassed by N. gruberi, as did the species Adelphamoeba galeacystis which should probably be assigned to the genus Naegleria. The species Naegleria jadini and Naegleria andersoni are not closely related to any other in the genus based on their rDNA patterns.

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

    Directory of Open Access Journals (Sweden)

    Borja Milá

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

  18. Multi-locus DNA sequencing of Toxoplasma gondii isolated from Brazilian pigs identifies genetically divergent strains

    Science.gov (United States)

    Frazão-Teixeira, E.; Sundar, N.; Dubey, J. P.; Grigg, M. E.; de Oliveira, F. C. R.

    2010-01-01

    Five Toxoplasma gondii isolates (TgPgBr1–5) were isolated from hearts and brains of pigs freshly purchased at the market of Campos dos Goytacazes, Northern Rio de Janeiro State, Brazil. Four of the five isolates were highly pathogenic in mice. Four genotypes were identified. Multi-locus PCR-DNA sequencing showed that each strain possessed a unique combination of archetypal and novel alleles not previously described in South America. The data suggest that different strains circulate in pigs destined for human consumption from those previously isolated from cats and chickens in Brazil. Further, multi-locus PCR-RFLP analyses failed to accurately genotype the Brazilian isolates due to the high presence of atypical alleles. This is the first report of multi-locus DNA sequencing of T. gondii isolates in pigs from Brazil. PMID:21051148

  19. Three human alcohol dehydrogenase subunits: cDNA structure and molecular and evolutionary divergence

    International Nuclear Information System (INIS)

    Ikuta, T.; Szeto, S.; Yoshida, A.

    1986-01-01

    Class I human alcohol dehydrogenase (ADH; alcohol:NAD + oxidoreductase, EC 1.1.1.1) consists of several homo- and heterodimers of α, β, and γ subunits that are governed by the ADH1, ADH2, and ADH3 loci. The authors previously cloned a full length of cDNA for the β subunit, and the complete sequence of 374 amino acid residues was established. cDNAs for the α and γ subunits were cloned and characterized. A human liver cDNA library, constructed in phage λgt11, was screened by using a synthetic oligonucleotide probe that was matched to the γ but not to the β sequence. Clone pUCADHγ21 and clone pUCADHα15L differed from β cDNA with respect to restriction sites and hybridization with the nucleotide probe. Clone pUCADHγ21 contained an insertion of 1.5 kilobase pairs (kbp) and encodes 374 amino acid residues compatible with the reported amino acid sequence of the γ subunit. Clone pUCADHα15L contained an insertion of 2.4 kbp and included nucleotide sequences that encode 374 amino acid residues for another subunit, the γ subunit. In addition, this clone contained the sequences that encode the COOH-terminal part of the β subunit at its extended 5' region. The amino acid sequences and coding regions of the cDNAs of the three subunits are very similar. A high degree of resemblance is observed also in their 3' noncoding regions. However, distinctive differences exist in the vicinity of the Zn-binding cysteine residue at position 46. Based on the cDNA sequences and the deduced amino acid sequences of the three subunits, their structural and evolutionary relationships are discussed

  20. Geographic divergence of "Sulfolobus islandicus" strains assessed by genomic analyses including electronic DNA hybridization confirms they are geovars.

    Science.gov (United States)

    Zuo, Guanghong; Hao, Bailin; Staley, James T

    2014-02-01

    Ten well-annotated genomes of "Sulfolobus islandicus" strains from different geographic locations have been released at the NCBI database. Whole genome based composition vector trees indicate that these strains show the same branching patterns as originally reported by multi-locus sequence analysis. To determine whether the ten strains meet the criteria for separate species, DNA-DNA hybridization (DDH) was performed in silico. DDH values of strains from the same geographic location, i.e., Iceland, Kamchatka and North America, ranged from 82.4 to 95.4 %, clearly qualifying them as members of the same species. The lowest DDH values found between locations ranged from 75.5 to 76.6 %, which exceed the 70 % DDH threshold for a species thereby indicating they are all members of the same species based on the currently accepted definition. The clear divergences of strains from the different geographic locations are sufficiently great to consider them as separate geovars. "S. islandicus" has not yet been validly named and a type strain has not been deposited in culture collections. We urgently recommend that those who study the organism fulfill the criteria of the International Code of Nomenclature of Bacteria in order to designate a type strain and to identify and deposit related strains of this species to make them available to the broader scientific community.

  1. Evolution of divergent DNA recognition specificities in VDE homing endonucleases from two yeast species

    Science.gov (United States)

    Posey, Karen L.; Koufopanou, Vassiliki; Burt, Austin; Gimble, Frederick S.

    2004-01-01

    Homing endonuclease genes (HEGs) are mobile DNA elements that are thought to confer no benefit to their host. They encode site-specific DNA endonucleases that perpetuate the element within a species population by homing and disseminate it between species by horizontal transfer. Several yeast species contain the VMA1 HEG that encodes the intein-associated VMA1-derived endonuclease (VDE). The evolutionary state of VDEs from 12 species was assessed by assaying their endonuclease activities. Only two enzymes are active, PI-ZbaI from Zygosaccharomyces bailii and PI-ScaI from Saccharomyces cariocanus. PI-ZbaI cleaves the Z.bailii recognition sequence significantly faster than the Saccharomyces cerevisiae site, which differs at six nucleotide positions. A mutational analysis indicates that PI-ZbaI cleaves the S.cerevisiae substrate poorly due to the absence of a contact that is analogous to one made in PI-SceI between Gln-55 and nucleotides +9/+10. PI-ZbaI cleaves the Z.bailii substrate primarily due to a single base-pair substitution (A/T+5 → T/A+5). Structural modeling of the PI-ZbaI/DNA complex suggests that Arg-331, which is absent in PI-SceI, contacts T/A+5, and the reduced activity observed in a PI-ZbaI R331A mutant provides evidence for this interaction. These data illustrate that homing endonucleases evolve altered specificity as they adapt to recognize alternative target sites. PMID:15280510

  2. SSU rDNA divergence in planktonic foraminifera: molecular taxonomy and biogeographic implications.

    Directory of Open Access Journals (Sweden)

    Aurore André

    Full Text Available The use of planktonic foraminifera in paleoceanography requires taxonomic consistency and precise assessment of the species biogeography. Yet, ribosomal small subunit (SSUr DNA analyses have revealed that most of the modern morpho-species of planktonic foraminifera are composed of a complex of several distinct genetic types that may correspond to cryptic or pseudo-cryptic species. These genetic types are usually delimitated using partial sequences located at the 3'end of the SSUrDNA, but typically based on empirical delimitation. Here, we first use patristic genetic distances calculated within and among genetic types of the most common morpho-species to show that intra-type and inter-type genetic distances within morpho-species may significantly overlap, suggesting that genetic types have been sometimes inconsistently defined. We further apply two quantitative and independent methods, ABGD (Automatic Barcode Gap Detection and GMYC (General Mixed Yule Coalescent to a dataset of published and newly obtained partial SSU rDNA for a more objective assessment of the species status of these genetic types. Results of these complementary approaches are highly congruent and lead to a molecular taxonomy that ranks 49 genetic types of planktonic foraminifera as genuine (pseudocryptic species. Our results advocate for a standardized sequencing procedure allowing homogenous delimitations of (pseudocryptic species. On the ground of this revised taxonomic framework, we finally provide an integrative taxonomy synthesizing geographic, ecological and morphological differentiations that can occur among the genuine (pseudocryptic species. Due to molecular, environmental or morphological data scarcities, many aspects of our proposed integrative taxonomy are not yet fully resolved. On the other hand, our study opens up the potential for a correct interpretation of environmental sequence datasets.

  3. SSU rDNA divergence in planktonic foraminifera: molecular taxonomy and biogeographic implications.

    Science.gov (United States)

    André, Aurore; Quillévéré, Frédéric; Morard, Raphaël; Ujiié, Yurika; Escarguel, Gilles; de Vargas, Colomban; de Garidel-Thoron, Thibault; Douady, Christophe J

    2014-01-01

    The use of planktonic foraminifera in paleoceanography requires taxonomic consistency and precise assessment of the species biogeography. Yet, ribosomal small subunit (SSUr) DNA analyses have revealed that most of the modern morpho-species of planktonic foraminifera are composed of a complex of several distinct genetic types that may correspond to cryptic or pseudo-cryptic species. These genetic types are usually delimitated using partial sequences located at the 3'end of the SSUrDNA, but typically based on empirical delimitation. Here, we first use patristic genetic distances calculated within and among genetic types of the most common morpho-species to show that intra-type and inter-type genetic distances within morpho-species may significantly overlap, suggesting that genetic types have been sometimes inconsistently defined. We further apply two quantitative and independent methods, ABGD (Automatic Barcode Gap Detection) and GMYC (General Mixed Yule Coalescent) to a dataset of published and newly obtained partial SSU rDNA for a more objective assessment of the species status of these genetic types. Results of these complementary approaches are highly congruent and lead to a molecular taxonomy that ranks 49 genetic types of planktonic foraminifera as genuine (pseudo)cryptic species. Our results advocate for a standardized sequencing procedure allowing homogenous delimitations of (pseudo)cryptic species. On the ground of this revised taxonomic framework, we finally provide an integrative taxonomy synthesizing geographic, ecological and morphological differentiations that can occur among the genuine (pseudo)cryptic species. Due to molecular, environmental or morphological data scarcities, many aspects of our proposed integrative taxonomy are not yet fully resolved. On the other hand, our study opens up the potential for a correct interpretation of environmental sequence datasets.

  4. Inferring divergence times within pikas (Ochotona spp.) using mtDNA and relaxed molecular dating techniques.

    Science.gov (United States)

    Lanier, Hayley C; Olson, Link E

    2009-10-01

    Although several studies have recently addressed phylogenetic relationships among Asian pikas (Ochotona spp.), the North American species have been relatively neglected and their monophyly generally unquestioned or assumed. Given the high degree of intraspecific diversity in pelage and call structure, the recent identification of previously unrecognized species of pika in Asia, and the increasing evidence for multiple trans-Beringian dispersals in several small mammal lineages, the monophyly of North American pikas warrants reexamination. In addition, previous studies have applied an externally calibrated rate to examine the timing of diversification within the genus. This method has been increasingly shown to return results that, at the very least, are overly narrow in their confidence intervals, and at the worst can be entirely spurious. For this study we combined GenBank sequences from the mitochondrial genes cyt b and ND4 with newly generated sequence data from O. hyperborea and O. collaris to investigate the origin of the North American lineages and the timing of phylogenetic diversification within the genus Ochotona. Specifically, we address three goals (1) summarize and reanalyze the molecular evidence for relationships within the genus using statistically supported models of evolution; (2) add additional sequences from O. collaris and O. hyperborea to rigorously test the monophyly of North American pikas; (3) examine the timing of the diversification within the genus using relaxed molecular clock methods. We found no evidence of multiple trans-Beringian dispersals into North America, thereby supporting the traditional hypothesis of a single invasion of North America. We also provide evidence that the major splits within the genus occurred in the Miocene, and the Nearctic pikas diverged sometime before the Pleistocene.

  5. Genetic Divergence in Domestic Japanese Quail Inferred from Mitochondrial DNA D-Loop and Microsatellite Markers.

    Science.gov (United States)

    Nunome, Mitsuo; Nakano, Mikiharu; Tadano, Ryo; Kawahara-Miki, Ryoka; Kono, Tomohiro; Takahashi, Shinji; Kawashima, Takaharu; Fujiwara, Akira; Nirasawa, Keijiro; Mizutani, Makoto; Matsuda, Yoichi

    2017-01-01

    To assess the genetic diversity of domestic Japanese quail (Coturnix japonica) populations, and their genetic relationships, we examined mitochondrial DNA (mtDNA) D-loop sequences and microsatellite markers for 19 Japanese quail populations. The populations included nine laboratory lines established in Japan (LWC, Quv, RWN, WE, AWE, AMRP, rb-TKP, NIES-L, and W), six meat-type quail lines reimported from Western countries (JD, JW, Estonia, NIES-Br, NIES-Fr, and NIES-Hn), one commercial population in Japan, and three wild quail populations collected from three Asian areas. The phylogenetic tree of mtDNA D-loop sequences revealed two distinct haplotype groups, Dloop-Group1 and Dloop-Group2. Dloop-Group1 included a dominant haplotype representing most of the quail populations, including wild quail. Dloop-Group2 was composed of minor haplotypes found in several laboratory lines, two meat-type lines, and a few individuals in commercial and wild quail populations. Taking the breeding histories of domestic populations into consideration, these results suggest that domestic quail populations may have derived from two sources, i.e., domestic populations established before and after World War II in Japan. A discriminant analysis of principal components and a Bayesian clustering analysis with microsatellite markers indicated that the domestic populations are clustered into four genetic groups. The two major groups were Microsat-Group1, which contained WE, and four WE-derived laboratory lines (LWC, Quv, RWN, and AWE), and Microsat-Group2 consisting of NIES-L, JD, JW, Estonia, NIES-Br, NIES-Fr, NIES-Hn, W, and commercial and wild populations. The remaining two lines (AMRP and rb-TKP) were each clustered into a separate clade. This hierarchical genetic difference between domestic quail populations is attributed to the genetic background derived from two different genetic sources-the pre-war and post-war populations-which is well supported by their breeding histories.

  6. A reinvestigation of phylogeny and divergence times of the Ablepharus kitaibelii species complex (Sauria, Scincidae) based on mtDNA and nuDNA genes.

    Science.gov (United States)

    Skourtanioti, Eirini; Kapli, Paschalia; Ilgaz, Çetin; Kumlutaş, Yusuf; Avcı, Aziz; Ahmadzadeh, Faraham; Crnobrnja-Isailović, Jelka; Gherghel, Iulian; Lymberakis, Petros; Poulakakis, Nikos

    2016-10-01

    Morphological and DNA data support that the East Mediterranean snake-eyed skink Ablepharus kitaibelii represents a species complex that includes four species A. kitaibelii, A. budaki, A. chernovi, and A. rueppellii, highlighting the need of its taxonomic reevaluation. Here, we used Bayesian and Maximum Likelihood methods to estimate the phylogenetic relationships of all members of the complex based on two mitochondrial (cyt b, 16S rRNA) and two nuclear markers (MC1R, and NKTR) and using Chalcides, Eumeces, and Eutropis as outgroups. The biogeographic history of the complex was also investigated through the application of several phylogeographic (BEAST) and biogeographic (BBM) analyses. Paleogeographic and paleoclimatic data were used to support the inferred phylogeographic patterns. The A. kitaibelli species complex exhibits high genetic diversity, revealing cases of hidden diversity and cases of non-monophyletic species such as A. kitaibelii and A. budaki. Our results indicate that A. pannonicus branches off first and a group that comprises specimens of A. kitaibelli and A. budaki from Kastelorizo Island group (southeast Greece) and southwest Turkey, respectively is differentiated from the rest A. kitaibelli and A. budaki populations and may represent a new species. The estimated divergence times place the origin of the complex in the Middle Miocene (∼16Mya) and the divergence of most currently recognized species in the Late Miocene. The inferred ancestral distribution suggests that the complex originated in Anatolia, supposing that several vicariance and dispersal events that are related with the formation of the Mid-Aegean Trench, the Anatolian Diagonal and the orogenesis of the mountain chains in southern and eastern Anatolia have led to current distribution pattern of A. kitaibelii species complex in the Balkans and Middle East. Copyright © 2016 Elsevier Inc. All rights reserved.

  7. Patterns of major divergence between the internal transcribed spacers of ribosomal DNA in Xenopus borealis and Xenopus laevis, and of minimal divergence within ribosomal coding regions.

    Science.gov (United States)

    Furlong, J C; Maden, B E

    1983-01-01

    We have determined the nucleotide sequences of the two internal transcribed spacers, the adjacent ribosomal coding sequences and the boundary between the external transcribed spacer and the 18S coding sequence in a cloned ribosomal transcription unit from Xenopus borealis. The transcribed spacers differ very extensively from those of X. laevis. Nevertheless, embedded in the internal transcribed spacers are several short sequence elements which are identical between the two species. These conserved elements are laterally displaced by substantial distances in the X. borealis sequence with respect to that of X. laevis. These relative displacements imply that insertions and deletions have played a major role in transcribed spacer divergence in Xenopus. This in turn implies that large regions of the transcribed spacers do not play a sequence-specific role in ribosome maturation. In contrast, the sequenced parts of the ribosomal coding regions, which encompass 670 nucleotides, differ at only three points from the corresponding sequences in X. laevis, each by a single substitution. These substitutions are readily accommodated by current models for rRNA higher order structure.

  8. Large sequence divergence of mitochondrial DNA genotypes of the control region within populations of the African antelope, kob (Kobus kob)

    DEFF Research Database (Denmark)

    Birungi, J.; Arctander, Peter

    2000-01-01

    conservation genetics, control region, Kobus kob, mitochondrial DNA, population expansion, population structure......conservation genetics, control region, Kobus kob, mitochondrial DNA, population expansion, population structure...

  9. Sequencing of whole plastid genomes and nuclear ribosomal DNA of Diospyros species (Ebenaceae) endemic to New Caledonia: many species, little divergence.

    Science.gov (United States)

    Turner, Barbara; Paun, Ovidiu; Munzinger, Jérôme; Chase, Mark W; Samuel, Rosabelle

    2016-06-01

    Some plant groups, especially on islands, have been shaped by strong ancestral bottlenecks and rapid, recent radiation of phenotypic characters. Single molecular markers are often not informative enough for phylogenetic reconstruction in such plant groups. Whole plastid genomes and nuclear ribosomal DNA (nrDNA) are viewed by many researchers as sources of information for phylogenetic reconstruction of groups in which expected levels of divergence in standard markers are low. Here we evaluate the usefulness of these data types to resolve phylogenetic relationships among closely related Diospyros species. Twenty-two closely related Diospyros species from New Caledonia were investigated using whole plastid genomes and nrDNA data from low-coverage next-generation sequencing (NGS). Phylogenetic trees were inferred using maximum parsimony, maximum likelihood and Bayesian inference on separate plastid and nrDNA and combined matrices. The plastid and nrDNA sequences were, singly and together, unable to provide well supported phylogenetic relationships among the closely related New Caledonian Diospyros species. In the nrDNA, a 6-fold greater percentage of parsimony-informative characters compared with plastid DNA was found, but the total number of informative sites was greater for the much larger plastid DNA genomes. Combining the plastid and nuclear data improved resolution. Plastid results showed a trend towards geographical clustering of accessions rather than following taxonomic species. In plant groups in which multiple plastid markers are not sufficiently informative, an investigation at the level of the entire plastid genome may also not be sufficient for detailed phylogenetic reconstruction. Sequencing of complete plastid genomes and nrDNA repeats seems to clarify some relationships among the New Caledonian Diospyros species, but the higher percentage of parsimony-informative characters in nrDNA compared with plastid DNA did not help to resolve the phylogenetic tree

  10. The complete chloroplast DNA sequence of the green alga Oltmannsiellopsis viridis reveals a distinctive quadripartite architecture in the chloroplast genome of early diverging ulvophytes

    Directory of Open Access Journals (Sweden)

    Lemieux Claude

    2006-02-01

    Full Text Available Abstract Background The phylum Chlorophyta contains the majority of the green algae and is divided into four classes. The basal position of the Prasinophyceae has been well documented, but the divergence order of the Ulvophyceae, Trebouxiophyceae and Chlorophyceae is currently debated. The four complete chloroplast DNA (cpDNA sequences presently available for representatives of these classes have revealed extensive variability in overall structure, gene content, intron composition and gene order. The chloroplast genome of Pseudendoclonium (Ulvophyceae, in particular, is characterized by an atypical quadripartite architecture that deviates from the ancestral type by a large inverted repeat (IR featuring an inverted rRNA operon and a small single-copy (SSC region containing 14 genes normally found in the large single-copy (LSC region. To gain insights into the nature of the events that led to the reorganization of the chloroplast genome in the Ulvophyceae, we have determined the complete cpDNA sequence of Oltmannsiellopsis viridis, a representative of a distinct, early diverging lineage. Results The 151,933 bp IR-containing genome of Oltmannsiellopsis differs considerably from Pseudendoclonium and other chlorophyte cpDNAs in intron content and gene order, but shares close similarities with its ulvophyte homologue at the levels of quadripartite architecture, gene content and gene density. Oltmannsiellopsis cpDNA encodes 105 genes, contains five group I introns, and features many short dispersed repeats. As in Pseudendoclonium cpDNA, the rRNA genes in the IR are transcribed toward the single copy region featuring the genes typically found in the ancestral LSC region, and the opposite single copy region harbours genes characteristic of both the ancestral SSC and LSC regions. The 52 genes that were transferred from the ancestral LSC to SSC region include 12 of those observed in Pseudendoclonium cpDNA. Surprisingly, the overall gene organization of

  11. Employing 454 amplicon pyrosequencing to reveal intragenomic divergence in the internal transcribed spacer rDNA region in fungi

    Science.gov (United States)

    Daniel L. Lindner; Tor Carlsen; Henrik Nilsson; Marie Davey; Trond Schumacher; Havard. Kauserud

    2013-01-01

    The rDNA internal transcribed spacer (ITS) region has been accepted as a DNA barcoding marker for fungi and is widely used in phylogenetic studies; however, intragenomic ITS variability has been observed in a broad range of taxa, including prokaryotes, plants, animals, and fungi, and this variability has the potential to inflate species richness estimates in molecular...

  12. DNA barcoding of gypsy moths from China (Lepidoptera: Erebidae) reveals new haplotypes and divergence patterns within gypsy moth subspecies

    Science.gov (United States)

    Fang Chen; Youqing Luo; Melody A. Keena; Ying Wu; Peng Wu; Juan Shi

    2015-01-01

    The gypsy moth from Asia (two subspecies) is considered a greater threat to North America than European gypsy moth, because of a broader host range and females being capable of flight. Variation within and among gypsy moths from China (nine locations), one of the native countries of Asian gypsy moth, were compared using DNA barcode sequences (658 bp of mtDNA cytochrome...

  13. Simulation model of converging-diverging (CD) nozzle to improve particle delivery system of deoxyribonucleic acid (DNA)

    Science.gov (United States)

    Sumarsono, Danardono A.; Ibrahim, Fera; Santoso, Satria P.; Sari, Gema P.

    2018-02-01

    Gene gun is a mechanical device which has been used to deliver DNA vaccine into the cells and tissues by increasing the uptake of DNA plasmid so it can generate a high immune response with less amount of DNA. Nozzle is an important part of the gene gun which used to accelerate DNA in particle form with a gas flow to reach adequate momentum to enter the epidermis of human skin and elicit immune response. We developed new designs of nozzle for gene gun to make DNA uptake more efficient in vaccination. We used Computational Fluid Dynamics (CFD) by Autodesk® Simulation 2015 to simulate static fluid pressure and velocity contour of supersonic wave and parametric distance to predict the accuracy of the new nozzle. The result showed that the nozzle could create a shockwave at the distance parametric to the object from 4 to 5 cm using fluid pressure varied between 0.8-1.2 MPa. This is indication a possibility that the DNA particle could penetrate under the mammalian skin. For the future research step, this new nozzle model could be considered for development the main component of the DNA delivery system in vaccination in vivo

  14. Acquisition of apparent DNA slippage structures during extensive evolutionary divergence of pcaD and catD genes encoding identical catalytic activities in Acinetobacter calcoaceticus.

    Science.gov (United States)

    Hartnett, G B; Ornston, L N

    1994-05-03

    The pca operon from the Gram- bacterium Acinetobacter calcoaceticus encodes all of the enzymes required for catabolism of protocatechuate to common intermediary metabolites. This report presents the 2754-nucleotide (nt) sequence of a HindIII restriction fragment containing pcaD, the 801-bp gene encoding beta-ketoadipate enol-lactone hydrolase I. The deduced primary structure of A. calcoaceticus PcaD shares 44% amino acid (aa) sequence identity with the aligned primary structure of CatD (beta-ketoadipate enol-lactone hydrolase II) from the same organism, and the overall nt sequence identity of the two genes is 51.8%. In the 56% of the genes where selection for identical aa residues was not imposed, pcaD and catD have diverged so extensively that nt sequence identity of the aligned segments is only 28.2%; the G+C contents of these segments from the respective genes differ by 8%. Conserved within the aligned PcaD and CatD aa sequences is a Ser residue corresponding to the nucleophile within the alpha/beta-fold of many hydrolytic enzymes. In this region of primary structure, PcaD and CatD appear to have maintained some different aa sequences derived from a common ancestor. Conservation of the different aa sequences during extreme evolutionary divergence suggests that separate segments of primary structure, conserved within either PcaD or CatD, may be functionally incompatible within recombinant enzymes. Consequently, selection for avoidance of genetic exchange between pcaD and catD could account for the thorough nt substitution in regions where identical aa were not selected. Sequence repetitions within pcaD suggest that the multiple mutations required for its extensive divergence from catD were achieved in part by acquisition of a complex DNA slippage structure.

  15. Phylogeographic Pattern and Extensive Mitochondrial DNA Divergence Disclose a Species Complex within the Chagas Disease Vector Triatoma dimidiata

    Science.gov (United States)

    Monteiro, Fernando A.; Peretolchina, Tatiana; Lazoski, Cristiano; Harris, Kecia; Dotson, Ellen M.; Abad-Franch, Fernando; Tamayo, Elsa; Pennington, Pamela M.; Monroy, Carlota; Cordon-Rosales, Celia; Salazar-Schettino, Paz Maria; Gómez-Palacio, Andrés; Grijalva, Mario J.; Beard, Charles B.; Marcet, Paula L.

    2013-01-01

    Background Triatoma dimidiata is among the main vectors of Chagas disease in Latin America. However, and despite important advances, there is no consensus about the taxonomic status of phenotypically divergent T. dimidiata populations, which in most recent papers are regarded as subspecies. Methodology and Findings A total of 126 cyt b sequences (621 bp long) were produced for specimens from across the species range. Forty-seven selected specimens representing the main cyt b clades observed (after a preliminary phylogenetic analysis) were also sequenced for an ND4 fragment (554 bp long) and concatenated with their respective cyt b sequences to produce a combined data set totalling 1175 bp/individual. Bayesian and Maximum-Likelihood phylogenetic analyses of both data sets (cyt b, and cyt b+ND4) disclosed four strongly divergent (all pairwise Kimura 2-parameter distances >0.08), monophyletic groups: Group I occurs from Southern Mexico through Central America into Colombia, with Ecuadorian specimens resembling Nicaraguan material; Group II includes samples from Western-Southwestern Mexico; Group III comprises specimens from the Yucatán peninsula; and Group IV consists of sylvatic samples from Belize. The closely-related, yet formally recognized species T. hegneri from the island of Cozumel falls within the divergence range of the T. dimidiata populations studied. Conclusions We propose that Groups I–IV, as well as T. hegneri, should be regarded as separate species. In the Petén of Guatemala, representatives of Groups I, II, and III occur in sympatry; the absence of haplotypes with intermediate genetic distances, as shown by multimodal mismatch distribution plots, clearly indicates that reproductive barriers actively promote within-group cohesion. Some sylvatic specimens from Belize belong to a different species – likely the basal lineage of the T. dimidiata complex, originated ∼8.25 Mya. The evidence presented here strongly supports the proposition that T

  16. Phylogeographic pattern and extensive mitochondrial DNA divergence disclose a species complex within the Chagas disease vector Triatoma dimidiata.

    Directory of Open Access Journals (Sweden)

    Fernando A Monteiro

    Full Text Available BACKGROUND: Triatoma dimidiata is among the main vectors of Chagas disease in Latin America. However, and despite important advances, there is no consensus about the taxonomic status of phenotypically divergent T. dimidiata populations, which in most recent papers are regarded as subspecies. METHODOLOGY AND FINDINGS: A total of 126 cyt b sequences (621 bp long were produced for specimens from across the species range. Forty-seven selected specimens representing the main cyt b clades observed (after a preliminary phylogenetic analysis were also sequenced for an ND4 fragment (554 bp long and concatenated with their respective cyt b sequences to produce a combined data set totalling 1175 bp/individual. Bayesian and Maximum-Likelihood phylogenetic analyses of both data sets (cyt b, and cyt b+ND4 disclosed four strongly divergent (all pairwise Kimura 2-parameter distances >0.08, monophyletic groups: Group I occurs from Southern Mexico through Central America into Colombia, with Ecuadorian specimens resembling Nicaraguan material; Group II includes samples from Western-Southwestern Mexico; Group III comprises specimens from the Yucatán peninsula; and Group IV consists of sylvatic samples from Belize. The closely-related, yet formally recognized species T. hegneri from the island of Cozumel falls within the divergence range of the T. dimidiata populations studied. CONCLUSIONS: We propose that Groups I-IV, as well as T. hegneri, should be regarded as separate species. In the Petén of Guatemala, representatives of Groups I, II, and III occur in sympatry; the absence of haplotypes with intermediate genetic distances, as shown by multimodal mismatch distribution plots, clearly indicates that reproductive barriers actively promote within-group cohesion. Some sylvatic specimens from Belize belong to a different species - likely the basal lineage of the T. dimidiata complex, originated ~8.25 Mya. The evidence presented here strongly supports the proposition

  17. A complex genetic switch involving overlapping divergent promoters and DNA looping regulates expression of conjugation genes of a gram-positive plasmid.

    Science.gov (United States)

    Ramachandran, Gayetri; Singh, Praveen K; Luque-Ortega, Juan Roman; Yuste, Luis; Alfonso, Carlos; Rojo, Fernando; Wu, Ling J; Meijer, Wilfried J J

    2014-10-01

    Plasmid conjugation plays a significant role in the dissemination of antibiotic resistance and pathogenicity determinants. Understanding how conjugation is regulated is important to gain insights into these features. Little is known about regulation of conjugation systems present on plasmids from Gram-positive bacteria. pLS20 is a native conjugative plasmid from the Gram-positive bacterium Bacillus subtilis. Recently the key players that repress and activate pLS20 conjugation have been identified. Here we studied in detail the molecular mechanism regulating the pLS20 conjugation genes using both in vivo and in vitro approaches. Our results show that conjugation is subject to the control of a complex genetic switch where at least three levels of regulation are integrated. The first of the three layers involves overlapping divergent promoters of different strengths regulating expression of the conjugation genes and the key transcriptional regulator RcoLS20. The second layer involves a triple function of RcoLS20 being a repressor of the main conjugation promoter and an activator and repressor of its own promoter at low and high concentrations, respectively. The third level of regulation concerns formation of a DNA loop mediated by simultaneous binding of tetrameric RcoLS20 to two operators, one of which overlaps with the divergent promoters. The combination of these three layers of regulation in the same switch allows the main conjugation promoter to be tightly repressed during conditions unfavorable to conjugation while maintaining the sensitivity to accurately switch on the conjugation genes when appropriate conditions occur. The implications of the regulatory switch and comparison with other genetic switches involving DNA looping are discussed.

  18. Expression of 5 S rRNA genes linked to 35 S rDNA in plants, their epigenetic modification and regulatory element divergence

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    Garcia Sònia

    2012-06-01

    Full Text Available Abstract Background In plants, the 5 S rRNA genes usually occur as separate tandems (S-type arrangement or, less commonly, linked to 35 S rDNA units (L-type. The activity of linked genes remains unknown so far. We studied the homogeneity and expression of 5 S genes in several species from family Asteraceae known to contain linked 35 S-5 S units. Additionally, their methylation status was determined using bisulfite sequencing. Fluorescence in situ hybridization was applied to reveal the sub-nuclear positions of rDNA arrays. Results We found that homogenization of L-type units went to completion in most (4/6 but not all species. Two species contained major L-type and minor S-type units (termed Ls-type. The linked genes dominate 5 S rDNA expression while the separate tandems do not seem to be expressed. Members of tribe Anthemideae evolved functional variants of the polymerase III promoter in which a residing C-box element differs from the canonical angiosperm motif by as much as 30%. On this basis, a more relaxed consensus sequence of a plant C-box: (5’-RGSWTGGGTG-3’ is proposed. The 5 S paralogs display heavy DNA methylation similarly as to their unlinked counterparts. FISH revealed the close association of 35 S-5 S arrays with nucleolar periphery indicating that transcription of 5 S genes may occur in this territory. Conclusions We show that the unusual linked arrangement of 5 S genes, occurring in several plant species, is fully compatible with their expression and functionality. This extraordinary 5 S gene dynamics is manifested at different levels, such as variation in intrachromosomal positions, unit structure, epigenetic modification and considerable divergence of regulatory motifs.

  19. A Novel Sequence-Based Feature for the Identification of DNA-Binding Sites in Proteins Using Jensen–Shannon Divergence

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    Truong Khanh Linh Dang

    2016-10-01

    Full Text Available The knowledge of protein-DNA interactions is essential to fully understand the molecular activities of life. Many research groups have developed various tools which are either structure- or sequence-based approaches to predict the DNA-binding residues in proteins. The structure-based methods usually achieve good results, but require the knowledge of the 3D structure of protein; while sequence-based methods can be applied to high-throughput of proteins, but require good features. In this study, we present a new information theoretic feature derived from Jensen–Shannon Divergence (JSD between amino acid distribution of a site and the background distribution of non-binding sites. Our new feature indicates the difference of a certain site from a non-binding site, thus it is informative for detecting binding sites in proteins. We conduct the study with a five-fold cross validation of 263 proteins utilizing the Random Forest classifier. We evaluate the functionality of our new features by combining them with other popular existing features such as position-specific scoring matrix (PSSM, orthogonal binary vector (OBV, and secondary structure (SS. We notice that by adding our features, we can significantly boost the performance of Random Forest classifier, with a clear increment of sensitivity and Matthews correlation coefficient (MCC.

  20. Biogeography of the Pistia clade (Araceae): based on chloroplast and mitochondrial DNA sequences and Bayesian divergence time inference.

    Science.gov (United States)

    Renner, Susanne S; Zhang, Li-Bing

    2004-06-01

    Pistia stratiotes (water lettuce) and Lemna (duckweeds) are the only free-floating aquatic Araceae. The geographic origin and phylogenetic placement of these unrelated aroids present long-standing problems because of their highly modified reproductive structures and wide geographical distributions. We sampled chloroplast (trnL-trnF and rpl20-rps12 spacers, trnL intron) and mitochondrial sequences (nad1 b/c intron) for all genera implicated as close relatives of Pistia by morphological, restriction site, and sequencing data, and present a hypothesis about its geographic origin based on the consensus of trees obtained from the combined data, using Bayesian, maximum likelihood, parsimony, and distance analyses. Of the 14 genera closest to Pistia, only Alocasia, Arisaema, and Typhonium are species-rich, and the latter two were studied previously, facilitating the choice of representatives that span the roots of these genera. Results indicate that Pistia and the Seychelles endemic Protarum sechellarum are the basalmost branches in a grade comprising the tribes Colocasieae (Ariopsis, Steudnera, Remusatia, Alocasia, Colocasia), Arisaemateae (Arisaema, Pinellia), and Areae (Arum, Biarum, Dracunculus, Eminium, Helicodiceros, Theriophonum, Typhonium). Unexpectedly, all Areae genera are embedded in Typhonium, which throws new light on the geographic history of Areae. A Bayesian analysis of divergence times that explores the effects of multiple fossil and geological calibration points indicates that the Pistia lineage is 90 to 76 million years (my) old. The oldest fossils of the Pistia clade, though not Pistia itself, are 45-my-old leaves from Germany; the closest outgroup, Peltandreae (comprising a few species in Florida, the Mediterranean, and Madagascar), is known from 60-my-old leaves from Europe, Kazakhstan, North Dakota, and Tennessee. Based on the geographic ranges of close relatives, Pistia likely originated in the Tethys region, with Protarum then surviving on the

  1. Diverging Cohesion?

    DEFF Research Database (Denmark)

    Charron, Nicholas

    2016-01-01

    Why do increases in globalisation in the face of European expansion lead to sharp levels of regional divergences in wealth in some countries but not in others? The central crux of this paper is that convergence/divergence trends in European states are conditioned by ‘state capacity’. State capacity...... – which we define here as a combination of impartial bureaucratic practices, corruption and the rule of law – limits, and in some cases reverses the tendency towards greater divergence linked to trade. Countries with high levels of state capacity – that is, those that have greater government effectiveness...... globalisation – European Union (EU) member states – using aggregated regional-level data from 1995 to 2008. Strong and robust empirical evidence is found for this claim....

  2. Phylogenetic relationship and time of divergence of Mus terricolor ...

    Indian Academy of Sciences (India)

    2016-06-06

    Jun 6, 2016 ... the divergence of different Mus lineages and 98 events in. Rattus after divergence from Mus lineage. Time of divergence. In this study, the rate of change of murid mtDNA was cal- culated taking 12 Mya (Rattus and Mus divergence time) as a calibration point. Tajima's relative rate test was also. Journal of ...

  3. Genetic divergence between Auxis thazard and A. rochei based on PCR-RFLP analysis of mtDNA D-loop region

    Digital Repository Service at National Institute of Oceanography (India)

    GirishKumar; Kunal, S.P.; Menezes, R.M.; Kocour, M.

    is mitochondrial DNA (mtDNA); because of its predominantly maternal inheritance, relatively rapid rate of base substitution, and lack of recombination (Avise et al., 1987). MtDNA sequence differences can either be measured directly through restriction site...

  4. Lack of Mitochondrial DNA Sequence Divergence between Two Subspecies of the Siberian Weasel from Korea: Mustela sibirica coreanus from the Korean Peninsula and M. s. quelpartis from Jeju Island

    Directory of Open Access Journals (Sweden)

    Hung Sun Koh

    2012-04-01

    Full Text Available The objective of this study was to determine the degree of mitochondrial DNA (mtDNA divergence between two subspecies of Mustela sibirica from Korea (M. s. coreanus on the Korean Peninsula and M. s. quelpartis on Jeju Island and to examine the taxonomic status of M. s. quelpartis. Thus, we obtained complete sequences of mtDNA cytochrome b gene (1,140 bp from the two subspecies, and these sequences were compared to a corresponding haplotype of M. s. coreanus, downloaded from GenBank. From this analysis, it was observed that the sequences from monogenic M. s. quelpartis on Jeju Island were identical to the sequences of four M. s. coreanus from four locations across the Korean Peninsula, and that the two subspecies formed a single clade; the average nucleotide distance between the two subspecies was 0.26% (range, 0.00 to 0.53%. We found that the subspecies quelpartis is not genetically distinct from the subspecies coreanus, and that this cytochrome b sequencing result does not support the current classification, distinguishing these two subspecies by pelage color. Further systematic analyses using morphometric characters and other DNA markers are necessary to confirm the taxonomic status of M. s. quelpartis.

  5. Expression of 5 S rRNA genes linked to 35 S rDNA in plants, their epigenetic modification and regulatory element divergence

    Czech Academy of Sciences Publication Activity Database

    Garcia, S.; Crhák Khaitová, Lucie; Kovařík, Aleš

    2012-01-01

    Roč. 12, JUN 20 (2012), ID 95 ISSN 1471-2229 R&D Projects: GA ČR GAP501/10/0208; GA ČR GBP501/12/G090 Institutional support: RVO:68081707 Keywords : ARABIDOPSIS -THALIANA * NUCLEOTIDE-SEQUENCES * DNA METHYLATION * GENUS ARTEMISIA Subject RIV: BO - Biophysics Impact factor: 4.354, year: 2012

  6. Ectopic expression of Arabidopsis FD and FD PARALOGUE in rice results in dwarfism with size reduction of spikelets.

    Science.gov (United States)

    Jang, Seonghoe; Li, Hsing-Yi; Kuo, Mei-Lin

    2017-03-14

    Key flowering genes, FD and FD PARALOGUE (FDP) encoding bZIP transcription factors that interact with a FLOWERING LOCUS T (FT) in Arabidopsis were ectopically expressed in rice since we found AtFD and AtFDP also interact with HEADING DATE 3a (Hd3a) and RICE FLOWERING LOCUS T 1 (RFT1). Transgenic rice plants overexpressing AtFD and AtFDP caused reduction in plant height and spikelet size with decreased expression of genes involved in cell elongation without significant flowering time alteration in spite of increased expression of OsMADS14 and OsMADS15, rice homologues of APETALA1 (AP1) in the leaves. Simultaneous overexpression of AtFD and AtFDP enhanced phenotypes seen with overexpression of either single gene while transgenic rice plants expressing AtFD or AtFDP under the control of phloem-specific Hd3a promoter were indistinguishable from wild-type rice. Candidate genes responsible for the phenotypes were identified by comparison of microarray hybridization and their expression pattern was also examined in WT and transgenic rice plants. It has so far not been reported that AtFD and AtFDP affect cell elongation in plants, and our findings provide novel insight into the possible roles of AtFD and AtFDP in the mesophyll cells of plants, and potential genetic tools for manipulation of crop architecture.

  7. Evolution of strigolactone receptors by gradual neo-functionalization of KAI2 paralogues.

    Science.gov (United States)

    Bythell-Douglas, Rohan; Rothfels, Carl J; Stevenson, Dennis W D; Graham, Sean W; Wong, Gane Ka-Shu; Nelson, David C; Bennett, Tom

    2017-06-29

    Strigolactones (SLs) are a class of plant hormones that control many aspects of plant growth. The SL signalling mechanism is homologous to that of karrikins (KARs), smoke-derived compounds that stimulate seed germination. In angiosperms, the SL receptor is an α/β-hydrolase known as DWARF14 (D14); its close homologue, KARRIKIN INSENSITIVE2 (KAI2), functions as a KAR receptor and likely recognizes an uncharacterized, endogenous signal ('KL'). Previous phylogenetic analyses have suggested that the KAI2 lineage is ancestral in land plants, and that canonical D14-type SL receptors only arose in seed plants; this is paradoxical, however, as non-vascular plants synthesize and respond to SLs. We have used a combination of phylogenetic and structural approaches to re-assess the evolution of the D14/KAI2 family in land plants. We analysed 339 members of the D14/KAI2 family from land plants and charophyte algae. Our phylogenetic analyses show that the divergence between the eu-KAI2 lineage and the DDK (D14/DLK2/KAI2) lineage that includes D14 occurred very early in land plant evolution. We show that eu-KAI2 proteins are highly conserved, and have unique features not found in DDK proteins. Conversely, we show that DDK proteins show considerable sequence and structural variation to each other, and lack clearly definable characteristics. We use homology modelling to show that the earliest members of the DDK lineage structurally resemble KAI2 and that SL receptors in non-seed plants likely do not have D14-like structure. We also show that certain groups of DDK proteins lack the otherwise conserved MORE AXILLARY GROWTH2 (MAX2) interface, and may thus function independently of MAX2, which we show is highly conserved throughout land plant evolution. Our results suggest that D14-like structure is not required for SL perception, and that SL perception has relatively relaxed structural requirements compared to KAI2-mediated signalling. We suggest that SL perception gradually evolved

  8. Divergence of host range and biological properties between natural isolate and full-length infectious cDNA clone of the Beet mild yellowing virus 2ITB.

    Science.gov (United States)

    Klein, Elodie; Brault, Véronique; Klein, Delphine; Weyens, Guy; Lefèbvre, Marc; Ziegler-Graff, Véronique; Gilmer, David

    2014-01-01

    Plant infection by poleroviruses is restricted to phloem tissues, preventing any classical leaf rub inoculation with viral RNA or virions. Efficient virus inoculation to plants is achieved by viruliferous aphids that acquire the virus by feeding on infected plants. The use of promoter-driven infectious cDNA is an alternative means to infect plants and allows reverse genetic studies to be performed. Using Beet mild yellowing virus isolate 2ITB (BMYV-2ITB), we produced a full-length infectious cDNA clone of the virus (named BMYV-EK) placed under the control of the T7 RNA polymerase and the Cauliflower mosaic virus 35S promoters. Infectivity of the engineered BMYV-EK virus was assayed in different plant species and compared with that of the original virus. We showed that in vitro- or in planta-derived transcripts were infectious in protoplasts and in whole plants. Importantly, the natural aphid vector Myzus persicae efficiently transmitted the viral progeny produced in infected plants. By comparing agroinoculation and aphid infection in a host range assay, we showed that the engineered BMYV-EK virus displayed a similar host range to BMYV-2ITB, except for Nicotiana benthamiana, which proved to be resistant to systemic infection with BMYV-EK. Finally, both the BMYV-EK P0 and the full-length clone were able to strongly interfere with post-transcriptional gene silencing. © 2013 BSPP AND JOHN WILEY & SONS LTD.

  9. Automated design of paralogue ratio test assays for the accurate and rapid typing of copy number variation

    Science.gov (United States)

    Veal, Colin D.; Xu, Hang; Reekie, Katherine; Free, Robert; Hardwick, Robert J.; McVey, David; Brookes, Anthony J.; Hollox, Edward J.; Talbot, Christopher J.

    2013-01-01

    Motivation: Genomic copy number variation (CNV) can influence susceptibility to common diseases. High-throughput measurement of gene copy number on large numbers of samples is a challenging, yet critical, stage in confirming observations from sequencing or array Comparative Genome Hybridization (CGH). The paralogue ratio test (PRT) is a simple, cost-effective method of accurately determining copy number by quantifying the amplification ratio between a target and reference amplicon. PRT has been successfully applied to several studies analyzing common CNV. However, its use has not been widespread because of difficulties in assay design. Results: We present PRTPrimer (www.prtprimer.org) software for automated PRT assay design. In addition to stand-alone software, the web site includes a database of pre-designed assays for the human genome at an average spacing of 6 kb and a web interface for custom assay design. Other reference genomes can also be analyzed through local installation of the software. The usefulness of PRTPrimer was tested within known CNV, and showed reproducible quantification. This software and database provide assays that can rapidly genotype CNV, cost-effectively, on a large number of samples and will enable the widespread adoption of PRT. Availability: PRTPrimer is available in two forms: a Perl script (version 5.14 and higher) that can be run from the command line on Linux systems and as a service on the PRTPrimer web site (www.prtprimer.org). Contact: cjt14@le.ac.uk Supplementary Information: Supplementary data are available at Bioinformatics online. PMID:23742985

  10. Phylogenomic analysis of vertebrate thrombospondins reveals fish-specific paralogues, ancestral gene relationships and a tetrapod innovation

    Directory of Open Access Journals (Sweden)

    Adams Josephine C

    2006-04-01

    Full Text Available Abstract Background Thrombospondins (TSPs are evolutionarily-conserved, extracellular, calcium-binding glycoproteins with important roles in cell-extracellular matrix interactions, angiogenesis, synaptogenesis and connective tissue organisation. Five TSPs, designated TSP-1 through TSP-5, are encoded in the human genome. All but one have known roles in acquired or inherited human diseases. To further understand the roles of TSPs in human physiology and pathology, it would be advantageous to extend the repertoire of relevant vertebrate models. In general the zebrafish is proving an excellent model organism for vertebrate biology, therefore we set out to evaluate the status of TSPs in zebrafish and two species of pufferfish. Results We identified by bioinformatics that three fish species encode larger numbers of TSPs than vertebrates, yet all these sequences group as homologues of TSP-1 to -4. By phylogenomic analysis of neighboring genes, we uncovered that, in fish, a TSP-4-like sequence is encoded from the gene corresponding to the tetrapod TSP-5 gene. Thus, all TSP genes show conservation of synteny between fish and tetrapods. In the human genome, the TSP-1, TSP-3, TSP-4 and TSP-5 genes lie within paralogous regions that provide insight into the ancestral genomic context of vertebrate TSPs. Conclusion A new model for TSP evolution in vertebrates is presented. The TSP-5 protein sequence has evolved rapidly from a TSP-4-like sequence as an innovation in the tetrapod lineage. TSP biology in fish is complicated by the presence of additional lineage- and species-specific TSP paralogues. These novel results give deeper insight into the evolution of TSPs in vertebrates and open new directions for understanding the physiological and pathological roles of TSP-4 and TSP-5 in humans.

  11. Evolution of Bacterial Global Modulators: Role of a Novel H-NS Paralogue in the EnteroaggregativeEscherichia coliStrain 042.

    Science.gov (United States)

    Prieto, A; Bernabeu, M; Aznar, S; Ruiz-Cruz, S; Bravo, A; Queiroz, M H; Juárez, A

    2018-01-01

    Bacterial genomes sometimes contain genes that code for homologues of global regulators, the function of which is unclear. In members of the family Enterobacteriaceae , cells express the global regulator H-NS and its paralogue StpA. In Escherichia coli , out of providing a molecular backup for H-NS, the role of StpA is poorly characterized. The enteroaggregative E. coli strain 042 carries, in addition to the hns and stpA genes, a third gene encoding an hns paralogue ( hns2 ). We present in this paper information about its biological function. Transcriptomic analysis has shown that the H-NS2 protein targets a subset of the genes targeted by H-NS. Genes targeted by H-NS2 correspond mainly with horizontally transferred (HGT) genes and are also targeted by the Hha protein, a fine-tuner of H-NS activity. Compared with H-NS, H-NS2 expression levels are lower. In addition, H-NS2 expression exhibits specific features: it is sensitive to the growth temperature and to the nature of the culture medium. This novel H-NS paralogue is widespread within the Enterobacteriaceae . IMPORTANCE Global regulators such as H-NS play key relevant roles enabling bacterial cells to adapt to a changing environment. H-NS modulates both core and horizontally transferred (HGT) genes, but the mechanism by which H-NS can differentially regulate these genes remains to be elucidated. There are several instances of bacterial cells carrying genes that encode homologues of the global regulators. The question is what the roles of these proteins are. We noticed that the enteroaggregative E. coli strain 042 carries a new hitherto uncharacterized copy of the hns gene. We decided to investigate why this pathogenic E. coli strain requires an extra H-NS paralogue, termed H-NS2. In our work, we show that H-NS2 displays specific expression and regulatory properties. H-NS2 targets a subset of H-NS-specific genes and may help to differentially modulate core and HGT genes by the H-NS cellular pool.

  12. Divergent flow isoelectric focusing

    Czech Academy of Sciences Publication Activity Database

    Šlais, Karel

    2008-01-01

    Roč. 29, č. 12 (2008), s. 2451-2457 ISSN 0173-0835 R&D Projects: GA AV ČR IAAX00310701; GA ČR GA203/06/1179 Institutional research plan: CEZ:AV0Z40310501 Keywords : isoelectric focusing * divergent flow * pI markers Subject RIV: CB - Analytical Chemistry, Separation Impact factor: 3.509, year: 2008

  13. Regularization of divergent integrals

    OpenAIRE

    Felder, Giovanni; Kazhdan, David

    2016-01-01

    We study the Hadamard finite part of divergent integrals of differential forms with singularities on submanifolds. We give formulae for the dependence of the finite part on the choice of regularization and express them in terms of a suitable local residue map. The cases where the submanifold is a complex hypersurface in a complex manifold and where it is a boundary component of a manifold with boundary, arising in string perturbation theory, are treated in more detail.

  14. Fast algorithms for computing phylogenetic divergence time.

    Science.gov (United States)

    Crosby, Ralph W; Williams, Tiffani L

    2017-12-06

    The inference of species divergence time is a key step in most phylogenetic studies. Methods have been available for the last ten years to perform the inference, but the performance of the methods does not yet scale well to studies with hundreds of taxa and thousands of DNA base pairs. For example a study of 349 primate taxa was estimated to require over 9 months of processing time. In this work, we present a new algorithm, AncestralAge, that significantly improves the performance of the divergence time process. As part of AncestralAge, we demonstrate a new method for the computation of phylogenetic likelihood and our experiments show a 90% improvement in likelihood computation time on the aforementioned dataset of 349 primates taxa with over 60,000 DNA base pairs. Additionally, we show that our new method for the computation of the Bayesian prior on node ages reduces the running time for this computation on the 349 taxa dataset by 99%. Through the use of these new algorithms we open up the ability to perform divergence time inference on large phylogenetic studies.

  15. divergence, pseudogenes, and

    Indian Academy of Sciences (India)

    Ribosomal internal transcribed spacer (ITS) sequences are commonly used for phylogenetic reconstruction because they are highly reiterated as components of rDNA repeats, and hence are often subject to rapid homogenization through concerted evolution. Concerted evolution leads to intragenomic uniformity of repeats ...

  16. Identification, chromosomal arrangements and expression analyses of the evolutionarily conserved prmt1 gene in chicken in comparison with its vertebrate paralogue prmt8.

    Directory of Open Access Journals (Sweden)

    Yi-Chun Wang

    Full Text Available Nine protein arginine methyltransferases (PRMTs are conserved in mammals and fish. Among these, PRMT1 is the major type I PRMT for asymmetric dimethylarginine (ADMA formation and is the most conserved and widely distributed one. Two chicken prmt1 splicing variants were assembled and confirmed by RT-PCR experiments. However, only two scaffolds containing single separate prmt1 exon with high GC contents are present in the current chicken genome assembly. Besides, prmt1 exons are scattered in separate small scaffolds in most avian species. Complete prmt1 gene has only been predicted from two falcon species with few neighboring genes. Crocodilians are considered close to the common ancestor shared by crocodilians and birds. The gene arrangements around prmt1 in American alligator are different from that in birds but are largely conserved in human. Orthologues of genes in a large segment of human chromosomal 19 around PRMT1 are missing or not assigned to the current chicken chromosomes. In comparison, prmt8, the prmt1 paralogue, is on chicken chromosome 1 with the gene arrangements downstream of prmt8 highly conserved in birds, crocodilians, and human. However, the ones upstream vary greatly in birds. Biochemically, we found that though prmt1 transcripts were detected, limited or none PRMT1 protein was present in chicken tissues. Moreover, a much higher level of PRMT8 protein was detected in chicken brain than in mouse brain. While PRMT8 is brain specific in other vertebrate species studied, low level of PRMT8 was present in chicken but not mouse liver and muscle. We also showed that the ADMA level in chicken was similar to that in mouse. This study provides the critical information of chicken PRMT1 and PRMT8 for future analyses of the function of protein arginine methyltransferases in birds.

  17. The critical role of protein arginine methyltransferase prmt8 in zebrafish embryonic and neural development is non-redundant with its paralogue prmt1.

    Directory of Open Access Journals (Sweden)

    Yu-ling Lin

    Full Text Available Protein arginine methyltransferase (PRMT 1 is the most conserved and widely distributed PRMT in eukaryotes. PRMT8 is a vertebrate-restricted paralogue of PRMT1 with an extra N-terminal sequence and brain-specific expression. We use zebrafish (Danio rerio as a vertebrate model to study PRMT8 function and putative redundancy with PRMT1. The transcripts of zebrafish prmt8 were specifically expressed in adult zebrafish brain and ubiquitously expressed from zygotic to early segmentation stage before the neuronal development. Whole-mount in situ hybridization revealed ubiquitous prmt8 expression pattern during early embryonic stages, similar to that of prmt1. Knockdown of prmt8 with antisense morpholino oligonucleotide phenocopied prmt1-knockdown, with convergence/extension defects at gastrulation. Other abnormalities observed later include short body axis, curled tails, small and malformed brain and eyes. Catalytically inactive prmt8 failed to complement the morphants, indicating the importance of methyltransferase activity. Full-length prmt8 but not prmt1 cRNA can rescue the phenotypic changes. Nevertheless, cRNA encoding Prmt1 fused with the N-terminus of Prmt8 can rescue the prmt8 morphants. In contrast, N-terminus- deleted but not full-length prmt8 cRNA can rescue the prmt1 morphants as efficiently as prmt1 cRNA. Abnormal brain morphologies illustrated with brain markers and loss of fluorescent neurons in a transgenic fish upon prmt8 knockdown confirm the critical roles of prmt8 in neural development. In summery, our study is the first report showing the expression and function of prmt8 in early zebrafish embryogenesis. Our results indicate that prmt8 may play important roles non-overlapping with prmt1 in embryonic and neural development depending on its specific N-terminus.

  18. Genomic patterns of species diversity and divergence in Eucalyptus.

    Science.gov (United States)

    Hudson, Corey J; Freeman, Jules S; Myburg, Alexander A; Potts, Brad M; Vaillancourt, René E

    2015-06-01

    We examined genome-wide patterns of DNA sequence diversity and divergence among six species of the important tree genus Eucalyptus and investigated their relationship with genomic architecture. Using c. 90 range-wide individuals of each Eucalyptus species (E. grandis, E. urophylla, E. globulus, E. nitens, E. dunnii and E. camaldulensis), genetic diversity and divergence were estimated from 2840 polymorphic diversity arrays technology markers covering the 11 chromosomes. Species differentiating markers (SDMs) identified in each of 15 pairwise species comparisons, along with species diversity (HHW ) and divergence (FST ), were projected onto the E. grandis reference genome. Across all species comparisons, SDMs totalled 1.1-5.3% of markers and were widely distributed throughout the genome. Marker divergence (FST and SDMs) and diversity differed among and within chromosomes. Patterns of diversity and divergence were broadly conserved across species and significantly associated with genomic features, including the proximity of markers to genes, the relative number of clusters of tandem duplications, and gene density within or among chromosomes. These results suggest that genomic architecture influences patterns of species diversity and divergence in the genus. This influence is evident across the six species, encompassing diverse phylogenetic lineages, geography and ecology. © 2015 University of Tasmania New Phytologist © 2015 New Phytologist Trust.

  19. A Multiparameter Network Reveals Extensive Divergence between C. elegans bHLH Transcription Factors

    DEFF Research Database (Denmark)

    Grove, C.; De Masi, Federico; Newburger, Daniel

    2009-01-01

    parameters remain undetermined. We comprehensively identify dimerization partners, spatiotemporal expression patterns, and DNA-binding specificities for the C. elegans bHLH family of TFs, and model these data into an integrated network. This network displays both specificity and promiscuity, as some b......HLH proteins, DNA sequences, and tissues are highly connected, whereas others are not. By comparing all bHLH TFs, we find extensive divergence and that all three parameters contribute equally to bHLH divergence. Our approach provides a framework for examining divergence for other protein families in C. elegans...

  20. Mitochondrial Involvement in Vertebrate Speciation? The Case of Mito-nuclear Genetic Divergence in Chameleons

    OpenAIRE

    Bar-Yaacov, Dan; Hadjivasiliou, Zena; Levin, Liron; Barshad, Gilad; Zarivach, Raz; Bouskila, Amos; Mishmar, Dan

    2015-01-01

    Compatibility between the nuclear (nDNA) and mitochondrial (mtDNA) genomes is important for organismal health. However, its significance for major evolutionary processes such as speciation is unclear, especially in vertebrates. We previously identified a sharp mtDNA-specific sequence divergence between morphologically indistinguishable chameleon populations (Chamaeleo chamaeleon recticrista) across an ancient Israeli marine barrier (Jezreel Valley). Because mtDNA introgression and gender-base...

  1. Conservation and divergence of autonomous pathway genes in the flowering regulatory network of Beta vulgaris.

    Science.gov (United States)

    Abou-Elwafa, Salah F; Büttner, Bianca; Chia, Tansy; Schulze-Buxloh, Gretel; Hohmann, Uwe; Mutasa-Göttgens, Effie; Jung, Christian; Müller, Andreas E

    2011-06-01

    The transition from vegetative growth to reproductive development is a complex process that requires an integrated response to multiple environmental cues and endogenous signals. In Arabidopsis thaliana, which has a facultative requirement for vernalization and long days, the genes of the autonomous pathway function as floral promoters by repressing the central repressor and vernalization-regulatory gene FLC. Environmental regulation by seasonal changes in daylength is under control of the photoperiod pathway and its key gene CO. The root and leaf crop species Beta vulgaris in the caryophyllid clade of core eudicots, which is only very distantly related to Arabidopsis, is an obligate long-day plant and includes forms with or without vernalization requirement. FLC and CO homologues with related functions in beet have been identified, but the presence of autonomous pathway genes which function in parallel to the vernalization and photoperiod pathways has not yet been reported. Here, this begins to be addressed by the identification and genetic mapping of full-length homologues of the RNA-regulatory gene FLK and the chromatin-regulatory genes FVE, LD, and LDL1. When overexpressed in A. thaliana, BvFLK accelerates bolting in the Col-0 background and fully complements the late-bolting phenotype of an flk mutant through repression of FLC. In contrast, complementation analysis of BvFVE1 and the presence of a putative paralogue in beet suggest evolutionary divergence of FVE homologues. It is further shown that BvFVE1, unlike FVE in Arabidopsis, is under circadian clock control. Together, the data provide first evidence for evolutionary conservation of components of the autonomous pathway in B. vulgaris, while also suggesting divergence or subfunctionalization of one gene. The results are likely to be of broader relevance because B. vulgaris expands the spectrum of evolutionarily diverse species which are subject to differential developmental and/or environmental regulation

  2. Context-Dependent Functional Divergence of the Notch Ligands DLL1 and DLL4 In Vivo.

    Directory of Open Access Journals (Sweden)

    Kristina Preuße

    2015-06-01

    Full Text Available Notch signalling is a fundamental pathway that shapes the developing embryo and sustains adult tissues by direct communication between ligand and receptor molecules on adjacent cells. Among the ligands are two Delta paralogues, DLL1 and DLL4, that are conserved in mammals and share a similar structure and sequence. They activate the Notch receptor partly in overlapping expression domains where they fulfil redundant functions in some processes (e.g. maintenance of the crypt cell progenitor pool. In other processes, however, they appear to act differently (e.g. maintenance of foetal arterial identity raising the questions of how similar DLL1 and DLL4 really are and which mechanism causes the apparent context-dependent divergence. By analysing mice that conditionally overexpress DLL1 or DLL4 from the same genomic locus (Hprt and mice that express DLL4 instead of DLL1 from the endogenous Dll1 locus (Dll1Dll4ki, we found functional differences that are tissue-specific: while DLL1 and DLL4 act redundantly during the maintenance of retinal progenitors, their function varies in the presomitic mesoderm (PSM where somites form in a Notch-dependent process. In the anterior PSM, every cell expresses both Notch receptors and ligands, and DLL1 is the only activator of Notch while DLL4 is not endogenously expressed. Transgenic DLL4 cannot replace DLL1 during somitogenesis and in heterozygous Dll1Dll4ki/+ mice, the Dll1Dll4ki allele causes a dominant segmentation phenotype. Testing several aspects of the complex Notch signalling system in vitro, we found that both ligands have a similar trans-activation potential but that only DLL4 is an efficient cis-inhibitor of Notch signalling, causing a reduced net activation of Notch. These differential cis-inhibitory properties are likely to contribute to the functional divergence of DLL1 and DLL4.

  3. Context-Dependent Functional Divergence of the Notch Ligands DLL1 and DLL4 In Vivo.

    Science.gov (United States)

    Preuße, Kristina; Tveriakhina, Lena; Schuster-Gossler, Karin; Gaspar, Cláudia; Rosa, Alexandra Isabel; Henrique, Domingos; Gossler, Achim; Stauber, Michael

    2015-06-01

    Notch signalling is a fundamental pathway that shapes the developing embryo and sustains adult tissues by direct communication between ligand and receptor molecules on adjacent cells. Among the ligands are two Delta paralogues, DLL1 and DLL4, that are conserved in mammals and share a similar structure and sequence. They activate the Notch receptor partly in overlapping expression domains where they fulfil redundant functions in some processes (e.g. maintenance of the crypt cell progenitor pool). In other processes, however, they appear to act differently (e.g. maintenance of foetal arterial identity) raising the questions of how similar DLL1 and DLL4 really are and which mechanism causes the apparent context-dependent divergence. By analysing mice that conditionally overexpress DLL1 or DLL4 from the same genomic locus (Hprt) and mice that express DLL4 instead of DLL1 from the endogenous Dll1 locus (Dll1Dll4ki), we found functional differences that are tissue-specific: while DLL1 and DLL4 act redundantly during the maintenance of retinal progenitors, their function varies in the presomitic mesoderm (PSM) where somites form in a Notch-dependent process. In the anterior PSM, every cell expresses both Notch receptors and ligands, and DLL1 is the only activator of Notch while DLL4 is not endogenously expressed. Transgenic DLL4 cannot replace DLL1 during somitogenesis and in heterozygous Dll1Dll4ki/+ mice, the Dll1Dll4ki allele causes a dominant segmentation phenotype. Testing several aspects of the complex Notch signalling system in vitro, we found that both ligands have a similar trans-activation potential but that only DLL4 is an efficient cis-inhibitor of Notch signalling, causing a reduced net activation of Notch. These differential cis-inhibitory properties are likely to contribute to the functional divergence of DLL1 and DLL4.

  4. Genomic innovations, transcriptional plasticity and gene loss underlying the evolution and divergence of two highly polyphagous and invasive Helicoverpa pest species.

    Science.gov (United States)

    Pearce, S L; Clarke, D F; East, P D; Elfekih, S; Gordon, K H J; Jermiin, L S; McGaughran, A; Oakeshott, J G; Papanikolaou, A; Perera, O P; Rane, R V; Richards, S; Tay, W T; Walsh, T K; Anderson, A; Anderson, C J; Asgari, S; Board, P G; Bretschneider, A; Campbell, P M; Chertemps, T; Christeller, J T; Coppin, C W; Downes, S J; Duan, G; Farnsworth, C A; Good, R T; Han, L B; Han, Y C; Hatje, K; Horne, I; Huang, Y P; Hughes, D S T; Jacquin-Joly, E; James, W; Jhangiani, S; Kollmar, M; Kuwar, S S; Li, S; Liu, N-Y; Maibeche, M T; Miller, J R; Montagne, N; Perry, T; Qu, J; Song, S V; Sutton, G G; Vogel, H; Walenz, B P; Xu, W; Zhang, H-J; Zou, Z; Batterham, P; Edwards, O R; Feyereisen, R; Gibbs, R A; Heckel, D G; McGrath, A; Robin, C; Scherer, S E; Worley, K C; Wu, Y D

    2017-07-31

    Helicoverpa armigera and Helicoverpa zea are major caterpillar pests of Old and New World agriculture, respectively. Both, particularly H. armigera, are extremely polyphagous, and H. armigera has developed resistance to many insecticides. Here we use comparative genomics, transcriptomics and resequencing to elucidate the genetic basis for their properties as pests. We find that, prior to their divergence about 1.5 Mya, the H. armigera/H. zea lineage had accumulated up to more than 100 more members of specific detoxification and digestion gene families and more than 100 extra gustatory receptor genes, compared to other lepidopterans with narrower host ranges. The two genomes remain very similar in gene content and order, but H. armigera is more polymorphic overall, and H. zea has lost several detoxification genes, as well as about 50 gustatory receptor genes. It also lacks certain genes and alleles conferring insecticide resistance found in H. armigera. Non-synonymous sites in the expanded gene families above are rapidly diverging, both between paralogues and between orthologues in the two species. Whole genome transcriptomic analyses of H. armigera larvae show widely divergent responses to different host plants, including responses among many of the duplicated detoxification and digestion genes. The extreme polyphagy of the two heliothines is associated with extensive amplification and neofunctionalisation of genes involved in host finding and use, coupled with versatile transcriptional responses on different hosts. H. armigera's invasion of the Americas in recent years means that hybridisation could generate populations that are both locally adapted and insecticide resistant.

  5. Complex patterns of genetic and phenotypic divergence in an island bird and the consequences for delimiting conservation units.

    Science.gov (United States)

    Phillimore, A B; Owens, I P F; Black, R A; Chittock, J; Burke, T; Clegg, S M

    2008-06-01

    Substantial phenotypic and genetic variation is often found below the species level and this may be useful in quantifying biodiversity and predicting future diversification. However, relatively few studies have tested whether different aspects of intraspecific variation show congruent patterns across populations. Here, we quantify several aspects of divergence between 13 insular populations of an island endemic bird, the Vanuatu white-eye (Zosterops flavifrons). The components of divergence studied are mitochondrial DNA (mtDNA), nuclear DNA microsatellites and morphology. These different aspects of divergence present subtly different scenarios. For instance, an mtDNA phylogenetic tree reveals a potential cryptic species on the most southerly island in Vanuatu and considerable divergence between at least two other major phylogroups. Microsatellite loci suggest that population genetic divergence between insular populations, both between and within phylogroups, is substantial, a result that is consistent with a low level of interisland gene flow. Finally, most populations were found to be strongly morphologically divergent, but no single population was morphologically diagnosable from all others. Taken together, our results show that, although many measures of divergence are concordant in this system, the number of divergent units identified varies widely depending on the characters considered and approach used. A continuum of divergence and a degree of discordance between different characters are both to be expected under simple models of evolution, but they present problems in terms of delimiting conservation units.

  6. String loop divergences and effective lagrangians

    International Nuclear Information System (INIS)

    Fischler, W.; Klebanov, I.; Susskind, L.

    1988-01-01

    We isolate logarithmic divergences from bosonic string amplitudes on a disc. These divergences are compared with 'tadpole' divergences in the effective field theory, with a covariant cosmological term implied by the counting of string coupling constants. We find an inconsistency between the two. This might be a problem in eliminating divergences from the bosonic string. (orig.)

  7. Divergence-free WKB theory

    International Nuclear Information System (INIS)

    Hyouguchi, Tadanori; Seto, Ryohei; Ueda, Masahito; Adachi, Satoshi

    2004-01-01

    We present a divergence-free WKB theory, which is a new semiclassical theory modified by nonperturbative quantum corrections. Conventionally, the WKB theory is constructed upon a trajectory that obeys the bare classical dynamics expressed by a quadratic equation in momentum space. Contrary to this, the divergence-free WKB theory is based on a higher-order algebraic equation in momentum space, which represents a dressed classical dynamics. More precisely, this higher-order algebraic equation is obtained by including quantum corrections to the quadratic equation, which is the bare classical limit. An additional solution of the higher-order algebraic equation enables us to construct a uniformly converging perturbative expansion of the wavefunction. Namely, our theory removes the notorious divergence of wavefunction at a turning point from the WKB theory. Moreover, our theory is able to produce wavefunctions and eigenenergies more accurate than those given by the traditional WKB method. In addition, the divergence-free WKB theory that is based on the cubic equation allows us to construct a uniformly valid wavefunction for the nonlinear Schroedinger equation (NLSE). A recent short letter [T. Hyouguchi, S. Adachi, M. Ueda, Phys. Rev. Lett. 88 (2002) 170404] is the opening of the divergence-free WKB theory. This paper presents full formalism of this theory and its several applications concerning wavefunction and eigenenergy to show that our theory is a natural extension of the traditional WKB theory that incorporates nonperturbative quantum corrections

  8. Using Dendritic Heat Maps to Simultaneously Display Genotype Divergence with Phenotype Divergence.

    Science.gov (United States)

    Kellom, Matthew; Raymond, Jason

    2016-01-01

    The advancement of techniques to visualize and analyze large-scale sequencing datasets is an area of active research and is rooted in traditional techniques such as heat maps and dendrograms. We introduce dendritic heat maps that display heat map results over aligned DNA sequence clusters for a range of clustering cutoffs. Dendritic heat maps aid in visualizing the effects of group differences on clustering hierarchy and relative abundance of sampled sequences. Here, we artificially generate two separate datasets with simplified mutation and population growth procedures with GC content group separation to use as example phenotypes. In this work, we use the term phenotype to represent any feature by which groups can be separated. These sequences were clustered in a fractional identity range of 0.75 to 1.0 using agglomerative minimum-, maximum-, and average-linkage algorithms, as well as a divisive centroid-based algorithm. We demonstrate that dendritic heat maps give freedom to scrutinize specific clustering levels across a range of cutoffs, track changes in phenotype inequity across multiple levels of sequence clustering specificity, and easily visualize how deeply rooted changes in phenotype inequity are in a dataset. As genotypes diverge in sample populations, clusters are shown to break apart into smaller clusters at higher identity cutoff levels, similar to a dendrogram. Phenotype divergence, which is shown as a heat map of relative abundance bin response, may or may not follow genotype divergences. This joined view highlights the relationship between genotype and phenotype divergence for treatment groups. We discuss the minimum-, maximum-, average-, and centroid-linkage algorithm approaches to building dendritic heat maps and make a case for the divisive "top-down" centroid-based clustering methodology as being the best option visualize the effects of changing factors on clustering hierarchy and relative abundance.

  9. Using Dendritic Heat Maps to Simultaneously Display Genotype Divergence with Phenotype Divergence.

    Directory of Open Access Journals (Sweden)

    Matthew Kellom

    Full Text Available The advancement of techniques to visualize and analyze large-scale sequencing datasets is an area of active research and is rooted in traditional techniques such as heat maps and dendrograms. We introduce dendritic heat maps that display heat map results over aligned DNA sequence clusters for a range of clustering cutoffs. Dendritic heat maps aid in visualizing the effects of group differences on clustering hierarchy and relative abundance of sampled sequences. Here, we artificially generate two separate datasets with simplified mutation and population growth procedures with GC content group separation to use as example phenotypes. In this work, we use the term phenotype to represent any feature by which groups can be separated. These sequences were clustered in a fractional identity range of 0.75 to 1.0 using agglomerative minimum-, maximum-, and average-linkage algorithms, as well as a divisive centroid-based algorithm. We demonstrate that dendritic heat maps give freedom to scrutinize specific clustering levels across a range of cutoffs, track changes in phenotype inequity across multiple levels of sequence clustering specificity, and easily visualize how deeply rooted changes in phenotype inequity are in a dataset. As genotypes diverge in sample populations, clusters are shown to break apart into smaller clusters at higher identity cutoff levels, similar to a dendrogram. Phenotype divergence, which is shown as a heat map of relative abundance bin response, may or may not follow genotype divergences. This joined view highlights the relationship between genotype and phenotype divergence for treatment groups. We discuss the minimum-, maximum-, average-, and centroid-linkage algorithm approaches to building dendritic heat maps and make a case for the divisive "top-down" centroid-based clustering methodology as being the best option visualize the effects of changing factors on clustering hierarchy and relative abundance.

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

    Directory of Open Access Journals (Sweden)

    Eichler Evan E

    2008-08-01

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

  11. Deep sympatric mitochondrial divergence without reproductive isolation in the common redstart Phoenicurus phoenicurus.

    Science.gov (United States)

    Hogner, Silje; Laskemoen, Terje; Lifjeld, Jan T; Porkert, Jiri; Kleven, Oddmund; Albayrak, Tamer; Kabasakal, Bekir; Johnsen, Arild

    2012-12-01

    Mitochondrial DNA usually shows low sequence variation within and high sequence divergence among species, which makes it a useful marker for phylogenetic inference and DNA barcoding. A previous study on the common redstart (Phoenicurus phoenicurus) revealed two very different mtDNA haplogroups (5% K2P distance). This divergence is comparable to that among many sister species; however, both haplogroups coexist and interbreed in Europe today. Herein, we describe the phylogeographic pattern of these lineages and test hypotheses for how such high diversity in mtDNA has evolved. We found no evidence for mitochondrial pseudogenes confirming that both haplotypes are of mitochondrial origin. When testing for possible reproductive barriers, we found no evidence for lineage-specific assortative mating and no difference in sperm morphology, indicating that they are not examples of cryptic species, nor likely to reflect the early stages of speciation. A gene tree based on a short fragment of cytochrome c oxidase subunit 1 from the common redstart and 10 other Phoenicurus species, showed no introgression from any of the extant congenerics. However, introgression from an extinct congeneric cannot be excluded. Sequences from two nuclear introns did not show a similar differentiation into two distinct groups. Mismatch distributions indicated that the lineages have undergone similar demographic changes. Taken together, these results confirm that deeply divergent mitochondrial lineages can coexist in biological species. Sympatric mtDNA divergences are relatively rare in birds, but the fact that they occur argues against the use of threshold mtDNA divergences in species delineation.

  12. Genetic, Ecological and Morphological Divergence between Populations of the Endangered Mexican Sheartail Hummingbird (Doricha eliza)

    Science.gov (United States)

    Licona-Vera, Yuyini; Ornelas, Juan Francisco

    2014-01-01

    The Mexican Sheartail (Doricha eliza), an endangered hummingbird, is endemic to Mexico where two populations have a disjunct distribution. One population is distributed along the northern tip of the Yucatan Peninsula whereas the other is mostly restricted to central Veracruz. Despite their disjunct distribution, previous work has failed to detect morphological or behavioral differences between these populations. Here we use variation in morphology, mtDNA and nuDNA sequences to determine the degree of morphological and molecular divergence between populations, their divergence time, and historical demography. We use species distribution modeling and niche divergence tests to infer the relative roles of vicariance and dispersal in driving divergence in the genus. Our Bayesian and maximum likelihood phylogenetic analyses revealed that Doricha eliza populations form a monophyletic clade and support their sister relationship with D. enicura. We found marked genetic differentiation, with reciprocal monophyly of haplotypes and highly restricted gene flow, supporting a history of isolation over the last 120,000 years. Genetic divergence between populations is consistent with the lack of overlap in environmental space and slight morphological differences between males. Our findings indicate that the divergence of the Veracruz and Yucatan populations is best explained by a combination of a short period of isolation exacerbated by subsequent divergence in climate conditions, and that rather than vicariance, the two isolated ranges of D. eliza are the product of recent colonization and divergence in isolation. PMID:24992589

  13. Genetic, ecological and morphological divergence between populations of the endangered Mexican Sheartail hummingbird (Doricha eliza.

    Directory of Open Access Journals (Sweden)

    Yuyini Licona-Vera

    Full Text Available The Mexican Sheartail (Doricha eliza, an endangered hummingbird, is endemic to Mexico where two populations have a disjunct distribution. One population is distributed along the northern tip of the Yucatan Peninsula whereas the other is mostly restricted to central Veracruz. Despite their disjunct distribution, previous work has failed to detect morphological or behavioral differences between these populations. Here we use variation in morphology, mtDNA and nuDNA sequences to determine the degree of morphological and molecular divergence between populations, their divergence time, and historical demography. We use species distribution modeling and niche divergence tests to infer the relative roles of vicariance and dispersal in driving divergence in the genus. Our Bayesian and maximum likelihood phylogenetic analyses revealed that Doricha eliza populations form a monophyletic clade and support their sister relationship with D. enicura. We found marked genetic differentiation, with reciprocal monophyly of haplotypes and highly restricted gene flow, supporting a history of isolation over the last 120,000 years. Genetic divergence between populations is consistent with the lack of overlap in environmental space and slight morphological differences between males. Our findings indicate that the divergence of the Veracruz and Yucatan populations is best explained by a combination of a short period of isolation exacerbated by subsequent divergence in climate conditions, and that rather than vicariance, the two isolated ranges of D. eliza are the product of recent colonization and divergence in isolation.

  14. Bacterial transformation: distribution, shared mechanisms and divergent control.

    Science.gov (United States)

    Johnston, Calum; Martin, Bernard; Fichant, Gwennaele; Polard, Patrice; Claverys, Jean-Pierre

    2014-03-01

    Natural bacterial transformation involves the internalization and chromosomal integration of DNA and has now been documented in ~80 species. Recent advances have established that phylogenetically distant species share conserved uptake and processing proteins but differ in the inducing cues and regulatory mechanisms that are involved. In this Review, we highlight divergent and common principles that govern the transformation process in different bacteria. We discuss how this cumulative knowledge enables the prediction of new transformable species and supports the idea that the main role of internalized DNA is in the generation of genetic diversity or in chromosome repair rather than in nutrition.

  15. Segmenting the human genome based on states of neutral genetic divergence.

    Science.gov (United States)

    Kuruppumullage Don, Prabhani; Ananda, Guruprasad; Chiaromonte, Francesca; Makova, Kateryna D

    2013-09-03

    Many studies have demonstrated that divergence levels generated by different mutation types vary and covary across the human genome. To improve our still-incomplete understanding of the mechanistic basis of this phenomenon, we analyze several mutation types simultaneously, anchoring their variation to specific regions of the genome. Using hidden Markov models on insertion, deletion, nucleotide substitution, and microsatellite divergence estimates inferred from human-orangutan alignments of neutrally evolving genomic sequences, we segment the human genome into regions corresponding to different divergence states--each uniquely characterized by specific combinations of divergence levels. We then parsed the mutagenic contributions of various biochemical processes associating divergence states with a broad range of genomic landscape features. We find that high divergence states inhabit guanine- and cytosine (GC)-rich, highly recombining subtelomeric regions; low divergence states cover inner parts of autosomes; chromosome X forms its own state with lowest divergence; and a state of elevated microsatellite mutability is interspersed across the genome. These general trends are mirrored in human diversity data from the 1000 Genomes Project, and departures from them highlight the evolutionary history of primate chromosomes. We also find that genes and noncoding functional marks [annotations from the Encyclopedia of DNA Elements (ENCODE)] are concentrated in high divergence states. Our results provide a powerful tool for biomedical data analysis: segmentations can be used to screen personal genome variants--including those associated with cancer and other diseases--and to improve computational predictions of noncoding functional elements.

  16. On Hölder Projective Divergences

    KAUST Repository

    Nielsen, Frank

    2017-03-16

    We describe a framework to build distances by measuring the tightness of inequalities and introduce the notion of proper statistical divergences and improper pseudo-divergences. We then consider the Holder ordinary and reverse inequalities and present two novel classes of Holder divergences and pseudo-divergences that both encapsulate the special case of the Cauchy-Schwarz divergence. We report closed-form formulas for those statistical dissimilarities when considering distributions belonging to the same exponential family provided that the natural parameter space is a cone (e.g., multivariate Gaussians) or affine (e.g., categorical distributions). Those new classes of Holder distances are invariant to rescaling and thus do not require distributions to be normalized. Finally, we show how to compute statistical Holder centroids with respect to those divergences and carry out center-based clustering toy experiments on a set of Gaussian distributions which demonstrate empirically that symmetrized Holder divergences outperform the symmetric Cauchy-Schwarz divergence.

  17. Genetic Divergence in Sugarcane Genotypes

    OpenAIRE

    Tahir, Mohammad; Rahman, Hidayatur; Gul, Rahmani; Ali, Amjad; Khalid, Muhammad

    2012-01-01

    To assess genetic divergence of sugarcane germplasm, an experiment comprising 25 sugarcane genotypes was conducted at Sugar Crops Research Institute (SCRI), Mardan, Khyber Pakhtunkhwa, Pakistan, in quadruple lattice design during 2008-09. Among the 14 parameters evaluated, majority exhibited significant differences while some showed nonsignificant mean squares. The initial correlation matrix revealed medium to high correlations. Principal Component Analysis (PCA) showed that there were two pr...

  18. Analytic practice: convergences and divergences.

    Science.gov (United States)

    Laks Eizirik, Cláudio

    2010-04-01

    The author discusses current convergences and divergences concerning analytic practice. After presenting a clinical vignette that can be understood differently according to different theoretical approaches, he discusses Wallerstein's proposal of a common ground in psychoanalysis and suggests that the present state of the art indicates that psychoanalysis is a pluralistic discipline, with different ways of training and practising it, and that the main challenge is to improve our ability to listen to and to learn from different approaches.

  19. ALLOZYME DIVERGENCE WITHIN THE BOVIDAE.

    Science.gov (United States)

    Georgiadis, Nicholas J; Kat, Pieter W; Oketch, Hellen; Patton, John

    1990-12-01

    We describe a phylogeny of the Bovidae based on 40 allozyme loci in 27 species, representing 10 of the 14 bovid tribes described by Vrba (1985). Giraffe represented a related family (Giraffidae). A phenogram was derived using the unweighted pair-group method with arithmetic means (UPGMA), based on Nei's genetic distances (ND) between species. A tree was also derived using the neighbor-joining technique, also based on ND. To provide a cladistic interpretation, the data were analyzed by a maximum parsimony method (phylogenetic analysis using parsimony, PAUP). We found marked divergence within the Bovidae, consistent with the appearance of the family in the early Miocene. Unexpectedly, the most divergent species was the impala, which occupied a basal position in all trees. Species in the tribe Alcelaphini were the most derived taxa in all trees. These patterns conflict strongly with the previous taxonomic alliance, based on immuno-distance and anatomical evidence, of the impala as a sister group of the Alcelaphini. All trees agreed that tribes described by Vrba (1985) are monophyletic, except the Neotragini, which was polyphyletic, with suni occupying a long branch by itself. The dikdik and klipspringer were consistently placed as sister taxa to species in the Antilopini. Three tribes (Aepycerotini, Tragelaphini and Cephalophini), whose fossils have not been found outside Africa, were basal in all trees, suggesting that bovids originated in Africa. Nodes connecting the remaining tribes were closely clustered, a pattern that agrees with fossil evidence of rapid divergence within the Bovidae in the mid-Miocene (about 15 mybp). The allozyme data suggested a second phase of rapid divergence within tribes during the Plio-Pleistocene, a pattern that also agrees with fossil evidence. Rates of bovid divergence have therefore been far from constant. However, the clustering of nodes imparts considerable uncertainty to the branching order leading to the derived tribes, and to a

  20. On metric divergences of probability measures

    Czech Academy of Sciences Publication Activity Database

    Vajda, Igor

    2009-01-01

    Roč. 45, č. 6 (2009), s. 885-900 ISSN 0023-5954 R&D Projects: GA MŠk(CZ) 1M0572; GA ČR GA102/07/1131 Institutional research plan: CEZ:AV0Z10750506 Keywords : Metric divergences * Hellinger divergence * Le Cam divergence * Jensen-Shannon divergence * Total variation Subject RIV: BD - Theory of Information Impact factor: 0.445, year: 2009 http://library.utia.cas.cz/separaty/2010/SI/vajda-on metric divergences of probability measures.pdf

  1. Mitogenomic evaluation of the historical biogeography of cichlids toward reliable dating of teleostean divergences

    Directory of Open Access Journals (Sweden)

    Miya Masaki

    2008-07-01

    Full Text Available Abstract Background Recent advances in DNA sequencing and computation offer the opportunity for reliable estimates of divergence times between organisms based on molecular data. Bayesian estimations of divergence times that do not assume the molecular clock use time constraints at multiple nodes, usually based on the fossil records, as major boundary conditions. However, the fossil records of bony fishes may not adequately provide effective time constraints at multiple nodes. We explored an alternative source of time constraints in teleostean phylogeny by evaluating a biogeographic hypothesis concerning freshwater fishes from the family Cichlidae (Perciformes: Labroidei. Results We added new mitogenomic sequence data from six cichlid species and conducted phylogenetic analyses using a large mitogenomic data set. We found a reciprocal monophyly of African and Neotropical cichlids and their sister group relationship to some Malagasy taxa (Ptychochrominae sensu Sparks and Smith. All of these taxa clustered with a Malagasy + Indo/Sri Lankan clade (Etroplinae sensu Sparks and Smith. The results of the phylogenetic analyses and divergence time estimations between continental cichlid clades were much more congruent with Gondwanaland origin and Cretaceous vicariant divergences than with Cenozoic transmarine dispersal between major continents. Conclusion We propose to add the biogeographic assumption of cichlid divergences by continental fragmentation as effective time constraints in dating teleostean divergence times. We conducted divergence time estimations among teleosts by incorporating these additional time constraints and achieved a considerable reduction in credibility intervals in the estimated divergence times.

  2. Statistical inference based on divergence measures

    CERN Document Server

    Pardo, Leandro

    2005-01-01

    The idea of using functionals of Information Theory, such as entropies or divergences, in statistical inference is not new. However, in spite of the fact that divergence statistics have become a very good alternative to the classical likelihood ratio test and the Pearson-type statistic in discrete models, many statisticians remain unaware of this powerful approach.Statistical Inference Based on Divergence Measures explores classical problems of statistical inference, such as estimation and hypothesis testing, on the basis of measures of entropy and divergence. The first two chapters form an overview, from a statistical perspective, of the most important measures of entropy and divergence and study their properties. The author then examines the statistical analysis of discrete multivariate data with emphasis is on problems in contingency tables and loglinear models using phi-divergence test statistics as well as minimum phi-divergence estimators. The final chapter looks at testing in general populations, prese...

  3. Log-Determinant Divergences Revisited: Alpha-Beta and Gamma Log-Det Divergences

    Directory of Open Access Journals (Sweden)

    Andrzej Cichocki

    2015-05-01

    Full Text Available This work reviews and extends a family of log-determinant (log-det divergences for symmetric positive definite (SPD matrices and discusses their fundamental properties. We show how to use parameterized Alpha-Beta (AB and Gamma log-det divergences to generate many well-known divergences; in particular, we consider the Stein’s loss, the S-divergence, also called Jensen-Bregman LogDet (JBLD divergence, Logdet Zero (Bhattacharyya divergence, Affine Invariant Riemannian Metric (AIRM, and other divergences. Moreover, we establish links and correspondences between log-det divergences and visualise them on an alpha-beta plane for various sets of parameters. We use this unifying framework to interpret and extend existing similarity measures for semidefinite covariance matrices in finite-dimensional Reproducing Kernel Hilbert Spaces (RKHS. This paper also shows how the Alpha-Beta family of log-det divergences relates to the divergences of multivariate and multilinear normal distributions. Closed form formulas are derived for Gamma divergences of two multivariate Gaussian densities; the special cases of the Kullback-Leibler, Bhattacharyya, Rényi, and Cauchy-Schwartz divergences are discussed. Symmetrized versions of log-det divergences are also considered and briefly reviewed. Finally, a class of divergences is extended to multiway divergences for separable covariance (or precision matrices.

  4. Ultraviolet divergences and supersymmetric theories

    Energy Technology Data Exchange (ETDEWEB)

    Sagnotti, A.

    1984-09-01

    This article is closely related to the one by Ferrara in these same Proceedings. It deals with what is perhaps the most fascinating property of supersymmetric theories, their improved ultraviolet behavior. My aim here is to present a survey of the state of the art as of August, 1984, and a somewhat more detailed discussion of the breakdown of the superspace power-counting beyond N = 2 superfields. A method is also described for simplifying divergence calculations that uses the locality of subtracted Feynman integrals. 74 references.

  5. Mitochondrial DNA divergence in Lygus lineolaris (Hemiptera: Miridae)

    Science.gov (United States)

    The genus Lygus is widely distributed in North America and Eurasia. The tarnished plant bug, Lygus lineolaris, is one of the most serious pest species within this genus having >300 different plant hosts. The intra-specific genetic diversity of L. lineolaris is being examined by employing mitochondri...

  6. Divergent thinking and constructing episodic simulations.

    Science.gov (United States)

    Addis, Donna Rose; Pan, Ling; Musicaro, Regina; Schacter, Daniel L

    2016-01-01

    Divergent thinking likely plays an important role in simulating autobiographical events. We investigated whether divergent thinking is differentially associated with the ability to construct detailed imagined future and imagined past events as opposed to recalling past events. We also examined whether age differences in divergent thinking might underlie the reduced episodic detail generated by older adults. The richness of episodic detail comprising autobiographical events in young and older adults was assessed using the Autobiographical Interview. Divergent thinking abilities were measured using the Alternative Uses Task. Divergent thinking was significantly associated with the amount of episodic detail for imagined future events. Moreover, while age was significantly associated with imagined episodic detail, this effect was strongly related to age-related changes in episodic retrieval rather than divergent thinking.

  7. Ramanujan summation of divergent series

    CERN Document Server

    Candelpergher, Bernard

    2017-01-01

    The aim of this monograph is to give a detailed exposition of the summation method that Ramanujan uses in Chapter VI of his second Notebook. This method, presented by Ramanujan as an application of the Euler-MacLaurin formula, is here extended using a difference equation in a space of analytic functions. This provides simple proofs of theorems on the summation of some divergent series. Several examples and applications are given. For numerical evaluation, a formula in terms of convergent series is provided by the use of Newton interpolation. The relation with other summation processes such as those of Borel and Euler is also studied. Finally, in the last chapter, a purely algebraic theory is developed that unifies all these summation processes. This monograph is aimed at graduate students and researchers who have a basic knowledge of analytic function theory.

  8. Divergence operator and related inequalities

    CERN Document Server

    Acosta, Gabriel

    2017-01-01

    This Brief is mainly devoted to two classical and related results: the existence of a right inverse of the divergence operator and the so-called Korn Inequalities. It is well known that both results are fundamental tools in the analysis of some classic differential equations, particularly in those arising in fluid dynamics and elasticity. Several connections between these two topics and improved Poincaré inequalities are extensively treated. From simple key ideas the book is growing smoothly in complexity. Beginning with the study of these problems on star-shaped domains the arguments are extended first to John domains and then to Hölder α domains where the need of weighted spaces arises naturally. In this fashion, the authors succeed in presenting in an unified and concise way several classic and recent developments in the field. These features certainly makes this Brief useful for students, post-graduate students, and researchers as well.

  9. Genetic divergence analysis in pumpkin

    International Nuclear Information System (INIS)

    Quamruzzaman, A.M.; Moniruzzaman, M.

    2013-01-01

    Genetic divergence among 18 punpkin genotypes was estimated using Mahalanohis's 1) statistic. Altogether lour clusters were formed where cluster I contained the highest number of genotypes (8) and cluster II contained the lowest (I). The highest intra-cluster distance was observed h.ir cluster I (0.83 I) and the lowest for clustcr IV (0.65 I). The highest inter-cluster distance was observed between cluster I and 11(24.346). Cluster II recorded the highest mean for fruit number/plant, TSS, fruit yield and niinitnuiii III cavity length and cavity diameter. Cluster III had the second highest mean for fruit diameter, fruit number/plant, individual unit weight, fruit yield and the fewest number of days to 1st Female flowering, earliness being a desirable trait. These crosses may produce new recombinants with desirable traits. (author)

  10. Armillaria phylogeny based on tef-1α sequences suggests ongoing divergent speciation within the boreal floristic kingdom

    Science.gov (United States)

    Ned B. Klopfenstein; John W. Hanna; Amy L. Ross-Davis; Jane E. Stewart; Yuko Ota; Rosario Medel-Ortiz; Miguel Armando Lopez-Ramirez; Ruben Damian Elias-Roman; Dionicio Alvarado-Rosales; Mee-Sook Kim

    2013-01-01

    Armillaria plays diverse ecological roles in forests worldwide, which has inspired interest in understanding phylogenetic relationships within and among species of this genus. Previous rDNA sequence-based phylogenetic analyses of Armillaria have shown general relationships among widely divergent taxa, but rDNA sequences were not reliable for separating closely related...

  11. Beam divergence scaling in neutral beam injectors

    International Nuclear Information System (INIS)

    Holmes, A.J.T.

    1976-01-01

    One of the main considerations in the design of neutral beam injectors is to monimize the divergence of the primary ion beam and hence maximize the beam transport and minimize the input of thermal gas. Experimental measurements of the divergence of a cylindrical ion beam are presented and these measurements are used to analyze the major components of ion beam divergence, namely: space charge expansion, gas-ion scattering, emittance and optical aberrations. The implication of these divergence components in the design of a neutral beam injector system is discussed and a method of maximizing the beam current is described for a given area of source plasma

  12. Detecting climatically driven phylogenetic and morphological divergence among spruce (Picea) species worldwide

    Science.gov (United States)

    Wang, Guo-Hong; Li, He; Zhao, Hai-Wei; Zhang, Wei-Kang

    2017-05-01

    This study aimed to elucidate the relationship between climate and the phylogenetic and morphological divergence of spruces (Picea) worldwide. Climatic and georeferenced data were collected from a total of 3388 sites distributed within the global domain of spruce species. A phylogenetic tree and a morphological tree for the global spruces were reconstructed based on DNA sequences and morphological characteristics. Spatial evolutionary and ecological vicariance analysis (SEEVA) was used to detect the ecological divergence among spruces. A divergence index (D) with (0, 1) scaling was calculated for each climatic factor at each node for both trees. The annual mean values, extreme values and annual range of the climatic variables were among the major determinants for spruce divergence. The ecological divergence was significant (P nodes in the phylogenetic tree, as well as for 196 of the 288 comparisons at 32 nodes in the morphological tree. Temperature parameters and precipitation parameters tended to be the main driving factors for the primary divergences of spruce phylogeny and morphology, respectively. Generally, the maximum D of the climatic variables was smaller in the basal nodes than in the remaining nodes. Notably, the primary divergence of morphology and phylogeny among the investigated spruces tended to be driven by different selective pressures. Given the climate scenario of severe and widespread drought over land areas in the next 30-90 years, our findings shed light on the prediction of spruce distribution under future climate change.

  13. Integration of Genetic and Phenotypic Data in 48 Lineages of Philippine Birds Shows Heterogeneous Divergence Processes and Numerous Cryptic Species.

    Science.gov (United States)

    Campbell, Kyle K; Braile, Thomas; Winker, Kevin

    2016-01-01

    The Philippine Islands are one of the most biologically diverse archipelagoes in the world. Current taxonomy, however, may underestimate levels of avian diversity and endemism in these islands. Although species limits can be difficult to determine among allopatric populations, quantitative methods for comparing phenotypic and genotypic data can provide useful metrics of divergence among populations and identify those that merit consideration for elevation to full species status. Using a conceptual approach that integrates genetic and phenotypic data, we compared populations among 48 species, estimating genetic divergence (p-distance) using the mtDNA marker ND2 and comparing plumage and morphometrics of museum study skins. Using conservative speciation thresholds, pairwise comparisons of genetic and phenotypic divergence suggested possible species-level divergences in more than half of the species studied (25 out of 48). In speciation process space, divergence routes were heterogeneous among taxa. Nearly all populations that surpassed high genotypic divergence thresholds were Passeriformes, and non-Passeriformes populations surpassed high phenotypic divergence thresholds more commonly than expected by chance. Overall, there was an apparent logarithmic increase in phenotypic divergence with respect to genetic divergence, suggesting the possibility that divergence among these lineages may initially be driven by divergent selection in this allopatric system. Also, genetic endemism was high among sampled islands. Higher taxonomy affected divergence in genotype and phenotype. Although broader lineage, genetic, phenotypic, and numeric sampling is needed to further explore heterogeneity among divergence processes and to accurately assess species-level diversity in these taxa, our results support the need for substantial taxonomic revisions among Philippine birds. The conservation implications are profound.

  14. Phylogeny, biogeography and divergence times in Passiflora (Passifloraceae).

    Science.gov (United States)

    Muschner, Valéria C; Zamberlan, Priscilla M; Bonatto, Sandro L; Freitas, Loreta B

    2012-12-01

    As part of a long-term investigation on the evolution of Passiflora L., we investigated the divergence ages of the genus and diversification of its subgenera, relating them with biogeographical and/or historical events, and other characteristics of this taxon. The main aim of the present work was to evaluate the biogeographic distribution of this genus to better understand its evolutionary history. This is the first time that representatives from South American and Old World Passifloraceae genera have been studied as a group comprising a total of 106 widely distributed species, with representative samples of the four suggested subgenera. Seven DNA regions were studied, comprising 7,431 nucleotides from plastidial, mitochondrial and nuclear genomes. Divergence time estimates were obtained by using a Bayesian Markov Chain Monte Carlo method and a random local clock model for each partition. Three major subgenera have been shown to be monophyletic and here we are proposing to include another subgenus in the Passiflora infrageneric classification. In general, divergence among the four subgenera in Passiflora is very ancient, ranging from ∼32 to ∼38 Mya, and Passifloraceae seems to follow a biogeographic scenario proposed for several plant groups, originating in Africa, crossing to Europe/Asia and arriving in the New World by way of land bridges. Our results indicated that Passiflora ancestors arrived in Central America and diversified quickly from there, with many long distance dispersion events.

  15. Phylogeny, biogeography and divergence times in Passiflora (Passifloraceae

    Directory of Open Access Journals (Sweden)

    Valéria C. Muschner

    2012-01-01

    Full Text Available As part of a long-term investigation on the evolution of Passiflora L., we investigated the divergence ages of the genus and diversification of its subgenera, relating them with biogeographical and/or historical events, and other characteristics of this taxon. The main aim of the present work was to evaluate the biogeographic distribution of this genus to better understand its evolutionary history. This is the first time that representatives from South American and Old World Passifloraceae genera have been studied as a group comprising a total of 106 widely distributed species, with representative samples of the four suggested subgenera. Seven DNA regions were studied, comprising 7,431 nucleotides from plastidial, mitochondrial and nuclear genomes. Divergence time estimates were obtained by using a Bayesian Markov Chain Monte Carlo method and a random local clock model for each partition. Three major subgenera have been shown to be monophyletic and here we are proposing to include another subgenus in the Passiflora infrageneric classification. In general, divergence among the four subgenera in Passiflora is very ancient, ranging from ~32 to ~38 Mya, and Passifloraceae seems to follow a biogeographic scenario proposed for several plant groups, originating in Africa, crossing to Europe/Asia and arriving in the New World by way of land bridges. Our results indicated that Passiflora ancestors arrived in Central America and diversified quickly from there, with many long distance dispersion events.

  16. k-Means Clustering with Hölder Divergences

    KAUST Repository

    Nielsen, Frank

    2017-10-24

    We introduced two novel classes of Hölder divergences and Hölder pseudo-divergences that are both invariant to rescaling, and that both encapsulate the Cauchy-Schwarz divergence and the skew Bhattacharyya divergences. We review the elementary concepts of those parametric divergences, and perform a clustering analysis on two synthetic datasets. It is shown experimentally that the symmetrized Hölder divergences consistently outperform significantly the Cauchy-Schwarz divergence in clustering tasks.

  17. Ancient DNA

    DEFF Research Database (Denmark)

    Willerslev, Eske; Cooper, Alan

    2004-01-01

    ancient DNA, palaeontology, palaeoecology, archaeology, population genetics, DNA damage and repair......ancient DNA, palaeontology, palaeoecology, archaeology, population genetics, DNA damage and repair...

  18. Lexicographic presentation of grammatical divergence in Sesotho ...

    African Journals Online (AJOL)

    Relying on existing insights from the field of theoretical lexicography this article gives an innovative application to the relation of divergence by introducing the notion of grammatical divergence. In bilingual dictionaries with English and Sesotho sa Leboa as language pair lexicographers are confronted with a real challenge ...

  19. Divergent Thinking and Age-Related Changes

    Science.gov (United States)

    Palmiero, Massimiliano; Di Giacomo, Dina; Passafiume, Domenico

    2014-01-01

    Aging can affect cognition in different ways. The extent to which aging affects divergent thinking is unclear. In this study, younger and older adults were compared at the performance on the Torrance Test of Creative Thinking in visual and verbal form. Results showed that older adults can think divergently as younger participants, although they…

  20. Global diversity and oceanic divergence of humpback whales (Megaptera novaeangliae).

    Science.gov (United States)

    Jackson, Jennifer A; Steel, Debbie J; Beerli, P; Congdon, Bradley C; Olavarría, Carlos; Leslie, Matthew S; Pomilla, Cristina; Rosenbaum, Howard; Baker, C Scott

    2014-07-07

    Humpback whales (Megaptera novaeangliae) annually undertake the longest migrations between seasonal feeding and breeding grounds of any mammal. Despite this dispersal potential, discontinuous seasonal distributions and migratory patterns suggest that humpbacks form discrete regional populations within each ocean. To better understand the worldwide population history of humpbacks, and the interplay of this species with the oceanic environment through geological time, we assembled mitochondrial DNA control region sequences representing approximately 2700 individuals (465 bp, 219 haplotypes) and eight nuclear intronic sequences representing approximately 70 individuals (3700 bp, 140 alleles) from the North Pacific, North Atlantic and Southern Hemisphere. Bayesian divergence time reconstructions date the origin of humpback mtDNA lineages to the Pleistocene (880 ka, 95% posterior intervals 550-1320 ka) and estimate radiation of current Northern Hemisphere lineages between 50 and 200 ka, indicating colonization of the northern oceans prior to the Last Glacial Maximum. Coalescent analyses reveal restricted gene flow between ocean basins, with long-term migration rates (individual migrants per generation) of less than 3.3 for mtDNA and less than 2 for nuclear genomic DNA. Genetic evidence suggests that humpbacks in the North Pacific, North Atlantic and Southern Hemisphere are on independent evolutionary trajectories, supporting taxonomic revision of M. novaeangliae to three subspecies. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

  1. Verbal and visual divergent thinking in aging.

    Science.gov (United States)

    Palmiero, Massimiliano; Nori, Raffaella; Piccardi, Laura

    2017-04-01

    According to the peak and decline model divergent thinking declines at a specific age (in or after middle age). However, if divergent thinking declines steadily in aging still has to be clarified. In order to explore the age-related changes in verbal and visual divergent thinking, in the present study a sample of 159 participants was divided in five age groups: young adults (18-35 years), middle-aged adults (36-55), young old (56-74), old (75-85) and the oldest-old (86-98). Two divergent thinking tasks were administered: the alternative uses for cardboard boxes, aimed at assessing verbal ideational fluency, flexibility and originality; the completion drawing task, aimed at assessing visual ideational fluency, flexibility and originality. Results showed that after peaking in the young adult group (20-35 years) all components of verbal and visual divergent thinking stabilized in the middle-aged adult group (36-55 years) and then started declining in the young old group (56-75). Interestingly, all components were found to be preserved after declining. Yet, verbal and visual divergent thinking were found at the same extent across age groups, with the exception of visual ideational fluency, that was higher in the young old group, the old group and the oldest-old group than verbal ideational fluency. These results support the idea that divergent thinking does not decline steadily in the elderly. Given that older people can preserve to some extent verbal and visual divergent thinking, these findings have important implications for active aging, that is, divergent thinking might be fostered in aging in order to prevent the cognitive decline.

  2. Two New Measures of Fuzzy Divergence and Their Properties

    Directory of Open Access Journals (Sweden)

    Om Parkash

    2006-06-01

    Full Text Available Several measures of directed divergence and their corresponding measures of fuzzy divergence are available in the exiting literature. Two new measures of fuzzy divergence have been developed and their desirable properties have been discussed.

  3. Divergence and convergence in nutrition science

    NARCIS (Netherlands)

    Penders, Bart; Spruit, Shannon L.; Sikkema, Jan; Maat, Jan; Schuurbiers, Daan

    2015-01-01

    Nutrigenomics diverged from mainstream nutrition science, ideologically, instrumentally and culturally, due to the establishment of a protective niche. That protection is fading. This article chronicles a case in which convergence between nutrigenomics and nutrition science is pursued. Here we

  4. Mitochondrial genome sequences reveal deep divergences among Anopheles punctulatus sibling species in Papua New Guinea

    Directory of Open Access Journals (Sweden)

    Logue Kyle

    2013-02-01

    Full Text Available Abstract Background Members of the Anopheles punctulatus group (AP group are the primary vectors of human malaria in Papua New Guinea. The AP group includes 13 sibling species, most of them morphologically indistinguishable. Understanding why only certain species are able to transmit malaria requires a better comprehension of their evolutionary history. In particular, understanding relationships and divergence times among Anopheles species may enable assessing how malaria-related traits (e.g. blood feeding behaviours, vector competence have evolved. Methods DNA sequences of 14 mitochondrial (mt genomes from five AP sibling species and two species of the Anopheles dirus complex of Southeast Asia were sequenced. DNA sequences from all concatenated protein coding genes (10,770 bp were then analysed using a Bayesian approach to reconstruct phylogenetic relationships and date the divergence of the AP sibling species. Results Phylogenetic reconstruction using the concatenated DNA sequence of all mitochondrial protein coding genes indicates that the ancestors of the AP group arrived in Papua New Guinea 25 to 54 million years ago and rapidly diverged to form the current sibling species. Conclusion Through evaluation of newly described mt genome sequences, this study has revealed a divergence among members of the AP group in Papua New Guinea that would significantly predate the arrival of humans in this region, 50 thousand years ago. The divergence observed among the mtDNA sequences studied here may have resulted from reproductive isolation during historical changes in sea-level through glacial minima and maxima. This leads to a hypothesis that the AP sibling species have evolved independently for potentially thousands of generations. This suggests that the evolution of many phenotypes, such as insecticide resistance will arise independently in each of the AP sibling species studied here.

  5. Mitochondrial Involvement in Vertebrate Speciation? The Case of Mito-nuclear Genetic Divergence in Chameleons

    Science.gov (United States)

    Bar-Yaacov, Dan; Hadjivasiliou, Zena; Levin, Liron; Barshad, Gilad; Zarivach, Raz; Bouskila, Amos; Mishmar, Dan

    2015-01-01

    Compatibility between the nuclear (nDNA) and mitochondrial (mtDNA) genomes is important for organismal health. However, its significance for major evolutionary processes such as speciation is unclear, especially in vertebrates. We previously identified a sharp mtDNA-specific sequence divergence between morphologically indistinguishable chameleon populations (Chamaeleo chamaeleon recticrista) across an ancient Israeli marine barrier (Jezreel Valley). Because mtDNA introgression and gender-based dispersal were ruled out, we hypothesized that mtDNA spatial division was maintained by mito-nuclear functional compensation. Here, we studied RNA-seq generated from each of ten chameleons representing the north and south populations and identified candidate nonsynonymous substitutions (NSSs) matching the mtDNA spatial distribution. The most prominent NSS occurred in 14 nDNA-encoded mitochondrial proteins. Increased chameleon sample size (N = 70) confirmed the geographic differentiation in POLRMT, NDUFA5, ACO1, LYRM4, MARS2, and ACAD9. Structural and functionality evaluation of these NSSs revealed high functionality. Mathematical modeling suggested that this mito-nuclear spatial divergence is consistent with hybrid breakdown. We conclude that our presented evidence and mathematical model underline mito-nuclear interactions as a likely role player in incipient speciation in vertebrates. PMID:26590214

  6. Conservation and divergence of immunoglobulin VH pseudogenes.

    OpenAIRE

    Cohen, J B; Givol, D

    1983-01-01

    The 12 immunoglobulin VH pseudogenes, that have been characterized to date, differ from most pseudogenes of other multigene families in two aspects: (i) they carry only one (11 cases) or at the most two (1 case) deleterious mutations and (ii) they show no evidence of increased divergence from intact VH genes. We describe here the first immunoglobulin VH pseudogene that does not have these characteristics. This pseudogene accumulated numerous deleterious mutations and diverged considerably fro...

  7. Site‐directed mutagenesis, in vivo electroporation and mass spectrometry in search for determinants of the subcellular targeting of Rab7b paralogue in the model eukaryote Paramecium octaurelia

    Directory of Open Access Journals (Sweden)

    E. Wyroba

    2016-04-01

    Full Text Available Protein products of the paralogous genes resulting from the whole genome duplication may acquire new function. The role of post‐translational modifications (PTM in proper targeting of Paramecium Rab7b paralogue – distinct from that of Rab7a directly involved in phagocytosis ‐ was studied using point mutagenesis, proteomic analysis and double immunofluorescence after in vivo electroporation of the mutagenized protein. Here we show that substitution of Thr200 by Ala200 resulted in diminished incorporation of [P32] by 37.4% and of 32 [C14–]UDP‐glucose by 24%, respectively, into recombinant Rab7b_200 in comparison to the non‐mutagenized control. Double confocal imaging revealed that Rab7b_200 was mistargeted upon electroporation into living cells contrary to non‐ mutagenized recombinant Rab7b correctly incorporated in the cytostome area. We identified the peptide ion at m/z=677.63+ characteristic for the glycan group attached to Thr200 in Rab7b using nano LC‐MS/MS and comparing the peptide map of this protein with that after deglycosylation with the mixture of five enzymes of different specificity. Based on the mass of this peptide ion and quantitative radioactive assays with [P32]and  [C14‐]UDP‐ glucose, the suggested composition of the adduct attached to Thr200 might be (Hex1(HexNAc1(Phos3 or (HexNAc1 (Deoxyhexose1 (Phos1 (HexA1. These data indicate that PTM of Thr200 located in the hypervariable C‐region of Rab7b in Paramecium is crucial for the proper localization/function of this protein. Moreover, these proteins differ also in other PTM: the number of phosphorylated amino acids in Rab7b is much higher than in Rab7a.   

  8. Site-directed mutagenesis, in vivo electroporation and mass spectrometry in search for determinants of the subcellular targeting of Rab7b paralogue in the model eukaryote Paramecium octaurelia.

    Science.gov (United States)

    Wyroba, E; Kwaśniak, P; Miller, K; Kobyłecki, K; Osińska, M

    2016-04-11

    Protein products of the paralogous genes resulting from the whole genome duplication may acquire new function. The role of post-translational modifications (PTM) in proper targeting of Paramecium Rab7b paralogue - distinct from that of Rab7a directly involved in phagocytosis - was studied using point mutagenesis, proteomic analysis and double immunofluorescence after in vivo electroporation of the mutagenized protein. Here we show that substitution of Thr200 by Ala200 resulted in diminished incorporation of [P32] by 37.4% and of 32 [C14-]UDP-glucose by 24%, respectively, into recombinant Rab7b_200 in comparison to the non-mutagenized control. Double confocal imaging revealed that Rab7b_200 was mistargeted upon electroporation into living cells contrary to non- mutagenized recombinant Rab7b correctly incorporated in the cytostome area. We identified the peptide ion at m/z=677.63+ characteristic for the glycan group attached to Thr200 in Rab7b using nano LC-MS/MS and comparing the peptide map of this protein with that after deglycosylation with the mixture of five enzymes of different specificity. Based on the mass of this peptide ion and quantitative radioactive assays with [P32]and  [C14-]UDP- glucose, the suggested composition of the adduct attached to Thr200 might be (Hex)1(HexNAc)1(Phos)3 or (HexNAc)1 (Deoxyhexose)1 (Phos)1 (HexA)1. These data indicate that PTM of Thr200 located in the hypervariable C-region of Rab7b in Paramecium is crucial for the proper localization/function of this protein. Moreover, these proteins differ also in other PTM: the number of phosphorylated amino acids in Rab7b is much higher than in Rab7a.

  9. Identifying Chinese species of Gammarus (Crustacea: Amphipoda using DNA barcoding

    Directory of Open Access Journals (Sweden)

    HOU Zhong-E

    2009-04-01

    Full Text Available Using a standard cytochrome c oxidase I sequence, DNA barcoding has been shown to be effective to distinguish known species and to discover cryptic species. Here we assessed the efficiency of DNA barcoding for the amphipod genus Gammarus from China. The maximum intraspecific divergence for widespread species, Gammarus lacustris, was 3.5%, and mean interspecific divergence reached 21.9%. We presented a conservative benchmark for determining provisional species using maximum intraspecific divergence of Gammarus lacustris. Thirty-one species possessed distinct barcode clusters. Two species were comprised of highly divergent clades with strong neighbor-joining bootstrap values, and likely indicated the presence of cryptic species. Although DNA barcoding is effective, future identification of species of Gammarus should incorporate DNA barcoding and morphological detection.

  10. Phenotypic and genetic divergence in three species of dart-poison frogs with contrasting parental behavior.

    Science.gov (United States)

    Summers, K; Bermingham, E; Weigt, L; McCafferty, S; Dahlstrom, L

    1997-01-01

    Why some species exhibit remarkable variation among populations while closely related species are relatively uniform remains unclear. The strawberry dart-poison frog (Dendrobates pumillo) exhibits spectacular color and pattern polmorphism among populations in the Bocas del Toro archipelago of Panama. In contrast, two other sympatric species of dart-poison frog, Phyllobates lugubris and Minyobates sp., show little color or pattern variation among island populations. Here we demonstrate that the color and pattern variation among populations of D. pumilio is not matched by higher levels of mitochondrial DNA sequence divergence relative to P. lugubris or Minyobates sp. Thus, neutral divergence in allopatry is unlikely to have caused the geographical differences observed in D. pumilio. We suggest that strong sexual selection associated with female parental care in D. pumilio, which contrasts the male parental care of P. lugubris and Minyobates sp., may have driven divergence in coloration and pattern in D. pumilio.

  11. Mitochondrial DNA evolution in the genus Equus.

    Science.gov (United States)

    George, M; Ryder, O A

    1986-11-01

    Employing mitochondrial DNA (mtDNA) restriction-endonuclease maps as the basis of comparison, we have investigated the evolutionary affinities of the seven species generally recognized as the genus Equus. Individual species' cleavage maps contained an average of 60 cleavage sites for 16 enzymes, of which 29 were invariant for all species. Based on an average divergence rate of 2%/Myr, the variation between species supports a divergence of extant lineages from a common ancestor approximately 3.9 Myr before the present. Comparisons of cleavage maps between Equus przewalskii (Mongolian wild horse) and E. caballus (domestic horse) yielded estimates of nucleotide sequence divergence ranging from 0.27% to 0.41%. This range was due to intraspecific variation, which was noted only for E. caballus. For pairwise comparisons within this family, estimates of sequence divergence ranged from 0% (E. hemionus onager vs. E. h. kulan) to 7.8% (E. przewalskii vs. E. h. onager). Trees constructed according to the parsimony principle, on the basis of 31 phylogenetically informative restriction sites, indicate that the three extant zebra species represent a monophyletic group with E. grevyi and E. burchelli antiquorum diverging most recently. The phylogenetic relationships of E. africanus and E. hemionus remain enigmatic on the basis of the mtDNA analysis, although a recent divergence is unsupported.

  12. Genetic diversity, recombination, and divergence in animal associated Penicillium dipodomyis.

    Directory of Open Access Journals (Sweden)

    Daniel A Henk

    Full Text Available Penicillium dipodomyis is thought to be an exclusively asexual fungus associated with Kangaroo Rats, Dipodomys species, and is unique among Penicillium species in growing at 37°C but producing no known toxins. Lack of recombination within P. dipodomyis would result in limited adaptive flexibility but possibly enhance local adaptation and host selection via maintenance of favourable genotypes. Here, analysis of DNA sequence data from five protein-coding genes shows that recombination occurs within P. dipodomyis on a small spatial scale. Furthermore, detection of mating-type alleles supports outcrossing and a sexual cycle in P. dipodomyis. P. dipodomyis was a weaker competitor in in vitro assays with other Penicillium species found in association with Kanagaroo rats. Bayesian species level analysis suggests that the P. dipodomyis lineage diverged from closely related species also found in cheek pouches of Kangaroo Rats and their stored seeds about 11 million years ago, a similar divergence time as Dipodomys from its sister rodent taxa.

  13. Evaluating the relationship between evolutionary divergence and phylogenetic accuracy in AFLP data sets.

    Science.gov (United States)

    García-Pereira, María Jesús; Caballero, Armando; Quesada, Humberto

    2010-05-01

    Using in silico amplified fragment length polymorphism (AFLP) fingerprints, we explore the relationship between sequence similarity and phylogeny accuracy to test when, in terms of genetic divergence, the quality of AFLP data becomes too low to be informative for a reliable phylogenetic reconstruction. We generated DNA sequences with known phylogenies using balanced and unbalanced trees with recent, uniform and ancient radiations, and average branch lengths (from the most internal node to the tip) ranging from 0.02 to 0.4 substitutions per site. The resulting sequences were used to emulate the AFLP procedure. Trees were estimated by maximum parsimony (MP), neighbor-joining (NJ), and minimum evolution (ME) methods from both DNA sequences and virtual AFLP fingerprints. The estimated trees were compared with the reference trees using a score that measures overall differences in both topology and relative branch length. As expected, the accuracy of AFLP-based phylogenies decreased dramatically in the more divergent data sets. Above a divergence of approximately 0.05, AFLP-based phylogenies were largely inaccurate irrespective of the distinct topology, radiation model, or phylogenetic method used. This value represents an upper bound of expected tree accuracy for data sets with a simple divergence history; AFLP data sets with a similar divergence but with unbalanced topologies and short ancestral branches produced much less accurate trees. The lack of homology of AFLP bands quickly increases with divergence and reaches its maximum value (100%) at a divergence of only 0.4. Low guanine-cytosine (GC) contents increase the number of nonhomologous bands in AFLP data sets and lead to less reliable trees. However, the effect of the lack of band homology on tree accuracy is surprisingly small relative to the negative impact due to the low information content of AFLP characters. Tree-building methods based on genetic distance displayed similar trends and outperformed parsimony

  14. Maternal diets trigger sex-specific divergent trajectories of gene expression and epigenetic systems in mouse placenta.

    Directory of Open Access Journals (Sweden)

    Anne Gabory

    Full Text Available Males and females responses to gestational overnutrition set the stage for subsequent sex-specific differences in adult onset non communicable diseases. Placenta, as a widely recognized programming agent, contibutes to the underlying processes. According to our previous findings, a high-fat diet during gestation triggers sex-specific epigenetic alterations within CpG and throughout the genome, together with the deregulation of clusters of imprinted genes. We further investigated the impact of diet and sex on placental histology, transcriptomic and epigenetic signatures in mice. Both basal gene expression and response to maternal high-fat diet were sexually dimorphic in whole placentas. Numerous genes showed sexually dimorphic expression, but only 11 genes regardless of the diet. In line with the key role of genes belonging to the sex chromosomes, 3 of these genes were Y-specific and 3 were X-specific. Amongst all the genes that were differentially expressed under a high-fat diet, only 16 genes were consistently affected in both males and females. The differences were not only quantitative but remarkably qualitative. The biological functions and networks of genes dysregulated differed markedly between the sexes. Seven genes of the epigenetic machinery were dysregulated, due to effects of diet, sex or both, including the Y- and X-linked histone demethylase paralogues Kdm5c and Kdm5d, which could mark differently male and female epigenomes. The DNA methyltransferase cofactor Dnmt3l gene expression was affected, reminiscent of our previous observation of changes in global DNA methylation. Overall, this striking sexual dimorphism of programming trajectories impose a considerable revision of the current dietary interventions protocols.

  15. The divergence theorem for divergence measure vectorfields on sets with fractal boundaries

    Czech Academy of Sciences Publication Activity Database

    Šilhavý, Miroslav

    2009-01-01

    Roč. 14, č. 5 (2009), s. 445-455 ISSN 1081-2865 Institutional research plan: CEZ:AV0Z10190503 Keywords : divergence measure vectorfields * fractal s * divergence theorem Subject RIV: BA - General Mathematics Impact factor: 1.065, year: 2009

  16. Vibhakti Divergence between Sanskrit and Hindi

    Science.gov (United States)

    Shukla, Preeti; Shukl, Devanand; Kulkarni, Amba

    Translation divergence at various levels between languages arises due to the different conventions followed by different languages for coding the information of grammatical relations. Though Sanskrit and Hindi belong to the same Indo-Aryan family and structurally as well as lexically Hindi inherits a lot from Sanskrit, yet divergences are observed at the level of function words such as vibhaktis. Pāṇini in his Aṣṭādhyāyī has assigned a default vibhakti to kārakas alongwith many scopes for exceptions. He handles these exceptions either by imposing a new kāraka role or by assigning a special vibhakti. However, these methods are not acceptable in Hindi in toto. Based on the nature of deviation, we propose seven cases of divergences in this paper.

  17. Extracellular DNA metabolism in Haloferax volcanii

    Directory of Open Access Journals (Sweden)

    Scott eChimileski

    2014-02-01

    Full Text Available Extracellular DNA is found in all environments and is a dynamic component of the micro-bial ecosystem. Microbial cells produce and interact with extracellular DNA through many endogenous mechanisms. Extracellular DNA is processed and internalized for use as genetic information and as a major source of macronutrients, and plays several key roles within prokaryotic biofilms. Hypersaline sites contain some of the highest extracellular DNA con-centrations measured in nature–a potential rich source of carbon, nitrogen and phosphorus for halophilic microorganisms. We conducted DNA growth studies for the halophilic archaeon Haloferax volcanii DS2 and show that this model Halobacteriales strain is capable of using exogenous double-stranded DNA as a nutrient. Further experiments with varying medium composition, DNA concentration and DNA types revealed that DNA is utilized primarily as a phosphorus source, that growth on DNA is concentration-dependent and that DNA isolated from different sources is metabolized selectively, with a bias against highly divergent methylated DNA sources. Additionally, fluorescence microscopy experiments showed that labeled DNA colocalized with Haloferax volcanii cells. The gene Hvo_1477 was also identified using a comparative genomic approach as a factor likely to be involved in extracellular DNA processing at the cell surface, and deletion of Hvo_1477 created an H. volcanii strain deficient in its ability to grow on extracellular DNA. Widespread distribution of Hvo_1477 homologs in archaea suggests metabolism of extracellular DNA may be of broad ecological and physiological relevance in this domain of life.

  18. Genetic studies of Australian Trichomya hirsuta (Bivalvia: Mytilidae suggest antitropical divergence of this species

    Directory of Open Access Journals (Sweden)

    Donald J. Colgan

    2018-03-01

    Full Text Available The hairy mussel Trichomya hirsuta (Lamarck, 1819 has disjunct known ranges in northeast Asia and Australia. There are substantial DNA sequence divergences for mitochondrial cytochrome c oxidase subunit I and 16S ribosomal RNA between specimens from these ranges showing that neither is likely to derive from a recent colonization. The most recent common ancestor of the observed haplotypes may have lived as long ago as the early Pliocene. It is, however, suggested here that the mussels from the two regions continue to be regarded, tentatively, as conspecific because intraspecific divergence of mitochondrial DNA sequences can be very high in Mytilidae. The present knowledge of fossil history suggests that the direction of colonization in Trichomya may have been from the Southern to the Northern Hemisphere in contrast with migrations of other genera of Mytilidae.

  19. Genetic divergence between two clinostomatid fish endoparasites ...

    African Journals Online (AJOL)

    1998-11-16

    . To identify usable oligonucleotide prim- ers, a trial study was conducted using parasite DNA and six different 10-mer primers. For amplification, we used a mix- ture including 0.125 ~I DNA polymerase (Takara Taq), 2.5 ~I.

  20. Diverging expectations in buyer-seller relationships

    DEFF Research Database (Denmark)

    Andersen, Poul Houman; Christensen, Poul Rind; Damgaard, Torben

    2009-01-01

    Many firms assume that outsourcing partnerships may allow them to strengthen their overall competitiveness. Lured by its intuitive appeal, several enter into such partnerships, only to realize that they represent a marginal rather than a magical solution to their quest for increasing market...... performance. An important reason for this is the diverging beliefs and expectations held by both parties in the buyer-seller dyad. The purpose of this contribution is to develop a framework for understanding the divergences in expectations and relationship norms in cross-cultural business relationships among...

  1. Lineage divergence and historical gene flow in the Chinese horseshoe bat (Rhinolophus sinicus.

    Directory of Open Access Journals (Sweden)

    Xiuguang Mao

    Full Text Available Closely related taxa living in sympatry provide good opportunities to investigate the origin of barriers to gene flow as well as the extent of reproductive isolation. The only two recognized subspecies of the Chinese rufous horseshoe bat Rhinolophus sinicus are characterized by unusual relative distributions in which R. s. septentrionalis is restricted to a small area within the much wider range of its sister taxon R. s. sinicus. To determine the history of lineage divergence and gene flow between these taxa, we applied phylogenetic, demographic and coalescent analyses to multi-locus datasets. MtDNA gene genealogies and microsatellite-based clustering together revealed three divergent lineages of sinicus, corresponding to Central China, East China and the offshore Hainan Island. However, the central lineage of sinicus showed a closer relationship with septentrionalis than with other lineages of R. s. sinicus, in contrary to morphological data. Paraphyly of sinicus could result from either past asymmetric mtDNA introgression between these two taxa, or could suggest septentrionalis evolved in situ from its more widespread sister subspecies. To test between these hypotheses, we applied coalescent-based phylogenetic reconstruction and Approximate Bayesian Computation (ABC. We found that septentrionalis is likely to be the ancestral taxon and therefore a recent origin of this subspecies can be ruled out. On the other hand, we found a clear signature of asymmetric mtDNA gene flow from septentrionalis into central populations of sinicus yet no nuclear gene flow, thus strongly pointing to historical mtDNA introgression. We suggest that the observed deeply divergent lineages within R. sinicus probably evolved in isolation in separate Pleistocene refugia, although their close phylogeographic correspondence with distinct eco-environmental zones suggests that divergent selection might also have promoted broad patterns of population genetic structure.

  2. Lineage divergence detected in the malaria vector Anopheles marajoara (Diptera: Culicidae in Amazonian Brazil

    Directory of Open Access Journals (Sweden)

    Povoa Marinete M

    2010-10-01

    Full Text Available Abstract Background Cryptic species complexes are common among anophelines. Previous phylogenetic analysis based on the complete mtDNA COI gene sequences detected paraphyly in the Neotropical malaria vector Anopheles marajoara. The "Folmer region" detects a single taxon using a 3% divergence threshold. Methods To test the paraphyletic hypothesis and examine the utility of the Folmer region, genealogical trees based on a concatenated (white + 3' COI sequences dataset and pairwise differentiation of COI fragments were examined. The population structure and demographic history were based on partial COI sequences for 294 individuals from 14 localities in Amazonian Brazil. 109 individuals from 12 localities were sequenced for the nDNA white gene, and 57 individuals from 11 localities were sequenced for the ribosomal DNA (rDNA internal transcribed spacer 2 (ITS2. Results Distinct A. marajoara lineages were detected by combined genealogical analysis and were also supported among COI haplotypes using a median joining network and AMOVA, with time since divergence during the Pleistocene (COI sequences at the 3' end were more variable, demonstrating significant pairwise differentiation (3.82% compared to the more moderate 2.92% detected by the Folmer region. Lineage 1 was present in all localities, whereas lineage 2 was restricted mainly to the west. Mismatch distributions for both lineages were bimodal, likely due to multiple colonization events and spatial expansion (~798 - 81,045 ya. There appears to be gene flow within, not between lineages, and a partial barrier was detected near Rio Jari in Amapá state, separating western and eastern populations. In contrast, both nDNA data sets (white gene sequences with or without the retention of the 4th intron, and ITS2 sequences and length detected a single A. marajoara lineage. Conclusions Strong support for combined data with significant differentiation detected in the COI and absent in the nDNA suggest that

  3. The Harmonic Series Diverges Again and Again

    Science.gov (United States)

    Kifowit, Steven J.; Stamps, Terra A.

    2006-01-01

    The harmonic series is one of the most celebrated infinite series of mathematics. A quick glance at a variety of modern calculus textbooks reveals that there are two very popular proofs of the divergence of the harmonic series. In this article, the authors survey these popular proofs along with many other proofs that are equally simple and…

  4. Viewpoint Environmental Slogans: Memes with Diverging ...

    African Journals Online (AJOL)

    Environmental slogans can be seen as memes, i.e. cultural constructs that, not unlike genes, replicate themselves from one generation to the next. Memes may, however, be divergently interpreted and some memes can even have unwanted side-effects. We wanted to find out how supporters of an environmental ...

  5. Fostering structural change? China's divergence and convergence ...

    African Journals Online (AJOL)

    The paper analyses the divergence and convergence of the characteristics of China's economic relationships with Africa – trade, investment and aid – with Africa's 'traditional' partners, i.e. Western industrialised countries. It argues that these relationships may foster structural transformation of African economies. The latter ...

  6. Divergence of Languages as Resources for Theorizing

    Science.gov (United States)

    Nguyen, Thi Hong Nhung

    2017-01-01

    This paper investigates the potential of conceptual divergences within and between languages for providing intellectual resources for theorizing. Specifically, it explores the role of multilingual researchers in using the possibilities of the plurality of intellectual cultures and languages they have access to for theorizing International Service…

  7. Stora's fine notion of divergent amplitudes

    Directory of Open Access Journals (Sweden)

    Joseph C. Várilly

    2016-11-01

    Full Text Available Stora and coworkers refined the notion of divergent quantum amplitude, somewhat upsetting the standard power-counting recipe. This unexpectedly clears the way to new prototypes for free and interacting field theories of bosons of any mass and spin.

  8. Short communication Divergent selection for reproduction affects ...

    African Journals Online (AJOL)

    Abstract. Merino lines that were divergently selected from the same base population from 1986 to 2009 for their ability to rear multiples were assessed for dag score in autumn and spring, breech wrinkle score, and crutching time. Animals in the Low (L) line had higher dag and breech wrinkle scores and took longer to be.

  9. Design of a divergence and alignment indicator

    International Nuclear Information System (INIS)

    Brenizer, J.S. Jr.; Raine, D.A.; Gao, J.; Chen, J.

    1996-01-01

    The divergence and alignment indicator (DAI) is an extension of the ASTM E803 L/D thermal neutron radiography L/D device that allows the user to determine both the beam centerline and the beam divergence. The DAI was made using aluminium plate and rods, and incorporated cadmium wire for contrast. Circular symmetry was utilized to simplify manufacture. The DAI was placed with the five posts against the film cassette or radioscopic imaging device in the physical center of the beam. The DAI was perpendicular to the selected beam radius when the front and back center Cd wire images overlap. The degree of misalignment was indicated by their image positions. After the DAI was aligned, analysis of the cadmium wire ''+'' image spacing yielded the beam divergence. The DAI was tested in a neutron beam which has an L/D of 30 but a small degree of divergence. The DAI was also imaged using an X-ray source. The point source predictions of Cd wire image locations showed good agreement with those measured from the X-ray radiograph. The neutron radiographic locations could be predicted using the point source equations, even though the neutron beam was a complex distributed source. (orig.)

  10. Taming infrared divergences in the effective potential

    International Nuclear Information System (INIS)

    Elias-Miro, J.; Konstandin, T.

    2014-06-01

    The Higgs effective potential in the Standard Model (SM), calculated perturbatively, generically suffers from infrared (IR) divergences when the (field-dependent) tree-level mass of the Goldstone bosons goes to zero. Such divergences can affect both the potential and its first derivative and become worse with increasing loop order. In this paper we show that these IR divergences are spurious, we perform a simple resummation of all IR-problematic terms known (up to three loops) and explain how to extend the resummation to cure all such divergences to any order. The method is of general applicability and would work in scenarios other than the SM. Our discussion has some bearing on a scenario recently proposed as a mechanism for gauge mediation of scale breaking in the ultraviolet, in which it is claimed that the low-energy Higgs potential is non-standard. We argue that all non-decoupling effects from the heavy sector can be absorbed in the renormalization of low-energy parameters leading to a SM-like effective theory.

  11. Hamiltonian representation of divergence-free fields

    International Nuclear Information System (INIS)

    Boozer, A.H.

    1984-11-01

    Globally divergence-free fields, such as the magnetic field and the vorticity, can be described by a two degree of freedom Hamiltonian. The Hamiltonian function provides a complete topological description of the field lines. The formulation also separates the dissipative and inertial time scale evolution of the magnetic and the vorticity fields

  12. Evaluation of genetic divergence and phylogenetic relationship ...

    African Journals Online (AJOL)

    AMOVA results among groups and among cultivars were 10 and 90%, respectively, while the estimated gene flow was 6.117. The overall Nei's gene diversity (0.238) and Shannon's information index (0.372) indicated high degree of genetic polymorphism revealed by the STMS molecular markers. So, genetic divergence in ...

  13. The Archimedes Principle and Gauss's Divergence Theorem

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 3; Issue 11. The Archimedes Principle and Gauss's Divergence Theorem. Subhashis Nag. General Article Volume 3 Issue 11 November 1998 pp 18-29. Fulltext. Click here to view fulltext PDF. Permanent link:

  14. Effects of asymmetric nuclear introgression, introgressive mitochondrial sweep, and purifying selection on phylogenetic reconstruction and divergence estimates in the Pacific clade of Locustella warblers.

    Science.gov (United States)

    Drovetski, Sergei V; Semenov, Georgy; Red'kin, Yaroslav A; Sotnikov, Vladimir N; Fadeev, Igor V; Koblik, Evgeniy A

    2015-01-01

    When isolated but reproductively compatible populations expand geographically and meet, simulations predict asymmetric introgression of neutral loci from a local to invading taxon. Genetic introgression may affect phylogenetic reconstruction by obscuring topology and divergence estimates. We combined phylogenetic analysis of sequences from one mtDNA and 12 nuDNA loci with analysis of gene flow among 5 species of Pacific Locustella warblers to test for presence of genetic introgression and its effects on tree topology and divergence estimates. Our data showed that nuDNA introgression was substantial and asymmetrical among all members of superspecies groups whereas mtDNA showed no introgression except a single species pair where the invader's mtDNA was swept by mtDNA of the local species. This introgressive sweep of mtDNA had the opposite direction of the nuDNA introgression and resulted in the paraphyly of the local species' mtDNA haplotypes with respect to those of the invader. Тhe multilocus nuDNA species tree resolved all inter- and intraspecific relationships despite substantial introgression. However, the node ages on the species tree may be underestimated as suggested by the differences in node age estimates based on non-introgressing mtDNA and introgressing nuDNA. In turn, the introgressive sweep and strong purifying selection appear to elongate internal branches in the mtDNA gene tree.

  15. Deep phylogeographic divergence and cytonuclear discordance in the grasshopper Oedaleus decorus.

    Science.gov (United States)

    Kindler, Eveline; Arlettaz, Raphaël; Heckel, Gerald

    2012-11-01

    The grasshopper Oedaleus decorus is a thermophilic insect with a large, mostly south-Palaearctic distribution range, stretching from the Mediterranean regions in Europe to Central-Asia and China. In this study, we analyzed the extent of phylogenetic divergence and the recent evolutionary history of the species based on 274 specimens from 26 localities across the distribution range in Europe. Phylogenetic relationships were determined using sequences of two mitochondrial loci (ctr, ND2) with neighbour-joining and Bayesian methods. Additionally, genetic differentiation was analyzed based on mitochondrial DNA and 11 microsatellite markers using F-statistics, model-free multivariate and model-based Bayesian clustering approaches. Phylogenetic analyses detected consistently two highly divergent, allopatrically distributed lineages within O. decorus. The divergence among these Western and Eastern lineages meeting in the region of the Alps was similar to the divergence of each lineage to the sister species O. asiaticus. Genetic differentiation for ctr was extremely high between Western and Eastern grasshopper populations (F(ct)=0.95). Microsatellite markers detected much lower but nevertheless very significant genetic structure among population samples. The nuclear data also demonstrated a case of cytonuclear discordance because the affiliation with mitochondrial lineages was incongruent in Northern Italy. Taken together these results provide evidence of an ancient separation within Oedaleus and either historical introgression of mtDNA among lineages and/or ongoing sex-specific gene flow in this grasshopper. Our study stresses the importance of multilocus approaches for unravelling the history and status of taxa of uncertain evolutionary divergence. Copyright © 2012 Elsevier Inc. All rights reserved.

  16. Mature habitats associated with genetic divergence despite strong dispersal ability in an arthropod

    Directory of Open Access Journals (Sweden)

    Taylor Derek J

    2007-04-01

    Full Text Available Abstract Background Populations may be bound by contemporary gene flow, selective sweeps, and extinction-recolonization processes. Indeed, existing molecular estimates indicate that species with low levels of gene flow are rare. However, strong priority effects and local selective regimes may hinder gene flow (despite dispersal sending populations on independent evolutionary trajectories. In this scenario (the monopolization hypothesis, population differentiation will increase with time and genealogical evidence should yield ample private haplotypes. Cyclical parthenogens (e.g. rotifers and cladocerans such as Daphnia have an increased capacity for rapid local adaptation and priority effects because sexual reproduction is followed by multiple generations of clonal selection and massive egg bank formation. We aimed to better understand the history of population differentiation and ongoing gene flow in Daphnia rosea s.l., by comparing population and regional divergences in mature unglaciated areas and younger previously glaciated areas. We also examined the timing and paths of colonization of previously-glaciated areas to assess the dispersal limitations of D. rosea s.l. We used DNA sequence variation (84 populations and >400 individuals at the mitochondrial ND2 and nuclear HSP90 loci from Holarctic populations for our genetic analyses. Results The genetic evidence indicated pronounced historical structure. Holarctic mtDNA phylogenies of D. rosea s.l. revealed three geographically restricted and divergent clades: European, Siberian and Japanese/American. The Japanese/American clade showed marked population genetic structure (FST > 0.8 that was weakly associated with geographic distance, and a high proportion of private haplotypes. Populations from older unglaciated habitats (i.e., Japan showed higher DNA sequence divergences than populations from presumed younger habitats (i.e. non-Beringian North America with nDNA and with mtDNA. Mismatch

  17. Evolution of DNA Methylation across Insects

    Science.gov (United States)

    Vogel, Kevin J.; Moore, Allen J.; Schmitz, Robert J.

    2017-01-01

    DNA methylation contributes to gene and transcriptional regulation in eukaryotes, and therefore has been hypothesized to facilitate the evolution of plastic traits such as sociality in insects. However, DNA methylation is sparsely studied in insects. Therefore, we documented patterns of DNA methylation across a wide diversity of insects. We predicted that underlying enzymatic machinery is concordant with patterns of DNA methylation. Finally, given the suggestion that DNA methylation facilitated social evolution in Hymenoptera, we tested the hypothesis that the DNA methylation system will be associated with presence/absence of sociality among other insect orders. We found DNA methylation to be widespread, detected in all orders examined except Diptera (flies). Whole genome bisulfite sequencing showed that orders differed in levels of DNA methylation. Hymenopteran (ants, bees, wasps and sawflies) had some of the lowest levels, including several potential losses. Blattodea (cockroaches and termites) show all possible patterns, including a potential loss of DNA methylation in a eusocial species whereas solitary species had the highest levels. Species with DNA methylation do not always possess the typical enzymatic machinery. We identified a gene duplication event in the maintenance DNA methyltransferase 1 (DNMT1) that is shared by some Hymenoptera, and paralogs have experienced divergent, nonneutral evolution. This diversity and nonneutral evolution of underlying machinery suggests alternative DNA methylation pathways may exist. Phylogenetically corrected comparisons revealed no evidence that supports evolutionary association between sociality and DNA methylation. Future functional studies will be required to advance our understanding of DNA methylation in insects. PMID:28025279

  18. Demography and genome divergence of lake and stream populations of an East African cichlid fish.

    Science.gov (United States)

    Egger, Bernd; Roesti, Marius; Böhne, Astrid; Roth, Olivia; Salzburger, Walter

    2017-10-01

    Disentangling the processes and mechanisms underlying adaptive diversification is facilitated by the comparative study of replicate population pairs that have diverged along a similar environmental gradient. Such a setting is realized in a cichlid fish from southern Lake Tanganyika, Astatotilapia burtoni, which occurs within the lake proper as well as in various affluent rivers. Previously, we demonstrated that independent lake and stream populations show similar adaptations to the two habitat regimes. However, little is known about the evolutionary and demographic history of the A. burtoni populations in question and the patterns of genome divergence among them. Here, we apply restriction site-associated DNA sequencing (RADseq) to examine the evolutionary history, the population structure and genomic differentiation of lake and stream populations in A. burtoni. A phylogenetic reconstruction based on genome-wide molecular data largely resolved the evolutionary relationships among populations, allowing us to re-evaluate the independence of replicate lake-stream population clusters. Further, we detected a strong pattern of isolation by distance, with baseline genomic divergence increasing with geographic distance and decreasing with the level of gene flow between lake and stream populations. Genome divergence patterns were heterogeneous and inconsistent among lake-stream population clusters, which is explained by differences in divergence times, levels of gene flow and local selection regimes. In line with the latter, we only detected consistent outlier loci when the most divergent lake-stream population pair was excluded. Several of the thus identified candidate genes have inferred functions in immune and neuronal systems and show differences in gene expression between lake and stream populations. © 2017 John Wiley & Sons Ltd.

  19. Endemic infrared divergences in QED3 at finite temperature

    International Nuclear Information System (INIS)

    Lo, Pok Man; Swanson, Eric S.

    2011-01-01

    We demonstrate that massless QED in three dimensions contains endemic infrared divergences. It is argued that these divergences do not affect observables; furthermore, it is possible to choose a gauge that renders the theory finite.

  20. Rapid divergence of mussel populations despite incomplete barriers to dispersal.

    Science.gov (United States)

    Maas, Diede L; Prost, Stefan; Bi, Ke; Smith, Lydia; Armstrong, Ellie E; Aji, Ludi P; Toha, Abdul H A; Gillespie, Rosemary G; Becking, Leontine E

    2018-03-25

    Striking genetic structure among marine populations at small spatial scales is becoming evident with extensive molecular studies. Such observations suggest isolation at small scales may play an important role in forming patterns of genetic diversity within species. Isolation-by-distance, isolation-by-environment, and historical priority effects are umbrella terms for a suite of processes that underlie genetic structure, but their relative importance at different spatial and temporal scales remains elusive. Here, we use marine lakes in Indonesia to assess genetic structure and test relative roles of the processes in shaping genetic differentiation in populations of a bivalve mussel (Brachidontes sp.). Marine lakes are landlocked water bodies of similar age (6,000 - 10,000 years), but with heterogeneous environments and varying degrees of connection to the sea. Using a population genomic approach (double-digest Restriction-site Associated DNA sequencing), we show strong genetic structuring across populations (range F ST : 0.07 - 0.24), and find limited gene flow through admixture plots. At large spatial scales (>1400km), a clear isolation-by-distance pattern was detected. At smaller spatial scales (<200km), this pattern is maintained, but accompanied by an association of genetic divergence with degree of connection. No signatures of isolation-by-environment were found. We hypothesize that (incomplete) dispersal barriers can cause initial isolation, allowing priority effects to give the numerical advantage necessary to initiate strong genetic structure. Priority effects may be strengthened by local adaptation, which our data potentially corroborates by showing a high correlation between mussel genotypes and temperature. Our study indicates an often-neglected role of evolution-mediated priority effects in shaping population divergence. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  1. Flow over convergent and divergent wall riblets

    Energy Technology Data Exchange (ETDEWEB)

    Koeltzsch, K.; Dinkelacker, A.; Grundmann, R. [Institut fuer Luft- und Raumfahrttechnik, Technische Universitaet Dresden, 36460 Merkers (Germany)

    2002-08-01

    Fast swimming sharks have small riblets on their skin, which are assumed to improve the swimming performance of the fish. Fluid dynamic experiments in water as well as in air confirm this assumption. With riblet surfaces as compared to smooth surfaces, drag reductions up to about 10% were measured. The overall riblet pattern on sharks shows parallel riblets directed from head to tail, but besides this overall pattern fast swimming sharks have also small areas with converging riblets and others with diverging riblets. In the present study the velocity field over convergent and divergent riblet patterns is investigated by hot-wire measurements in turbulent pipe flow. Significant changes in the near wall velocity field were found. (orig.)

  2. Increasing interpersonal trust through divergent thinking

    Directory of Open Access Journals (Sweden)

    Roberta eSellaro

    2014-06-01

    Full Text Available Interpersonal trust is an essential ingredient of many social relationships but how stable is it actually, and how is it controlled? There is evidence that the degree of trust into others might be rather volatile and can be affected by manipulations like drawing attention to personal interdependence or independence. Here we investigated whether the degree of interpersonal trust can be biased by inducing either a more integrative or a more cognitive-control mode by means of a creativity task requiring divergent or convergent thinking, respectively. Participants then performed the Trust Game, which provides an index of interpersonal trust by assessing the money units one participant (the trustor transfers to another participant (the trustee. As expected, participants transferred significantly more money to the trustee after engaging in divergent thinking as compared to convergent thinking. This observation provides support for the idea that interpersonal trust is controlled by domain-general (i.e., not socially dedicated cognitive states.

  3. Enhancing Divergent Search through Extinction Events

    DEFF Research Database (Denmark)

    Lehman, Joel; Miikkulainen, Risto

    2015-01-01

    A challenge in evolutionary computation is to create representations as evolvable as those in natural evolution. This paper hypothesizes that extinction events, i.e. mass extinctions, can significantly increase evolvability, but only when combined with a divergent search algorithm, i.e. a search...... driven towards diversity (instead of optimality). Extinctions amplify diversity-generation by creating unpredictable evolutionary bottlenecks. Persisting through multiple such bottlenecks is more likely for lineages that diversify across many niches, resulting in indirect selection pressure...... for the capacity to evolve. This hypothesis is tested through experiments in two evolutionary robotics domains. The results show that combining extinction events with divergent search increases evolvability, while combining them with convergent search offers no similar benefit. The conclusion is that extinction...

  4. PUBLIC INTEGRITY AND THE DIVERGENCE FROM IT

    Directory of Open Access Journals (Sweden)

    Simona‐Roxana ULMAN

    2013-12-01

    Full Text Available Public Integrity is one of the public sector’s essential objectives to attain. In contradiction, as a divergence from it, corruption is one of the persistent problems of the societies over years and it affects the credibility of public institutions and its ambassadors in front of the citizens and of the other related countries. All nations complain of corruption and, as it is observed in the Corruption Perception Index 2012, no country has a maximum score which shows that a country is totally clean. In this context, the study of the most important elements of the public integrity concept, the identification of what causes the divergence from it and the solutions detection become a relevant option for economic literature. In this context, the main objective of this paper is to emphasize the public integrity concept and its main aspects and to make a comparison between countries to achieve a large perspective of the world’s public integrity juncture.

  5. Automatic transfer functions based on informational divergence.

    Science.gov (United States)

    Ruiz, Marc; Bardera, Anton; Boada, Imma; Viola, Ivan; Feixas, Miquel; Sbert, Mateu

    2011-12-01

    In this paper we present a framework to define transfer functions from a target distribution provided by the user. A target distribution can reflect the data importance, or highly relevant data value interval, or spatial segmentation. Our approach is based on a communication channel between a set of viewpoints and a set of bins of a volume data set, and it supports 1D as well as 2D transfer functions including the gradient information. The transfer functions are obtained by minimizing the informational divergence or Kullback-Leibler distance between the visibility distribution captured by the viewpoints and a target distribution selected by the user. The use of the derivative of the informational divergence allows for a fast optimization process. Different target distributions for 1D and 2D transfer functions are analyzed together with importance-driven and view-based techniques. © 2010 IEEE

  6. COMPARATIVE FINANCIAL STATEMENTS. CONVERGENCE VERSUS DIVERGENCE

    Directory of Open Access Journals (Sweden)

    Nicolae ECOBICI

    2010-09-01

    Full Text Available In this paper I compared the Romanian financial statements with the US GAAP financial statements in terms of two criteria: first the reference period and secondly the shape, structure and content of financial statements. Nowadays the two accounting systems, the French and Anglo-Saxon, tend to harmonize. I will present the convergences and the divergences between the financial statements of Romania, subject to OMFP 3055/2009, in parallel with the Anglo-Saxon accounting system.

  7. Phylogeography of the Alpine salamander, Salamandra atra (Salamandridae) and the influence of the Pleistocene climatic oscillations on population divergence.

    Science.gov (United States)

    Riberon, A; Miaud, C; Grossenbacher, K; Taberlet, P

    2001-10-01

    Fifty individuals of the endemic Alpine salamander, Salamandra atra, representing 13 populations throughout the range of the two currently recognized subspecies, atra and aurorae, were examined for sequence variation in a large portion (1050 bp) of the mitochondrial cytochrome b gene. We revealed a large number of mitochondrial DNA (mtDNA) haplotypes (10). Interpopulation sequence divergence was very low, ranging from 0 to 3.1%. The relationships among haplotypes were poorly resolved. The divergence time estimate between several mtDNA haplotypes suggested a pre-Pleistocene differentiation approximately 3 million years ago. Moreover, the impact of the Pleistocene glaciations on the phylogeographical patterns appears to have been secondary, although a somewhat reduced genetic variability was found in populations living in areas that were directly affected by the glaciation.

  8. Two families of astrophysical diverging lens models

    Science.gov (United States)

    Er, Xinzhong; Rogers, Adam

    2018-03-01

    In the standard gravitational lensing scenario, rays from a background source are bent in the direction of a foreground lensing mass distribution. Diverging lens behaviour produces deflections in the opposite sense to gravitational lensing, and is also of astrophysical interest. In fact, diverging lensing due to compact distributions of plasma has been proposed as an explanation for the extreme scattering events that produce frequency-dependent dimming of extragalactic radio sources, and may also be related to the refractive radio wave phenomena observed to affect the flux density of pulsars. In this work we study the behaviour of two families of astrophysical diverging lenses in the geometric optics limit, the power law, and the exponential plasma lenses. Generally, the members of these model families show distinct behaviour in terms of image formation and magnification, however the inclusion of a finite core for certain power-law lenses can produce a caustic and critical curve morphology that is similar to the well-studied Gaussian plasma lens. Both model families can produce dual radial critical curves, a novel distinction from the tangential distortion usually produced by gravitational (converging) lenses. The deflection angle and magnification of a plasma lens vary with the observational frequency, producing wavelength-dependent magnifications that alter the amplitudes and the shape of the light curves. Thus, multiwavelength observations can be used to physically constrain the distribution of the electron density in such lenses.

  9. Polygamy slows down population divergence in shorebirds

    Science.gov (United States)

    Jackson, Josephine D'Urban; dos Remedios, Natalie; Maher, Kathryn; Zefania, Sama; Haig, Susan M.; Oyler-McCance, Sara J.; Blomqvist, Donald; Burke, Terry; Bruford, Michael W.; Székely, Tamás; Küpper, Clemens

    2017-01-01

    Sexual selection may act as a promotor of speciation since divergent mate choice and competition for mates can rapidly lead to reproductive isolation. Alternatively, sexual selection may also retard speciation since polygamous individuals can access additional mates by increased breeding dispersal. High breeding dispersal should hence increase gene flow and reduce diversification in polygamous species. Here, we test how polygamy predicts diversification in shorebirds using genetic differentiation and subspecies richness as proxies for population divergence. Examining microsatellite data from 79 populations in 10 plover species (Genus: Charadrius) we found that polygamous species display significantly less genetic structure and weaker isolation-by-distance effects than monogamous species. Consistent with this result, a comparative analysis including 136 shorebird species showed significantly fewer subspecies for polygamous than for monogamous species. By contrast, migratory behavior neither predicted genetic differentiation nor subspecies richness. Taken together, our results suggest that dispersal associated with polygamy may facilitate gene flow and limit population divergence. Therefore, intense sexual selection, as occurs in polygamous species, may act as a brake rather than an engine of speciation in shorebirds. We discuss alternative explanations for these results and call for further studies to understand the relationships between sexual selection, dispersal, and diversification.

  10. An Exponential Regulator for Rapidity Divergences

    Energy Technology Data Exchange (ETDEWEB)

    Li, Ye [Fermilab; Neill, Duff [MIT, Cambridge, CTP; Zhu, Hua Xing [MIT, Cambridge, CTP

    2016-04-01

    Finding an efficient and compelling regularization of soft and collinear degrees of freedom at the same invariant mass scale, but separated in rapidity is a persistent problem in high-energy factorization. In the course of a calculation, one encounters divergences unregulated by dimensional regularization, often called rapidity divergences. Once regulated, a general framework exists for their renormalization, the rapidity renormalization group (RRG), leading to fully resummed calculations of transverse momentum (to the jet axis) sensitive quantities. We examine how this regularization can be implemented via a multi-differential factorization of the soft-collinear phase-space, leading to an (in principle) alternative non-perturbative regularization of rapidity divergences. As an example, we examine the fully-differential factorization of a color singlet's momentum spectrum in a hadron-hadron collision at threshold. We show how this factorization acts as a mother theory to both traditional threshold and transverse momentum resummation, recovering the classical results for both resummations. Examining the refactorization of the transverse momentum beam functions in the threshold region, we show that one can directly calculate the rapidity renormalized function, while shedding light on the structure of joint resummation. Finally, we show how using modern bootstrap techniques, the transverse momentum spectrum is determined by an expansion about the threshold factorization, leading to a viable higher loop scheme for calculating the relevant anomalous dimensions for the transverse momentum spectrum.

  11. On the Benefits of Divergent Search for Evolved Representations

    DEFF Research Database (Denmark)

    Lehman, Joel; Risi, Sebastian; Stanley, Kenneth O

    2012-01-01

    explicit objectives that are consequently divergent may implicitly reward lineages that continually diverge, thereby indirectly selecting for evolvable representations that are better able to diverge further. This paper reviews a range of past results that support such a hypothesis from a method called...

  12. Chromosomal divergence and evolutionary inferences in Rhodniini based on the chromosomal location of ribosomal genes

    Directory of Open Access Journals (Sweden)

    Sebastian Pita

    2013-05-01

    Full Text Available In this study, we used fluorescence in situ hybridisation to determine the chromosomal location of 45S rDNA clusters in 10 species of the tribe Rhodniini (Hemiptera: Reduviidae: Triatominae. The results showed striking inter and intraspecific variability, with the location of the rDNA clusters restricted to sex chromosomes with two patterns: either on one (X chromosome or both sex chromosomes (X and Y chromosomes. This variation occurs within a genus that has an unchanging diploid chromosome number (2n = 22, including 20 autosomes and 2 sex chromosomes and a similar chromosome size and genomic DNA content, reflecting a genome dynamic not revealed by these chromosome traits. The rDNA variation in closely related species and the intraspecific polymorphism in Rhodnius ecuadoriensis suggested that the chromosomal position of rDNA clusters might be a useful marker to identify recently diverged species or populations. We discuss the ancestral position of ribosomal genes in the tribe Rhodniini and the possible mechanisms involved in the variation of the rDNA clusters, including the loss of rDNA loci on the Y chromosome, transposition and ectopic pairing. The last two processes involve chromosomal exchanges between both sex chromosomes, in contrast to the widely accepted idea that the achiasmatic sex chromosomes of Heteroptera do not interchange sequences.

  13. Chromosomal divergence and evolutionary inferences in Rhodniini based on the chromosomal location of ribosomal genes

    Science.gov (United States)

    Pita, Sebastián; Panzera, Francisco; Ferrandis, Inés; Galvão, Cleber; Gómez-Palacio, Andrés; Panzera, Yanina

    2013-01-01

    In this study, we used fluorescence in situ hybridisation to determine the chromosomal location of 45S rDNA clusters in 10 species of the tribe Rhodniini (Hemiptera: Reduviidae: Triatominae). The results showed striking inter and intraspecific variability, with the location of the rDNA clusters restricted to sex chromosomes with two patterns: either on one (X chromosome) or both sex chromosomes (X and Y chromosomes). This variation occurs within a genus that has an unchanging diploid chromosome number (2n = 22, including 20 autosomes and 2 sex chromosomes) and a similar chromosome size and genomic DNA content, reflecting a genome dynamic not revealed by these chromosome traits. The rDNA variation in closely related species and the intraspecific polymorphism in Rhodnius ecuadoriensis suggested that the chromosomal position of rDNA clusters might be a useful marker to identify recently diverged species or populations. We discuss the ancestral position of ribosomal genes in the tribe Rhodniini and the possible mechanisms involved in the variation of the rDNA clusters, including the loss of rDNA loci on the Y chromosome, transposition and ectopic pairing. The last two processes involve chromosomal exchanges between both sex chromosomes, in contrast to the widely accepted idea that the achiasmatic sex chromosomes of Heteroptera do not interchange sequences. PMID:23778665

  14. Divergent natural selection promotes immigrant inviability at early and late stages of evolutionary divergence.

    Science.gov (United States)

    Ingley, Spencer J; Johnson, Jerald B

    2016-03-01

    Natural selection's role in speciation has been of fundamental importance since Darwin first outlined his theory. Recently, work has focused on understanding how selection drives trait divergence, and subsequently reproductive isolation. "Immigrant inviability," a barrier that arises from selection against immigrants in their nonnative environment, appears to be of particular importance. Although immigrant inviability is likely ubiquitous, we know relatively little about how selection acts on traits to drive immigrant inviability, and how important immigrant inviability is at early-versus-late stages of divergence. We present a study evaluating the role of predation in the evolution of immigrant inviability in recently diverged population pairs and a well-established species pair of Brachyrhaphis fishes. We evaluate performance in a high-predation environment by assessing survival in the presence of a predator, and swimming endurance in a low-predation environment. We find strong signatures of local adaptation and immigrant inviability of roughly the same magnitude both early and late in divergence. We find remarkably conserved selection for burst-speed swimming (important in predator evasion), and selection for increased size in low-predation environments. Our results highlight the consistency with which selection acts during speciation, and suggest that similar factors might promote initial population differentiation and maintain differentiation at late stages of divergence. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

  15. Beam divergence correction method for neutron resonance spin echo spectroscope

    International Nuclear Information System (INIS)

    Maruyama, Ryuji; Tasaki, Seiji; Hino, Masahiro; Kitaguchi, Masaaki; Kawabata, Yuji; Ebisawa, Toru

    2005-01-01

    A beam divergence correction method for Neutron resonance spin echo (NRSE) spectroscope was proposed and the effectiveness is evaluated by simulation. When a beam divergence correction coil was introduced into NRSE spectroscope and the optimum magnetic field was given, the visibility of spin echo signal was recovered by controlling scattering of phase difference generated by beam divergence. The effectiveness of the correction method was proved by the above result. Principle of NRSE spectroscopy, decrease of spin polarization rate by beam divergence and its correction method, structure of divergence angle correction coil and the magnetic field calculation and result of simulation are described. (S.Y.)

  16. Variational divergence in wave scattering theory with Kirchhoffean trial functions

    Science.gov (United States)

    Bird, J. F.

    1986-01-01

    In a recent study of variational improvement of the Kirchhoff approximation for electromagnetic scattering by rough surfaces, a key ingredient in the variational principle was found to diverge for important configurations (e.g., backscatter) if the polarization had any vertical component. The cause and a cure of this divergence are discussed here. The divergence is demonstrated to occur for arbitrary perfectly conducting scatterers and its universal characterstics are determined, by means of a general divergence criterion that is derived. A variational cure for the divergence is prescribed, and it is tested successfully on a standard scattering model.

  17. Gene duplication and divergence produce divergent MHC genotypes without disassortative mating

    Science.gov (United States)

    Dearborn, Donald C.; Gager, Andrea B.; McArthur, Andrew G.; Gilmour, Morgan E.; Mandzhukova, Elena; Mauck, Robert A.

    2016-01-01

    Genes of the major histocompatibility complex (MHC) exhibit heterozygote advantage in immune defense, which in turn can select for MHC-disassortative mate choice. However, many species lack this expected pattern of MHC-disassortative mating. A possible explanation lies in evolutionary processes following gene duplication: if two duplicated MHC genes become functionally diverged from each other, offspring will inherit diverse multilocus genotypes even under random mating. We used locus-specific primers for high throughput sequencing of two expressed MHC Class II B genes in Leach's storm-petrels, Oceanodroma leucorhoa, and found that exon 2 alleles fall into two gene-specific monophyletic clades. We tested for disassortative versus random mating at these two functionally diverged Class II B genes, using multiple metrics and different subsets of exon 2 sequence data. With good statistical power, we consistently found random assortment of mates at MHC. Despite random mating, birds had MHC genotypes with functionally diverged alleles, averaging 13 amino acid differences in pairwise comparisons of exon 2 alleles within individuals. To test whether this high MHC diversity in individuals is driven by evolutionary divergence of the two duplicated genes, we built a phylogenetic permutation model. The model showed that genotypic diversity was strongly impacted by sequence divergence between the most common allele of each gene, with a smaller additional impact of monophyly of the two genes. Divergence of allele sequences between genes may have reduced the benefits of actively seeking MHC-dissimilar mates, in which case the evolutionary history of duplicated genes is shaping the adaptive landscape of sexual selection. PMID:27376487

  18. The Eurozone Dynamic Cohesion: Convergence or Divergence

    Directory of Open Access Journals (Sweden)

    Antonin Rusek

    2013-08-01

    Full Text Available The long term economic dynamics of the Eurozone’s original 12 countries (Greece, Italy, Spain, Portugal, Ireland, Germany, Netherlands, Luxembourg, Belgium, Austria, Finland, France is analyzed and compared. It is today increasingly recognized that the diverging competitiveness between the Eurozone members is at the root of the current crisis. But the competitiveness dynamics and its impact on the crucial fiscal and financial variables during the common currency existence is seldom analyzed and compared, especially as far as the different groups of countries (and/or different areas within the Eurozone are concerned.

  19. Divergence-based tests for model diagnostic

    Czech Academy of Sciences Publication Activity Database

    Hobza, Tomáš; Esteban, M. D.; Morales, D.; Marhuenda, Y.

    2008-01-01

    Roč. 78, č. 13 (2008), s. 1702-1710 ISSN 0167-7152 R&D Projects: GA MŠk 1M0572 Grant - others:Instituto Nacional de Estadistica (ES) MTM2006-05693 Institutional research plan: CEZ:AV0Z10750506 Keywords : goodness of fit * devergence statistics * GLM * model checking * bootstrap Subject RIV: BB - Applied Statistics, Operational Research Impact factor: 0.445, year: 2008 http://library.utia.cas.cz/separaty/2008/SI/hobza-divergence-based%20tests%20for%20model%20diagnostic.pdf

  20. Projection Pursuit Through ϕ-Divergence Minimisation

    Directory of Open Access Journals (Sweden)

    Jacques Touboul

    2010-06-01

    Full Text Available In his 1985 article (“Projection pursuit”, Huber demonstrates the interest of his method to estimate a density from a data set in a simple given case. He considers the factorization of density through a Gaussian component and some residual density. Huber’s work is based on maximizing Kullback–Leibler divergence. Our proposal leads to a new algorithm. Furthermore, we will also consider the case when the density to be factorized is estimated from an i.i.d. sample. We will then propose a test for the factorization of the estimated density. Applications include a new test of fit pertaining to the elliptical copulas.

  1. Diverging expectations in buyer-seller relationships

    DEFF Research Database (Denmark)

    Andersen, Poul Houman; Christensen, Poul Rind; Damgaard, Torben

    2009-01-01

    Many firms assume that outsourcing partnerships may allow them to strengthen their overall competitiveness. Lured by its intuitive appeal, several enter into such partnerships, only to realize that they represent a marginal rather than a magical solution to their quest for increasing market...... SMEs. We discuss four relational expectations derived from the B2B literature on relational norms for addressing these divergences: Quality, frequency and scope of communication, role specifications and coordination of work nature of planning horizons, and trustworthiness and link these to relationship...

  2. Postglacial recolonization patterns and genetic relationships among whitefish ( Coregonus sp.) populations in Denmark, inferred from mitochondrial DNA and microsatellite markers

    DEFF Research Database (Denmark)

    Hansen, Michael Møller; Mensberg, Karen-Lise Dons; Berg, Søren

    1999-01-01

    The genetic relationships among morphologically and geographically divergent populations of whitefish (genus: Coregonus) from Denmark and the Baltic Sea region were studied by analysis of microsatellites and polymerase chain reaction- restriction fragment length polymorphism (PCR-RFLP) analysis...... of mitochondrial DNA (mtDNA) segments, The endangered North Sea houting (classified as C. oxyrhynchus) differs morphologically and physiologically from other Danish whitefish (C. lavaretus). However, limited divergence of North Sea houting was observed both at the level of mtDNA and microsatellites...

  3. Genetic isolation and morphological divergence mediated by high-energy rapids in two cichlid genera from the lower Congo rapids

    Directory of Open Access Journals (Sweden)

    Stiassny Melanie LJ

    2010-05-01

    Full Text Available Abstract Background It is hypothesized that one of the mechanisms promoting diversification in cichlid fishes in the African Great Lakes has been the well-documented pattern of philopatry along shoreline habitats leading to high levels of genetic isolation among populations. However lake habitats are not the only centers of cichlid biodiversity - certain African rivers also contain large numbers of narrowly endemic species. Patterns of isolation and divergence in these systems have tended to be overlooked and are not well understood. Results We examined genetic and morphological divergence among populations of two narrowly endemic cichlid species, Teleogramma depressum and Lamprologus tigripictilis, from a 100 km stretch of the lower Congo River using both nDNA microsatellites and mtDNA markers along with coordinate-based morphological techniques. In L. tigripictilis, the strongest genetic break was concordant with measurable phenotypic divergence but no morphological disjunction was detected for T. depressum despite significant differentiation at mtDNA and nDNA microsatellite markers. Conclusions The genetic markers revealed patterns of philopatry and estimates of genetic isolation that are among the highest reported for any African cichlid species over a comparable geographic scale. We hypothesize that the high levels of philopatry observed are generated and maintained by the extreme hydrology of the lower Congo River.

  4. Dissecting molecular stress networks: identifying nodes of divergence between life-history phenotypes.

    Science.gov (United States)

    Schwartz, Tonia S; Bronikowski, Anne M

    2013-02-01

    The complex molecular network that underlies physiological stress response is comprised of nodes (proteins, metabolites, mRNAs, etc.) whose connections span cells, tissues and organs. Variable nodes are points in the network upon which natural selection may act. Thus, identifying variable nodes will reveal how this molecular stress network may evolve among populations in different habitats and how it might impact life-history evolution. Here, we use physiological and genetic assays to test whether laboratory-born juveniles from natural populations of garter snakes (Thamnophis elegans), which have diverged in their life-history phenotypes, vary concomitantly at candidate nodes of the stress response network, (i) under unstressed conditions and (ii) in response to an induced stress. We found that two common measures of stress (plasma corticosterone and liver gene expression of heat shock proteins) increased under stress in both life-history phenotypes. In contrast, the phenotypes diverged at four nodes both under unstressed conditions and in response to stress: circulating levels of reactive oxygen species (superoxide, H(2)O(2)); liver gene expression of GPX1 and erythrocyte DNA damage. Additionally, allele frequencies for SOD2 diverge from neutral markers, suggesting diversifying selection on SOD2 alleles. This study supports the hypothesis that these life-history phenotypes have diverged at the molecular level in how they respond to stress, particularly in nodes regulating oxidative stress. Furthermore, the differences between the life-history phenotypes were more pronounced in females. We discuss the responses to stress in the context of the associated life-history phenotype and the evolutionary pressures thought to be responsible for divergence between the phenotypes. © 2012 Blackwell Publishing Ltd.

  5. Genetic hitchhiking associated with life history divergence and colonization of North America in the European corn borer moth.

    Science.gov (United States)

    Dopman, Erik B

    2011-05-01

    A primary goal for evolutionary biology is to reveal the genetic basis for adaptive evolution and reproductive isolation. Using Z and E pheromone strains the European corn borer (ECB) moth, I address this problem through multilocus analyses of DNA polymorphism. I find that the locus Triose phosphate isomerase (Tpi) is a statistically significant outlier in coalescent simulations of demographic histories of population divergence, including strict allopatric isolation, restricted migration, secondary contact, and population growth or decline. This result corroborates a previous QTL study that identified the Tpi chromosomal region as a repository for gene(s) contributing to divergence in life history. Patterns of nucleotide polymorphism at Tpi suggest a recent selective sweep and genetic hitchhiking associated with colonization of North America from Europe ~200 generations ago. These results indicate that gene genealogies initially diverge during speciation because of selective sweeps, but differential introgression may play a role in the maintenance of differentiation for sympatric populations.

  6. Genetic divergence among invasive and native populations of Plagioscion squamosissimus (Perciformes, Sciaenidae) in Neotropical regions.

    Science.gov (United States)

    Panarari-Antunes, R S; Prioli, A J; Prioli, S M A P; Gomes, V N; Júlio, H F; Agostinho, C S; Silva Filho, J P; Boni, T A; Prioli, L M

    2012-06-01

    The genetic divergence among invasive and native populations of Plagioscion squamosissimus from four Neotropical hydrographic basins was assessed using the hypervariable domain of the mitochondrial DNA (mtDNA) control region. Plagioscion squamosissimus is native to the neighbouring hydrographic basins of the Parnaíba and Amazon Rivers, and the latter includes the Araguaia-Tocantins drainage, but it is invasive in other basins due to introductions. The mtDNA nucleotide polymorphism supported the hypothesis that the Amazon and Parnaíba populations constitute the same species and are separated into two independent evolutionary lineages. Absence of nucleotide polymorphism was observed within and among P. squamosissimus populations invasive to the uppper and middle Paraná River basins. Nucleotide divergence was null or low comparing the Paraná invasive populations with the populations native to the Parnaíba River basin, whereas it was significantly high compared to Tocantins populations. These results ascertain that P. squamosissimus populations invasive to the upper Paraná River basin and to the middle Paraná River basin downstream of the Itaipu dam are derived from the Parnaíba River basin. The genetic data presented are potentially useful to assist further studies on P. squamosissimus taxonomic and geographic distribution, development of ecological guidelines for managing populations invasive to the upper Paraná River basin and for preservation of native fish diversity. © 2012 The Authors. Journal of Fish Biology © 2012 The Fisheries Society of the British Isles.

  7. Mitochondrial DNA.

    Science.gov (United States)

    Wright, Russell G.; Bottino, Paul J.

    1986-01-01

    Provides background information for teachers on mitochondrial DNA, pointing out that it may have once been a free-living organism. Includes a ready-to-duplicate exercise titled "Using Microchondrial DNA to Measure Evolutionary Distance." (JN)

  8. The colonization of land by animals: molecular phylogeny and divergence times among arthropods

    Directory of Open Access Journals (Sweden)

    Lyons-Weiler Maureen

    2004-01-01

    Full Text Available Abstract Background The earliest fossil evidence of terrestrial animal activity is from the Ordovician, ~450 million years ago (Ma. However, there are earlier animal fossils, and most molecular clocks suggest a deep origin of animal phyla in the Precambrian, leaving open the possibility that animals colonized land much earlier than the Ordovician. To further investigate the time of colonization of land by animals, we sequenced two nuclear genes, glyceraldehyde-3-phosphate dehydrogenase and enolase, in representative arthropods and conducted phylogenetic and molecular clock analyses of those and other available DNA and protein sequence data. To assess the robustness of animal molecular clocks, we estimated the deuterostome-arthropod divergence using the arthropod fossil record for calibration and tunicate instead of vertebrate sequences to represent Deuterostomia. Nine nuclear and 15 mitochondrial genes were used in phylogenetic analyses and 61 genes were used in molecular clock analyses. Results Significant support was found for the unconventional pairing of myriapods (millipedes and centipedes with chelicerates (spiders, scorpions, horseshoe crabs, etc. using nuclear and mitochondrial genes. Our estimated time for the divergence of millipedes (Diplopoda and centipedes (Chilopoda was 442 ± 50 Ma, and the divergence of insects and crustaceans was estimated as 666 ± 58 Ma. Our results also agree with previous studies suggesting a deep divergence (~1100 – 900 Ma for arthropods and deuterostomes, considerably predating the Cambrian Explosion seen in the animal fossil record. Conclusions The consistent support for a close relationship between myriapods and chelicerates, using mitochondrial and nuclear genes and different methods of analysis, suggests that this unexpected result is not an artefact of analysis. We propose the name Myriochelata for this group of animals, which includes many that immobilize prey with venom. Our molecular clock

  9. Modeling DNA

    Science.gov (United States)

    Robertson, Carol

    2016-01-01

    Deoxyribonucleic acid (DNA) is life's most amazing molecule. It carries the genetic instructions that almost every organism needs to develop and reproduce. In the human genome alone, there are some three billion DNA base pairs. The most difficult part of teaching DNA structure, however, may be getting students to visualize something as small as a…

  10. MiR-221/222 target the DNA methyltransferase MGMT in glioma cells.

    Directory of Open Access Journals (Sweden)

    Cristina Quintavalle

    Full Text Available Glioblastoma multiforme (GBM is one of the most deadly types of cancer. To date, the best clinical approach for treatment is based on administration of temozolomide (TMZ in combination with radiotherapy. Much evidence suggests that the intracellular level of the alkylating enzyme O(6-methylguanine-DNA methyltransferase (MGMT impacts response to TMZ in GBM patients. MGMT expression is regulated by the methylation of its promoter. However, evidence indicates that this is not the only regulatory mechanism present. Here, we describe a hitherto unknown microRNA-mediated mechanism of MGMT expression regulation. We show that miR-221 and miR-222 are upregulated in GMB patients and that these paralogues target MGMT mRNA, inducing greater TMZ-mediated cell death. However, miR-221/miR-222 also increase DNA damage and, thus, chromosomal rearrangements. Indeed, miR-221 overexpression in glioma cells led to an increase in markers of DNA damage, an effect rescued by re-expression of MGMT. Thus, chronic miR-221/222-mediated MGMT downregulation may render cells unable to repair genetic damage. This, associated also to miR-221/222 oncogenic potential, may poor GBM prognosis.

  11. MiR-221/222 target the DNA methyltransferase MGMT in glioma cells.

    Science.gov (United States)

    Quintavalle, Cristina; Mangani, Davide; Roscigno, Giuseppina; Romano, Giulia; Diaz-Lagares, Angel; Iaboni, Margherita; Donnarumma, Elvira; Fiore, Danilo; De Marinis, Pasqualino; Soini, Ylermi; Esteller, Manel; Condorelli, Gerolama

    2013-01-01

    Glioblastoma multiforme (GBM) is one of the most deadly types of cancer. To date, the best clinical approach for treatment is based on administration of temozolomide (TMZ) in combination with radiotherapy. Much evidence suggests that the intracellular level of the alkylating enzyme O(6)-methylguanine-DNA methyltransferase (MGMT) impacts response to TMZ in GBM patients. MGMT expression is regulated by the methylation of its promoter. However, evidence indicates that this is not the only regulatory mechanism present. Here, we describe a hitherto unknown microRNA-mediated mechanism of MGMT expression regulation. We show that miR-221 and miR-222 are upregulated in GMB patients and that these paralogues target MGMT mRNA, inducing greater TMZ-mediated cell death. However, miR-221/miR-222 also increase DNA damage and, thus, chromosomal rearrangements. Indeed, miR-221 overexpression in glioma cells led to an increase in markers of DNA damage, an effect rescued by re-expression of MGMT. Thus, chronic miR-221/222-mediated MGMT downregulation may render cells unable to repair genetic damage. This, associated also to miR-221/222 oncogenic potential, may poor GBM prognosis.

  12. Mouse Rad9b is essential for embryonic development and promotes resistance to DNA damage

    Science.gov (United States)

    Leloup, Corinne; Hopkins, Kevin M.; Wang, Xiangyuan; Zhu, Aiping; Wolgemuth, Debra J.; Lieberman, Howard B.

    2010-01-01

    RAD9 participates in promoting resistance to DNA damage, cell cycle checkpoint control, DNA repair, apoptosis, embryogenesis, and regulation of transcription. A paralogue of RAD9 (named RAD9B) has been identified. To define the function of mouse Rad9b (Mrad9b), embryonic stem (ES) cells with a targeted gene deletion were constructed and used to generate Mrad9b mutant mice. Mrad9b−/− embryos are resorbed after E7.5 while some of the heterozygotes die between E12.5 and a few days after birth. Mrad9b is expressed in embryonic brain and Mrad9b+/− embryos exhibit abnormal neural tube closure. Mrad9b−/− mouse embryonic fibroblasts are not viable. Mrad9b−/− ES cells are more sensitive to gamma rays and mitomycin C than Mrad9b+/+ controls, but show normal gamma-ray-induced G2/M checkpoint control. There is no evidence of spontaneous genomic instability in Mrad9b−/− cells. Our findings thus indicate that Mrad9b is essential for embryonic development and mediates resistance to certain DNA damaging agents. PMID:20842695

  13. Growth divergence: a challenging opportunity for dendrochronology

    Science.gov (United States)

    Buras, Allan; Sass-Klaassen, Ute; Wilmking, Martin

    2017-04-01

    Dendrochronology is an essential cornerstone of paleoclimatology and the evaluation of climate change impacts on forest ecosystems. However, a growing body of literature indicates that the standard dendrochronological approach may too rigorously neglect individualistic tree-growth (e.g. Wilmking et al., 2004, Buras et al., 2016). Amongst others, these studies showed convincing evidence that individual trees of the same species sampled at one site expressed different long-term growth patterns and therefore differing climate-growth relationships. This phenomenon is commonly termed growth divergence (GD) and possibly weakens our ability to correctly estimate past climate variability as discussed in the context of the so-called divergence phenomenon (D'Arrigo et al., 2008). In this context, climate change may naturally select for trees on the stand-level which are better adapted to future conditions. Although GD has been reported for several sites, the standard dendrochronological approach yet does not consider the existence of GD. A possible reason for this methodological persistence is the lack of detailed information on the frequency, magnitude, and impact of GD occurrence. To assess GD occurrence and related tree-individual variations in climate-growth response we conducted a global GD study by using 134 ring-width data representing 52 tree species and 16 genera distributed over 115 sites across 22 countries. Our analyses clearly reveal GD to be a common phenomenon as occurring in 85 % of all sites. GD was clearly related to the degree of tree-individual differences in climate-growth response. Respective transfer functions which appropriately accounted for GD by selection of tree-cohorts with a high share of long-term variance on average increased the precision and stability of tree-ring based climate reconstructions. Concluding, incorporation of GD assessments into the dendrochronological approach has a strong potential to improve the precision of our predictions

  14. Mutation of the p53 gene precedes aneuploid clonal divergence in colorectal carcinoma.

    OpenAIRE

    Carder, P. J.; Cripps, K. J.; Morris, R.; Collins, S.; White, S.; Bird, C. C.; Wyllie, A. H.

    1995-01-01

    To establish whether p53 mutation precedes or follows clonal divergence in human colorectal carcinomas, 17 tumours were analysed at multiple sites (2-5 each) for single-strand conformation polymorphisms (SSCP) within exons 5-8 of the p53 gene. A previous study had demonstrated subclones of differing DNA ploidy in these tumours, but all showed immunocytochemical evidence for p53 stabilisation, using the monoclonal antibody PAb 1801. Mutations within exons 5-8 of p53 were identified by the pres...

  15. Dna Sequencing

    Science.gov (United States)

    Tabor, Stanley; Richardson, Charles C.

    1995-04-25

    A method for sequencing a strand of DNA, including the steps off: providing the strand of DNA; annealing the strand with a primer able to hybridize to the strand to give an annealed mixture; incubating the mixture with four deoxyribonucleoside triphosphates, a DNA polymerase, and at least three deoxyribonucleoside triphosphates in different amounts, under conditions in favoring primer extension to form nucleic acid fragments complementory to the DNA to be sequenced; labelling the nucleic and fragments; separating them and determining the position of the deoxyribonucleoside triphosphates by differences in the intensity of the labels, thereby to determine the DNA sequence.

  16. Rapid Hepatitis C Virus Divergence among Chronically Infected Individuals

    OpenAIRE

    Cruz-Rivera, Mayra; Carpio-Pedroza, Juan Carlos; Escobar-Gutiérrez, Alejandro; Lozano, Daniela; Vergara-Castaneda, Arely; Rivera-Osorio, Pilar; Martinez-Guarneros, Armando; Chacon, Carlos A. Vazquez; Fonseca-Coronado, Salvador; Vaughan, Gilberto

    2013-01-01

    Here, we analyze the viral divergence among hepatitis C virus (HCV) chronic cases infected with genotype 1. The intrahost viral evolution was assessed by deep sequencing using the 454 Genome Sequencer platform. The results showed a rapid nucleotide sequence divergence. This notorious short-term viral evolution is of the utmost importance for the study of HCV transmission, because direct links between related samples were virtually lost. Thus, rapid divergence of HCV significantly affects gene...

  17. Hamiltonian mechanics and divergence-free fields

    International Nuclear Information System (INIS)

    Boozer, A.H.

    1986-08-01

    The field lines, or integral curves, of a divergence-free field in three dimensions are shown to be topologically equivalent to the trajectories of a Hamiltonian with two degrees of freedom. The consideration of fields that depend on a parameter allow the construction of a canonical perturbation theory which is valid even if the perturbation is large. If the parametric dependence of the magnetic, or the vorticity field is interpreted as time dependence, evolution equations are obtained which give Kelvin's theorem or the flux conservation theorem for ideal fluids and plasmas. The Hamiltonian methods prove especially useful for study of fields in which the field lines must be known throughout a volume of space

  18. Some Divergence Properties of Asset Price Models

    Directory of Open Access Journals (Sweden)

    Wolfgang Stummer

    2001-12-01

    Full Text Available Abstract: We consider asset price processes Xt which are weak solutions of one-dimensional stochastic differential equations of the form (equation (2 Such price models can be interpreted as non-lognormally-distributed generalizations of the geometric Brownian motion. We study properties of the Iα-divergence between the law of the solution Xt and the corresponding drift-less measure (the special case α=1 is the relative entropy. This will be applied to some context in statistical information theory as well as to arbitrage theory and contingent claim valuation. For instance, the seminal option pricing theorems of Black-Scholes and Merton appear as a special case.

  19. DIVERGING DISCOURSES ON THE SYR DARYA

    Directory of Open Access Journals (Sweden)

    Eelke Kraak

    2012-01-01

    Full Text Available The hydraulic mission of the Soviet Union has transformed Central Asia’s Syr Darya River into a governable entity. After the dissolution of the Soviet Union the river system disintegrated and conflict arose over the operation of the main dam and reservoir of the river: the Toktogul. Uzbekistan and Kyrgyzstan have widely different and diverging sanctioned discourses on how the dam should be operated and on the nature of the water itself. These discourses have had a significant impact on the hydro-politics of the river basin and the operation of the dam. The central argument of this paper is that both the decline of the Aral Sea, and the potential conflict between the states are driven by the same modernist governmentality of the river.

  20. Reliability and Security - Convergence or Divergence

    Directory of Open Access Journals (Sweden)

    Emil BURTESCU

    2010-01-01

    Full Text Available Reliability, as every technical field, must adapt to the new demands imposed by reality. Started initially as a field designed to control and ensure the smooth functionality of an element or technical system, reliability has reached the stage where the discussion is about the reliability management, similar to the other top-level fields. Security has its own contribution to the reliability of a system; a reliable system is a system with reliable security. In order for a system to be reliable, that means clear and safe, all its components must be reliable. In the following pages we will talk about the two main facts - reliability and security - to determine both the convergence and the divergence points.

  1. Culturally divergent responses to mortality salience.

    Science.gov (United States)

    Ma-Kellams, Christine; Blascovich, Jim

    2011-08-01

    Two experiments compared the effects of death thoughts, or mortality salience, on European and Asian Americans. Research on terror management theory has demonstrated that in Western cultural groups, individuals typically employ self-protective strategies in the face of death-related thoughts. Given fundamental East-West differences in self-construal (i.e., the independent vs. interdependent self), we predicted that members of Eastern cultural groups would affirm other people, rather than defend and affirm the self, after encountering conditions of mortality salience. We primed European Americans and Asian Americans with either a death or a control prime and examined the effect of this manipulation on attitudes about a person who violates cultural norms (Study 1) and on attributions about the plight of an innocent victim (Study 2). Mortality salience promoted culturally divergent responses, leading European Americans to defend the self and Asian Americans to defend other people.

  2. Divergent Geophysical Evolution of Vesta and Ceres

    Science.gov (United States)

    Raymond, C. A.; Ermakov, A.; Castillo, J. C.; Fu, R. R.; McSween, H. Y., Jr.; McCord, T. B.; Park, R. S.; Russell, C. T.; De Sanctis, M. C.; Jaumann, R.; Konopliv, A. S.

    2017-12-01

    The Dawn mission explored two massive protoplanets in the main asteroid belt, Vesta and Ceres, that are fossils from the earliest epoch of solar system formation. Dawn's data provide evidence that these bodies formed very early, within the first few million years after CAIs, yet they followed divergent evolutionary paths. Vesta formed elements in the HED clan. Discovery of hydrated material on Vesta's surface implies that volatile delivery to the inner solar system was an important process. Thus, while the basic HED paradigm was confirmed, we learned that differentiation on a small planet is more complex than envisioned. Dwarf planet Ceres was known to be water-rich before Dawn arrived. However, contrary to the expected ice-rich, viscously-relaxed smooth surface resulting from physical differentiation and freezing of an ancient subsurface ocean, its surface has many craters, implying a mechanically strong thick crust. The lack of large craters and Ceres' gravitationally-relaxed shape at long wavelengths implies that a strong crust overlies a weaker deep interior. The globally homogeneous distribution of minerals across the surface indicates that Ceres' interior experienced pervasive alteration. Topography and morphology of the surface reveals smoother, apparently resurfaced areas, generally at lower elevation, and rougher areas with greater relief. Local morphology such as crater floor deposits, isolated mountains, and enigmatic bright areas indicate recently active processes on Ceres, likely driven by brine cryovolcanism. Causes of the divergent evolution of these bodies include their accretionary environment, timing of accretion and size. Acknowledgements: Part of this research was carried out at the Jet Propulsion Laboratory, California Institute of Technology, under contract to the National Aeronautics and Space Administration.

  3. Adaptive divergence in wine yeasts and their wild relatives suggests a prominent role for introgressions and rapid evolution at noncoding sites.

    Science.gov (United States)

    Almeida, Pedro; Barbosa, Raquel; Bensasson, Douda; Gonçalves, Paula; Sampaio, José Paulo

    2017-04-01

    In Saccharomyces cerevisiae, the main yeast in wine fermentation, the opportunity to examine divergence at the molecular level between a domesticated lineage and its wild counterpart arose recently due to the identification of the closest relatives of wine strains, a wild population associated with Mediterranean oaks. As genomic data are available for a considerable number of representatives belonging to both groups, we used population genomics to estimate the degree and distribution of nucleotide variation between wine yeasts and their closest wild relatives. We found widespread genomewide divergence, particularly at noncoding sites, which, together with above average divergence in trans-acting DNA binding proteins, may suggest an important role for divergence at the level of transcriptional regulation. Nine outlier regions putatively under strong divergent selection were highlighted by a genomewide scan under stringent conditions. Several cases of introgressions, originating in the sibling species Saccharomyces paradoxus, were also identified in the Mediterranean oak population. FZF1 and SSU1, mostly known for conferring sulphite resistance in wine yeasts, were among the introgressed genes, although not fixed. Because the introgressions detected in our study are not found in wine strains, we hypothesize that ongoing divergent ecological selection segregates the two forms between the different niches. Together, our results provide a first insight into the extent and kind of divergence between wine yeasts and their closest wild relatives. © 2017 John Wiley & Sons Ltd.

  4. Sequence divergence between spelt and common wheat

    Czech Academy of Sciences Publication Activity Database

    Liu, M.; Zhao, Q.; Qi, F.; Stiller, J.; Tang, Q.; Miao, J.; Vrána, Jan; Holušová, Kateřina; Liu, D.; Doležel, Jaroslav; Manners, J. M.; Han, B. P.; Liu, C.

    2018-01-01

    Roč. 131, č. 5 (2018), s. 1125-1132 ISSN 0040-5752 R&D Projects: GA MŠk(CZ) LO1204 Institutional support: RVO:61389030 Keywords : BREAD WHEAT * DNA * DIVERSITY Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Genetics and heredity (medical genetics to be 3) Impact factor: 4.132, year: 2016

  5. Latitudinal variation in genetic divergence of populations and the potential for future speciation.

    Science.gov (United States)

    Martin, Paul R; McKay, John K

    2004-05-01

    The increase in biological diversity with decreasing latitude is widely appreciated but the cause of the pattern is unknown. This pattern reflects latitudinal variation in both the origin of new species (cladogenesis) and the number of species that coexist. Here we address latitudinal variation in species origination, by examining population genetic processes that influence speciation. Previous data suggest a greater number of speciation events at lower latitudes. If speciation events occur more frequently at lower latitudes, we predicted that genetic divergence among populations within species, an important component of cladogenesis, should be greater among lower latitude populations. We tested this prediction using within-species patterns of mtDNA variation across 60 vertebrate species that collectively spanned six continents, two oceans, and 119 degrees latitude. We found greater genetic divergence of populations, controlling for geographic distance, at lower latitudes within species. This pattern remained statistically significant after removing populations that occur in localities previously covered by continental glaciers during the last glaciation. Results suggest that lower latitude populations within species exhibit greater evolutionary independence, increasing the likelihood that mutation, recombination, selection, and/or drift will lead to divergence of traits important for reproductive isolation and speciation. Results are consistent with a greater influence of seasonality, reduced energy, and/or glacial (Milankovitch) cycles acting on higher latitude populations, and represent one of the few tests of predictions of latitudinal variation in speciation rates using population genetic data.

  6. Identification and characterisation of a highly divergent geminivirus: evolutionary and taxonomic implications.

    Science.gov (United States)

    Bernardo, Pauline; Golden, Michael; Akram, Mohammad; Naimuddin; Nadarajan, Nagaswamy; Fernandez, Emmanuel; Granier, Martine; Rebelo, Anthony G; Peterschmitt, Michel; Martin, Darren P; Roumagnac, Philippe

    2013-10-01

    During a large scale "non a priori" survey in 2010 of South African plant-infecting single stranded DNA viruses, a highly divergent geminivirus genome was isolated from a wild spurge, Euphorbia caput-medusae. In addition to being infectious in E. caput-medusae, the cloned viral genome was also infectious in tomato and Nicotiana benthamiana. The virus, named Euphorbia caput-medusae latent virus (EcmLV) due to the absence of infection symptoms displayed by its natural host, caused severe symptoms in both tomato and N. benthamiana. The genome organisation of EcmLV is unique amongst geminiviruses and it likely expresses at least two proteins without any detectable homologues within public sequence databases. Although clearly a geminivirus, EcmLV is so divergent that we propose its placement within a new genus that we have tentatively named Capulavirus. Using a set of highly divergent geminiviruses genomes, it is apparent that recombination has likely been a primary process in the genus-level diversification of geminiviruses. It is also demonstrated how this insight, taken together with phylogenetic analyses of predicted coat protein and replication associated protein (Rep) amino acid sequences indicate that the most recent common ancestor of the geminiviruses was likely a dicot-infecting virus that, like modern day mastreviruses and becurtoviruses, expressed its Rep from a spliced complementary strand transcript. Copyright © 2013 The Authors. Published by Elsevier B.V. All rights reserved.

  7. Evolution of pygmy angelfishes: Recent divergences, introgression, and the usefulness of color in taxonomy

    KAUST Repository

    Gaither, Michelle R.

    2014-05-01

    The pygmy angelfishes (genus Centropyge, family Pomacanthidae) are brightly colored species that occupy reef habitats in every tropical ocean. Some species are rarely observed because they occur below conventional scuba depths. Their striking coloration can command thousands of U.S. dollars in the aquarium trade, and closely related species are often distinguished only by coloration. These factors have impeded phylogenetic resolution, and every phylogeographic survey to date has reported discordance between coloration, taxonomy, and genetic partitions. Here we report a phylogenetic survey of 29 of the 34 recognized species (N= 94 plus 23 outgroups), based on two mtDNA and three nuclear loci, totaling 2272. bp. The resulting ML and Baysian trees are highly concordant and indicate that the genus Centropyge is paraphyletic, consistent with a previous analysis of the family Pomacanthidae. Two recognized genera (Apolemichthys and Genicanthus) nest within Centropyge, and two subgenera (Xiphypops and Paracentropyge) comprise monophyletic lineages that should be elevated to genus level. Based on an age estimate of 38. Ma for the family Pomacanthidae, Centropyge diverged from the closest extant genus Pygoplites about 33. Ma, three deep lineages within Centropyge diverged about 18-28. Ma, and four species complexes diverged 3-12. Ma. However, in 11 of 13 cases, putative species in these complexes are indistinguishable based on morphology and genetics, being defined solely by coloration. These cases indicate either emerging species or excessive taxonomic splitting based on brightly colored variants. © 2014 Elsevier Inc.

  8. Testing evolutionary hypotheses for phenotypic divergence using landscape genetics.

    Science.gov (United States)

    Funk, W Chris; Murphy, Melanie A

    2010-02-01

    Understanding the evolutionary causes of phenotypic variation among populations has long been a central theme in evolutionary biology. Several factors can influence phenotypic divergence, including geographic isolation, genetic drift, divergent natural or sexual selection, and phenotypic plasticity. But the relative importance of these factors in generating phenotypic divergence in nature is still a tantalizing and unresolved problem in evolutionary biology. The origin and maintenance of phenotypic divergence is also at the root of many ongoing debates in evolutionary biology, such as the extent to which gene flow constrains adaptive divergence (Garant et al. 2007) and the relative importance of genetic drift, natural selection, and sexual selection in initiating reproductive isolation and speciation (Coyne & Orr 2004). In this issue, Wang & Summers (2010) test the causes of one of the most fantastic examples of phenotypic divergence in nature: colour pattern divergence among populations of the strawberry poison frog (Dendrobates pumilio) in Panama and Costa Rica (Fig. 1). This study provides a beautiful example of the use of the emerging field of landscape genetics to differentiate among hypotheses for phenotypic divergence. Using landscape genetic analyses, Wang & Summers were able to reject the hypotheses that colour pattern divergence is due to isolation-by-distance (IBD) or landscape resistance. Instead, the hypothesis left standing is that colour divergence is due to divergent selection, in turn driving reproductive isolation among populations with different colour morphs. More generally, this study provides a wonderful example of how the emerging field of landscape genetics, which has primarily been applied to questions in conservation and ecology, now plays an essential role in evolutionary research.

  9. Alkaline Extraction of DNA from Pathogenic Fungi for PCR-RFLP Analysis

    OpenAIRE

    Matsumoto, Masaru; Mishima, Shinobu; Matsuyama, Nobuaki; 松元, 賢; 松山, 宣明

    1997-01-01

    For the preparation of DNA samples from fungal mycelia alkaline extraction method was applied and assessed its usefulness for PCR-RFLP analysis. Using alkaline treatment protocols, 18S ribosomal DNAs (rDNA) derived from fungal genomic DNA of Pyricularia oryzae, P. zingiberi, Rhizoctonia solani and R. oryzae were PCR-amplified and digested with Hha I, Msp I and Hae ill. RFLP analysis with HhaI showed the divergent polymorphism between genus Pyricularia and Rhizoctonia. The alkaline DNA extract...

  10. Divergent transcription: a driving force for new gene origination?

    Science.gov (United States)

    Wu, Xuebing; Sharp, Phillip A

    2013-11-21

    The mammalian genome is extensively transcribed, a large fraction of which is divergent transcription from promoters and enhancers that is tightly coupled with active gene transcription. Here, we propose that divergent transcription may shape the evolution of the genome by new gene origination. Copyright © 2013 Elsevier Inc. All rights reserved.

  11. The Relationship Between Lateral Dominance and Divergent Cognitive Thought.

    Science.gov (United States)

    Williams, Barbara B.

    This study was designed to explore the relationship of lateral dominance to divergent cognitive thought. According to the screening results of the Harris Tests of Lateral Dominance, 36 subjects ranging from 9-12 years were divided equally into three groups of left, right, and mixed lateral dominance. In order to measure divergent cognitive…

  12. Evidence of multiple divergent mitochondrial lineages within the ...

    African Journals Online (AJOL)

    On this basis, the mitochondrial cytochrome c oxidase subunit 1 (COI) was used to reconstruct the phylogeny of Bicoxidens and reveal divergent lineages within the genus. Maximum likelihood and Bayesian inference analyses recovered a paraphyletic Bicoxidens phylogram with divergent lineages present in three species ...

  13. The direct Flow parametric Proof of Gauss' Divergence Theorem revisited

    DEFF Research Database (Denmark)

    Markvorsen, Steen

    The standard proof of the divergence theorem in undergraduate calculus courses covers the theorem for static domains between two graph surfaces. We show that within first year undergraduate curriculum, the flow proof of the dynamic version of the divergence theorem - which is usually considered o...

  14. Structure and expression of a divergent canine class I gene

    Energy Technology Data Exchange (ETDEWEB)

    Burnett, R.C.; Geraghty, D.E. [Fred Hutchinson Cancer Research Center, Seattle, WA (United States)

    1995-11-01

    We have isolated and characterized a canine class I MHC (dog leukocyte Ag, DLA) gene, DLA-79. The deduced protein sequence shares only 65% identity with a previously published canine class I cDNA, designated DLA-A, and exhibits 64% amino acid identity with the HLA-A, -B, -C consensus. The peptide-binding region of DLA-79 is unusual. Three of four highly conserved tyrosine residues (Tyr 7, 59, 159, and 171), proposed to interact with the N terminus of peptide-Ag, are substituted. Additionally, the long {alpha}-helix lining the peptide-binding region in the {alpha}1 domain contains one more amino acid residue than that observed in typical class I. Together, these features suggest that DLA-79 binds a distinct subset of peptides or other ligands. This gene has been expressed in a class I null human lymphoblastoid cell line, and the encoded heavy chain associated with {beta}{sub 2}-microglobulin and was transported to the cell surface. Ribonuclease protection analysis detected low levels of gene-specific mRNA in a broad variety of dog tissues. The highest levels were found in skeletal muscle, a tissue expressing relatively low levels of classical class I Ag. These data suggest that DLA-79 is functional and plays a specialized role in the immune response. Nucleotide sequence analysis of second exon sequences (encoding the {alpha}1 domain) identified only two alleles in five dogs of different breeds; a third variant was found in a coyote. The divergent structure, relatively low mRNA expression, and limited polymorphism of this gene suggest that DLA-79 is not a classical or class Ia gene, but rather, an analogue of the MHC class Ib gene of humans and rodents. 49 refs., 7 figs., 1 tab.

  15. One-loop divergences in the quantum theory of supergravity

    International Nuclear Information System (INIS)

    Nieuwenhuizen, P. van; Vermaseren, J.A.M.

    1976-01-01

    Supergravity does not lead to a finite quantum theory of gravitation when coupled to the spin 1, 1/2 matter multiplet. The S-matrix of photon-photon scattering diverges; its divergences are proportional to the square of the photon energy-momentum tensor, in agreement with electro-magnetic duality and chiral invariance. The graviton self-energy corrections are divergent in pure supergravity as well as in the coupled Maxwell-Einstein system and satisfy their Ward identity because the supersymmetry ghost field is commuting. The photon-graviton vertex corrections diverge, as expected from the non-invariance of the action under local scale transformations, and satisfy the equivalence principle at the quantum level. The photon self-energy is divergent. (Auth.)

  16. Niche divergence accelerates evolution in Asian endemic Procapra gazelles.

    Science.gov (United States)

    Hu, Junhua; Jiang, Zhigang; Chen, Jing; Qiao, Huijie

    2015-05-07

    Ecological niche divergence and adaptation to new environments are thought to play important roles in driving speciation. Whether recently evolved species show evidence for niche divergence or conservation is vital towards understanding the role of ecology in the process of speciation. The genus Procapra is an ancient, monophyletic lineage endemic to Asia that contains three extant species (P. gutturosa, P. przewalskii and P. picticaudata). These species mainly inhabit the Qinghai-Tibetan and Mongolian Plateaus, and today have primarily allopatric distributions. We applied a series of geographic information system-based analyses to test for environmental variation and niche divergence among these three species. We found substantial evidence for niche divergence in species' bioclimatic preferences, which supports the hypothesis that niche divergence accelerates diversification in Procapra. Our results provide important insight into the evolutionary history of ungulates in Asia and help to elucidate how environmental changes accelerate lineage diversification.

  17. Escort entropies and divergences and related canonical distribution

    International Nuclear Information System (INIS)

    Bercher, J.-F.

    2011-01-01

    We discuss two families of two-parameter entropies and divergences, derived from the standard Renyi and Tsallis entropies and divergences. These divergences and entropies are found as divergences or entropies of escort distributions. Exploiting the nonnegativity of the divergences, we derive the expression of the canonical distribution associated to the new entropies and a observable given as an escort-mean value. We show that this canonical distribution extends, and smoothly connects, the results obtained in nonextensive thermodynamics for the standard and generalized mean value constraints. -- Highlights: → Two-parameter entropies are derived from q-entropies and escort distributions. → The related canonical distribution is derived. → This connects and extends known results in nonextensive statistics.

  18. Active learning for noisy oracle via density power divergence.

    Science.gov (United States)

    Sogawa, Yasuhiro; Ueno, Tsuyoshi; Kawahara, Yoshinobu; Washio, Takashi

    2013-10-01

    The accuracy of active learning is critically influenced by the existence of noisy labels given by a noisy oracle. In this paper, we propose a novel pool-based active learning framework through robust measures based on density power divergence. By minimizing density power divergence, such as β-divergence and γ-divergence, one can estimate the model accurately even under the existence of noisy labels within data. Accordingly, we develop query selecting measures for pool-based active learning using these divergences. In addition, we propose an evaluation scheme for these measures based on asymptotic statistical analyses, which enables us to perform active learning by evaluating an estimation error directly. Experiments with benchmark datasets and real-world image datasets show that our active learning scheme performs better than several baseline methods. Copyright © 2013 Elsevier Ltd. All rights reserved.

  19. Exceptional giftedness in early adolescence and intrafamilial divergent thinking.

    Science.gov (United States)

    Runco, M A; Albert, R S

    1986-08-01

    Two groups of boys and their parents (N=54) were given five divergent thinking tests as one part of a longitudinal investigation on exceptional giftedness in early adolescence. One groups of adolescents was selected because their IQs were above 150, and the other group, was selected because of their outstanding math-science abilities. Canonical and bivariate analyses indicated that there was a strong correlation between the adolescents' divergent thinking test scores and their parents' divergent thinking test scores (Rc=.55). Additionally, there was some indication that these correlations differed in the two exceptionally gifted groups, with the high-IQ group having divergent thinking test scores related to those of both parents, and the math-science group having divergent thinking test scores related only to those of their mothers. These findings are very consistent with earlier investigations on exceptionally gifted adolescents.

  20. Isolation with asymmetric gene flow during the nonsynchronous divergence of dry forest birds.

    Science.gov (United States)

    Oswald, Jessica A; Overcast, Isaac; Mauck, William M; Andersen, Michael J; Smith, Brian Tilston

    2017-03-01

    Dry forest bird communities in South America are often fragmented by intervening mountains and rainforests, generating high local endemism. The historical assembly of dry forest communities likely results from dynamic processes linked to numerous population histories among codistributed species. Nevertheless, species may diversify in the same way through time if landscape and environmental features, or species ecologies, similarly structure populations. Here we tested whether six co-distributed taxon pairs that occur in the dry forests of the Tumbes and Marañón Valley of northwestern South America show concordant patterns and modes of diversification. We employed a genome reduction technique, double-digest restriction site-associated DNA sequencing, and obtained 4407-7186 genomewide SNPs. We estimated demographic history in each taxon pair and inferred that all pairs had the same best-fit demographic model: isolation with asymmetric gene flow from the Tumbes into the Marañón Valley, suggesting a common diversification mode. Overall, we also observed congruence in effective population size (N e ) patterns where ancestral N e were 2.9-11.0× larger than present-day Marañón Valley populations and 0.3-2.0× larger than Tumbesian populations. Present-day Marañón Valley N e was smaller than Tumbes. In contrast, we found simultaneous population isolation due to a single event to be unlikely as taxon pairs diverged over an extended period of time (0.1-2.9 Ma) with multiple nonoverlapping divergence periods. Our results show that even when populations of codistributed species asynchronously diverge, the mode of their differentiation can remain conserved over millions of years. Divergence by allopatric isolation due to barrier formation does not explain the mode of differentiation between these two bird assemblages; rather, migration of individuals occurred before and after geographic isolation. © 2017 John Wiley & Sons Ltd.

  1. Experimental evidence indicating that mastreviruses probably did not co-diverge with their hosts

    Directory of Open Access Journals (Sweden)

    Owor Betty E

    2009-07-01

    Full Text Available Abstract Background Despite the demonstration that geminiviruses, like many other single stranded DNA viruses, are evolving at rates similar to those of RNA viruses, a recent study has suggested that grass-infecting species in the genus Mastrevirus may have co-diverged with their hosts over millions of years. This "co-divergence hypothesis" requires that long-term mastrevirus substitution rates be at least 100,000-fold lower than their basal mutation rates and 10,000-fold lower than their observable short-term substitution rates. The credibility of this hypothesis, therefore, hinges on the testable claim that negative selection during mastrevirus evolution is so potent that it effectively purges 99.999% of all mutations that occur. Results We have conducted long-term evolution experiments lasting between 6 and 32 years, where we have determined substitution rates of between 2 and 3 × 10-4 substitutions/site/year for the mastreviruses Maize streak virus (MSV and Sugarcane streak Réunion virus (SSRV. We further show that mutation biases are similar for different geminivirus genera, suggesting that mutational processes that drive high basal mutation rates are conserved across the family. Rather than displaying signs of extremely severe negative selection as implied by the co-divergence hypothesis, our evolution experiments indicate that MSV and SSRV are predominantly evolving under neutral genetic drift. Conclusion The absence of strong negative selection signals within our evolution experiments and the uniformly high geminivirus substitution rates that we and others have reported suggest that mastreviruses cannot have co-diverged with their hosts.

  2. The Mitochondrial Genomes of a Myxozoan Genus Kudoa Are Extremely Divergent in Metazoa.

    Directory of Open Access Journals (Sweden)

    Fumihiko Takeuchi

    Full Text Available The Myxozoa are oligo-cellular parasites with alternate hosts--fish and annelid worms--and some myxozoan species harm farmed fish. The phylum Myxozoa, comprising 2,100 species, was difficult to position in the tree of life, due to its fast evolutionary rate. Recent phylogenomic studies utilizing an extensive number of nuclear-encoded genes have confirmed that Myxozoans belong to Cnidaria. Nevertheless, the evolution of parasitism and extreme body simplification in Myxozoa is not well understood, and no myxozoan mitochondrial DNA sequence has been reported to date. To further elucidate the evolution of Myxozoa, we sequenced the mitochondrial genomes of the myxozoan species Kudoa septempunctata, K. hexapunctata and K. iwatai and compared them with those of other metazoans. The Kudoa mitochondrial genomes code for ribosomal RNAs, transfer RNAs, eight proteins for oxidative phosphorylation and three proteins of unknown function, and they are among the metazoan mitochondrial genomes coding the fewest proteins. The mitochondrial-encoded proteins were extremely divergent, exhibiting the fastest evolutionary rate in Metazoa. Nevertheless, the dN/dS ratios of the protein genes in genus Kudoa were approximately 0.1 and similar to other cnidarians, indicating that the genes are under negative selection. Despite the divergent genetic content, active oxidative phosphorylation was indicated by the transcriptome, metabolism and structure of mitochondria in K. septempunctata. As possible causes, we attributed the divergence to the population genetic characteristics shared between the two most divergent clades, Ctenophora and Myxozoa, and to the parasitic lifestyle of Myxozoa. The fast-evolving, functional mitochondria of the genus Kudoa expanded our understanding of metazoan mitochondrial evolution.

  3. Divergência genética entre cultivares de gérbera utilizando marcadores RAPD Genetic divergence among cultivars of gerbera using RAPD markers

    Directory of Open Access Journals (Sweden)

    Rodrigo Kelson Silva Rezende

    2009-11-01

    Full Text Available No processo de produção comercial de mudas de gérbera, a cor da flor é uma das principais características morfológicas de interesse agronômico, sendo uma característica importante em programas de melhoramento genético. A utilização de marcadores moleculares pode servir para direcionar cruzamentos, confirmar novos híbridos ou genótipos mutantes e identificar novos genótipos para fins comerciais. Nesse contexto, o objetivo deste trabalho foi analisar a divergência genética entre seis cultivares de Gerbera jamesonii ('Jaguar Yellow', 'Jaguar Cream', 'Jaguar Lemon', 'Jaguar Salmon Pastel', 'Jaguar Red', 'Jaguar Deep Rose'. A análise de divergência genética entre as cultivares de gérbera foi realizada utilizando-se 21 primers, os quais amplificaram 37 fragmentos polimórficos de DNA, que foram usados para estimar o coeficiente de Jaccard, o qual apresentou uma média de 0,38, variando de 0,28 a 0,56. A estrutura genética entre as cultivares foi estimada pelo UPGMA, revelando dois grupos distintos, a 38% de similaridade genética. A maior similaridade genética encontrada (56% foi entre as cultivares 'Jaguar Yellow' e 'Jaguar Lemon'. Os resultados demonstram que a técnica RAPD oferece uma maneira rápida, relativamente barata e útil para a caracterização da divergência genética entre as diferentes cultivares de Gerbera jamesonii com relação à cor da flor.During the commercial production of gerbera seedlings, flower color is one of the main morphological aspects that have an agronomic interest and becoming an important feature in genetic breeding programs. The use of molecular markers may serve to direct crossings, new hybrids and mutants, besides confirm and identify new genotypes for commercial purposes. In that context, this work aimed to analyze the genetic divergence among six cultivars of Gerbera jamesonii ('Jaguar Yellow', 'Jaguar Cream', 'Jaguar Lemon', 'Jaguar Salmon Pastel', 'Jaguar Red', 'Jaguar Deep Rose'. The

  4. Evolution of DNA Methylation across Insects.

    Science.gov (United States)

    Bewick, Adam J; Vogel, Kevin J; Moore, Allen J; Schmitz, Robert J

    2017-03-01

    DNA methylation contributes to gene and transcriptional regulation in eukaryotes, and therefore has been hypothesized to facilitate the evolution of plastic traits such as sociality in insects. However, DNA methylation is sparsely studied in insects. Therefore, we documented patterns of DNA methylation across a wide diversity of insects. We predicted that underlying enzymatic machinery is concordant with patterns of DNA methylation. Finally, given the suggestion that DNA methylation facilitated social evolution in Hymenoptera, we tested the hypothesis that the DNA methylation system will be associated with presence/absence of sociality among other insect orders. We found DNA methylation to be widespread, detected in all orders examined except Diptera (flies). Whole genome bisulfite sequencing showed that orders differed in levels of DNA methylation. Hymenopteran (ants, bees, wasps and sawflies) had some of the lowest levels, including several potential losses. Blattodea (cockroaches and termites) show all possible patterns, including a potential loss of DNA methylation in a eusocial species whereas solitary species had the highest levels. Species with DNA methylation do not always possess the typical enzymatic machinery. We identified a gene duplication event in the maintenance DNA methyltransferase 1 (DNMT1) that is shared by some Hymenoptera, and paralogs have experienced divergent, nonneutral evolution. This diversity and nonneutral evolution of underlying machinery suggests alternative DNA methylation pathways may exist. Phylogenetically corrected comparisons revealed no evidence that supports evolutionary association between sociality and DNA methylation. Future functional studies will be required to advance our understanding of DNA methylation in insects. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  5. Comparative genome scan detects host-related divergent selection in the grasshopper Hesperotettix viridis.

    Science.gov (United States)

    Apple, Jennifer L; Grace, Tony; Joern, Anthony; St Amand, Paul; Wisely, Samantha M

    2010-09-01

    In this study, we used a comparative genome scan to examine patterns of population differentiation with respect to host plant use in Hesperotettix viridis, a Nearctic oligophagous grasshopper locally specialized on various Asteraceae including Solidago, Gutierrezia, and Ericameria. We identified amplified fragment length polymorphism (AFLP) loci with significantly elevated F(ST) (outlier loci) in multiple different-host and same-host comparisons of populations while controlling for geographic distance. By comparing the number and identities of outlier loci in different-host vs. same-host comparisons, we found evidence of host plant-related divergent selection for some population comparisons (Solidago- vs. Gutierrezia-feeders), while other comparisons (Ericameria- vs. Gutierrezia-feeders) failed to demonstrate a strong role for host association in population differentiation. In comparisons of Solidago- vs. Gutierrezia-feeding populations, a relatively high number of outlier loci observed repeatedly in different-host comparisons (35% of all outliers and 2.7% of all 625 AFLP loci) indicated a significant role for host-related selection in contributing to overall genomic differentiation in this grasshopper. Mitochondrial DNA sequence data revealed a star-shaped phylogeny with no host- or geography-related structure, low nucleotide diversity, and high haplotype diversity, suggesting a recent population expansion. mtDNA data do not suggest a long period of isolation in separate glacial refugia but are instead more compatible with a single glacial refugium and more recent divergence in host use. Our study adds to research documenting heterogeneity in differentiation across the genome as a consequence of divergent natural selection, a phenomenon that may occur as part of the process of ecological speciation. © 2010 Blackwell Publishing Ltd.

  6. Homology among divergent Paleozoic tetrapod clades.

    Science.gov (United States)

    Carroll, R L

    1999-01-01

    A stringent definition of homology is necessary to establish phylogenetic relationships among Paleozoic amphibians. Many derived characters exhibited by divergent clades of Carboniferous lepospondyls resemble those achieved convergently among Cenozoic squamates that have elongate bodies and reduced limbs, and by lineages of modern amphibians that have undergone miniaturization. Incongruent character distribution, poorly resolved cladograms and functionally improbable character transformations determined by phylogenetic analysis suggest that convergence was also common among Paleozoic amphibians with a skull length under 3 cm, including lepospondyls, early amniotes and the putative ancestors of modern amphibians. For this reason, it is injudicious to equate apparent synapomorphy (perceived common presence of a particular derived character in two putative sister-taxa) with strict homology of phylogenetic origin. Identification of homology by the similarity of structure, anatomical position and pattern of development is insufficient to establish the synapomorphy of bone and limb loss or precocial ossification of vertebral centra, which are common among small Paleozoic amphibians. The only way in which synapomorphies can be established definitively is through the discovery and recognition of the trait in question in basal members of each of the clades under study, and in their immediate common ancestors.

  7. Divergent mortality trends by ethnicity in Fiji.

    Science.gov (United States)

    Taylor, Richard; Carter, Karen; Naidu, Shivnay; Linhart, Christine; Azim, Syed; Rao, Chalapati; Lopez, Alan D

    2013-12-01

    To examine trends in infant mortality rate (IMR), adult mortality and life expectancy (LE) in the two major Fijian ethnic groups since 1975. Estimates of IMR, adult mortality (15-59 years) and LE by ethnicity are calculated from previously unreported Fiji Ministry of Health data and extracted from published sources. Over 1975-2008: IMR decreased from 33 to 20 deaths/1,000 live births in i-Taukei (Fiji Melanesians); and 38 to 18 in Fijians of Indian descent. Increased adult male mortality among i-Taukei and decline among Fijians of Indian descent led to an equal probability of dying in 2007 of 29%; while in female adults the probability trended upwards in i-Taukei to 25%, and declined in Fijians of Indian descent to 17%. Life expectancy in both ethnicities increased until 1985 (to 64 years for males; 68 for females) then forming a plateau in males of both ethnicities, and Fijian females of Indian descent, but declining in i-Taukei females to 66 years in 2007. Despite IMR declines over 1975-2008, LE for i-Taukei and Fijians of Indian descent has not increased since 1985, and has actually decreased in i-Taukei women, consistent with trends in adult mortality (15-59 years). Mortality analyses in Fiji that consider the entire population mask divergent trends in the major ethnic groups. This situation is most likely a consequence of non-communicable disease mortality, requiring further assessment and a strengthened response.

  8. Function of Junk: Pericentromeric Satellite DNA in Chromosome Maintenance.

    Science.gov (United States)

    Jagannathan, Madhav; Yamashita, Yukiko M

    2018-04-02

    Satellite DNAs are simple tandem repeats that exist at centromeric and pericentromeric regions on eukaryotic chromosomes. Unlike the centromeric satellite DNA that comprises the vast majority of natural centromeres, function(s) for the much more abundant pericentromeric satellite repeats are poorly understood. In fact, the lack of coding potential allied with rapid divergence of repeat sequences across eukaryotes has led to their dismissal as "junk DNA" or "selfish parasites." Although implicated in various biological processes, a conserved function for pericentromeric satellite DNA remains unidentified. We have addressed the role of satellite DNA through studying chromocenters, a cytological aggregation of pericentromeric satellite DNA from multiple chromosomes into DNA-dense nuclear foci. We have shown that multivalent satellite DNA-binding proteins cross-link pericentromeric satellite DNA on chromosomes into chromocenters. Disruption of chromocenters results in the formation of micronuclei, which arise by budding off the nucleus during interphase. We propose a model that satellite DNAs are critical chromosome elements that are recognized by satellite DNA-binding proteins and incorporated into chromocenters. We suggest that chromocenters function to preserve the entire chromosomal complement in a single nucleus, a fundamental and unquestioned feature of eukaryotic genomes. We speculate that the rapid divergence of satellite DNA sequences between closely related species results in discordant chromocenter function and may underlie speciation and hybrid incompatibility. © 2017 Jagannathan and Yamashita; Published by Cold Spring Harbor Laboratory Press.

  9. DNA glue

    DEFF Research Database (Denmark)

    Filichev, Vyacheslav V; Astakhova, Irina V.; Malakhov, Andrei D.

    2008-01-01

    Significant alterations in thermal stability of parallel DNA triplexes and antiparallel duplexes were observed upon changing the attachment of ethynylpyrenes from para to ortho in the structure of phenylmethylglycerol inserted as a bulge into DNA (TINA). Insertions of two ortho-TINAs as a pseudo...

  10. DNA Vaccines

    Indian Academy of Sciences (India)

    DNA vaccine, immune response, antibodies, infectious diseases. GENERAL I ARTICLE. DNA Vaccines. P N Rangarajan. History of Vaccine Development. The year 1996 marked the 200th anniversary of the first vaccine developed against smallpox by Edward Jenner. In the now- famous 1796 experiment, Jenner scratched ...

  11. Hyperstretching DNA

    NARCIS (Netherlands)

    Schakenraad, Koen; Biebricher, Andreas S.; Sebregts, Maarten; Ten Bensel, Brian; Peterman, Erwin J.G.; Wuite, Gijs J L; Heller, Iddo; Storm, Cornelis; Van Der Schoot, Paul

    2017-01-01

    The three-dimensional structure of DNA is highly susceptible to changes by mechanical and biochemical cues in vivo and in vitro. In particular, large increases in base pair spacing compared to regular B-DNA are effected by mechanical (over)stretching and by intercalation of compounds that are widely

  12. Origins and divergence of the Roma (gypsies).

    Science.gov (United States)

    Gresham, D; Morar, B; Underhill, P A; Passarino, G; Lin, A A; Wise, C; Angelicheva, D; Calafell, F; Oefner, P J; Shen, P; Tournev, I; de Pablo, R; Kuĉinskas, V; Perez-Lezaun, A; Marushiakova, E; Popov, V; Kalaydjieva, L

    2001-12-01

    The identification of a growing number of novel Mendelian disorders and private mutations in the Roma (Gypsies) points to their unique genetic heritage. Linguistic evidence suggests that they are of diverse Indian origins. Their social structure within Europe resembles that of the jatis of India, where the endogamous group, often defined by profession, is the primary unit. Genetic studies have reported dramatic differences in the frequencies of mutations and neutral polymorphisms in different Romani populations. However, these studies have not resolved ambiguities regarding the origins and relatedness of Romani populations. In this study, we examine the genetic structure of 14 well-defined Romani populations. Y-chromosome and mtDNA markers of different mutability were analyzed in a total of 275 individuals. Asian Y-chromosome haplogroup VI-68, defined by a mutation at the M82 locus, was present in all 14 populations and accounted for 44.8% of Romani Y chromosomes. Asian mtDNA-haplogroup M was also identified in all Romani populations and accounted for 26.5% of female lineages in the sample. Limited diversity within these two haplogroups, measured by the variation at eight short-tandem-repeat loci for the Y chromosome, and sequencing of the HVS1 for the mtDNA are consistent with a small group of founders splitting from a single ethnic population in the Indian subcontinent. Principal-components analysis and analysis of molecular variance indicate that genetic structure in extant endogamous Romani populations has been shaped by genetic drift and differential admixture and correlates with the migrational history of the Roma in Europe. By contrast, social organization and professional group divisions appear to be the product of a more recent restitution of the caste system of India.

  13. Speed-consistency Based Safety Evaluation for Freeway Diverging Segments

    Directory of Open Access Journals (Sweden)

    Zhang Ting

    2017-01-01

    Full Text Available Diverging segments are potential bottlenecks because of frequent lane change and deceleration maneuvers. Speed study has been proven to be an effective way to understand the safety performance of diverging segments. This paper addresses the safety level of diverging segments in terms of speed consistency. Speed data is extracted by Tracker based on aerial video imager collected at the diverging segment of MaQun interchange of G42 in Nanjing, China. The operating speed of vehicles is assumed to follow the Linear Regression Model with two explanatory variables—initial velocity and running distance, and the estimated operating speed is amended un der actual traffic conditions. Furthermore, average speed, speed difference and the coefficient of variation are used as safety indicators to establish the speed evaluation criteria. Last but not the least, based on vague set of material-units, the safety level of diverging segments in terms of the velocity arrives at level III, which means that consideration must be given about the safety of diverging segments. The proposed methodology can be used to estimate the safety of diverging segments.

  14. Recent ecological divergence despite migration in sockeye salmon (Oncorhynchus nerka)

    Science.gov (United States)

    Pavey, Scott A.; Nielsen, Jennifer L.; Hamon, Troy R.

    2010-01-01

    Ecological divergence may result when populations experience different selection regimes, but there is considerable discussion about the role of migration at the beginning stages of divergence before reproductive isolating mechanisms have evolved. However, detection of past migration is difficult in current populations and tools to differentiate genetic similarities due to migration versus recent common ancestry are only recently available. Using past volcanic eruption times as a framework, we combine morphological analyses of traits important to reproduction with a coalescent-based genetic analysis of two proximate sockeye salmon (Oncorhynchus nerka) populations. We find that this is the most recent (~500 years, 100 generations) natural ecological divergence recorded in a fish species, and report that this divergence is occurring despite migration. Although studies of fish divergence following the retreat of glaciers (10,000–15,000 years ago) have contributed extensively to our understanding of speciation, the Aniakchak system of sockeye salmon provides a rare example of the initial stages of ecological divergence following natural colonization. Our results show that even in the face of continued migration, populations may diverge in the absence of a physical barrier.

  15. Genomics of divergence along a continuum of parapatric population differentiation.

    Directory of Open Access Journals (Sweden)

    Philine G D Feulner

    2015-02-01

    Full Text Available The patterns of genomic divergence during ecological speciation are shaped by a combination of evolutionary forces. Processes such as genetic drift, local reduction of gene flow around genes causing reproductive isolation, hitchhiking around selected variants, variation in recombination and mutation rates are all factors that can contribute to the heterogeneity of genomic divergence. On the basis of 60 fully sequenced three-spined stickleback genomes, we explore these different mechanisms explaining the heterogeneity of genomic divergence across five parapatric lake and river population pairs varying in their degree of genetic differentiation. We find that divergent regions of the genome are mostly specific for each population pair, while their size and abundance are not correlated with the extent of genome-wide population differentiation. In each pair-wise comparison, an analysis of allele frequency spectra reveals that 25-55% of the divergent regions are consistent with a local restriction of gene flow. Another large proportion of divergent regions (38-75% appears to be mainly shaped by hitchhiking effects around positively selected variants. We provide empirical evidence that alternative mechanisms determining the evolution of genomic patterns of divergence are not mutually exclusive, but rather act in concert to shape the genome during population differentiation, a first necessary step towards ecological speciation.

  16. Evolutionary divergence of chloroplast FAD synthetase proteins

    Directory of Open Access Journals (Sweden)

    Arilla-Luna Sonia

    2010-10-01

    Full Text Available Abstract Background Flavin adenine dinucleotide synthetases (FADSs - a group of bifunctional enzymes that carry out the dual functions of riboflavin phosphorylation to produce flavin mononucleotide (FMN and its subsequent adenylation to generate FAD in most prokaryotes - were studied in plants in terms of sequence, structure and evolutionary history. Results Using a variety of bioinformatics methods we have found that FADS enzymes localized to the chloroplasts, which we term as plant-like FADS proteins, are distributed across a variety of green plant lineages and constitute a divergent protein family clearly of cyanobacterial origin. The C-terminal module of these enzymes does not contain the typical riboflavin kinase active site sequence, while the N-terminal module is broadly conserved. These results agree with a previous work reported by Sandoval et al. in 2008. Furthermore, our observations and preliminary experimental results indicate that the C-terminus of plant-like FADS proteins may contain a catalytic activity, but different to that of their prokaryotic counterparts. In fact, homology models predict that plant-specific conserved residues constitute a distinct active site in the C-terminus. Conclusions A structure-based sequence alignment and an in-depth evolutionary survey of FADS proteins, thought to be crucial in plant metabolism, are reported, which will be essential for the correct annotation of plant genomes and further structural and functional studies. This work is a contribution to our understanding of the evolutionary history of plant-like FADS enzymes, which constitute a new family of FADS proteins whose C-terminal module might be involved in a distinct catalytic activity.

  17. DNA probes

    International Nuclear Information System (INIS)

    Castelino, J.

    1992-01-01

    The creation of DNA probes for detection of specific nucleotide segments differs from ligand detection in that it is a chemical rather than an immunological reaction. Complementary DNA or RNA is used in place of the antibody and is labelled with 32 P. So far, DNA probes have been successfully employed in the diagnosis of inherited disorders, infectious diseases, and for identification of human oncogenes. The latest approach to the diagnosis of communicable and parasitic infections is based on the use of deoxyribonucleic acid (DNA) probes. The genetic information of all cells is encoded by DNA and DNA probe approach to identification of pathogens is unique because the focus of the method is the nucleic acid content of the organism rather than the products that the nucleic acid encodes. Since every properly classified species has some unique nucleotide sequences that distinguish it from every other species, each organism's genetic composition is in essence a finger print that can be used for its identification. In addition to this specificity, DNA probes offer other advantages in that pathogens may be identified directly in clinical specimens

  18. Divergence analysis of atomic ionization processes and isoelectronic series

    International Nuclear Information System (INIS)

    Lopez-Rosa, S.; Angulo, J. C.; Antolin, J.; Esquivel, R. O.

    2009-01-01

    Fisher divergences (FDs) and Jensen-Shannon divergences (JSDs) are used in this work to quantify the informational discrepancies between the one-particle electron densities of neutral atoms, singly charged ions, and isoelectronic series. These dissimilarity magnitudes, computed for a set of 319 atomic systems in both position and momentum spaces, provide relevant information concerning pattern, structure, and periodicity properties of the ionization processes. In particular an apparent correlation between extremal values of the atomic ionization potential and the divergences is found. Results are compared with those obtained by quantum similarity techniques.

  19. Short-range quantitative precipitation forecasts using a divergent initialization

    Science.gov (United States)

    Salmon, E. M.; Warner, T. T.

    1983-01-01

    Data simulations and real data tests indicate that the treatment of the initial divergence field in a mesoscale weather prediction model strongly influences the quality of the first 6 hours of a rainfall forecast. Of the procedures tested for determining the initial divergence field for the predictions, the best technique is found to be the Tarbell et al. (1981) diagnostic procedure, where a diabatic form of the omega equation is used to obtain a three-dimensional vertical motion field that in turn can be used in conjunction with a continuity equation to obtain the horizontal divergence fields.

  20. Neogene-dominated diversification in neotropical montane lichens: dating divergence events in the lichen-forming fungal genus Oropogon (Parmeliaceae).

    Science.gov (United States)

    Leavitt, Steven D; Esslinger, Theodore L; Lumbsch, H Thorsten

    2012-11-01

    Diversification in neotropical regions has been attributed to both Tertiary geological events and Pleistocene climatic fluctuations. However, the timing and processes driving speciation in these regions remain unexplored in many important groups. Here, we address the timing of diversification in the neotropical lichenized fungal genus Oropogon (Ascomycota) and assess traditional species boundaries. We analyzed sequence data from three loci to assess phenotypically circumscribed Oropogon species from the Oaxacan Highlands, Mexico. We provide a comparison of dated divergence estimates between concatenated gene trees and a calibrated multilocus species-tree using substitution rates for two DNA regions. We also compare estimates from a data set excluding ambiguously aligned regions and a data set including the hyper-variable regions in two ribosomal markers. Phylogenetic reconstructions were characterized by well-supported monophyletic clades corresponding to traditionally circumscribed species, with the exception of a single taxon. Divergence estimates indicate that most diversification of the sampled Oropogon species occurred throughout the Oligocene and Miocene, although diversification of a single closely related clade appears to have occurred during the late Pliocene and into the Pleistocene. Divergence estimates calculated from a data set with ambiguously aligned regions removed were much more recent than those from the full data set. Overall, our analyses place the majority of divergence events of Oropogon species from the Oaxacan Highlands within the Neogene and provide strong evidence that climatic changes during the Pleistocene were not a major factor driving speciation in the lichenized genus Oropogon in neotropical highlands.

  1. Molecular phylogeny, historical biogeography, and divergence time estimates for swallowtail butterflies of the genus Papilio (Lepidoptera: Papilionidae).

    Science.gov (United States)

    Zakharov, Evgueni V; Caterino, Michael S; Sperling, Felix A H

    2004-04-01

    Swallowtail butterflies are recognized as model organisms in ecology, evolutionary biology, genetics, and conservation biology but present numerous unresolved phylogenetic problems. We inferred phylogenetic relationships for 51 of about 205 species of the genus Papilio (sensu lato) from 3.3-Kilobase (kb) sequences of mitochondrial and nuclear DNA (2.3 kb of cytochrome oxidases I and II and 1.0 kb of elongation factor 1 alpha). Congruent phylogenetic trees were recovered within Papilio from analyses of combined data using maximum likelihood, Bayesian analysis, and maximum parsimony bootstrap consensus. Several disagreements with the traditional classification of Papilio were found. Five major previously hypothesized subdivisions within Papilio were well supported: Heraclides, Pterourus, Chilasa, Papilio (sensu stricto), and Eleppone. Further studies are required to clarify relationships within traditional "Princeps," which was paraphyletic. Several biologically interesting characteristics of Papilio appear to have polyphyletic origins, including mimetic adults, larval host associations, and larval morphology. Early diversification within Papilio is estimated at 55-65 million years ago based on a combination of biogeographic time constraints rather than fossils. This divergence time suggests that Papilio has slower apparent substitution rates than do Drosophila and fig-pollinating wasps and/or divergences corrected using best-fit substitution models are still being consistently underestimated. The amount of sequence divergence between Papilio subdivisions is equivalent to divergences between genera in other tribes of the Papilionidae, and between genera of moths of the noctuid subfamily Heliothinae.

  2. Sexual selection and population divergence II. Divergence in different sexual traits and signal modalities in field crickets (Teleogryllus oceanicus).

    Science.gov (United States)

    Pascoal, Sonia; Mendrok, Magdalena; Wilson, Alastair J; Hunt, John; Bailey, Nathan W

    2017-06-01

    Sexual selection can target many different types of traits. However, the relative influence of different sexually selected traits during evolutionary divergence is poorly understood. We used the field cricket Teleogryllus oceanicus to quantify and compare how five traits from each of three sexual signal modalities and components diverge among allopatric populations: male advertisement song, cuticular hydrocarbon (CHC) profiles and forewing morphology. Population divergence was unexpectedly consistent: we estimated the among-population (genetic) variance-covariance matrix, D, for all 15 traits, and D max explained nearly two-thirds of its variation. CHC and wing traits were most tightly integrated, whereas song varied more independently. We modeled the dependence of among-population trait divergence on genetic distance estimated from neutral markers to test for signatures of selection versus neutral divergence. For all three sexual trait types, phenotypic variation among populations was largely explained by a neutral model of divergence. Our findings illustrate how phenotypic integration across different types of sexual traits might impose constraints on the evolution of mating isolation and divergence via sexual selection. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

  3. Mining environmental high-throughput sequence data sets to identify divergent amplicon clusters for phylogenetic reconstruction and morphotype visualization.

    Science.gov (United States)

    Gimmler, Anna; Stoeck, Thorsten

    2015-08-01

    Environmental high-throughput sequencing (envHTS) is a very powerful tool, which in protistan ecology is predominantly used for the exploration of diversity and its geographic and local patterns. We here used a pyrosequenced V4-SSU rDNA data set from a solar saltern pond as test case to exploit such massive protistan amplicon data sets beyond this descriptive purpose. Therefore, we combined a Swarm-based blastn network including 11 579 ciliate V4 amplicons to identify divergent amplicon clusters with targeted polymerase chain reaction (PCR) primer design for full-length small subunit of the ribosomal DNA retrieval and probe design for fluorescence in situ hybridization (FISH). This powerful strategy allows to benefit from envHTS data sets to (i) reveal the phylogenetic position of the taxon behind divergent amplicons; (ii) improve phylogenetic resolution and evolutionary history of specific taxon groups; (iii) solidly assess an amplicons (species') degree of similarity to its closest described relative; (iv) visualize the morphotype behind a divergent amplicons cluster; (v) rapidly FISH screen many environmental samples for geographic/habitat distribution and abundances of the respective organism and (vi) to monitor the success of enrichment strategies in live samples for cultivation and isolation of the respective organisms. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

  4. DNA data

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Raw DNA chromatogram data produced by the ABI 373, 377, 3130 and 3730 automated sequencing machines in ABI format. These are from fish (primarily Sebastes spp.,...

  5. DNA methylation

    DEFF Research Database (Denmark)

    Williams, Kristine; Christensen, Jesper; Helin, Kristian

    2012-01-01

    DNA methylation is involved in key cellular processes, including X-chromosome inactivation, imprinting and transcriptional silencing of specific genes and repetitive elements. DNA methylation patterns are frequently perturbed in human diseases such as imprinting disorders and cancer. The recent...... discovery that the three members of the TET protein family can convert 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC) has provided a potential mechanism leading to DNA demethylation. Moreover, the demonstration that TET2 is frequently mutated in haematopoietic tumours suggests that the TET...... proteins are important regulators of cellular identity. Here, we review the current knowledge regarding the function of the TET proteins, and discuss various mechanisms by which they contribute to transcriptional control. We propose that the TET proteins have an important role in regulating DNA methylation...

  6. DNA nanotechnology

    Science.gov (United States)

    Seeman, Nadrian C.; Sleiman, Hanadi F.

    2018-01-01

    DNA is the molecule that stores and transmits genetic information in biological systems. The field of DNA nanotechnology takes this molecule out of its biological context and uses its information to assemble structural motifs and then to connect them together. This field has had a remarkable impact on nanoscience and nanotechnology, and has been revolutionary in our ability to control molecular self-assembly. In this Review, we summarize the approaches used to assemble DNA nanostructures and examine their emerging applications in areas such as biophysics, diagnostics, nanoparticle and protein assembly, biomolecule structure determination, drug delivery and synthetic biology. The introduction of orthogonal interactions into DNA nanostructures is discussed, and finally, a perspective on the future directions of this field is presented.

  7. Mitochondrial and nuclear DNA reveals a complete lineage sorti ng ...

    African Journals Online (AJOL)

    The present study utilised phylogenetic and population structure analyses of molecular sequence data from mitochondrial (cytochrome b) and nuclear (S7 intron 1) DNA markers to evaluate the genetic structure of the species. Two reproductively isolated lineages, 8.7% and 1.1% divergent, respectively, were identified.

  8. Highly Divergent Hepaciviruses from African Cattle

    Science.gov (United States)

    Corman, Victor Max; Grundhoff, Adam; Baechlein, Christine; Fischer, Nicole; Gmyl, Anatoly; Wollny, Robert; Dei, Dickson; Ritz, Daniel; Binger, Tabea; Adankwah, Ernest; Marfo, Kwadwo Sarfo; Annison, Lawrence; Annan, Augustina; Adu-Sarkodie, Yaw; Oppong, Samuel; Becher, Paul; Drosten, Christian

    2015-01-01

    ABSTRACT The hepatitis C virus (HCV; genus Hepacivirus) is a highly relevant human pathogen. Unique hepaciviruses (HV) were discovered recently in animal hosts. The direct ancestor of HCV has not been found, but the genetically most closely related animal HVs exist in horses. To investigate whether other peridomestic animals also carry HVs, we analyzed sera from Ghanaian cattle for HVs by reverse transcription-PCR (RT-PCR). Nine of 106 specimens from different sampling sites contained HV RNA (8.5%) at median viral loads of 1.6 × 105 copies/ml. Infection seemed unrelated to cattle age and gender. Near-full-genome sequencing of five representative viruses confirmed taxonomic classifications. Cattle HVs formed two distinct phylogenetic lineages that differed by up to 17.7% on the nucleotide level in the polyprotein-encoding region, suggesting cocirculation of different virus subtypes. A conserved microRNA122-binding site in the 5′ internal ribosomal entry site suggested liver tropism of cattle HVs. Phylogenetic analyses suggested the circulation of HVs in cattle for several centuries. Cattle HVs were genetically highly divergent from all other HVs, including HCV. HVs from genetically related equine and bovine hosts were not monophyletic, corroborating host shifts during the evolution of the genus Hepacivirus. Similar to equine HVs, the genetic diversity of cattle HVs was low compared to that of HCV genotypes. This suggests an influence of the human-modified ecology of peridomestic animals on virus diversity. Further studies should investigate the occurrence of cattle HVs in other geographic areas and breeds, virus pathogenicity in cattle, and the potential exposure of human risk groups, such as farmers, butchers, and abattoir workers. IMPORTANCE HCV (genus Hepacivirus) is a major human pathogen, causing liver failure and cancer. Unique hepaciviruses (HVs) were discovered over the last few years in animals, but the direct ancestor of HCV has not been found. The

  9. Accuracy of therapist perceptions of patients' alliance: Exploring the divergence.

    Science.gov (United States)

    Hartmann, Armin; Joos, Andreas; Orlinsky, David Elliot; Zeeck, Almut

    2015-01-01

    The therapeutic alliance is a well-established predictor of psychotherapy outcome, yet much research has shown that therapists' and patients' views of the alliance can diverge substantially. Therapists systematically underestimate their patients' perceived level of alliance, and the correlation between therapist and patient estimates of patient alliance is only moderate. The present study explored the divergence between therapists' and patients' perspectives on patients' alliance experience, and its relations to therapists' concurrent work involvement and session process experiences. Data from 98 patients treated by 26 therapists with psychodynamic psychotherapy were analyzed. Therapist-patient divergence was significantly related to therapists' case-wise work involvement, but not to therapist's views of session process. The best predictor of therapist-patient divergence was therapists experiencing a "distressed practice" work involvement pattern. Although therapists' work involvement experiences are not commonly investigated, they can be a relevant predictor of therapy processes.

  10. UDOT diverging diamond interchange (DDI) observations and experience.

    Science.gov (United States)

    2012-04-01

    This report presents the results of a functionality evaluation, by the I-15 Utah County Corridor Expansion (CORE) traffic team, of the first Diverging Diamond Interchange (DDI) in Utah, located at the intersection of American Fork Main Street (Pionee...

  11. Stora's fine notion of divergent amplitudes

    International Nuclear Information System (INIS)

    Várilly, Joseph C.; Gracia-Bondía, José M.

    2016-01-01

    Stora and coworkers refined the notion of divergent quantum amplitude, somewhat upsetting the standard power-counting recipe. This unexpectedly clears the way to new prototypes for free and interacting field theories of bosons of any mass and spin.

  12. Interspecific genetic divergence in grey mullets from the Goa region

    Digital Repository Service at National Institute of Oceanography (India)

    Menezes, M.R.; Martins, M.; Naik, S.

    Genetic divergence and phylogenetic relationships among Mugil cephalus, Liza subviridis and Valamugil cunnesius were investigated by examining the electrophoretic patterns of ten enzymes and sarcoplasmic proteins. Among the 19 loci detected, eight...

  13. Stora's fine notion of divergent amplitudes

    Energy Technology Data Exchange (ETDEWEB)

    Várilly, Joseph C., E-mail: joseph.varilly@ucr.ac.cr [Escuela de Matemática, Universidad de Costa Rica, San José 11501 (Costa Rica); Gracia-Bondía, José M. [Departamento de Física Teórica, Universidad de Zaragoza, Zaragoza 50009 (Spain); Departamento de Física, Universidad de Costa Rica, San Pedro 11501 (Costa Rica)

    2016-11-15

    Stora and coworkers refined the notion of divergent quantum amplitude, somewhat upsetting the standard power-counting recipe. This unexpectedly clears the way to new prototypes for free and interacting field theories of bosons of any mass and spin.

  14. Higher level phylogeny and the first divergence time estimation of Heteroptera (Insecta: Hemiptera based on multiple genes.

    Directory of Open Access Journals (Sweden)

    Min Li

    Full Text Available Heteroptera, or true bugs, are the largest, morphologically diverse and economically important group of insects with incomplete metamorphosis. However, the phylogenetic relationships within Heteroptera are still in dispute and most of the previous studies were based on morphological characters or with single gene (partial or whole 18S rDNA. Besides, so far, divergence time estimates for Heteroptera totally rely on the fossil record, while no studies have been performed on molecular divergence rates. Here, for the first time, we used maximum parsimony (MP, maximum likelihood (ML and Bayesian inference (BI with multiple genes (18S rDNA, 28S rDNA, 16S rDNA and COI to estimate phylogenetic relationships among the infraorders, and meanwhile, the Penalized Likelihood (r8s and Bayesian (BEAST molecular dating methods were employed to estimate divergence time of higher taxa of this suborder. Major results of the present study included: Nepomorpha was placed as the most basal clade in all six trees (MP trees, ML trees and Bayesian trees of nuclear gene data and four-gene combined data, respectively with full support values. The sister-group relationship of Cimicomorpha and Pentatomomorpha was also strongly supported. Nepomorpha originated in early Triassic and the other six infraorders originated in a very short period of time in middle Triassic. Cimicomorpha and Pentatomomorpha underwent a radiation at family level in Cretaceous, paralleling the proliferation of the flowering plants. Our results indicated that the higher-group radiations within hemimetabolous Heteroptera were simultaneously with those of holometabolous Coleoptera and Diptera which took place in the Triassic. While the aquatic habitat was colonized by Nepomorpha already in the Triassic, the Gerromorpha independently adapted to the semi-aquatic habitat in the Early Jurassic.

  15. Higher level phylogeny and the first divergence time estimation of Heteroptera (Insecta: Hemiptera) based on multiple genes.

    Science.gov (United States)

    Li, Min; Tian, Ying; Zhao, Ying; Bu, Wenjun

    2012-01-01

    Heteroptera, or true bugs, are the largest, morphologically diverse and economically important group of insects with incomplete metamorphosis. However, the phylogenetic relationships within Heteroptera are still in dispute and most of the previous studies were based on morphological characters or with single gene (partial or whole 18S rDNA). Besides, so far, divergence time estimates for Heteroptera totally rely on the fossil record, while no studies have been performed on molecular divergence rates. Here, for the first time, we used maximum parsimony (MP), maximum likelihood (ML) and Bayesian inference (BI) with multiple genes (18S rDNA, 28S rDNA, 16S rDNA and COI) to estimate phylogenetic relationships among the infraorders, and meanwhile, the Penalized Likelihood (r8s) and Bayesian (BEAST) molecular dating methods were employed to estimate divergence time of higher taxa of this suborder. Major results of the present study included: Nepomorpha was placed as the most basal clade in all six trees (MP trees, ML trees and Bayesian trees of nuclear gene data and four-gene combined data, respectively) with full support values. The sister-group relationship of Cimicomorpha and Pentatomomorpha was also strongly supported. Nepomorpha originated in early Triassic and the other six infraorders originated in a very short period of time in middle Triassic. Cimicomorpha and Pentatomomorpha underwent a radiation at family level in Cretaceous, paralleling the proliferation of the flowering plants. Our results indicated that the higher-group radiations within hemimetabolous Heteroptera were simultaneously with those of holometabolous Coleoptera and Diptera which took place in the Triassic. While the aquatic habitat was colonized by Nepomorpha already in the Triassic, the Gerromorpha independently adapted to the semi-aquatic habitat in the Early Jurassic.

  16. Barcoding the butterflies of southern South America: Species delimitation efficacy, cryptic diversity and geographic patterns of divergence.

    Science.gov (United States)

    Lavinia, Pablo D; Núñez Bustos, Ezequiel O; Kopuchian, Cecilia; Lijtmaer, Darío A; García, Natalia C; Hebert, Paul D N; Tubaro, Pablo L

    2017-01-01

    Because the tropical regions of America harbor the highest concentration of butterfly species, its fauna has attracted considerable attention. Much less is known about the butterflies of southern South America, particularly Argentina, where over 1,200 species occur. To advance understanding of this fauna, we assembled a DNA barcode reference library for 417 butterfly species of Argentina, focusing on the Atlantic Forest, a biodiversity hotspot. We tested the efficacy of this library for specimen identification, used it to assess the frequency of cryptic species, and examined geographic patterns of genetic variation, making this study the first large-scale genetic assessment of the butterflies of southern South America. The average sequence divergence to the nearest neighbor (i.e. minimum interspecific distance) was 6.91%, ten times larger than the mean distance to the furthest conspecific (0.69%), with a clear barcode gap present in all but four of the species represented by two or more specimens. As a consequence, the DNA barcode library was extremely effective in the discrimination of these species, allowing a correct identification in more than 95% of the cases. Singletons (i.e. species represented by a single sequence) were also distinguishable in the gene trees since they all had unique DNA barcodes, divergent from those of the closest non-conspecific. The clustering algorithms implemented recognized from 416 to 444 barcode clusters, suggesting that the actual diversity of butterflies in Argentina is 3%-9% higher than currently recognized. Furthermore, our survey added three new records of butterflies for the country (Eurema agave, Mithras hannelore, Melanis hillapana). In summary, this study not only supported the utility of DNA barcoding for the identification of the butterfly species of Argentina, but also highlighted several cases of both deep intraspecific and shallow interspecific divergence that should be studied in more detail.

  17. Estimation of population divergence times from non-overlapping genomic sequences: examples from dogs and wolves.

    Science.gov (United States)

    Skoglund, Pontus; Götherström, Anders; Jakobsson, Mattias

    2011-04-01

    Despite recent technological advances in DNA sequencing, incomplete coverage remains to be an issue in population genomics, in particular for studies that include ancient samples. Here, we describe an approach to estimate population divergence times for non-overlapping sequence data that is based on probabilities of different genealogical topologies under a structured coalescent model. We show that the approach can be adapted to accommodate common problems such as sequencing errors and postmortem nucleotide misincorporations, and we use simulations to investigate biases involved with estimating genealogical topologies from empirical data. The approach relies on three reference genomes and should be particularly useful for future analysis of genomic data that comprise of nonoverlapping sets of sequences, potentially from different points in time. We applied the method to shotgun sequence data from an ancient wolf together with extant dogs and wolves and found striking resemblance to previously described fine-scale population structure among dog breeds. When comparing modern dogs to four geographically distinct wolves, we find that the divergence time between dogs and an Indian wolf is smallest, followed by the divergence times to a Chinese wolf and a Spanish wolf, and a relatively long divergence time to an Alaskan wolf, suggesting that the origin of modern dogs is somewhere in Eurasia, potentially southern Asia. We find that less than two-thirds of all loci in the boxer and poodle genomes are more similar to each other than to a modern gray wolf and that--assuming complete isolation without gene flow--the divergence time between gray wolves and modern European dogs extends to 3,500 generations before the present, corresponding to approximately 10,000 years ago (95% confidence interval [CI]: 9,000-13,000). We explicitly study the effect of gene flow between dogs and wolves on our estimates and show that a low rate of gene flow is compatible with an even earlier

  18. DNA expressions - A formal notation for DNA

    NARCIS (Netherlands)

    Vliet, Rudy van

    2015-01-01

    We describe a formal notation for DNA molecules that may contain nicks and gaps. The resulting DNA expressions denote formal DNA molecules. Different DNA expressions may denote the same molecule. Such DNA expressions are called equivalent. We examine which DNA expressions are minimal, which

  19. Dimensional regularization and infrared divergences in quantum electrodynamics

    International Nuclear Information System (INIS)

    Marculescu, S.

    1979-01-01

    Dimensional continuation was devised as a powerful regularization method for ultraviolet divergences in quantum field theories. Recently it was clear, at least for quantum electrodynamics, that such a method could be employed for factorizing out infrared divergences from the on-shell S-matrix elements. This provides a renormalization scheme on the electron mass-shell without using a gauge violating ''photon mass''. (author)

  20. On the ambiguity of functions represented by divergent power series

    Czech Academy of Sciences Publication Activity Database

    Caprini, I.; Fischer, Jan; Vrkoč, Ivo

    2010-01-01

    Roč. 60, č. 12 (2010), s. 1264-1272 ISSN 0168-9274. [Conference on Approximation and Extrapolation of Convergent and Divergent Sequences and Series. Luminy, 28.09.2009-02.10.2009] Institutional research plan: CEZ:AV0Z10100502; CEZ:AV0Z10190503 Keywords : divergent perturbation series * curvilinear integrals Subject RIV: BF - Elementary Particles and High Energy Physics Impact factor: 0.919, year: 2010

  1. What Is Mitochondrial DNA?

    Science.gov (United States)

    ... DNA What is mitochondrial DNA? What is mitochondrial DNA? Although most DNA is packaged in chromosomes within ... proteins. For more information about mitochondria and mitochondrial DNA: Molecular Expressions, a web site from the Florida ...

  2. Speciation on oceanic islands: rapid adaptive divergence vs. cryptic speciation in a Guadalupe Island songbird (Aves: Junco.

    Directory of Open Access Journals (Sweden)

    Pau Aleixandre

    Full Text Available The evolutionary divergence of island populations, and in particular the tempo and relative importance of neutral and selective factors, is of central interest to the study of speciation. The rate of phenotypic evolution upon island colonization can vary greatly among taxa, and cases of convergent evolution can further confound the inference of correct evolutionary histories. Given the potential lability of phenotypic characters, molecular dating of insular lineages analyzed in a phylogenetic framework provides a critical tool to test hypotheses of phenotypic divergence since colonization. The Guadalupe junco is the only insular form of the polymorphic dark-eyed junco (Junco hyemalis, and shares eye and plumage color with continental morphs, yet presents an enlarged bill and reduced body size. Here we use variation in mtDNA sequence, morphological traits and song variables to test whether the Guadalupe junco evolved rapidly following a recent colonization by a mainland form of the dark-eyed junco, or instead represents a well-differentiated "cryptic" lineage adapted to the insular environment through long-term isolation, with plumage coloration a result of evolutionary convergence. We found high mtDNA divergence of the island lineage with respect to both continental J. hyemalis and J. phaeonotus, representing a history of isolation of about 600,000 years. The island lineage was also significantly differentiated in morphological and male song variables. Moreover, and contrary to predictions regarding diversity loss on small oceanic islands, we document relatively high levels of both haplotypic and song-unit diversity on Guadalupe Island despite long-term isolation in a very small geographic area. In contrast to prevailing taxonomy, the Guadalupe junco is an old, well-differentiated evolutionary lineage, whose similarity to mainland juncos in plumage and eye color is due to evolutionary convergence. Our findings confirm the role of remote islands

  3. Utility of divergent domains of 28S ribosomal RNA in species discrimination of paramphistomes (Trematoda: Digenea: Paramphistomoidea).

    Science.gov (United States)

    Shylla, Jollin A; Ghatani, Sudeep; Tandon, Veena

    2013-12-01

    Among the digenetic trematodes, paramphistomes are known to be the causative agent of "amphistomiasis" or the stomach fluke disease of domestic and wild animals, mainly ruminants. The use of 28S (divergent domains) and 18S rRNA for phylogenetic inference is significantly warranted for these flukes since it is as yet limited to merely the exploration of the second internal transcribed spacer (ITS2) region. The present study intended to explore the divergent domains (D1-D3) of 28S rRNA and simultaneously equate the phylogenetic information with 18S rRNA in paramphistomes. Divergence of the 28S rRNA domains was evident amongst the divergent (D) domains, where D1 domain emerged as the most variable and D2, the most robust domain, since the latter could provide a higher resolution of the species. D2 was the only domain that comprised compensatory mutations in the helices of its structural constraints; this domain is thus well suited for species distinction and may be considered a potential DNA barcode complementary to mitochondrial DNA. 28S (D1 + D2 + D3) rRNA provided a significant resolution of the taxa corroborating with the taxonomy of these flukes and thus proved to be more robust as a phylogenetic marker for lower levels than 18S rRNA. Phylogenetic inferences of paramphitomes are still scarcely explored; additional data from other taxa belonging to this family may estimate better the biodiversity of these flukes.

  4. Genetic divergence and phylogeography in the genus Nyctalus (Mammalia, Chiroptera): implications for population history of the insular bat Nyctalus azoreum.

    Science.gov (United States)

    Salgueiro, P; Ruedi, M; Coelho, M M; Palmeirim, J M

    2007-06-01

    We used three mitochondrial DNA fragments with different substitution rates (ND1, Cyt b and the CR) to infer phylogenetic relationships among six species of the genus Nyctalus, and compare levels of genetic divergence between the insular, vulnerable Nyctalus azoreum and its continental counterpart to assess the origins of the Azorean bat. The larger species found throughout the Palaearctic region (N. lasiopterus, N. aviator and N. noctula) share a unique chromosome formula (2n=42) and form a monophyletic clade in our reconstructions. Nyctalus plancyi (=velutinus), a Chinese taxon with 2n=36 chromosomes, is sometimes included in N. noctula, but is genetically very divergent from the latter and deserves full species status. All Cyt b and CR haplotypes of N. azoreum are closely related and only found in the Azores archipelago, but when compared to continental sequences of N. leisleri, levels of mtDNA divergence are unusually low for mammalian species. This contrasts with the high level of differentiation that N. azoreum has attained in its morphology, ecology, and echolocation calls, suggesting a recent split followed by fast evolutionary change. The molecular data suggest that N. azoreum originated from a European population of N. leisleri, and that the colonisation of the Azores occurred at the end of the Pleistocene. The Madeiran populations of N. leisleri also appear to have a European origin, whereas those of the Canary Islands probably came from North Africa. In spite of its recent origin and low genetic divergence, the Azorean bat is well differentiated and consequently represents a unique evolutionary unit with great conservation value.

  5. DNA barcoding and the differentiation between North American and West European Phormia regina (Diptera, Calliphoridae, Chrysomyinae)

    Science.gov (United States)

    Jordaens, Kurt; Sonet, Gontran; Braet, Yves; De Meyer, Marc; Backeljau, Thierry; Goovaerts, Frankie; Bourguignon, Luc; Desmyter, Stijn

    2013-01-01

    Abstract Phormia regina (the black fly) is a common Holarctic blow fly species which serves as a primary indicator taxon to estimate minimal post mortem intervals. It is also a major research model in physiological and neurological studies on insect feeding. Previous studies have shown a sequence divergence of up to 4.3% in the mitochondrial COI gene between W European and N American P. regina populations. Here, we DNA barcoded P. regina specimens from six N American and 17 W European populations and confirmed a mean sequence divergence of ca. 4% between the populations of the two continents, while sequence divergence within each continent was a ten-fold lower. Comparable mean mtDNA sequence divergences were observed for COII (3.7%) and cyt b (5.3%), but mean divergence was lower for 16S (0.4–0.6%). Intercontinental divergence at nuclear DNA was very low (≤ 0.1% for both 28S and ITS2), and we did not detect any morphological differentiation between N American and W European specimens. Therefore, we consider the strong differentiation at COI, COII and cyt b as intraspecific mtDNA sequence divergence that should be taken into account when using P. regina in forensic casework or experimental research. PMID:24453556

  6. Saccharomyces cerevisiae: population divergence and resistance to oxidative stress in clinical, domesticated and wild isolates.

    Directory of Open Access Journals (Sweden)

    Stephanie Diezmann

    Full Text Available BACKGROUND: Saccharomyces cerevisiae has been associated with human life for millennia in the brewery and bakery. Recently it has been recognized as an emerging opportunistic pathogen. To study the evolutionary history of S. cerevisiae, the origin of clinical isolates and the importance of a virulence-associated trait, population genetics and phenotypic assays have been applied to an ecologically diverse set of 103 strains isolated from clinics, breweries, vineyards, fruits, soil, commercial supplements and insect guts. METHODOLOGY/PRINCIPAL FINDINGS: DNA sequence data from five nuclear DNA loci were analyzed for population structure and haplotype distribution. Additionally, all strains were tested for survival of oxidative stress, a trait associated with microbial pathogenicity. DNA sequence analyses identified three genetic subgroups within the recombining S. cerevisiae strains that are associated with ecology, geography and virulence. Shared alleles suggest that the clinical isolates contain genetic contribution from the fruit isolates. Clinical and fruit isolates exhibit high levels of recombination, unlike the genetically homogenous soil isolates in which no recombination was detected. However, clinical and soil isolates were more resistant to oxidative stress than any other population, suggesting a correlation between survival in oxidative stress and yeast pathogenicity. CONCLUSIONS/SIGNIFICANCE: Population genetic analyses of S. cerevisiae delineated three distinct groups, comprising primarily the (i human-associated brewery and vineyard strains, (ii clinical and fruit isolates (iii and wild soil isolates from eastern U.S. The interactions between S. cerevisiae and humans potentiate yeast evolution and the development of genetically, ecologically and geographically divergent groups.

  7. Novel core promoter elements and a cognate transcription factor in the divergent unicellular eukaryote Trichomonas vaginalis.

    Science.gov (United States)

    Smith, Alias J; Chudnovsky, Lorissa; Simoes-Barbosa, Augusto; Delgadillo-Correa, Maria G; Jonsson, Zophonias O; Wohlschlegel, James A; Johnson, Patricia J

    2011-04-01

    A highly conserved DNA initiator (Inr) element has been the only core promoter element described in the divergent unicellular eukaryote Trichomonas vaginalis, although genome analyses reveal that only ∼75% of protein-coding genes appear to contain an Inr. In search of another core promoter element(s), a nonredundant database containing 5' untranslated regions of expressed T. vaginalis genes was searched for overrepresented DNA motifs and known eukaryotic core promoter elements. In addition to identifying the Inr, two elements that lack sequence similarity to the known protein-coding gene core promoter, motif 3 (M3) and motif 5 (M5), were identified. Mutational and functional analyses demonstrate that both are novel core promoter elements. M3 [(A/G/T)(A/G)C(G/C)G(T/C)T(T/A/G)] resembles a Myb recognition element (MRE) and is bound specifically by a unique protein with a Myb-like DNA binding domain. The M5 element (CCTTT) overlaps the transcription start site and replaces the Inr as an alternative, gene-specific initiator element. Transcription specifically initiates at the second cytosine within M5, in contrast to characteristic initiation by RNA polymerase II at an adenosine. In promoters that combine M3 with either M5 or Inr, transcription initiation is regulated by the M3 motif.

  8. Novel Core Promoter Elements and a Cognate Transcription Factor in the Divergent Unicellular Eukaryote Trichomonas vaginalis▿

    Science.gov (United States)

    Smith, Alias J.; Chudnovsky, Lorissa; Simoes-Barbosa, Augusto; Delgadillo-Correa, Maria G.; Jonsson, Zophonias O.; Wohlschlegel, James A.; Johnson, Patricia J.

    2011-01-01

    A highly conserved DNA initiator (Inr) element has been the only core promoter element described in the divergent unicellular eukaryote Trichomonas vaginalis, although genome analyses reveal that only ∼75% of protein-coding genes appear to contain an Inr. In search of another core promoter element(s), a nonredundant database containing 5′ untranslated regions of expressed T. vaginalis genes was searched for overrepresented DNA motifs and known eukaryotic core promoter elements. In addition to identifying the Inr, two elements that lack sequence similarity to the known protein-coding gene core promoter, motif 3 (M3) and motif 5 (M5), were identified. Mutational and functional analyses demonstrate that both are novel core promoter elements. M3 [(A/G/T)(A/G)C(G/C)G(T/C)T(T/A/G)] resembles a Myb recognition element (MRE) and is bound specifically by a unique protein with a Myb-like DNA binding domain. The M5 element (CCTTT) overlaps the transcription start site and replaces the Inr as an alternative, gene-specific initiator element. Transcription specifically initiates at the second cytosine within M5, in contrast to characteristic initiation by RNA polymerase II at an adenosine. In promoters that combine M3 with either M5 or Inr, transcription initiation is regulated by the M3 motif. PMID:21245378

  9. Sex-biased transcriptome divergence along a latitudinal gradient.

    Science.gov (United States)

    Allen, Scott L; Bonduriansky, Russell; Sgro, Carla M; Chenoweth, Stephen F

    2017-03-01

    Sex-dependent gene expression is likely an important genomic mechanism that allows sex-specific adaptation to environmental changes. Among Drosophila species, sex-biased genes display remarkably consistent evolutionary patterns; male-biased genes evolve faster than unbiased genes in both coding sequence and expression level, suggesting sex differences in selection through time. However, comparatively little is known of the evolutionary process shaping sex-biased expression within species. Latitudinal clines offer an opportunity to examine how changes in key ecological parameters also influence sex-specific selection and the evolution of sex-biased gene expression. We assayed male and female gene expression in Drosophila serrata along a latitudinal gradient in eastern Australia spanning most of its endemic distribution. Analysis of 11 631 genes across eight populations revealed strong sex differences in the frequency, mode and strength of divergence. Divergence was far stronger in males than females and while latitudinal clines were evident in both sexes, male divergence was often population specific, suggesting responses to localized selection pressures that do not covary predictably with latitude. While divergence was enriched for male-biased genes, there was no overrepresentation of X-linked genes in males. By contrast, X-linked divergence was elevated in females, especially for female-biased genes. Many genes that diverged in D. serrata have homologs also showing latitudinal divergence in Drosophila simulans and Drosophila melanogaster on other continents, likely indicating parallel adaptation in these distantly related species. Our results suggest that sex differences in selection play an important role in shaping the evolution of gene expression over macro- and micro-ecological spatial scales. © 2017 John Wiley & Sons Ltd.

  10. Cardiac Strain Imaging With Coherent Compounding of Diverging Waves.

    Science.gov (United States)

    Grondin, Julien; Sayseng, Vincent; Konofagou, Elisa E

    2017-08-01

    Current methods of cardiac strain imaging at high frame rate suffer from motion matching artifacts or poor lateral resolution. Coherent compounding has been shown to improve echocardiographic image quality while maintaining a high frame rate, but has never been used to image cardiac strain. However, myocardial velocity can have an impact on coherent compounding due to displacements between frames. The objective of this paper was to investigate the feasibility and performance of coherent compounding for cardiac strain imaging at a low and a high myocardial velocity. Left-ventricular contraction in short-axis view was modeled as an annulus with radial thickening and circumferential rotation. Simulated radio-frequency channel data with a cardiac phased array were obtained using three different beamforming methods: single diverging wave, coherent compounding of diverging waves, and conventional focusing. Axial and lateral displacements and strains as well as radial strains were estimated and compared to their true value. In vivo feasibility of cardiac strain imaging with coherent compounding was performed and compared to single diverging wave imaging. At low myocardial velocities, the axial, lateral, and radial strain relative error for nine compounded waves (16.3%, 40.4%, and 18.9%) were significantly lower than those obtained with single diverging wave imaging (19.9%, 80.3%, and 30.6%) and closer to that obtained with conventional focusing (16.7%, 43.7%, and 16%). In vivo left-ventricular radial strains exhibited higher quality with nine compounded waves than with single diverging wave imaging. These results indicate that cardiac strain can be imaged using coherent compounding of diverging waves with a better performance than with single diverging wave imaging while maintaining a high frame rate, and therefore, has the potential to improve diagnosis of myocardial strain-based cardiac diseases.

  11. Crystal Structure of the Vaccinia Virus Uracil-DNA Glycosylase in Complex with DNA.

    Science.gov (United States)

    Burmeister, Wim P; Tarbouriech, Nicolas; Fender, Pascal; Contesto-Richefeu, Céline; Peyrefitte, Christophe N; Iseni, Frédéric

    2015-07-17

    Vaccinia virus polymerase holoenzyme is composed of the DNA polymerase catalytic subunit E9 associated with its heterodimeric co-factor A20·D4 required for processive genome synthesis. Although A20 has no known enzymatic activity, D4 is an active uracil-DNA glycosylase (UNG). The presence of a repair enzyme as a component of the viral replication machinery suggests that, for poxviruses, DNA synthesis and base excision repair is coupled. We present the 2.7 Å crystal structure of the complex formed by D4 and the first 50 amino acids of A20 (D4·A201-50) bound to a 10-mer DNA duplex containing an abasic site resulting from the cleavage of a uracil base. Comparison of the viral complex with its human counterpart revealed major divergences in the contacts between protein and DNA and in the enzyme orientation on the DNA. However, the conformation of the dsDNA within both structures is very similar, suggesting a dominant role of the DNA conformation for UNG function. In contrast to human UNG, D4 appears rigid, and we do not observe a conformational change upon DNA binding. We also studied the interaction of D4·A201-50 with different DNA oligomers by surface plasmon resonance. D4 binds weakly to nonspecific DNA and to uracil-containing substrates but binds abasic sites with a Kd of DNA complex structure of a family I UNG gives new insight into the role of D4 as a co-factor of vaccinia virus DNA polymerase and allows a better understanding of the structural determinants required for UNG action. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  12. Crystal Structure of the Vaccinia Virus Uracil-DNA Glycosylase in Complex with DNA*

    Science.gov (United States)

    Burmeister, Wim P.; Tarbouriech, Nicolas; Fender, Pascal; Contesto-Richefeu, Céline; Peyrefitte, Christophe N.; Iseni, Frédéric

    2015-01-01

    Vaccinia virus polymerase holoenzyme is composed of the DNA polymerase catalytic subunit E9 associated with its heterodimeric co-factor A20·D4 required for processive genome synthesis. Although A20 has no known enzymatic activity, D4 is an active uracil-DNA glycosylase (UNG). The presence of a repair enzyme as a component of the viral replication machinery suggests that, for poxviruses, DNA synthesis and base excision repair is coupled. We present the 2.7 Å crystal structure of the complex formed by D4 and the first 50 amino acids of A20 (D4·A201–50) bound to a 10-mer DNA duplex containing an abasic site resulting from the cleavage of a uracil base. Comparison of the viral complex with its human counterpart revealed major divergences in the contacts between protein and DNA and in the enzyme orientation on the DNA. However, the conformation of the dsDNA within both structures is very similar, suggesting a dominant role of the DNA conformation for UNG function. In contrast to human UNG, D4 appears rigid, and we do not observe a conformational change upon DNA binding. We also studied the interaction of D4·A201–50 with different DNA oligomers by surface plasmon resonance. D4 binds weakly to nonspecific DNA and to uracil-containing substrates but binds abasic sites with a Kd of DNA complex structure of a family I UNG gives new insight into the role of D4 as a co-factor of vaccinia virus DNA polymerase and allows a better understanding of the structural determinants required for UNG action. PMID:26045555

  13. Controls to validate plasma samples for cell free DNA quantification

    DEFF Research Database (Denmark)

    Pallisgaard, Niels; Spindler, Karen-Lise Garm; Andersen, Rikke Fredslund

    2015-01-01

    Recent research has focused on the utility of cell free DNA (cfDNA) in serum and plasma for clinical application, especially in oncology. The literature holds promise of cfDNA as a valuable tumour marker to be used for treatment selection, monitoring and follow-up. The results, however......, are diverging due to methodological differences with lack of standardisation and definition of sensitivity. The new biological information has not yet come into routine use. The present study presents external standardisation by spiking with non-human DNA fragments to control for loss of DNA during sample...... preparation and measurement. It also suggests a method to control for admixture of DNA from normal lymphocytes by utilizing the unique immunoglobulin gene rearrangement in the B-cells. The results show that this approach improves the quality of the analysis and lowers the risk of falsely increased values...

  14. Diverse Applications of Environmental DNA Methods in Parasitology.

    Science.gov (United States)

    Bass, David; Stentiford, Grant D; Littlewood, D T J; Hartikainen, Hanna

    2015-10-01

    Nucleic acid extraction and sequencing of genes from organisms within environmental samples encompasses a variety of techniques collectively referred to as environmental DNA or 'eDNA'. The key advantages of eDNA analysis include the detection of cryptic or otherwise elusive organisms, large-scale sampling with fewer biases than specimen-based methods, and generation of data for molecular systematics. These are particularly relevant for parasitology because parasites can be difficult to locate and are morphologically intractable and genetically divergent. However, parasites have rarely been the focus of eDNA studies. Focusing on eukaryote parasites, we review the increasing diversity of the 'eDNA toolbox'. Combining eDNA methods with complementary tools offers much potential to understand parasite communities, disease risk, and parasite roles in broader ecosystem processes such as food web structuring and community assembly. Crown Copyright © 2015. Published by Elsevier Ltd. All rights reserved.

  15. DNA nanotechnology

    OpenAIRE

    Nadrian C Seeman

    2003-01-01

    Since Watson and Crick’s determination of its structure nearly 50 years ago, DNA has come to fill our lives in many areas, from genetic counseling to forensics, from genomics to gene therapy. These, and other ways in which DNA affects human activities, are related to its function as genetic material, not just our genetic material, but the genetic material of all living organisms. Here, we will ignore DNA’s biological role; rather, we will discuss how the properties that make it so successful ...

  16. Tandem repeat variation in human and great ape populations and its impact on gene expression divergence.

    Science.gov (United States)

    Bilgin Sonay, Tugce; Carvalho, Tiago; Robinson, Mark D; Greminger, Maja P; Krützen, Michael; Comas, David; Highnam, Gareth; Mittelman, David; Sharp, Andrew; Marques-Bonet, Tomàs; Wagner, Andreas

    2015-11-01

    Tandem repeats (TRs) are stretches of DNA that are highly variable in length and mutate rapidly. They are thus an important source of genetic variation. This variation is highly informative for population and conservation genetics. It has also been associated with several pathological conditions and with gene expression regulation. However, genome-wide surveys of TR variation in humans and closely related species have been scarce due to technical difficulties derived from short-read technology. Here we explored the genome-wide diversity of TRs in a panel of 83 human and nonhuman great ape genomes, in a total of six different species, and studied their impact on gene expression evolution. We found that population diversity patterns can be efficiently captured with short TRs (repeat unit length, 1-5 bp). We examined the potential evolutionary role of TRs in gene expression differences between humans and primates by using 30,275 larger TRs (repeat unit length, 2-50 bp). Genes that contained TRs in the promoters, in their 3' untranslated region, in introns, and in exons had higher expression divergence than genes without repeats in the regions. Polymorphic small repeats (1-5 bp) had also higher expression divergence compared with genes with fixed or no TRs in the gene promoters. Our findings highlight the potential contribution of TRs to human evolution through gene regulation. © 2015 Bilgin Sonay et al.; Published by Cold Spring Harbor Laboratory Press.

  17. Evaluation of Monocot and Eudicot Divergence Using the Sugarcane Transcriptome1[w

    Science.gov (United States)

    Vincentz, Michel; Cara, Frank A.A.; Okura, Vagner K.; da Silva, Felipe R.; Pedrosa, Guilherme L.; Hemerly, Adriana S.; Capella, Adriana N.; Marins, Mozart; Ferreira, Paulo C.; França, Suzelei C.; Grivet, Laurent; Vettore, Andre L.; Kemper, Edson L.; Burnquist, Willian L.; Targon, Maria L.P.; Siqueira, Walter J.; Kuramae, Eiko E.; Marino, Celso L.; Camargo, Luis E.A.; Carrer, Helaine; Coutinho, Luis L.; Furlan, Luiz R.; Lemos, Manoel V.F.; Nunes, Luiz R.; Gomes, Suely L.; Santelli, Roberto V.; Goldman, Maria H.; Bacci, Maurício; Giglioti, Eder A.; Thiemann, Otávio H.; Silva, Flávio H.; Van Sluys, Marie-Anne; Nobrega, Francisco G.; Arruda, Paulo; Menck, Carlos F.M.

    2004-01-01

    Over 40,000 sugarcane (Saccharum officinarum) consensus sequences assembled from 237,954 expressed sequence tags were compared with the protein and DNA sequences from other angiosperms, including the genomes of Arabidopsis and rice (Oryza sativa). Approximately two-thirds of the sugarcane transcriptome have similar sequences in Arabidopsis. These sequences may represent a core set of proteins or protein domains that are conserved among monocots and eudicots and probably encode for essential angiosperm functions. The remaining sequences represent putative monocot-specific genetic material, one-half of which were found only in sugarcane. These monocot-specific cDNAs represent either novelties or, in many cases, fast-evolving sequences that diverged substantially from their eudicot homologs. The wide comparative genome analysis presented here provides information on the evolutionary changes that underlie the divergence of monocots and eudicots. Our comparative analysis also led to the identification of several not yet annotated putative genes and possible gene loss events in Arabidopsis. PMID:15020759

  18. Ancient DNA and the tropics: a rodent's tale.

    Science.gov (United States)

    Gutiérrez-García, Tania A; Vázquez-Domínguez, Ella; Arroyo-Cabrales, Joaquín; Kuch, Melanie; Enk, Jacob; King, Christine; Poinar, Hendrik N

    2014-06-01

    Most genetic studies of Holocene fauna have been performed with ancient samples from dry and cold regions, in which preservation of fossils is facilitated and molecular damage is reduced. Ancient DNA work from tropical regions has been precluded owing to factors that limit DNA preservation (e.g. temperature, hydrolytic damage). We analysed ancient DNA from rodent jawbones identified as Ototylomys phyllotis, found in Holocene and Late Pleistocene stratigraphic layers from Loltún, a humid tropical cave located in the Yucatan peninsula. We extracted DNA and amplified six short overlapping fragments of the cytochrome b gene, totalling 666 bp, which represents an unprecedented success considering tropical ancient DNA samples. We performed genetic, phylogenetic and divergence time analyses, combining sequences from ancient and modern O. phyllotis, in order to assess the ancestry of the Loltún samples. Results show that all ancient samples fall into a unique clade that diverged prior to the divergence of the modern O. phyllotis, supporting it as a distinct Pleistocene form of the Ototylomys genus. Hence, this rodent's tale suggests that the sister group to modern O. phyllotis arose during the Miocene-Pliocene, diversified during the Pleistocene and went extinct in the Holocene. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

  19. DAST in Flight Showing Diverging Wingtip Oscillations

    Science.gov (United States)

    1980-01-01

    normal stiffness. This was done because stiffness requires structural weight but ensures freedom from flutter-an uncontrolled, divergent oscillation of the structure, driven by aerodynamic forces and resulting in structural failure. The program used refined theoretical tools to predict at what speed flutter would occur. It then designed a high-response control system to counteract the motion and permit a much lighter wing structure. The wing had, in effect, 'electronic stiffness.' Flight research with this concept was extremely hazardous because an error in either the flutter prediction or control system implementation would result in wing structural failure and the loss of the vehicle. Because of this, flight demonstration of a sub-scale vehicle made sense from the standpoint of both safety and cost. The program anticipated structural failure during the course of the flight research. The Firebee II was a supersonic drone selected as the DAST testbed because its wing could be easily replaced, it used only tail-mounted control surfaces, and it was available as surplus from the U. S. Air Force. It was capable of 5-g turns (that is, turns producing acceleration equal to 5 times that of gravity). Langley outfitted a drone with an aeroelastic, supercritical research wing suitable for a Mach 0.98 cruise transport with a predicted flutter speed of Mach 0.95 at an altitude of 25,000 feet. Dryden and Langley, in conjunction with Boeing, designed and fabricated a digital flutter suppression system (FSS). Dryden developed an RPRV (remotely piloted research vehicle) flight control system; integrated the wing, FSS, and vehicle systems; and conducted the flight program. In addition to a digital flight control system and aeroelastic wings, each DAST drone had research equipment mounted in its nose and a mid-air retrieval system in its tail. The drones were originally launched from the NASA B-52 bomber and later from a DC-130. The DAST vehicle's flight was monitored from the sky by an F

  20. A chloroplast DNA phylogeny of lilacs (Syringa, Oleaceae): plastome groups show a strong correlation with crossing groups.

    Science.gov (United States)

    Kim, K J; Jansen, R K

    1998-09-01

    Phylogenetic relationships and genomic compatibility were compared for 60 accessions of Syringa using chloroplast DNA (cpDNA) and nuclear ribosomal DNA (rDNA) markers. A total of 669 cpDNA variants, 653 of which were potentially phylogenetically informative, was detected using 22 restriction enzymes. Phylogenetic analyses reveal four strongly supported plastome groups that correspond to four genetically incompatible crossing groups. Relationships of the four plastome groups (I(II(III,IV))) correlate well with the infrageneric classification except for ser. Syringa and Pinnatifoliae. Group I, which includes subg. Ligustrina, forms a basal lineage within Syringa. Group II includes ser. Syringa and Pinnatifoliae and the two series have high compatibility and low sequence divergence. Group III consists of three well-defined species groups of ser. Pubescentes. Group IV comprises all members of ser. Villosae and has the lowest interspecific cpDNA sequence divergences. Comparison of cpDNA sequence divergence with crossability data indicates that hybrids have not been successfully generated between species with divergence greater than 0.7%. Hybrid barriers are strong among the four major plastome groups, which have sequence divergence estimates ranging from 1.096 to 1.962%. In contrast, fully fertile hybrids occur between species pairs with sequence divergence below 0.4%. Three regions of the plastome have length variants of greater than 100 bp, and these indels identify 12 different plastome types that correlate with phylogenetic trees produced from cpDNA restriction site data. Biparentally inherited nuclear rDNA and maternally inherited cpDNA length variants enable the identification of the specific parentage of several lilac hybrids.

  1. Comparative Study of Genome Divergence in Salmonids with Various Rates of Genetic Isolation

    Directory of Open Access Journals (Sweden)

    Elena A. Shubina

    2013-01-01

    Full Text Available The aim of the study is a comparative investigation of changes that certain genome parts undergo during speciation. The research was focused on divergence of coding and noncoding sequences in different groups of salmonid fishes of the Salmonidae (Salmo, Parasalmo, Oncorhynchus, and Salvelinus genera and the Coregonidae families under different levels of reproductive isolation. Two basic approaches were used: (1 PCR-RAPD with a 20–22 nt primer design with subsequent cloning and sequencing of the products and (2 a modified endonuclease restriction analysis. The restriction fragments were shown with sequencing to represent satellite DNA. Effects of speciation are found in repetitive sequences. The revelation of expressed sequences in the majority of the employed anonymous loci allows for assuming the adaptive selection during allopatric speciation in isolated char forms.

  2. Concrete ensemble Kalman filters with rigorous catastrophic filter divergence.

    Science.gov (United States)

    Kelly, David; Majda, Andrew J; Tong, Xin T

    2015-08-25

    The ensemble Kalman filter and ensemble square root filters are data assimilation methods used to combine high-dimensional, nonlinear dynamical models with observed data. Ensemble methods are indispensable tools in science and engineering and have enjoyed great success in geophysical sciences, because they allow for computationally cheap low-ensemble-state approximation for extremely high-dimensional turbulent forecast models. From a theoretical perspective, the dynamical properties of these methods are poorly understood. One of the central mysteries is the numerical phenomenon known as catastrophic filter divergence, whereby ensemble-state estimates explode to machine infinity, despite the true state remaining in a bounded region. In this article we provide a breakthrough insight into the phenomenon, by introducing a simple and natural forecast model that transparently exhibits catastrophic filter divergence under all ensemble methods and a large set of initializations. For this model, catastrophic filter divergence is not an artifact of numerical instability, but rather a true dynamical property of the filter. The divergence is not only validated numerically but also proven rigorously. The model cleanly illustrates mechanisms that give rise to catastrophic divergence and confirms intuitive accounts of the phenomena given in past literature.

  3. Ayahuasca enhances creative divergent thinking while decreasing conventional convergent thinking.

    Science.gov (United States)

    Kuypers, K P C; Riba, J; de la Fuente Revenga, M; Barker, S; Theunissen, E L; Ramaekers, J G

    2016-09-01

    Ayahuasca is a South American psychotropic plant tea traditionally used in Amazonian shamanism. The tea contains the psychedelic 5-HT2A receptor agonist N,N-dimethyltryptamine (DMT), plus β-carboline alkaloids with monoamine oxidase-inhibiting properties. Increasing evidence from anecdotal reports and open-label studies indicates that ayahuasca may have therapeutic effects in treatment of substance use disorders and depression. A recent study on the psychological effects of ayahuasca found that the tea reduces judgmental processing and inner reactivity, classic goals of mindfulness psychotherapy. Another psychological facet that could potentially be targeted by ayahuasca is creative divergent thinking. This mode of thinking can enhance and strengthen psychological flexibility by allowing individuals to generate new and effective cognitive, emotional, and behavioral strategies. The present study aimed to assess the potential effects of ayahuasca on creative thinking. We visited two spiritual ayahuasca workshops and invited participants to conduct creativity tests before and during the acute effects of ayahuasca. In total, 26 participants consented. Creativity tests included the "pattern/line meanings test" (PLMT) and the "picture concept test" (PCT), both assessing divergent thinking and the latter also assessing convergent thinking. While no significant effects were found for the PLMT, ayahuasca intake significantly modified divergent and convergent thinking as measured by the PCT. While convergent thinking decreased after intake, divergent thinking increased. The present data indicate that ayahuasca enhances creative divergent thinking. They suggest that ayahuasca increases psychological flexibility, which may facilitate psychotherapeutic interventions and support clinical trial initiatives.

  4. Gut microbiota may predict host divergence time during Glires evolution.

    Science.gov (United States)

    Li, Huan; Qu, Jiapeng; Li, Tongtong; Yao, Minjie; Li, Jiaying; Li, Xiangzhen

    2017-03-01

    The gut microbial communities of animals play key roles in host evolution. However, the possible relationship between gut microbiota and host divergence time remains unknown. Here, we investigated the gut microbiota of eight Glires species (four lagomorph species and four rodent species) distributed throughout the Qinghai-Tibet plateau and Inner Mongolia grassland. Lagomorphs and rodents had distinct gut microbial compositions. Three out of four lagomorph species were dominated by Firmicutes, while rodents were dominated by Bacteroidetes in general. The alpha diversity values (Shannon diversity and evenness) exhibited significant differences between any two species within the lagomorphs, whereas there were no significant differences among rodents. The structure of the gut microbiota showed significant differences between lagomorphs and rodents. In addition, we calculated host phylogeny and divergence times, and used a phylogenetic approach to reconstruct how the animal gut microbiota has diverged from their ancestral species. Some core bacterial genera (e.g. Prevotella and Clostridium) shared by more than nine-tenths of all the Glires individuals associated with plant polysaccharide degradation showed marked changes within lagomorphs. Differences in Glires gut microbiota (based on weighted UniFrac and Bray-Curtis dissimilarity metrics) were positively correlated with host divergence time. Our results thus suggest the gut microbial composition is associated with host phylogeny, and further suggest that dissimilarity of animal gut microbiota may predict host divergence time. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  5. Rotational and divergent kinetic energy in the mesoscale model ALADIN

    Directory of Open Access Journals (Sweden)

    V. Blažica

    2013-03-01

    Full Text Available Kinetic energy spectra from the mesoscale numerical weather prediction (NWP model ALADIN with horizontal resolution 4.4 km are split into divergent and rotational components which are then compared at horizontal scales below 300 km and various vertical levels. It is shown that about 50% of kinetic energy in the free troposphere in ALADIN is divergent energy. The percentage increases towards 70% near the surface and in the upper troposphere towards 100 hPa. The maximal percentage of divergent energy is found at stratospheric levels around 100 hPa and at scales below 100 km which are not represented by the global models. At all levels, the divergent energy spectra are characterised by shallower slopes than the rotational energy spectra, and the difference increases as horizontal scales become larger. A very similar vertical distribution of divergent energy is obtained by using the standard ALADIN approach for the computation of spectra based on the extension zone and by applying detrending approach commonly used in mesoscale NWP community.

  6. DNA Investigations.

    Science.gov (United States)

    Mayo, Ellen S.; Bertino, Anthony J.

    1991-01-01

    Presents a simulation activity that allow students to work through the exercise of DNA profiling and to grapple with some analytical and ethical questions involving a couple arranging with a surrogate mother to have a baby. Can be used to teach the principles of restriction enzyme digestion, gel electrophoresis, and probe hybridization. (MDH)

  7. Divergence of gene regulation through chromosomal rearrangements

    Directory of Open Access Journals (Sweden)

    Messing Joachim

    2010-11-01

    based not only on insertions but also on excisions that cause DNA double-strand breaks and trigger illegitimate recombination.

  8. Rapid evolutionary divergence of Gossypium barbadense and G. hirsutum mitochondrial genomes.

    Science.gov (United States)

    Tang, Mingyong; Chen, Zhiwen; Grover, Corrinne E; Wang, Yumei; Li, Shuangshuang; Liu, Guozheng; Ma, Zhiying; Wendel, Jonathan F; Hua, Jinping

    2015-10-12

    The mitochondrial genome from upland cotton, G. hirsutum, was previously sequenced. To elucidate the evolution of mitochondrial genomic diversity within a single genus, we sequenced the mitochondrial genome from Sea Island cotton (Gossypium barbadense L.). Mitochondrial DNA from week-old etiolated seedlings was extracted from isolated organelles using discontinuous sucrose density gradient method. Mitochondrial genome was sequenced with Solexa using paired-end, 90 bp read. The clean reads were assembled into contigs using ABySS and finished via additional fosmid and BAC sequencing. Finally, the genome was annotated and analyzed using different softwares. The G. barbadense (Sea Island cotton) mitochondrial genome was fully sequenced (677,434-bp) and compared to the mitogenome of upland cotton. The G. barbadense mitochondrial DNA contains seven more genes than that of upland cotton, with a total of 40 protein coding genes (excluding possible pseudogenes), 6 rRNA genes, and 29 tRNA genes. Of these 75 genes, atp1, mttB, nad4, nad9, rrn5, rrn18, and trnD(GTC)-cp were each represented by two identical copies. A single 64 kb repeat was largely responsible for the 9 % difference in genome size between the two mtDNAs. Comparison of genome structures between the two mitochondrial genomes revealed 8 rearranged syntenic regions and several large repeats. The largest repeat was missing from the master chromosome in G. hirsutum. Both mitochondrial genomes contain a duplicated copy of rps3 (rps3-2) in conjunction with a duplication of repeated sequences. Phylogenetic and divergence considerations suggest that a 544-bp fragment of rps3 was transferred to the nuclear genome shortly after divergence of the A- and D- genome diploid cottons. These results highlight the insights to the evolution of structural variation between Sea Island and upland cotton mitochondrial genomes.

  9. Phylogeny and divergence times of gymnosperms inferred from single-copy nuclear genes.

    Science.gov (United States)

    Lu, Ying; Ran, Jin-Hua; Guo, Dong-Mei; Yang, Zu-Yu; Wang, Xiao-Quan

    2014-01-01

    Phylogenetic reconstruction is fundamental to study evolutionary biology and historical biogeography. However, there was not a molecular phylogeny of gymnosperms represented by extensive sampling at the genus level, and most published phylogenies of this group were constructed based on cytoplasmic DNA markers and/or the multi-copy nuclear ribosomal DNA. In this study, we use LFY and NLY, two single-copy nuclear genes that originated from an ancient gene duplication in the ancestor of seed plants, to reconstruct the phylogeny and estimate divergence times of gymnosperms based on a complete sampling of extant genera. The results indicate that the combined LFY and NLY coding sequences can resolve interfamilial relationships of gymnosperms and intergeneric relationships of most families. Moreover, the addition of intron sequences can improve the resolution in Podocarpaceae but not in cycads, although divergence times of the cycad genera are similar to or longer than those of the Podocarpaceae genera. Our study strongly supports cycads as the basal-most lineage of gymnosperms rather than sister to Ginkgoaceae, and a sister relationship between Podocarpaceae and Araucariaceae and between Cephalotaxaceae-Taxaceae and Cupressaceae. In addition, intergeneric relationships of some families that were controversial, and the relationships between Taxaceae and Cephalotaxaceae and between conifers and Gnetales are discussed based on the nuclear gene evidence. The molecular dating analysis suggests that drastic extinctions occurred in the early evolution of gymnosperms, and extant coniferous genera in the Northern Hemisphere are older than those in the Southern Hemisphere on average. This study provides an evolutionary framework for future studies on gymnosperms.

  10. Phylogeny and Divergence Times of Lemurs Inferred with Recent and Ancient Fossils in the Tree.

    Science.gov (United States)

    Herrera, James P; Dávalos, Liliana M

    2016-09-01

    Paleontological and neontological systematics seek to answer evolutionary questions with different data sets. Phylogenies inferred for combined extant and extinct taxa provide novel insights into the evolutionary history of life. Primates have an extensive, diverse fossil record and molecular data for living and extinct taxa are rapidly becoming available. We used two models to infer the phylogeny and divergence times for living and fossil primates, the tip-dating (TD) and fossilized birth-death process (FBD). We collected new morphological data, especially on the living and extinct endemic lemurs of Madagascar. We combined the morphological data with published DNA sequences to infer near-complete (88% of lemurs) time-calibrated phylogenies. The results suggest that primates originated around the Cretaceous-Tertiary boundary, slightly earlier than indicated by the fossil record and later than previously inferred from molecular data alone. We infer novel relationships among extinct lemurs, and strong support for relationships that were previously unresolved. Dates inferred with TD were significantly older than those inferred with FBD, most likely related to an assumption of a uniform branching process in the TD compared with a birth-death process assumed in the FBD. This is the first study to combine morphological and DNA sequence data from extinct and extant primates to infer evolutionary relationships and divergence times, and our results shed new light on the tempo of lemur evolution and the efficacy of combined phylogenetic analyses. © The Author(s) 2016. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  11. The highest-copy repeats are methylated in the small genome of the early divergent vascular plant Selaginella moellendorffii

    Directory of Open Access Journals (Sweden)

    Quan Hui

    2008-06-01

    Full Text Available Abstract Background The lycophyte Selaginella moellendorffii is a vascular plant that diverged from the fern/seed plant lineage at least 400 million years ago. Although genomic information for S. moellendorffii is starting to be produced, little is known about basic aspects of its molecular biology. In order to provide the first glimpse to the epigenetic landscape of this early divergent vascular plant, we used the methylation filtration technique. Methylation filtration genomic libraries select unmethylated DNA clones due to the presence of the methylation-dependent restriction endonuclease McrBC in the bacterial host. Results We conducted a characterization of the DNA methylation patterns of the S. moellendorffii genome by sequencing a set of S. moellendorffii shotgun genomic clones, along with a set of methylation filtered clones. Chloroplast DNA, which is typically unmethylated, was enriched in the filtered library relative to the shotgun library, showing that there is DNA methylation in the extremely small S. moellendorffii genome. The filtered library also showed enrichment in expressed and gene-like sequences, while the highest-copy repeats were largely under-represented in this library. These results show that genes and repeats are differentially methylated in the S. moellendorffii genome, as occurs in other plants studied. Conclusion Our results shed light on the genome methylation pattern in a member of a relatively unexplored plant lineage. The DNA methylation data reported here will help understanding the involvement of this epigenetic mark in fundamental biological processes, as well as the evolutionary aspects of epigenetics in land plants.

  12. Divergence of the mRNA targets for the Ssb proteins of bacteriophages T4 and RB69

    Directory of Open Access Journals (Sweden)

    Petrov Vasiliy M

    2004-09-01

    Full Text Available Abstract The single-strand binding (Ssb protein of phage T4 (T4 gp32, product of gene 32 is a mRNA-specific autogenous translational repressor, in addition to being a sequence-independent ssDNA-binding protein that participates in phage DNA replication, repair and recombination. It is not clear how this physiologically essential protein distinguishes between specific RNA and nonspecific nucleic acid targets. Here, we present phylogenetic evidence suggesting that ssDNA and specific RNA bind the same gp32 domain and that plasticity of this domain underlies its ability to configure certain RNA structures for specific binding. We have cloned and characterized gene 32 of phage RB69, a relative of T4 We observed that RB69 gp32 and T4 gp32 have nearly identical ssDNA binding domains, but diverge in their C-terminal domains. In T4 gp32, it is known that the C-terminal domain interacts with the ssDNA-binding domain and with other phage-induced proteins. In translation assays, we show that RB69 gp32 is, like T4 gp32, an autogenous translational repressor. We also show that the natural mRNA targets (translational operators for the 2 proteins are diverged in sequence from each other and yet can be repressed by either gp32. Results of chemical and RNase sensitivity assays indicate that the gp32 mRNA targets from the 2 related phages have similar structures, but differ in their patterns of contact with the 2 repressors. These and other observations suggest that a range of gp32-RNA binding specificities may evolve in nature due to plasticity of the protein-nucleic acid interaction and its response to modulation by the C-terminal domain of this translational repressor.

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

    Science.gov (United States)

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

    2009-03-01

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

  14. Genetic divergence in sesame based on morphological and agronomic traits

    Directory of Open Access Journals (Sweden)

    Nair Helena Castro Arriel

    2007-01-01

    Full Text Available The evaluation of diversity in germplasm collections is important for both plant breeders and germplasmcurators to optimize the use of the variability available. Diversity can be estimated by different genetic markers. The purposeof this study was to estimate the genetic divergence of 30 morphological and agronomic traits in 108 sesame genotypes bymultivariate analysis. The Cole-Rodgers index was used to establish the dissimilarity matrices. The principal componentanalysis identified the traits that contributed most to the divergence and the genotypes were clustered by Tocher’s optimization.Despite the narrow genetic basis, the markers were efficient to characterize the genotypes and identify the most similar groupsor duplicate and divergent genotypes. Greatest variation was found for the traits number of capsules per plant and grain yield.

  15. Molecular phylogeny and divergence of the map turtles (Emydidae: Graptemys).

    Science.gov (United States)

    Thomson, Robert C; Spinks, Phillip Q; Shaffer, H Bradley

    2018-04-01

    The map turtles (genus Graptemys) comprise a morphologically diverse clade that forms a major component of the southeastern US hotspot of chelonian diversity. Map turtles have experienced both recent and rapid diversification resulting in long-standing uncertainty regarding species boundaries and phylogenetic relationships within the genus as well as timing of their divergence. We present a phylogeny for the group that includes geographically representative sampling for all described species and subspecies. We make use of an empirical prior on rates of molecular evolution to estimate divergence times with a molecular clock under a coalescent framework. Together, the phylogeny and divergence time estimates suggest that diversification has been both more recent and more rapid than has so far been suspected. We provide a well-supported evolutionary framework for Graptemys that is necessary for understanding map turtle diversity, biogeography, and for conservation of this threatened clade of turtles. Copyright © 2017 Elsevier Inc. All rights reserved.

  16. Ice flux divergence anomalies on 79north Glacier, Greenland

    DEFF Research Database (Denmark)

    Seroussi, H.; Morlighem, M.; Rignot, E.

    2011-01-01

    onto a regular grid using a scheme (here block kriging) that does not conserve mass or ice flux. This problem is not unique to 79north Glacier but is common to all conventional ice thickness surveys of glaciers and ice sheets; and fundamentally limits the application of ice thickness grids to high......The ice flux divergence of a glacier is an important quantity to examine because it determines the rate of temporal change of its thickness. Here, we combine high-resolution ice surface velocity observations of Nioghalvfjerdsfjorden (79north) Glacier, a major outlet glacier in north Greenland......, with a dense grid of ice thickness data collected with an airborne radar sounder in 1998, to examine its ice flux divergence. We detect large variations, up to 100 m/yr, in flux divergence on grounded ice that are incompatible with what we know of the glacier surface mass balance, basal mass balance...

  17. Repeated adaptive divergence of microhabitat specialization in avian feather lice

    Directory of Open Access Journals (Sweden)

    Johnson Kevin P

    2012-06-01

    Full Text Available Abstract Background Repeated adaptive radiations are evident when phenotypic divergence occurs within lineages, but this divergence into different forms is convergent when compared across lineages. Classic examples of such repeated adaptive divergence occur in island (for example, Caribbean Anolis lizards and lake systems (for example, African cichlids. Host-parasite systems in many respects are analogous to island systems, where host species represent isolated islands for parasites whose life cycle is highly tied to that of their hosts. Thus, host-parasite systems might exhibit interesting cases of repeated adaptive divergence as seen in island and lake systems. The feather lice of birds spend their entire life cycle on the body of the host and occupy distinct microhabitats on the host: head, wing, body and generalist. These microhabitat specialists show pronounced morphological differences corresponding to how they escape from host preening. We tested whether these different microhabitat specialists were a case of repeated adaptive divergence by constructing both morphological and molecular phylogenies for a diversity of avian feather lice, including many examples of head, wing, body and generalist forms. Results Morphological and molecular based phylogenies were highly incongruent, which could be explained by rampant convergence in morphology related to microhabitat specialization on the host. In many cases lice from different microhabitat specializations, but from the same group of birds, were sister taxa. Conclusions This pattern indicates a process of repeated adaptive divergence of these parasites within host group, but convergence when comparing parasites across host groups. These results suggest that host-parasite systems might be another case in which repeated adaptive radiations could be relatively common, but potentially overlooked, because morphological convergence can obscure evolutionary relationships.

  18. Elucidating population histories using genomic DNA sequences.

    Science.gov (United States)

    Vigilant, Linda

    2009-04-01

    In 1993, Cliff Jolly suggested that rather than debating species definitions and classifications, energy would be better spent investigating multidimensional patterns of variation and gene flow among populations. Until now, however, genetic studies of wild primate populations have been limited to very small portions of the genome. Access to complete genome sequences of humans, chimpanzees, macaques, and other primates makes it possible to design studies surveying substantial amounts of DNA sequence variation at multiple genetic loci in representatives of closely related but distinct wild primate populations. Such data can be analyzed with new approaches that estimate not only when populations diverged but also the relative amounts and directions of subsequent gene flow. These analyses will reemphasize the difficulty of achieving consistent species and subspecies definitions by revealing the extent of variation in the amount and duration of gene flow accompanying population divergences.

  19. Use of Kullback–Leibler divergence for forgetting

    Czech Academy of Sciences Publication Activity Database

    Kárný, Miroslav; Andrýsek, Josef

    2009-01-01

    Roč. 23, č. 1 (2009), s. 1-15 ISSN 0890-6327 R&D Projects: GA MŠk 2C06001; GA MŠk 1M0572; GA ČR GA102/08/0567 Institutional research plan: CEZ:AV0Z10750506 Keywords : Bayesian estimation * Kullback–Leibler divergence * functional approximation of estimation * parameter tracking by stabilized forgetting * ARX model Subject RIV: BB - Applied Statistics, Operational Research Impact factor: 1.347, year: 2009 http://library.utia.cas.cz/separaty/2008/AS/karny-use%20of%20kullback-leibler%20divergence%20for%20forgetting.pdf

  20. Divergence from factorizable distributions and matroid representations by partitions

    Czech Academy of Sciences Publication Activity Database

    Matúš, František

    2009-01-01

    Roč. 55, č. 12 (2009), s. 5375-5381 ISSN 0018-9448 R&D Projects: GA AV ČR IAA100750603; GA ČR GA201/04/0393 Institutional research plan: CEZ:AV0Z10750506 Keywords : Information divergence * relative entropy * Shannon entropy * exponential family * hierarchical model * log-linear model * contingency table * Gibbs distribution * matroid representation * secret sharing scheme * maximum likelihood. Subject RIV: BA - General Mathematics Impact factor: 2.357, year: 2009 http://library.utia.cas.cz/separaty/2009/MTR/matus-divergence from factorizable distributions and matroid representations by partitions.pdf

  1. The C-terminal domain of the bacterial SSB protein acts as a DNA maintenance hub at active chromosome replication forks.

    Directory of Open Access Journals (Sweden)

    Audrey Costes

    2010-12-01

    Full Text Available We have investigated in vivo the role of the carboxy-terminal domain of the Bacillus subtilis Single-Stranded DNA Binding protein (SSB(Cter as a recruitment platform at active chromosomal forks for many proteins of the genome maintenance machineries. We probed this SSB(Cter interactome using GFP fusions and by Tap-tag and biochemical analysis. It includes at least 12 proteins. The interactome was previously shown to include PriA, RecG, and RecQ and extended in this study by addition of DnaE, SbcC, RarA, RecJ, RecO, XseA, Ung, YpbB, and YrrC. Targeting of YpbB to active forks appears to depend on RecS, a RecQ paralogue, with which it forms a stable complex. Most of these SSB partners are conserved in bacteria, while others, such as the essential DNA polymerase DnaE, YrrC, and the YpbB/RecS complex, appear to be specific to B. subtilis. SSB(Cter deletion has a moderate impact on B. subtilis cell growth. However, it markedly affects the efficiency of repair of damaged genomic DNA and arrested replication forks. ssbΔCter mutant cells appear deficient in RecA loading on ssDNA, explaining their inefficiency in triggering the SOS response upon exposure to genotoxic agents. Together, our findings show that the bacterial SSB(Cter acts as a DNA maintenance hub at active chromosomal forks that secures their propagation along the genome.

  2. DNA Chip

    Indian Academy of Sciences (India)

    Imagine a world without identity cards; no I-cards for the college or office or bank account or anything! All you are carrying is a small (say, 2cm x 2cm) 'DNA-chip', which has the whole of your genetic profile on it. Your identity cannot get more authentic than that. Imagine a world where marriages are not decided by matching ...

  3. DNA repair

    International Nuclear Information System (INIS)

    Setlow, R.

    1978-01-01

    Some topics discussed are as follows: difficulty in extrapolating data from E. coli to mammalian systems; mutations caused by UV-induced changes in DNA; mutants deficient in excision repair; other postreplication mechanisms; kinds of excision repair systems; detection of repair by biochemical or biophysical means; human mutants deficient in repair; mutagenic effects of UV on XP cells; and detection of UV-repair defects among XP individuals

  4. Stool DNA Test

    Science.gov (United States)

    ... The stool DNA test is a noninvasive laboratory test that identifies DNA changes in the cells of a stool sample. ... the presence of cancer. If a stool DNA test detects abnormal DNA, additional testing may be used to investigate the ...

  5. Patterns in nuclear and mitochondrial DNA reveal historical and recent isolation in the black-tailed godwit (Limosa limosa)

    NARCIS (Netherlands)

    Trimbos, Krijn B.; Doorenweerd, Camiel; Kraaijeveld, Ken; Musters, C.J.M.; Groen, Niko M.; Knijff, Peter de; Piersma, Theunis; de Snoo, Geert R.

    2014-01-01

    On the basis of morphological differences, three subspecies of Black-tailed Godwit (Limosa limosa) have been recognized (L. l. limosa, L. l. islandica and L. l. melanuroides). In previous studies mitochondrial DNA (mtDNA) sequence data showed minimal genetic divergence between the three subspecies

  6. Patterns in Nuclear and Mitochondrial DNA Reveal Historical and Recent Isolation in the Black-Tailed Godwit (

    NARCIS (Netherlands)

    Trimbos, K.B.; Doorenweerd, C.; Kraaijeveld, K.; Musters, C.J.M.; Groen, N.M.; de Knijff, P.; Piersma, T.; de Snoo, G.R.

    2014-01-01

    On the basis of morphological differences, three subspecies of Black-tailed Godwit (Limosa limosa) have been recognized (L. l. limosa, L. l. islandica and L. l. melanuroides). In previous studies mitochondrial DNA (mtDNA) sequence data showed minimal genetic divergence between the three subspecies

  7. Patterns in Nuclear and Mitochondrial DNA Reveal Historical and Recent Isolation in the Black-Tailed Godwit (Limosa limosa)

    NARCIS (Netherlands)

    Trimbos, K.B.; Doorenweerd, C.; Kraaijeveld, K.; Musters, C.J.M.; Groen, N.M.; Kniff, de P.; Piersma, T.; Snoo, de G.R.

    2014-01-01

    On the basis of morphological differences, three subspecies of Black-tailed Godwit (Limosa limosa) have been recognized (L. l. limosa, L. l. islandica and L. l. melanuroides). In previous studies mitochondrial DNA (mtDNA) sequence data showed minimal genetic divergence between the three subspecies

  8. The role of East Asian monsoon system in shaping population divergence and dynamics of a constructive desert shrub Reaumuria soongarica.

    Science.gov (United States)

    Yin, Hengxia; Yan, Xia; Shi, Yong; Qian, Chaoju; Li, Zhonghu; Zhang, Wen; Wang, Lirong; Li, Yi; Li, Xiaoze; Chen, Guoxiong; Li, Xinrong; Nevo, Eviatar; Ma, Xiao-Fei

    2015-10-29

    Both of the uplift of Qinghai-Tibet Plateau (QTP) and the development of East Asian monsoon system (EAMS) could have comprehensively impacted the formation and evolution of Arid Central Asia (ACA). To understand how desert plants endemic to ACA responded to these two factors, we profiled the historical population dynamics and distribution range shift of a constructive desert shrub Reaumuria soongarica (Tamaricaceae) based on species wide investigation of sequence variation of chloroplast DNA and nuclear ribosomal ITS. Phylogenetic analysis uncovered a deep divergence occurring at ca. 2.96 Mya between the western and eastern lineages of R. soongarica, and ecological niche modeling analysis strongly supported that the monsoonal climate could have fragmented its habitats in both glacial and interglacial periods and impelled its intraspecific divergence. Additionally, the population from the east monsoonal zone expanded rapidly, suggesting that the local monsoonal climate significantly impacted its population dynamics. The isolation by distance tests supported strong maternal gene flow along the direction of the East Asian winter monsoon, whose intensification induced the genetic admixture along the latitudinal populations of R. soongarica. Our results presented a new case that the development of EAMS had prominently impacted the intraspecific divergence and population dynamics of this desert plant.

  9. Analysis of genetic divergence in Durum wheat (Triticum Durum Desf.)

    African Journals Online (AJOL)

    A field experiment was conducted at Geregera and Kone testing sites of Sirinka Agricultural Research Center, northeastern Ethiopia. The objective of the experiment was to estimate the genetic divergence among durum wheat germplasm of diverse origin and clustering them into homogenous groups for further hybridization ...

  10. Genetic divergence in Ethiopian coriander accessions and its ...

    African Journals Online (AJOL)

    The genetic divergence among 49 Ethiopian coriander (Coriandrum sativum L.) accessions was assessed using employing Mahalanobi's distance (D2) analysis based on 15 characters. The accessions were grouped in to eight clusters. Cluster II and III were the largest each with 12 accessions, followed by clusters I and V ...

  11. Estimation of divergence times for major lineages of galliform birds ...

    African Journals Online (AJOL)

    STORAGESEVER

    2010-05-24

    May 24, 2010 ... Determining an absolute timescale for avian evolutionary history has been recently challenged by the relaxed molecular clock methods, that rates of molecular evolution can vary significantly among organisms. In this study, we used relaxed molecular clocks to date the divergence of major lineages of.

  12. Stimulating Divergent Thinking in Junior High Career Education.

    Science.gov (United States)

    Ranke, Charlotte; Champoux, Ellen M.

    1981-01-01

    Describes a middle school career-oriented teaching unit with emphasis on teaching for divergent thinking. The unit provides hands-on opportunities for eighth-grade students to explore careers using the knowledge and skills developed in their home economics class. The careers are restaurant management, hospitality service, and interior design. (CT)

  13. Functional Analysis of HIV/AIDS Stigma: Consensus or Divergence?

    Science.gov (United States)

    Hosseinzadeh, Hassan; Hossain, Syeda Zakia

    2011-01-01

    Functional theory proposes that attitudes may serve a variety of purposes for individuals. This study aimed to determine whether stigmatized attitudes toward HIV/AIDS serve the same function for all (consensus function) or serve different functions for different individuals (divergence function) by assessing various aspects of HIV/AIDS stigma…

  14. Estimation of divergence times for major lineages of galliform birds ...

    African Journals Online (AJOL)

    Estimation of divergence times for major lineages of galliform birds: Evidence from complete mitochondrial genome sequences. X-Z Kan, X-F Li, Z-P Lei, L Chen, H Gao, Z-Y Yang, J-K Yang, Z-C Guo, L Yu, L-Q Zhang, C-J Qian ...

  15. Globalization and the Colonial Origins of the Great Divergence

    NARCIS (Netherlands)

    Zwart, de P.

    2016-01-01

    In Globalization and the Colonial Origins of the Great Divergence Pim de Zwart examines the Dutch East India Company’s intercontinental trade and its effects on living standards in various regions on the edges of the Indian Ocean in the seventeenth and eighteenth centuries. Contrary to conventional

  16. Divergent apparent temperature sensitivity of terrestrial ecosystem respiration

    Science.gov (United States)

    Bing Song; Shuli Niu; Ruise Luo; Yiqi Luo; Jiquan Chen; Guirui Yu; Janusz Olejnik; Georg Wohlfahrt; Gerard Kiely; Ako Noormets; Leonardo Montagnani; Alessandro Cescatti; Vincenzo Magliulo; Beverly Elizabeth Law; Magnus Lund; Andrej Varlagin; Antonio Raschi; Matthias Peichl; Mats B. Nilsson; Lutz Merbold

    2014-01-01

    Recent studies revealed convergent temperature sensitivity of ecosystem respiration (Re) within aquatic ecosystems and between terrestrial and aquatic ecosystems. We do not know yet whether various terrestrial ecosystems have consistent or divergent temperature sensitivity. Here, we synthesized 163 eddy covariance flux sites across the world and...

  17. Navier–Stokes flow in converging–diverging distensible tubes

    Directory of Open Access Journals (Sweden)

    Taha Sochi

    2015-09-01

    Full Text Available We use a method based on the lubrication approximation in conjunction with a residual-based mass-continuity iterative solution scheme to compute the flow rate and pressure field in distensible converging–diverging tubes for Navier–Stokes fluids. We employ an analytical formula derived from a one-dimensional version of the Navier–Stokes equations to describe the underlying flow model that provides the residual function. This formula correlates the flow rate to the boundary pressures in straight cylindrical elastic tubes with constant-radius. We validate our findings by the convergence toward a final solution with fine discretization as well as by comparison to the Poiseuille-type flow in its convergence toward analytic solutions found earlier in rigid converging–diverging tubes. We also tested the method on limiting special cases of cylindrical elastic tubes with constant-radius where the numerical solutions converged to the expected analytical solutions. The distensible model has also been endorsed by its convergence toward the rigid Poiseuille-type model with increasing the tube wall stiffness. Lubrication-based one-dimensional finite element method was also used for verification. In this investigation five converging–diverging geometries are used for demonstration, validation and as prototypes for modeling converging–diverging geometries in general.

  18. Transcutaneous vagus nerve stimulation (tVNS) enhances divergent thinking.

    Science.gov (United States)

    Colzato, Lorenza S; Ritter, Simone M; Steenbergen, Laura

    2018-03-01

    Creativity is one of the most important cognitive skills in our complex and fast-changing world. Previous correlative evidence showed that gamma-aminobutyric acid (GABA) is involved in divergent but not convergent thinking. In the current study, a placebo/sham-controlled, randomized between-group design was used to test a causal relation between vagus nerve and creativity. We employed transcutaneous vagus nerve stimulation (tVNS), a novel non-invasive brain stimulation technique to stimulate afferent fibers of the vagus nerve and speculated to increase GABA levels, in 80 healthy young volunteers. Creative performance was assessed in terms of divergent thinking (Alternate Uses Task) and convergent thinking tasks (Remote Associates Test, Creative Problem Solving Task, Idea Selection Task). Results demonstrate active tVNS, compared to sham stimulation, enhanced divergent thinking. Bayesian analysis reported the data to be inconclusive regarding a possible effect of tVNS on convergent thinking. Therefore, our findings corroborate the idea that the vagus nerve is causally involved in creative performance. Even thought we did not directly measure GABA levels, our results suggest that GABA (likely to be increased in active tVNS condition) supports the ability to select among competing options in high selection demand (divergent thinking) but not in low selection demand (convergent thinking). Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

  19. Genome-wide screening reveals the emergence and divergence of ...

    Indian Academy of Sciences (India)

    Receptor tyrosine kinases (RTKs) are key components of cell–cell signalling required for growth and development of multicellular organisms. It is therefore likely that the divergence of RTKs and associated components played a significant role in the evolution of multicellular organisms. We have carried out the present study ...

  20. Genetic Divergence in Ducks for Economic Traits | Kalita | Animal ...

    African Journals Online (AJOL)

    D2 Statistics was used to identify the genetic divergence in 4 groups of duck, namely Khaki Campbell (KC), Desi (D), Khaki Campbell x Desi (KC x D) and Desi x Khaki Campbell (D x KC) reared under rural conditions at the Siphajar, Darrang District, Assam, India. The study showed that both Khaki Campbell and Desi or ...

  1. Divergent Explanatory Production (DEP): The Relationship between Resilience and Creativity

    Science.gov (United States)

    Hernández, Óscar Sánchez; Méndez, Francisco Xavier; Garber, Judy

    2015-01-01

    Introduction: The aim of the study is to describe and analyze a new test and construct, Divergent Explanatory Production (DEP), defined as the ability to observe adverse situations from various points of view. At the theoretical level, it is a bridge between the reformulated model of learned helplessness (as a resilience model), and creative…

  2. Micropolar Fluids Using B-spline Divergence Conforming Spaces

    KAUST Repository

    Sarmiento, Adel

    2014-06-06

    We discretized the two-dimensional linear momentum, microrotation, energy and mass conservation equations from micropolar fluids theory, with the finite element method, creating divergence conforming spaces based on B-spline basis functions to obtain pointwise divergence free solutions [8]. Weak boundary conditions were imposed using Nitsche\\'s method for tangential conditions, while normal conditions were imposed strongly. Once the exact mass conservation was provided by the divergence free formulation, we focused on evaluating the differences between micropolar fluids and conventional fluids, to show the advantages of using the micropolar fluid model to capture the features of complex fluids. A square and an arc heat driven cavities were solved as test cases. A variation of the parameters of the model, along with the variation of Rayleigh number were performed for a better understanding of the system. The divergence free formulation was used to guarantee an accurate solution of the flow. This formulation was implemented using the framework PetIGA as a basis, using its parallel stuctures to achieve high scalability. The results of the square heat driven cavity test case are in good agreement with those reported earlier.

  3. Missouri's experience with a diverging diamond interchange : lessons learned.

    Science.gov (United States)

    2010-05-01

    The first DDI in the nation opened to traffic on June 21, 2009, in Springfield, Missouri. The interchange in : Springfield where the Kansas Expressway (MO-13) passes over I-44 is a huge success. A diverging diamond : interchange (DDI), sometimes refe...

  4. Reproduction of Merino sheep subjected to divergent selection on ...

    African Journals Online (AJOL)

    Reproduction of Merino sheep subjected to divergent selection on maternal values for lambs weaned per ewe joined. SWP Cloete, A Durand. Abstract. No Abstract. Full Text: EMAIL FREE FULL TEXT EMAIL FREE FULL TEXT · DOWNLOAD FULL TEXT DOWNLOAD FULL TEXT · AJOL African Journals Online. HOW TO ...

  5. Sand-mediated divergence between shallow reef communities on ...

    African Journals Online (AJOL)

    Sand-mediated divergence between shallow reef communities on horizontal and vertical substrata in the western Indian Ocean. SN Porter, GM Branch, KJ Sink. Abstract. Distinctions are rarely made between vertical and horizontal surfaces when assessing reef community composition, yet physical differences are expected ...

  6. Lambing behaviour of Merino ewes from lines subjected to divergent ...

    African Journals Online (AJOL)

    Lambing behaviour of Merino ewes from lines subjected to divergent selection for multiple rearing ability from the same base population. ... likely than those in the H line to graze. The latter group of ewes was more likely to stand with their offspring at this stage. South African Journal of Animal Science Vol.32(1) 2002: 57-65 ...

  7. Genetic divergence in selected durum wheat genotypes of Ethiopian ...

    African Journals Online (AJOL)

    genotypes of diverse origin, and clustering them into homogenous groups for the hybridisation programme. Genetic divergence analysis was done based on multivariate analysis using Mahalanobis's D2 statistic, which grouped the durum wheat genotypes into ten clusters. The highest inter-cluster distance was between ...

  8. Genome-wide screening reveals the emergence and divergence of ...

    Indian Academy of Sciences (India)

    Domain organization of all the predicted RTKs was verified using SMART and found to be similar to the general RTK domain organization, which includes extracellular domain (ECD)/TM domain ... magnipapillata genome, showed that HTK30 lies in a ..... Gu J and Gu X 2003 Natural history and functional divergence of.

  9. Divergence time estimates of mammals from molecular clocks and ...

    Indian Academy of Sciences (India)

    Prakash

    2009-10-30

    Oct 30, 2009 ... Ankle bone morphology provides important information about attachment surfaces for muscles and tendons and hence the functional adaptations of the animal during its life and phylogenetic relationships. Based on tarsal bone morphology, it was inferred that Deccanolestes was. Divergence time estimates ...

  10. The odd couple: Diverging paths in language policy and educational ...

    African Journals Online (AJOL)

    This paper examines the divergences between what educational policy calls for in South African schools with regard to language and learning and what takes place in schools. It argues that South African constitutional and education policy statements employ an idea of languages as bound entities and systems, and ...

  11. Analysis of growth characteristics in short-term divergently selected ...

    African Journals Online (AJOL)

    weeks of age body weight in divergent lines of Japanese quail. Growth curves for both sexes within each selection group resembled the general sigmoid shape of a typical growth curve. Gompertz model curves and the observed growth curves were ...

  12. Acceptance and Divergence from Engineering Design Procedures Implicating Knowledge Flow

    DEFF Research Database (Denmark)

    Jensen, Ole Kjeldal; Ahmed, Saeema

    2009-01-01

    that a complex understanding of procedures and reasons for divergence needs to be adopted, where implicit as well as explicit procedures are recognised and managed. Three distinct types of implicit procedures were uncovered through the study: 1) historical implicit procedures; 2) social interpretations...

  13. Divergence-Free Wavelets on the Hypercube : General Boundary Conditions

    NARCIS (Netherlands)

    Stevenson, R.

    2016-01-01

    On the n-dimensional hypercube, for given k∈N, wavelet Riesz bases are constructed for the subspace of divergence-free vector fields of the Sobolev space Hk((0,1)n)n with general homogeneous Dirichlet boundary conditions, including slip or no-slip boundary conditions. Both primal and suitable dual

  14. Factor analysis models via I-divergence optimization

    NARCIS (Netherlands)

    Finesso, L.; Spreij, P.

    2016-01-01

    Given a positive definite covariance matrix Σˆ of dimension n, we approximate it with a covariance of the form HH⊤+D, where H has a prescribed number k0 is diagonal. The quality of the approximation is gauged by the I-divergence between the zero mean normal laws with covariances

  15. Assessing DNA Barcodes for Species Identification in North American Reptiles and Amphibians in Natural History Collections.

    Science.gov (United States)

    Chambers, E Anne; Hebert, Paul D N

    2016-01-01

    High rates of species discovery and loss have led to the urgent need for more rapid assessment of species diversity in the herpetofauna. DNA barcoding allows for the preliminary identification of species based on sequence divergence. Prior DNA barcoding work on reptiles and amphibians has revealed higher biodiversity counts than previously estimated due to cases of cryptic and undiscovered species. Past studies have provided DNA barcodes for just 14% of the North American herpetofauna, revealing the need for expanded coverage. This study extends the DNA barcode reference library for North American herpetofauna, assesses the utility of this approach in aiding species delimitation, and examines the correspondence between current species boundaries and sequence clusters designated by the BIN system. Sequences were obtained from 730 specimens, representing 274 species (43%) from the North American herpetofauna. Mean intraspecific divergences were 1% and 3%, while average congeneric sequence divergences were 16% and 14% in amphibians and reptiles, respectively. BIN assignments corresponded with current species boundaries in 79% of amphibians, 100% of turtles, and 60% of squamates. Deep divergences (>2%) were noted in 35% of squamate and 16% of amphibian species, and low divergences (reptiles and 23% of amphibians, patterns reflected in BIN assignments. Sequence recovery declined with specimen age, and variation in recovery success was noted among collections. Within collections, barcodes effectively flagged seven mislabeled tissues, and barcode fragments were recovered from five formalin-fixed specimens. This study demonstrates that DNA barcodes can effectively flag errors in museum collections, while BIN splits and merges reveal taxa belonging to deeply diverged or hybridizing lineages. This study is the first effort to compile a reference library of DNA barcodes for herpetofauna on a continental scale.

  16. Effects of Mountain Uplift and Climatic Oscillations on Phylogeography and Species Divergence in Four Endangered Notopterygium Herbs

    Directory of Open Access Journals (Sweden)

    Khurram Shahzad

    2017-11-01

    Full Text Available Mountain uplift and climatic fluctuations are important driving forces that have affected the geographic distribution and population dynamics history of organisms. However, it is unclear how geological and climatic events might have affected the phylogeographic history and species divergence in high-alpine herbal plants. In this study, we analyzed the population demographic history and species differentiation of four endangered Notopterygium herbs on the high-altitude Qinghai–Tibetan Plateau (QTP and adjacent areas. We combined phylogeographic analysis with species distribution modeling to detect the genetic variations in four Notopterygium species (N. incisum, N. franchetii, N. oviforme, and N. forrestii. In total, 559 individuals from 74 populations of the four species were analyzed based on three maternally inherited chloroplast fragments (matK, rbcL, and trnS-trnG and one nuclear DNA region (internal transcribed spacer, ITS. Fifty-five chloroplast DNA (cpDNA and 48 ITS haplotypes were identified in the four species. All of the cpDNA and ITS haplotypes were species-specific, except N. franchetii and N. oviforme shared one cpDNA haplotype, H32. Phylogenetic analysis suggested that all four species formed a monophyletic clade with high bootstrap support, where N. franchetii and N. oviforme were sisters. In addition, each Notopterygium species generated an individual clade that corresponded to their respective species in the ITS tree. Population dynamics analyses and species distribution modeling showed that the two widely distributed herbs N. incisum and N. franchetii exhibited obvious demographic expansions during the Pleistocene ice ages. Molecular dating suggested that the divergence of the four Notopterygium species occurred approximately between 3.6 and 1.2 Mya, and it was significantly associated with recent extensive uplifts of the QTP. Our results support the hypothesis that mountain uplift and Quaternary climatic oscillations

  17. Patterns of DNA barcode variation in Canadian marine molluscs.

    Science.gov (United States)

    Layton, Kara K S; Martel, André L; Hebert, Paul D N

    2014-01-01

    Molluscs are the most diverse marine phylum and this high diversity has resulted in considerable taxonomic problems. Because the number of species in Canadian oceans remains uncertain, there is a need to incorporate molecular methods into species identifications. A 648 base pair segment of the cytochrome c oxidase subunit I gene has proven useful for the identification and discovery of species in many animal lineages. While the utility of DNA barcoding in molluscs has been demonstrated in other studies, this is the first effort to construct a DNA barcode registry for marine molluscs across such a large geographic area. This study examines patterns of DNA barcode variation in 227 species of Canadian marine molluscs. Intraspecific sequence divergences ranged from 0-26.4% and a barcode gap existed for most taxa. Eleven cases of relatively deep (>2%) intraspecific divergence were detected, suggesting the possible presence of overlooked species. Structural variation was detected in COI with indels found in 37 species, mostly bivalves. Some indels were present in divergent lineages, primarily in the region of the first external loop, suggesting certain areas are hotspots for change. Lastly, mean GC content varied substantially among orders (24.5%-46.5%), and showed a significant positive correlation with nearest neighbour distances. DNA barcoding is an effective tool for the identification of Canadian marine molluscs and for revealing possible cases of overlooked species. Some species with deep intraspecific divergence showed a biogeographic partition between lineages on the Atlantic, Arctic and Pacific coasts, suggesting the role of Pleistocene glaciations in the subdivision of their populations. Indels were prevalent in the barcode region of the COI gene in bivalves and gastropods. This study highlights the efficacy of DNA barcoding for providing insights into sequence variation across a broad taxonomic group on a large geographic scale.

  18. Rivers, refuges and population divergence of fire-eye antbirds (Pyriglena) in the Amazon Basin.

    Science.gov (United States)

    Maldonado-Coelho, M; Blake, J G; Silveira, L F; Batalha-Filho, H; Ricklefs, R E

    2013-05-01

    The identification of ecological and evolutionary mechanisms that might account for the elevated biotic diversity in tropical forests is a central theme in evolutionary biology. This issue is especially relevant in the Neotropical region, where biological diversity is the highest in the world, but where few studies have been conducted to test factors causing population differentiation and speciation. We used mtDNA sequence data to examine the genetic structure within white-backed fire-eye (Pyriglena leuconota) populations along the Tocantins River valley in the south-eastern Amazon Basin, and we confront the predictions of the river and the Pleistocene refuge hypotheses with patterns of genetic variation observed in these populations. We also investigated whether these patterns reflect the recently detected shift in the course of the Tocantins River. We sampled a total of 32 individuals east of, and 52 individuals west of, the Tocantins River. Coalescent simulations and phylogeographical and population genetics analytical approaches revealed that mtDNA variation observed for fire-eye populations provides little support for the hypothesis that populations were isolated in glacial forest refuges. Instead, our data strongly support a key prediction of the river hypothesis. Our study shows that the Tocantins River has probably been the historical barrier promoting population divergence in fire-eye antbirds. Our results have important implications for a better understanding of the importance of large Amazonian rivers in vertebrate diversification in the Neotropics. © 2013 The Authors. Journal of Evolutionary Biology © 2013 European Society For Evolutionary Biology.

  19. Selection and geographic isolation influence hummingbird speciation: genetic, acoustic and morphological divergence in the wedge-tailed sabrewing (Campylopterus curvipennis

    Directory of Open Access Journals (Sweden)

    Ornelas Juan

    2011-02-01

    Full Text Available Abstract Background Mesoamerica is one of the most threatened biodiversity hotspots in the world, yet we are far from understanding the geologic history and the processes driving population divergence and speciation for most endemic taxa. In species with highly differentiated populations selective and/or neutral factors can induce rapid changes to traits involved in mate choice, promoting reproductive isolation between allopatric populations that can eventually lead to speciation. We present the results of genetic differentiation, and explore drift and selection effects in promoting acoustic and morphological divergence among populations of Campylopterus curvipennis, a lekking hummingbird with an extraordinary vocal variability across Mesoamerica. Results Analyses of two mitochondrial genes and ten microsatellite loci genotyped for 160 individuals revealed the presence of three lineages with no contemporary gene flow: C. c. curvipennis, C. c. excellens, and C. c. pampa disjunctly distributed in the Sierra Madre Oriental, the Tuxtlas region and the Yucatan Peninsula, respectively. Sequence mtDNA and microsatellite data were congruent with two diversification events: an old vicariance event at the Isthmus of Tehuantepec (c. 1.4 Ma, and a more recent Pleistocene split, isolating populations in the Tuxtlas region. Hummingbirds of the excellens group were larger, and those of the pampa group had shorter bills, and lineages that have been isolated the longest shared fewer syllables and differed in spectral and temporal traits of a shared syllable. Coalescent simulations showed that fixation of song types has occurred faster than expected under neutrality but the null hypothesis that morphological divergence resulted from drift was not rejected. Conclusions Our phylogeographic analyses uncovered the presence of three Mesoamerican wedge-tailed sabrewing lineages, which diverged at different time scales. These results highlight the importance of the

  20. DNA Microarrays

    Science.gov (United States)

    Nguyen, C.; Gidrol, X.

    Genomics has revolutionised biological and biomedical research. This revolution was predictable on the basis of its two driving forces: the ever increasing availability of genome sequences and the development of new technology able to exploit them. Up until now, technical limitations meant that molecular biology could only analyse one or two parameters per experiment, providing relatively little information compared with the great complexity of the systems under investigation. This gene by gene approach is inadequate to understand biological systems containing several thousand genes. It is essential to have an overall view of the DNA, RNA, and relevant proteins. A simple inventory of the genome is not sufficient to understand the functions of the genes, or indeed the way that cells and organisms work. For this purpose, functional studies based on whole genomes are needed. Among these new large-scale methods of molecular analysis, DNA microarrays provide a way of studying the genome and the transcriptome. The idea of integrating a large amount of data derived from a support with very small area has led biologists to call these chips, borrowing the term from the microelectronics industry. At the beginning of the 1990s, the development of DNA chips on nylon membranes [1, 2], then on glass [3] and silicon [4] supports, made it possible for the first time to carry out simultaneous measurements of the equilibrium concentration of all the messenger RNA (mRNA) or transcribed RNA in a cell. These microarrays offer a wide range of applications, in both fundamental and clinical research, providing a method for genome-wide characterisation of changes occurring within a cell or tissue, as for example in polymorphism studies, detection of mutations, and quantitative assays of gene copies. With regard to the transcriptome, it provides a way of characterising differentially expressed genes, profiling given biological states, and identifying regulatory channels.

  1. Chromosomal structures and repetitive sequences divergence in Cucumis species revealed by comparative cytogenetic mapping.

    Science.gov (United States)

    Zhang, Yunxia; Cheng, Chunyan; Li, Ji; Yang, Shuqiong; Wang, Yunzhu; Li, Ziang; Chen, Jinfeng; Lou, Qunfeng

    2015-09-25

    Differentiation and copy number of repetitive sequences affect directly chromosome structure which contributes to reproductive isolation and speciation. Comparative cytogenetic mapping has been verified an efficient tool to elucidate the differentiation and distribution of repetitive sequences in genome. In present study, the distinct chromosomal structures of five Cucumis species were revealed through genomic in situ hybridization (GISH) technique and comparative cytogenetic mapping of major satellite repeats. Chromosome structures of five Cucumis species were investigated using GISH and comparative mapping of specific satellites. Southern hybridization was employed to study the proliferation of satellites, whose structural characteristics were helpful for analyzing chromosome evolution. Preferential distribution of repetitive DNAs at the subtelomeric regions was found in C. sativus, C hystrix and C. metuliferus, while majority was positioned at the pericentromeric heterochromatin regions in C. melo and C. anguria. Further, comparative GISH (cGISH) through using genomic DNA of other species as probes revealed high homology of repeats between C. sativus and C. hystrix. Specific satellites including 45S rDNA, Type I/II, Type III, Type IV, CentM and telomeric repeat were then comparatively mapped in these species. Type I/II and Type IV produced bright signals at the subtelomeric regions of C. sativus and C. hystrix simultaneously, which might explain the significance of their amplification in the divergence of Cucumis subgenus from the ancient ancestor. Unique positioning of Type III and CentM only at the centromeric domains of C. sativus and C. melo, respectively, combining with unique southern bands, revealed rapid evolutionary patterns of centromeric DNA in Cucumis. Obvious interstitial telomeric repeats were observed in chromosomes 1 and 2 of C. sativus, which might provide evidence of the fusion hypothesis of chromosome evolution from x = 12 to x = 7 in

  2. Adaptive divergence in a scleractinian coral: physiological adaptation of Seriatopora hystrix to shallow and deep reef habitats

    Directory of Open Access Journals (Sweden)

    van Oppen Madeleine JH

    2011-10-01

    Full Text Available Abstract Background Divergent natural selection across environmental gradients has been acknowledged as a major driver of population and species divergence, however its role in the diversification of scleractinian corals remains poorly understood. Recently, it was demonstrated that the brooding coral Seriatopora hystrix and its algal endosymbionts (Symbiodinium are genetically partitioned across reef environments (0-30 m on the far northern Great Barrier Reef. Here, we explore the potential mechanisms underlying this differentiation and assess the stability of host-symbiont associations through a reciprocal transplantation experiment across habitats ('Back Reef', 'Upper Slope' and 'Deep Slope', in combination with molecular (mtDNA and ITS2-DGGE and photo-physiological analyses (respirometry and HPLC. Results The highest survival rates were observed for native transplants (measured 14 months after transplantation, indicating differential selective pressures between habitats. Host-symbiont assemblages remained stable during the experimental duration, demonstrating that the ability to "shuffle" or "switch" symbionts is restricted in S. hystrix. Photo-physiological differences were observed between transplants originating from the shallow and deep habitats, with indirect evidence of an increased heterotrophic capacity in native deep-water transplants (from the 'Deep Slope' habitat. Similar photo-acclimatisation potential was observed between transplants originating from the two shallow habitats ('Back Reef' and 'Upper Slope', highlighting that their genetic segregation over depth may be due to other, non-photo-physiological traits under selection. Conclusions This study confirms that the observed habitat partitioning of S. hystrix (and associated Symbiodinium is reflective of adaptive divergence along a depth gradient. Gene flow appears to be reduced due to divergent selection, highlighting the potential role of ecological mechanisms, in addition to

  3. East-west genetic differentiation in Musk Ducks (Biziura lobata) of Australia suggests late Pleistocene divergence at the Nullarbor Plain

    Science.gov (United States)

    Guay, P.-J.; Chesser, R.T.; Mulder, R.A.; Afton, A.D.; Paton, D.C.; McCracken, K.G.

    2010-01-01

    Musk Ducks (Biziura lobata) are endemic to Australia and occur as two geographically isolated populations separated by the Nullarbor Plain, a vast arid region in southern Australia. We studied genetic variation in Musk Duck populations at coarse (eastern versus western Australia) and fine scales (four sites within eastern Australia). We found significant genetic structure between eastern and western Australia in the mtDNA control region (??ST = 0. 747), one nuclear intron (??ST = 0.193) and eight microsatellite loci (FST = 0.035). In contrast, there was little genetic structure between Kangaroo Island and adjacent mainland regions within eastern Australia. One small population of Musk Ducks in Victoria (Lake Wendouree) differed from both Kangaroo Island and the remainder of mainland eastern Australia, possibly due to genetic drift exacerbated by inbreeding and small population size. The observed low pairwise distance between the eastern and western mtDNA lineages (0.36%) suggests that they diverged near the end of the Pleistocene, a period characterised by frequent shifts between wet and arid conditions in central Australia. Our genetic results corroborate the display call divergence and Mathews' (Austral Avian Record 2:83-107, 1914) subspecies classification, and confirm that eastern and western populations of Musk Duck are currently isolated from each other. ?? 2010 Springer Science+Business Media B.V.

  4. A Role for the Host DNA Damage Response in Hepatitis B Virus cccDNA Formation-and Beyond?

    Science.gov (United States)

    Schreiner, Sabrina; Nassal, Michael

    2017-05-22

    Chronic hepatitis B virus (HBV) infection puts more than 250 million people at a greatly increased risk to develop end-stage liver disease. Like all hepadnaviruses, HBV replicates via protein-primed reverse transcription of a pregenomic (pg) RNA, yielding an unusually structured, viral polymerase-linked relaxed-circular (RC) DNA as genome in infectious particles. Upon infection, RC-DNA is converted into nuclear covalently closed circular (ccc) DNA. Associating with cellular proteins into an episomal minichromosome, cccDNA acts as template for new viral RNAs, ensuring formation of progeny virions. Hence, cccDNA represents the viral persistence reservoir that is not directly targeted by current anti-HBV therapeutics. Eliminating cccDNA will thus be at the heart of a cure for chronic hepatitis B. The low production of HBV cccDNA in most experimental models and the associated problems in reliable cccDNA quantitation have long hampered a deeper understanding of cccDNA molecular biology. Recent advancements including cccDNA-dependent cell culture systems have begun to identify select host DNA repair enzymes that HBV usurps for RC-DNA to cccDNA conversion. While this list is bound to grow, it may represent just one facet of a broader interaction with the cellular DNA damage response (DDR), a network of pathways that sense and repair aberrant DNA structures and in the process profoundly affect the cell cycle, up to inducing cell death if repair fails. Given the divergent interactions between other viruses and the DDR it will be intriguing to see how HBV copes with this multipronged host system.

  5. A Role for the Host DNA Damage Response in Hepatitis B Virus cccDNA Formation—and Beyond?

    Directory of Open Access Journals (Sweden)

    Sabrina Schreiner

    2017-05-01

    Full Text Available Chronic hepatitis B virus (HBV infection puts more than 250 million people at a greatly increased risk to develop end-stage liver disease. Like all hepadnaviruses, HBV replicates via protein-primed reverse transcription of a pregenomic (pg RNA, yielding an unusually structured, viral polymerase-linked relaxed-circular (RC DNA as genome in infectious particles. Upon infection, RC-DNA is converted into nuclear covalently closed circular (ccc DNA. Associating with cellular proteins into an episomal minichromosome, cccDNA acts as template for new viral RNAs, ensuring formation of progeny virions. Hence, cccDNA represents the viral persistence reservoir that is not directly targeted by current anti-HBV therapeutics. Eliminating cccDNA will thus be at the heart of a cure for chronic hepatitis B. The low production of HBV cccDNA in most experimental models and the associated problems in reliable cccDNA quantitation have long hampered a deeper understanding of cccDNA molecular biology. Recent advancements including cccDNA-dependent cell culture systems have begun to identify select host DNA repair enzymes that HBV usurps for RC-DNA to cccDNA conversion. While this list is bound to grow, it may represent just one facet of a broader interaction with the cellular DNA damage response (DDR, a network of pathways that sense and repair aberrant DNA structures and in the process profoundly affect the cell cycle, up to inducing cell death if repair fails. Given the divergent interactions between other viruses and the DDR it will be intriguing to see how HBV copes with this multipronged host system.

  6. Mating system divergence affects the distribution of sequence diversity within and among populations of recently diverged subspecies of Clarkia xantiana (Onagraceae).

    Science.gov (United States)

    Pettengill, James B; Briscoe Runquist, Ryan D; Moeller, David A

    2016-01-01

    The population biology of outcrossing and self-fertilizing taxa is thought to differ because of the advantage that selfers have in colonizing unoccupied sites where mates and pollinators may be limiting (Baker's Law). This reduced tendency for outcrossers to colonize new sites, along with their greater dependence on pollinators to disperse pollen, has the potential to differently influence the genetic diversity and structure of outcrossing and selfing populations. We conducted a comparative population genetic study of two sister outcrossing and selfing subspecies of Clarkia xantiana that have very recently diverged. We used DNA sequence variation (>40 kb from eight nuclear loci) from large samples of individuals from 14 populations to assess geographic patterns of genetic diversity and make inferences about the demographic and colonization histories of each subspecies. We show that sequence variation is strongly reduced across all selfing populations. The demographic history of selfing populations exhibits recent colonization bottlenecks, whereas such bottlenecks are rarely observed for the outcrosser. The greater effect of genetic drift in the selfer has resulted in strong population genetic structure, but with no pattern of isolation by distance. By contrast, the stronger effect of gene flow in the outcrosser has resulted in considerably less structure, but a significant pattern of isolation by distance. Taken together, our results suggest that selfing populations are not at migration-drift equilibrium, are affected by strong episodes of genetic drift during colonization, and experience little or no subsequent gene flow from other populations after those founder events. © 2016 Botanical Society of America.

  7. Divergência genética em linhagens de melancia Genetic divergence in watermelon lines

    Directory of Open Access Journals (Sweden)

    Flávio de França Souza

    2005-06-01

    Full Text Available A divergência genética entre 31 genótipos de melancia foi avaliada por meio da análise de variáveis canônicas e de técnicas de agrupamento (Tocher e método hierárquico de Ward baseadas na distância generalizada de Mahalanobis (D²ii'. Trinta linhagens, obtidas a partir de acessos coletados no Nordeste brasileiro e a cultivar 'Crimson Sweet' foram avaliadas quanto ao número de dias para o aparecimento da primeira flor masculina e da primeira flor feminina (NDM e NDF; número do nó da primeira flor masculina e da primeira flor feminina (NGM e NGF; número de frutos por planta (NFP; comprimento de rama principal (CRP; peso médio de fruto (PMF; teor de sólidos solúveis (TSS; diâmetro transversal e longitudinal do fruto (DTF e DLF e espessura média de casca (EMC. O experimento foi realizado em delineamento de blocos ao acaso com três repetições, compostas por parcelas de sete plantas. As características que mais contribuíram para a divergência entre as linhagens foram número de frutos por planta, diâmetro longitudinal, teor de sólidos solúveis e peso médio de fruto. Foram formados três grupos por meio do método de otimização de Tocher, três por meio do método hierárquico de Ward e quatro grupos pela dispersão gráfica baseada nas duas primeiras variáveis canônicas. Neste caso, o grupo I compôs-se de sete linhagens de Pernambuco e uma da Bahia; o grupo II reuniu todas as 21 linhagens do Maranhão; os grupos III e IV foram compostos pela linhagem 97-0247.008 (Pernambuco e pela cultivar Crimson Sweet, respectivamente. As linhagens 87-019.021 e 87-019.022 foram as mais semelhantes, enquanto a linhagem 87-019.023 e 'Crimson Sweet' apresentaram maior dissimilaridade pela distância generalizada Mahalanobis (D²ii'. Os cruzamentos mais promissores serão aqueles realizados entre Crimson Sweet e as linhagens do grupo II. Cruzamentos entre Crimson Sweet e as linhagens do grupo I serão interessantes para a obtenção de

  8. How and why DNA barcodes underestimate the diversity of microbial eukaryotes.

    Directory of Open Access Journals (Sweden)

    Gwenael Piganeau

    Full Text Available BACKGROUND: Because many picoplanktonic eukaryotic species cannot currently be maintained in culture, direct sequencing of PCR-amplified 18S ribosomal gene DNA fragments from filtered sea-water has been successfully used to investigate the astounding diversity of these organisms. The recognition of many novel planktonic organisms is thus based solely on their 18S rDNA sequence. However, a species delimited by its 18S rDNA sequence might contain many cryptic species, which are highly differentiated in their protein coding sequences. PRINCIPAL FINDINGS: Here, we investigate the issue of species identification from one gene to the whole genome sequence. Using 52 whole genome DNA sequences, we estimated the global genetic divergence in protein coding genes between organisms from different lineages and compared this to their ribosomal gene sequence divergences. We show that this relationship between proteome divergence and 18S divergence is lineage dependent. Unicellular lineages have especially low 18S divergences relative to their protein sequence divergences, suggesting that 18S ribosomal genes are too conservative to assess planktonic eukaryotic diversity. We provide an explanation for this lineage dependency, which suggests that most species with large effective population sizes will show far less divergence in 18S than protein coding sequences. CONCLUSIONS: There is therefore a trade-off between using genes that are easy to amplify in all species, but which by their nature are highly conserved and underestimate the true number of species, and using genes that give a better description of the number of species, but which are more difficult to amplify. We have shown that this trade-off differs between unicellular and multicellular organisms as a likely consequence of differences in effective population sizes. We anticipate that biodiversity of microbial eukaryotic species is underestimated and that numerous "cryptic species" will become

  9. Assessment of genetic variability among Indian sheep breeds using mitochondrial DNA cytochrome-b region

    Directory of Open Access Journals (Sweden)

    A. D. Sawaimul

    2014-10-01

    Full Text Available Aim: The present study was conducted to estimate genetic distance, the phylogenetic relationship, and time of divergences using mitochondrial DNA (mtDNA. Materials and Methods: The total 216 unrelated samples were collected from native breeding tract of six Indian sheep breeds. The genomic DNA was isolated and screened for restriction enzyme polymorphisms for cytochrome b (Cyt-b region of mtDNA with seven restriction enzymes. Results: The genetic distance among sheep breeds was ranging between 0.02833 and 0.0946. The phylogenetic analysis revealed that Malpura and Chokla were found closer relationship forming distinct cluster followed by Deccani individual were clustered with Nellore sheep, whereas Nali and Sonadi were distant to each other having separate cluster. Estimated divergence time among Indian sheep breeds were ranging about 1.41-4.73 million years ago (MYA with an average of 3.063±0.27 MYA. It showed that Malpura and Sonadi sheep revealed highest divergence time as 4.73 MYA whereas Malpura and Chokla show the lowest as 1.41 MYA. Conclusion: In conclusion, the restriction fragment length polymorphisms-polymerase chain reaction (RFLP-PCR of the Cyt-b region of mtDNA is suitable and cost effective tool for estimating the genetic variability, phylogenetic relationship, and time of divergence among Indian sheep breeds. These findings will help to formulate proper breeding strategies for conservation and utilization of sheep breeds.

  10. Mitochondrial DNA evolution in the Anaxyrus boreas species group

    Science.gov (United States)

    Goebel, A.M.; Ranker, T.A.; Corn, P.S.; Olmstead, R.G.

    2009-01-01

    The Anaxyrus boreas species group currently comprises four species in western North America including the broadly distributed A. boreas, and three localized species, Anaxyrus nelsoni, Anaxyrus exsul and Anaxyrus canorus. Phylogenetic analyses of the mtDNA 12S rDNA, cytochrome oxidase I, control region, and restriction sites data, identified three major haplotype clades. The Northwest clade (NW) includes both subspecies of A. boreas and divergent minor clades in the middle Rocky Mountains, coastal, and central regions of the west and Pacific Northwest. The Southwest (SW) clade includes A. exsul, A. nelsoni, and minor clades in southern California. Anaxyrus canorus, previously identified as paraphyletic, has populations in both the NW and SW major clades. The Eastern major clade (E) includes three divergent lineages from southern Utah, the southern Rocky Mountains, and north of the Great Basin at the border of Utah and Nevada. These results identify new genetic variation in the eastern portion of the toad's range and are consistent with previous regional studies from the west coast. Low levels of control region sequence divergence between major clades (2.2-4.7% uncorrected pair-wise distances) are consistent with Pleistocene divergence and suggest that the phylogeographic history of the group was heavily influenced by dynamic Pleistocene glacial and climatic changes, and especially pluvial changes, in western North America. Results reported here may impact conservation plans in that the current taxonomy does not reflect the diversity in the group. ?? 2008 Elsevier Inc.

  11. Balancing selection on a regulatory region exhibiting ancient variation that predates human-neandertal divergence.

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    Omer Gokcumen

    2013-04-01

    Full Text Available Ancient population structure shaping contemporary genetic variation has been recently appreciated and has important implications regarding our understanding of the structure of modern human genomes. We identified a ∼36-kb DNA segment in the human genome that displays an ancient substructure. The variation at this locus exists primarily as two highly divergent haplogroups. One of these haplogroups (the NE1 haplogroup aligns with the Neandertal haplotype and contains a 4.6-kb deletion polymorphism in perfect linkage disequilibrium with 12 single nucleotide polymorphisms (SNPs across diverse populations. The other haplogroup, which does not contain the 4.6-kb deletion, aligns with the chimpanzee haplotype and is likely ancestral. Africans have higher overall pairwise differences with the Neandertal haplotype than Eurasians do for this NE1 locus (p<10⁻¹⁵. Moreover, the nucleotide diversity at this locus is higher in Eurasians than in Africans. These results mimic signatures of recent Neandertal admixture contributing to this locus. However, an in-depth assessment of the variation in this region across multiple populations reveals that African NE1 haplotypes, albeit rare, harbor more sequence variation than NE1 haplotypes found in Europeans, indicating an ancient African origin of this haplogroup and refuting recent Neandertal admixture. Population genetic analyses of the SNPs within each of these haplogroups, along with genome-wide comparisons revealed significant FST (p = 0.00003 and positive Tajima's D (p = 0.00285 statistics, pointing to non-neutral evolution of this locus. The NE1 locus harbors no protein-coding genes, but contains transcribed sequences as well as sequences with putative regulatory function based on bioinformatic predictions and in vitro experiments. We postulate that the variation observed at this locus predates Human-Neandertal divergence and is evolving under balancing selection, especially among European

  12. Gene conversion limits divergence of mammalian TLR1 and TLR6

    Directory of Open Access Journals (Sweden)

    Dunoyer-Geindre Sylvie

    2007-08-01

    Full Text Available Abstract Background Toll-like receptors (TLR recognize pathogen-associated molecular patterns and are important mediators of the innate immune system. TLR1 and TLR6 are paralogs and located in tandem on the same chromosome in mammals. They form heterodimers with TLR2 and bind lipopeptide components of gram-positive and gram-negative bacterial cell walls. To identify conserved stretches in TLR1 and TLR6, that may be important for their function, we compared their protein sequences in nine mammalian species(Homo sapiens, Pan troglodytes, Macaca mulatta, Mus musculus, Rattus norvegicus; Erinaceus europaeus, Bos Taurus, Sus scrofa and Canis familiaris. Results The N-terminal sequences of the orthologous proteins showed greater similarity than corresponding paralog sequences. However, we identified a region of 300 amino acids towards the C-terminus of TLR1 and TLR6, where paralogs had a greater degree of sequence identity than orthologs. Preservation of DNA sequence identity of paralogs in this region was observed in all nine mammalian species investigated, and is due to independent gene conversion events. The regions having undergone gene conversion in each species are almost identical and encode the leucine-rich repeat motifs 16 to 19, the C-terminal cap motif, the transmembrane domain and most of the intracellular Toll/interleukin-1 receptor (TIR domain. Conclusion Our results show that, for a specific conserved region, divergence of TLR1 and TLR6 is limited by gene conversion, most likely because of the need for co-evolution with multiple intracellular and extracellular binding partners. Thus, gene conversion provides a mechanism for limiting the divergence of functional regions of protein paralogs, while allowing other domains to evolve diversified functions.

  13. Uncovering genes with divergent mRNA-protein dynamics in Streptomyces coelicolor.

    Directory of Open Access Journals (Sweden)

    Karthik P Jayapal

    2008-05-01

    Full Text Available Many biological processes are intrinsically dynamic, incurring profound changes at both molecular and physiological levels. Systems analyses of such processes incorporating large-scale transcriptome or proteome profiling can be quite revealing. Although consistency between mRNA and proteins is often implicitly assumed in many studies, examples of divergent trends are frequently observed. Here, we present a comparative transcriptome and proteome analysis of growth and stationary phase adaptation in Streptomyces coelicolor, taking the time-dynamics of process into consideration. These processes are of immense interest in microbiology as they pertain to the physiological transformations eliciting biosynthesis of many naturally occurring therapeutic agents. A shotgun proteomics approach based on mass spectrometric analysis of isobaric stable isotope labeled peptides (iTRAQ enabled identification and rapid quantification of approximately 14% of the theoretical proteome of S. coelicolor. Independent principal component analyses of this and DNA microarray-derived transcriptome data revealed that the prominent patterns in both protein and mRNA domains are surprisingly well correlated. Despite this overall correlation, by employing a systematic concordance analysis, we estimated that over 30% of the analyzed genes likely exhibited significantly divergent patterns, of which nearly one-third displayed even opposing trends. Integrating this data with biological information, we discovered that certain groups of functionally related genes exhibit mRNA-protein discordance in a similar fashion. Our observations suggest that differences between mRNA and protein synthesis/degradation mechanisms are prominent in microbes while reaffirming the plausibility of such mechanisms acting in a concerted fashion at a protein complex or sub-pathway level.

  14. Divergence in homoeolog expression of the grain length-associated gene GASR7 during wheat allohexaploidization

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    Dongdong Zhang

    2015-02-01

    Full Text Available Hexaploid wheat has triplicated homoeologs for most of the genes that are located in subgenomes A, B, and D. GASR7, a member of the Snakin/GASA gene family, has been associated with grain length development in wheat. However, little is known about divergence of its homoeolog expression in wheat polyploids. We studied the expression patterns of the GASR7 homoeologs in immature seeds in a synthetic hexaploid wheat line whose kernels are slender like those of its maternal parent (Triticum turgidum, AABB, PI 94655 in contrast to the round seed shape of its paternal progenitor (Aegilops tauschii, DD, AS2404. We found that the B homoeolog of GASR7 was the main contributor to the total expression level of this gene in both the maternal tetraploid progenitor and the hexaploid progeny, whereas the expression levels of the A and D homoeologs were much lower. To understand possible mechanisms regulating different GASR7 homoeologs, we firstly analyzed the promoter sequences of three homoeologous genes and found that all of them contained gibberellic acid (GA response elements, with the TaGASR7B promoter (pTaGASR7B uniquely characterized by an additional predicted transcriptional enhancer. This was confirmed by the GA treatment of spikes where all three homoeologs were induced, with a much stronger response for TaGASR7B. McrBC enzyme assays showed that the methylation status at pTaGASR7D was increased during allohexaploidization, consistent with the repressed expression of TaGASR7D. For pTaGASR7A, the distribution of repetitive sequence-derived 24-nucleotide (nt small interfering RNAs (siRNAs were found which suggests possible epigenetic regulation because 24-nt siRNAs are known to mediate RNA-dependent DNA methylation. Our results thus indicate that both genetic and epigenetic mechanisms may be involved in the divergence of GASR7 homoeolog expression in polyploid wheat.

  15. Climate change promotes hybridisation between deeply divergent species

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    Daniele Canestrelli

    2017-03-01

    Full Text Available Rare hybridisations between deeply divergent animal species have been reported for decades in a wide range of taxa, but have often remained unexplained, mainly considered chance events and reported as anecdotal. Here, we combine field observations with long-term data concerning natural hybridisations, climate, land-use, and field-validated species distribution models for two deeply divergent and naturally sympatric toad species in Europe (Bufo bufo and Bufotes viridis species groups. We show that climate warming and seasonal extreme temperatures are conspiring to set the scene for these maladaptive hybridisations, by differentially affecting life-history traits of both species. Our results identify and provide evidence of an ultimate cause for such events, and reveal that the potential influence of climate change on interspecific hybridisations goes far beyond closely related species. Furthermore, climate projections suggest that the chances for these events will steadily increase in the near future.

  16. Divergence-free MHD Simulations with the HERACLES Code

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    Vides J.

    2013-12-01

    Full Text Available Numerical simulations of the magnetohydrodynamics (MHD equations have played a significant role in plasma research over the years. The need of obtaining physical and stable solutions to these equations has led to the development of several schemes, all requiring to satisfy and preserve the divergence constraint of the magnetic field numerically. In this paper, we aim to show the importance of maintaining this constraint numerically. We investigate in particular the hyperbolic divergence cleaning technique applied to the ideal MHD equations on a collocated grid and compare it to the constrained transport technique that uses a staggered grid to maintain the property. The methods are implemented in the software HERACLES and several numerical tests are presented, where the robustness and accuracy of the different schemes can be directly compared.

  17. Little evidence for dynamic divergences in ultraviscous molecular liquids

    DEFF Research Database (Denmark)

    Hecksher, Tina; Nielsen, Albena; Olsen, Niels Boye

    2008-01-01

    The physics of the ultraviscous liquid phase preceding glass formation continues to pose major problems that remain unsolved. It is actively debated, for instance, whether the marked increase of the relaxation time reflects an underlying phase transition to a state of infinite relaxation time....... To elucidate the empirical evidence for this intriguing scenario, some of the most accurate relaxationtime data available for any class of ultraviscous liquids-those obtained by dielectric relaxation experiments on organic liquids just above the glass transition-were compiled. Analysis of data for 42 liquids...... shows that there is no compelling evidence for the Vogel-Fulcher-Tammann (VFT) prediction that the relaxation time diverges at a finite temperature.We conclude that theories with a dynamic divergence of the VFT formlack a direct experimental basis....

  18. Divergent series, summability and resurgence II simple and multiple summability

    CERN Document Server

    Loday-Richaud, Michèle

    2016-01-01

    Addressing the question how to “sum” a power series in one variable when it diverges, that is, how to attach to it analytic functions, the volume gives answers by presenting and comparing the various theories of k-summability and multisummability. These theories apply in particular to all solutions of ordinary differential equations. The volume includes applications, examples and revisits, from a cohomological point of view, the group of tangent-to-identity germs of diffeomorphisms of C studied in volume 1. With a view to applying the theories to solutions of differential equations, a detailed survey of linear ordinary differential equations is provided which includes Gevrey asymptotic expansions, Newton polygons, index theorems and Sibuya’s proof of the meromorphic classification theorem that characterizes the Stokes phenomenon for linear differential equations. This volume is the second of a series of three entitled Divergent Series, Summability and Resurgence. It is aimed at graduate students and res...

  19. Contrasting the Chromosomal Organization of Repetitive DNAs in Two Gryllidae Crickets with Highly Divergent Karyotypes.

    Science.gov (United States)

    Palacios-Gimenez, Octavio M; Carvalho, Carlos Roberto; Ferrari Soares, Fernanda Aparecida; Cabral-de-Mello, Diogo C

    2015-01-01

    A large percentage of eukaryotic genomes consist of repetitive DNA that plays an important role in the organization, size and evolution. In the case of crickets, chromosomal variability has been found using classical cytogenetics, but almost no information concerning the organization of their repetitive DNAs is available. To better understand the chromosomal organization and diversification of repetitive DNAs in crickets, we studied the chromosomes of two Gryllidae species with highly divergent karyotypes, i.e., 2n(♂) = 29,X0 (Gryllus assimilis) and 2n = 9, neo-X1X2Y (Eneoptera surinamensis). The analyses were performed using classical cytogenetic techniques, repetitive DNA mapping and genome-size estimation. Conserved characteristics were observed, such as the occurrence of a small number of clusters of rDNAs and U snDNAs, in contrast to the multiple clusters/dispersal of the H3 histone genes. The positions of U2 snDNA and 18S rDNA are also conserved, being intermingled within the largest autosome. The distribution and base-pair composition of the heterochromatin and repetitive DNA pools of these organisms differed, suggesting reorganization. Although the microsatellite arrays had a similar distribution pattern, being dispersed along entire chromosomes, as has been observed in some grasshopper species, a band-like pattern was also observed in the E. surinamensis chromosomes, putatively due to their amplification and clustering. In addition to these differences, the genome of E. surinamensis is approximately 2.5 times larger than that of G. assimilis, which we hypothesize is due to the amplification of repetitive DNAs. Finally, we discuss the possible involvement of repetitive DNAs in the differentiation of the neo-sex chromosomes of E. surinamensis, as has been reported in other eukaryotic groups. This study provided an opportunity to explore the evolutionary dynamics of repetitive DNAs in two non-model species and will contribute to the understanding of

  20. Contrasting the Chromosomal Organization of Repetitive DNAs in Two Gryllidae Crickets with Highly Divergent Karyotypes.

    Directory of Open Access Journals (Sweden)

    Octavio M Palacios-Gimenez

    Full Text Available A large percentage of eukaryotic genomes consist of repetitive DNA that plays an important role in the organization, size and evolution. In the case of crickets, chromosomal variability has been found using classical cytogenetics, but almost no information concerning the organization of their repetitive DNAs is available. To better understand the chromosomal organization and diversification of repetitive DNAs in crickets, we studied the chromosomes of two Gryllidae species with highly divergent karyotypes, i.e., 2n(♂ = 29,X0 (Gryllus assimilis and 2n = 9, neo-X1X2Y (Eneoptera surinamensis. The analyses were performed using classical cytogenetic techniques, repetitive DNA mapping and genome-size estimation. Conserved characteristics were observed, such as the occurrence of a small number of clusters of rDNAs and U snDNAs, in contrast to the multiple clusters/dispersal of the H3 histone genes. The positions of U2 snDNA and 18S rDNA are also conserved, being intermingled within the largest autosome. The distribution and base-pair composition of the heterochromatin and repetitive DNA pools of these organisms differed, suggesting reorganization. Although the microsatellite arrays had a similar distribution pattern, being dispersed along entire chromosomes, as has been observed in some grasshopper species, a band-like pattern was also observed in the E. surinamensis chromosomes, putatively due to their amplification and clustering. In addition to these differences, the genome of E. surinamensis is approximately 2.5 times larger than that of G. assimilis, which we hypothesize is due to the amplification of repetitive DNAs. Finally, we discuss the possible involvement of repetitive DNAs in the differentiation of the neo-sex chromosomes of E. surinamensis, as has been reported in other eukaryotic groups. This study provided an opportunity to explore the evolutionary dynamics of repetitive DNAs in two non-model species and will contribute to the

  1. Singular divergence instability thresholds of kinematically constrained circulatory systems

    Energy Technology Data Exchange (ETDEWEB)

    Kirillov, O.N., E-mail: o.kirillov@hzdr.de [Magnetohydrodynamics Division, Helmholtz-Zentrum Dresden-Rossendorf, P.O. Box 510119, D-01314 Dresden (Germany); Challamel, N. [University of South Brittany, LIMATB, Lorient (France); Darve, F. [Laboratoire Sols Solides Structures, UJF-INPG-CNRS, Grenoble (France); Lerbet, J. [IBISC, Universite d' Evry Val d' Essone, 40 Rue Pelvoux, CE 1455 Courcouronnes, 91020 Evry Cedex (France); Nicot, F. [Cemagref, Unite de Recherche Erosion Torrentielle Neige et Avalanches, Grenoble (France)

    2014-01-10

    Static instability or divergence threshold of both potential and circulatory systems with kinematic constraints depends singularly on the constraints' coefficients. Particularly, the critical buckling load of the kinematically constrained Ziegler's pendulum as a function of two coefficients of the constraint is given by the Plücker conoid of degree n=2. This simple mechanical model exhibits a structural instability similar to that responsible for the Velikhov–Chandrasekhar paradox in the theory of magnetorotational instability.

  2. Real and metaphorical hunger: the case of The Divergent Trilogy

    OpenAIRE

    Paravano, Cristina

    2015-01-01

    The present contribution investigates how the issue of hunger becomes a means of expressing and communicating personal and social identity in Veronica Roth’s best seller trilogy Divergent (2011-13). Roth portrays a dystopian future developing a multifaceted concept of hunger, both real and figurative, and using food as a cultural metaphor. The trilogy is set in a post-apocalyptic Chicago, whose population is divided into five allegorical factions, according to a number of personal and social ...

  3. One-loop divergences for f (R ) gravity

    Science.gov (United States)

    Ruf, Michael S.; Steinwachs, Christian F.

    2018-02-01

    We calculate the divergent part of the one-loop effective action for f (R ) gravity on an arbitrary background manifold. Our result generalizes previous results for quantum corrections in f (R ) gravity, which have been limited to spaces of constant curvature. We discuss a new technical aspect connected to operators with degenerate principal symbol. Our result has important applications in cosmology and allows us to study the quantum equivalence between f (R ) theories and scalar-tensor theories.

  4. Divergence via Abstraction' Practices for Inventing New Puzzles

    OpenAIRE

    Sugiyama, Kozo; Maeda, Atsuhiko; Mizumoto, Akinori

    2003-01-01

    To invent new puzzles, we take a systematic approach called divergence via abstraction. Existing popular puzzles called permutation puzzles and cyclic puzzles are abstracted and converted into other media such as graphs, blocks, sounds, and robots, while preserving their logic. We implement puzzle generators on different media and variations of generated puzzles are shown. Merits and demerits of new puzzles are evaluated comparing with the original puzzles. This systematic approach can flexib...

  5. Relative Entropies and Jensen Divergences in the Classical Limit

    Directory of Open Access Journals (Sweden)

    A. M. Kowalski

    2015-01-01

    Full Text Available Metrics and distances in probability spaces have shown to be useful tools for physical purposes. Here we use this idea, with emphasis on Jensen Divergences and relative entropies, to investigate features of the road towards the classical limit. A well-known semiclassical model is used and recourse is made to numerical techniques, via the well-known Bandt and Pompe methodology, to extract probability distributions from the pertinent time-series associated with dynamical data.

  6. Divergent detonation wave processes in PBX based on RDX

    Energy Technology Data Exchange (ETDEWEB)

    Mendes, Ricardo A.L.; Campos, Jose L.S. de A.; Plaksin, Igor Y.; Ribeiro, Jose M.B.M. [Fac. of Sciences and Technology of the University of Coimbra, Pinhal de Marrocos, Polo II, 3030-201 Coimbra (Portugal)

    2004-06-01

    In order to characterize the initial phase of the divergent detonation wave in PBX, a hemispheric explosive sample was initiated by a long cylindrical charge of the same explosive. The tested PBX is composed of 85 wt% of RDX and 15 wt% of binder based on HTPB. This PBX-RDX presents an effective density of 1.57 g/cm{sup 3}, and a detonation velocity of 7.90 mm/{mu}s. (Abstract Copyright [2004], Wiley Periodicals, Inc.)

  7. Seasonality and the evolutionary divergence of plant parasites

    OpenAIRE

    Castel, Magda; poggi, Sylvain; Andrivon, Didier; Mailleret, Ludovic

    2011-01-01

    The coexistence of closely related plant parasites is widespread. Yet, understanding the ecological determinants of evolutionary divergence in plant parasites remains an issue. Niche differentiation through resource specialization has been widely researched, but it hardly explains the coexistence of parasites exploiting the same host plant. Time-partitioning has so far received less attention, although in temperate climates, parasites may specialize on either the early or the late season. Acc...

  8. Seasonality and the evolutionary divergence of plant parasites

    OpenAIRE

    Hamelin, Frédéric,; Castel, Magda; Poggi, Sylvain; Andrivon, Didier; Mailleret, Ludovic

    2011-01-01

    The coexistence of closely related plant parasites is widespread. Yet, understanding the ecological determinants of evolutionary divergence in plant parasites remains an issue. Niche differentiation through resource specialization has been widely researched, but it hardly explains the coexistence of parasites exploiting the same host plant. Time-partitioning has so far received less attention, although in temperate climates, parasites may specialize either in the early or in the late season. ...

  9. Infra-red divergences and Regge behaviour in QCD

    International Nuclear Information System (INIS)

    Jaroszewicz, T.

    1980-01-01

    We analyze high energy behaviour of multi-gluon exchange amplitudes in the leading-lns approximation in perturbation theory. Working in the Coulomb gauge and employing Ward identities we derive an integral equation for the n-gluon system in the exchange channel. We find that the Regge behaviour is associated with exponentiation of leading infrared divergences, and the position of the j-plane singularities is determined by the colour quantum numbers of the exchanged system. (author)

  10. Divergence of Cs-137 sources fluence used in brachytherapy

    International Nuclear Information System (INIS)

    Vianello, E.A.; Almeida, C.E. de

    1998-01-01

    In this work the experimental determination of correction factor for fluence divergence (kln) of linear Cs-137 sources CDCS J4, with Farmer ionization chamber model 2571 in a central and perpendicular plan to source axis, for distances range from 1 to 7 cm., has been presented. The experimental results were compared to calculating by Kondo and Randolph (1960) isotropic theory and Bielajew (1990) anisotropic theory. (Author)

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

    Directory of Open Access Journals (Sweden)

    Rovito Sean M

    2012-12-01

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

  12. Beam divergence changing mechanism for short-range inter-unmanned aerial vehicle optical communications.

    Science.gov (United States)

    Heng, Kiang Huat; Zhong, Wen-De; Cheng, Tee Hiang; Liu, Ning; He, Yingjie

    2009-03-10

    The problems associated with using a single fixed beam divergence for short-range inter-unmanned aerial vehicle free-space optical communications are discussed. To overcome the problems, a beam divergence changing mechanism is proposed. Four different methods are then proposed to implement the beam divergence changing mechanism. The performance of these methods is evaluated in terms of transmission distance under adverse weather conditions. The results show that the performance is greatly improved when the beam divergence changing mechanism is used.

  13. Differentiation of movement behaviour in an adaptively diverging salamander population.

    Science.gov (United States)

    Hendrix, Ralf; Schmidt, Benedikt R; Schaub, Michael; Krause, E Tobias; Steinfartz, Sebastian

    2017-11-01

    Dispersal is considered to be a species-specific trait, but intraspecific variation can be high. However, when and how this complex trait starts to differentiate during the divergence of species/lineages is unknown. Here, we studied the differentiation of movement behaviour in a large salamander population (Salamandra salamandra), in which individual adaptations to different habitat conditions drive the genetic divergence of this population into two subpopulations. In this system, salamanders have adapted to the deposition and development of their larvae in ephemeral ponds vs. small first-order streams. In general, the pond habitat is characterized as a spatially and temporally highly unpredictable habitat, while streams provide more stable and predictable conditions for the development of larvae. We analysed the fine-scale genetic distribution of larvae, and explored whether the adaptation to different larval habitat conditions has in turn also affected dispersal strategies and home range size of adult salamanders. Based on the genetic assignment of adult individuals to their respective larval habitat type, we show that pond-adapted salamanders occupied larger home ranges, displayed long-distance dispersal and had a higher variability of movement types than the stream-adapted individuals. We argue that the differentiation of phenotypically plastic traits such as dispersal and movement characteristics can be a crucial component in the course of adaptation to new habitat conditions, thereby promoting the genetic divergence of populations. © 2017 John Wiley & Sons Ltd.

  14. 'String amplitudes': What can we do about the divergent integrals?

    International Nuclear Information System (INIS)

    Amano, Kaoru

    1990-01-01

    The rules for perturbative construction of scattering amplitude constitute the most well-established part of the string theory. They lead to neat integral expressions that represent the amplitude as the sum over the geometry of the string world sheet. However, if one really tries to evaluate the expression, one has to go a long way from there, for the integral does not represent the amplitude in any direct way. The present report focuses on this problem. A study is made to show that the traditional integrals purporting to be string amplitudes are divergent and to identify a remedy. Obviously, any divergent amplitude is not acceptable in a case like the one-loop four-point amplitude. Although the origin of the divergences seems to relate to physical singularities, the integral fails to give imaginary part required for unitarity but only gives infinities which are not desired. Respecting the observation that the integral representation corresponds to the Euclidean Feynman integral, one may modify the integral by postulating an offshell integral for a certain Euclidean, then continuing the function analytically, and defining the physical amplitude by the limit value of the function. This would take one to the correct Minkowskian expression. Some examples are also shown. (N.K.)

  15. Divergence of iron metabolism in wild Malaysian yeast.

    Science.gov (United States)

    Lee, Hana N; Mostovoy, Yulia; Hsu, Tiffany Y; Chang, Amanda H; Brem, Rachel B

    2013-12-09

    Comparative genomic studies have reported widespread variation in levels of gene expression within and between species. Using these data to infer organism-level trait divergence has proven to be a key challenge in the field. We have used a wild Malaysian population of S. cerevisiae as a test bed in the search to predict and validate trait differences based on observations of regulatory variation. Malaysian yeast, when cultured in standard medium, activated regulatory programs that protect cells from the toxic effects of high iron. Malaysian yeast also showed a hyperactive regulatory response during culture in the presence of excess iron and had a unique growth defect in conditions of high iron. Molecular validation experiments pinpointed the iron metabolism factors AFT1, CCC1, and YAP5 as contributors to these molecular and cellular phenotypes; in genome-scale sequence analyses, a suite of iron toxicity response genes showed evidence for rapid protein evolution in Malaysian yeast. Our findings support a model in which iron metabolism has diverged in Malaysian yeast as a consequence of a change in selective pressure, with Malaysian alleles shifting the dynamic range of iron response to low-iron concentrations and weakening resistance to extreme iron toxicity. By dissecting the iron scarcity specialist behavior of Malaysian yeast, our work highlights the power of expression divergence as a signpost for biologically and evolutionarily relevant variation at the organismal level. Interpreting the phenotypic relevance of gene expression variation is one of the primary challenges of modern genomics.

  16. Seasonality and the evolutionary divergence of plant parasites.

    Science.gov (United States)

    Hamelin, Frédéric M; Castel, Magda; Poggi, Sylvain; Andrivon, Didier; Mailleret, Ludovic

    2011-12-01

    The coexistence of closely related plant parasites is widespread. Yet, understanding the ecological determinants of evolutionary divergence in plant parasites remains an issue. Niche differentiation through resource specialization has been widely researched, but it hardly explains the coexistence of parasites exploiting the same host plant. Time-partitioning has so far received less attention, although in temperate climates, parasites may specialize on either the early or the late season. Accordingly, we investigated whether seasonality can also promote phenotypic divergence. For plant parasites, seasonality generally engenders periodic host absence. To account for abrupt seasonal events, we made use of an epidemic model that combines continuous and discrete dynamics. Based on the assumption of a trade-off between in-season transmission and inter-season survival, we found through an "evolutionary invasion analysis" that evolutionary divergence of the parasite phenotype can occur. Since such a trade-off has been reported, this study provides further ecological bases for the coexistence of closely related plant parasites. Moreover, this study provides original insights into the coexistence of sibling plant pathogens which perform either a single or several infection cycles within a season (mono- and polycyclic diseases, or uni- and multivoltine life cycles).

  17. Divergent sexual selection via male competition: ecology is key.

    Science.gov (United States)

    Lackey, A C R; Boughman, J W

    2013-08-01

    Sexual selection and ecological differences are important drivers of speciation. Much research has focused on female choice, yet the role of male competition in ecological speciation has been understudied. Here, we test how mating habitats impact sexual selection and speciation through male competition. Using limnetic and benthic species of threespine stickleback fish, we find that different mating habitats select differently on male traits through male competition. In mixed habitat with both vegetated and open areas, selection favours two trait combinations of male body size and nuptial colour: large with little colour and small with lots of colour. This matches what we see in reproductively isolated stickleback species, suggesting male competition could promote trait divergence and reproductive isolation. In contrast, when only open habitat exists, selection favours one trait combination, large with lots of colour, which would hinder trait divergence and reproductive isolation. Other behavioural mechanisms in male competition that might promote divergence, such as avoiding aggression with heterospecifics, are insufficient to maintain separate species. This work highlights the importance of mating habitats in male competition for both sexual selection and speciation. © 2013 The Authors. Journal of Evolutionary Biology © 2013 European Society For Evolutionary Biology.

  18. A limit of the quantum Rényi divergence

    International Nuclear Information System (INIS)

    Datta, Nilanjana; Leditzky, Felix

    2014-01-01

    Recently, an interesting quantity called the quantum Rényi divergence (or ‘sandwiched’ Rényi relative entropy) was defined for pairs of positive semi-definite operators ρ and σ. It depends on a parameter α and acts as a parent quantity for other relative entropies which have important operational significance in quantum information theory: the quantum relative entropy and the min- and max-relative entropies. There is, however, another relative entropy, called the 0-relative Rényi entropy, which plays a key role in the analysis of various quantum information-processing tasks in the one-shot setting. We prove that the 0-relative Rényi entropy is obtainable from the quantum Rényi divergence only if ρ and σ have equal supports. This, along with existing results in the literature, suggests that it suffices to consider two essential parent quantities from which operationally relevant entropic quantities can be derived—the quantum Rényi divergence with parameter α ⩾ 1/2, and the α-relative Rényi entropy with α ∈ [0, 1). (paper)

  19. Genetic divergence between genotypes for male and female broilers

    Directory of Open Access Journals (Sweden)

    Rogério de Carvalho Veloso

    2015-01-01

    Full Text Available ABSTRACT: The aim of this study was to verify the genetic divergence amongst three broiler genotype, from both sexes, by means of a multivariate performance analysis and carcass traits. Nine hundred and ninety sexed, one-day chicks were utilized; belonged to the following genetic groups: Cobb 500, Hubbard Flex, and Ross 308. The study evaluated the daily average weight gain, the daily average ration consumption, feed conversion, body weight, weight and performance for breast, and carcass over the period from 1 to 35, and from 1 to 42 days of age. Performance of the genetic groups was evaluated by means of multivariate analysis of variance and by Fisher's linear discriminant function, using Roy's largest eigenvalue and Roy's union-intersection test for multiple comparisons. The genetic divergence study was carried out through the analysis of canonical variables and through Tocher method. Female animals from Cobb 500, Hubbard Flex, and Ross 308 genetic groups presented different canonical averages from males of the same groups. First two canonical variables explained 88.10% of variation between genetic groups. Genetic divergence between the evaluated groups allowed formation of two clusters with the following genotypes: Cluster 1 - Cobb 500, Hubbard Flex and Ross 308 females; Cluster 2 - Cobb 500, Hubbard Flex and Ross 308 males.

  20. Exploring Canadian Echinoderm Diversity through DNA Barcodes.

    Science.gov (United States)

    Layton, Kara K S; Corstorphine, Erin A; Hebert, Paul D N

    2016-01-01

    DNA barcoding has proven an effective tool for species identification in varied groups of marine invertebrates including crustaceans, molluscs, polychaetes and echinoderms. In this study, we further validate its utility by analyzing almost half of the 300 species of Echinodermata known from Canadian waters. COI sequences from 999 specimens were assigned to 145 BINs. In most cases, species discrimination was straightforward due to the large difference (25-fold) between mean intra- (0.48%) and inter- (12.0%) specific divergence. Six species were flagged for further taxonomic investigation because specimens assigned to them fell into two or three discrete sequence clusters. The potential influence of larval dispersal capacity and glacial events on patterns of genetic diversity is discussed for 19 trans-oceanic species. Although additional research is needed to clarify biogeographic patterns and resolve taxonomic questions, this study represents an important step in the assembly of a DNA barcode library for all Canadian echinoderms, a valuable resource for future biosurveillance programs.

  1. Genetic divergence among hybrids of 'Cravo' mandarin with 'Pêra' sweet orange Divergência genética entre híbridos de tangerina 'Cravo' com laranja 'Pêra'

    Directory of Open Access Journals (Sweden)

    Roberto Pedroso de Oliveira

    2003-02-01

    Full Text Available Molecular markers have been used as tools in breading programs of sexual hybridation, allowing the genetic characterization of a large number of genotypes. The RADP markers are the most used since the employed techniques are simple and of low cost. To evaluate the genetic divergence among F1 hybrids of 'Cravo' mandarin (Citrus reticulata Blanco and 'Pêra' sweet orange (C. sinensis (L. Osbeck, this study analyses the variability and similarity of the hybrids among themselves and with their parents. Random Amplified Polimorfic DNA marker analysis, with 102 primers, were applied to a population composed of 94 hybrids and their parents. Multivariate genetic divergence analysis of the principal components and Tocher grouping were carried out only considering the polymorphic fragments. Genetic distances were calculated by the arithmetic complement of the Jaccard index. Bidimensional dispersion graphs among hybrid and parent distances and of the divergence analysis by principal components were constructed. High genetic similarity among Cravo and Pêra varieties and their hybrids was verified, showing a casual distribution from the hybrids in relation to the parents, but in intermediary positions. The principal component analysis showed little applicability in the study of hybrid genetic divergence. The hybrids and parents were classified in groups based on the genetic similarity, using the Tocher optimization method.Os marcadores moleculares têm sido utilizados como ferramentas em programas de melhoramento por hibridação sexual, permitindo a caracterização genética de grande número de genótipos. Os marcadores moleculares RAPD são os mais utilizados pois as técnicas empregadas são simples e de baixo custo. Avaliou-se a divergência genética entre híbridos F1 de tangerina 'Cravo' (Citrus reticulata Blanco com laranja 'Pêra' (C. sinensis (L. Osbeck e estudou-se a variabilidade e a similaridade desses materiais entre si e em relação aos

  2. Understanding Creative Cultural Divergence: A Bakhtinian Reflection from a Culture-Crossing Scholar

    Science.gov (United States)

    Hsu, Pei-Ling

    2012-01-01

    I respond to Baron and Chen's article on creative cultural divergence, which they describe as the novel pedagogy of diverging from culturally generated educational expectations. Their article provides an analysis on how an experienced Taiwanese teacher drew on different forms of creative cultural divergence to facilitate students' critical…

  3. Species history and divergence times of viviparous and oviparous Chinese toad-headed sand lizards (Phrynocephalus) on the Qinghai-Tibetan Plateau.

    Science.gov (United States)

    Jin, Y-T; Brown, R P

    2013-08-01

    The Qinghai-Tibetan Plateau (QTP) is an important biogeographical area and has recently become a focus for biodiversity studies. Phyrnocephalus lizards form a widespread Eurasian group with oviparous and viviparous reproductive modes, but two previous mtDNA studies of species from around the QTP have provided different phylogenetic hypotheses. We analysed three loci (mtDNA, RAG-1, AME) from all recognised Chinese Phrynocephalus species to reconstruct the speciation history of the group and to estimate species divergence times. The effects of mtDNA partitioning strategy on phylogenetic inference were examined. Bayes factor comparisons of marginal likelihoods (mLs) estimated using stepping-stone sampling revealed that partitioning strategy had a major impact on mL. Nevertheless, it had a negligible effect on the inferred tree topology. The impact of hard-bound uniform or equivalent soft-bound gamma speciation time calibration priors as well as the use of a fixed topology (as opposed to integration over all possible species histories) on divergence time estimation were also assessed, and found to have little impact on posterior estimates. All three gene trees and the species tree supported the hypothesis that the Chinese species form oviparous and viviparous sister clades. This was in agreement with an early mtDNA study but differed from a subsequent reanalysis of the mtDNA data. Inclusion of mtDNA from more widely distributed Phrynocephalus (from previous studies) indicates that the oviparous P. interscapularis from Central Asia lies outside the clade of Chinese viviparous and oviparous species, but that other Asian oviparous species lie within the Chinese oviparous clade. The median of the posterior on the divergence time of Chinese oviparous and viviparous species was 9.7 Ma ago (95% interval: 7.2-13.0 Ma ago), which coincides with major uplifting of the QTP and indicates that viviparity evolved when this clade became restricted to regions of high elevation. We

  4. Comparison of three genomic DNA extraction methods to obtain high DNA quality from maize.

    Science.gov (United States)

    Abdel-Latif, Amani; Osman, Gamal

    2017-01-01

    The world's top three cereals, based on their monetary value, are rice, wheat, and corn. In cereal crops, DNA extraction is difficult owing to rigid non-cellulose components in the cell wall of leaves and high starch and protein content in grains. The advanced techniques in molecular biology require pure and quick extraction of DNA. The majority of existing DNA extraction methods rely on long incubation and multiple precipitations or commercially available kits to produce contaminant-free high molecular weight DNA. In this study, we compared three different methods used for the isolation of high-quality genomic DNA from the grains of cereal crop, Zea mays , with minor modifications. The DNA from the grains of two maize hybrids, M10 and M321, was extracted using extraction methods DNeasy Qiagen Plant Mini Kit, CTAB-method (with/without 1% PVP) and modified Mericon extraction. Genes coding for 45S ribosomal RNA are organized in tandem arrays of up to several thousand copies and contain codes for 18S, 5.8S and 26S rRNA units separated by internal transcribed spacers ITS1 and ITS2. While the rRNA units are evolutionary conserved, ITS regions show high level of interspecific divergence and have been used frequently in genetic diversity and phylogenetic studies. In this study, the genomic DNA was then amplified with PCR using primers specific for ITS gene. PCR products were then visualized on agarose gel. The modified Mericon extraction method was found to be the most efficient DNA extraction method, capable to provide high DNA yields with better quality, affordable cost and less time.

  5. Phylogeography and allopatric divergence of cypress species (Cupressus L. in the Qinghai-Tibetan Plateau and adjacent regions

    Directory of Open Access Journals (Sweden)

    Ciren Zhaxi

    2010-06-01

    Full Text Available Abstract Background Although allopatric speciation is viewed as the most common way in which species originate, allopatric divergence among a group of closely related species has rarely been examined at the population level through phylogeographic analysis. Here we report such a case study on eight putative cypress (Cupressus species, which each have a mainly allopatric distribution in the Qinghai-Tibetan Plateau (QTP and adjacent regions. The analysis involved sequencing three plastid DNA fragments (trnD-trnT, trnS-trnG and trnL-trnF in 371 individuals sampled from populations at 66 localities. Results Both phylogenetic and network analyses showed that most DNA haplotypes recovered or haplotype-clustered lineages resolved were largely species-specific. Across all species, significant phylogeographic structure (NST >GST, P C. duclouxiana and C. chengiana, which are distributed in the eastern QTP region, contained more haplotypes and higher diversity than five species with restricted distributions in the western highlands of the QTP. The remaining species, C. funebris, is widely cultivated and contained very little cpDNA diversity. Conclusions It is concluded that the formation of high mountain barriers separating deep valleys in the QTP and adjacent regions caused by various uplifts of the plateau since the early Miocene most likely promoted allopatric divergence in Cupressus by restricting gene flow and fixing local, species-specific haplotypes in geographically isolated populations. The low levels of intraspecific diversity present in most species might stem from population bottlenecks brought about by recurrent periods of unfavorable climate and more recently by the negative impacts of human activities on species' distributions. Our findings shed new light on the importance of geographical isolation caused by the uplift of the QTP on the development of high plant species diversity in the QTP biodiversity hotspot.

  6. HPV DNA test

    Science.gov (United States)

    ... HPV testing in women; Cervical cancer - HPV DNA test; Cancer of cervix - HPV DNA test ... The HPV DNA test may be done during a Pap smear . You lie on a table and place your feet in stirrups. The ...

  7. Molecular Genetic Markers of Intra- and Interspecific Divergence within Starfish and Sea Urchins (Echinodermata).

    Science.gov (United States)

    Petrov, N B; Vladychenskaya, I P; Drozdov, A L; Kedrova, O S

    2016-09-01

    A fragment of the mitochondrial COI gene from isolates of several echinoderm species was sequenced. The isolates were from three species of starfish from the Asteriidae family (Asterias amurensis and Aphelasterias japonica collected in the Sea of Japan and Asterias rubens collected in the White Sea) and from the sea urchin Echinocardium cordatum (family Loveniidae) collected in the Sea of Japan. Additionally, regions including internal transcribed spacers and 5.8S rRNA (ITS1 - 5.8S rDNA - ITS2) were sequenced for the three studied starfish species. Phylogenetic analysis of the obtained COI sequences together with earlier determined homologous COI sequences from Ast. forbesii, Ast. rubens, and Echinocardium laevigaster from the North Atlantic and E. cordatum from the Yellow and North Seas (GenBank) placed them into strictly conspecific clusters with high bootstrap support (99% in all cases). Only two exceptions - Ast. rubens DQ077915 sequence placed with the Ast. forbesii cluster and Aph. japonica DQ992560 sequence placed with the Ast. amurensis cluster - were likely results of species misidentification. The intraspecific polymorphism for the COI gene within the Asteriidae family varied within a range of 0.2-0.9% as estimated from the genetic distances. The corresponding intrageneric and intergeneric values were 10.4-12.1 and 21.8-29.8%, respectively. The interspecific divergence for the COI gene in the sea urchin of Echinocardium genus (family Loveniidae) was significantly higher (17.1-17.7%) than in the starfish, while intergeneric divergence (14.6-25.7%) was similar to that in asteroids. The interspecific genetic distances for the nuclear transcribed sequences (ITS1 - 5.8S rDNA - ITS2) within the Asteriidae family were lower (3.1-4.5%), and the intergeneric distances were significantly higher (32.8-35.0%), compared to the corresponding distances for the COI gene. These results suggest that the investigated molecular-genetic markers could be used for segregation

  8. Synthesis of DNA

    Science.gov (United States)

    Mariella, Jr., Raymond P.

    2008-11-18

    A method of synthesizing a desired double-stranded DNA of a predetermined length and of a predetermined sequence. Preselected sequence segments that will complete the desired double-stranded DNA are determined. Preselected segment sequences of DNA that will be used to complete the desired double-stranded DNA are provided. The preselected segment sequences of DNA are assembled to produce the desired double-stranded DNA.

  9. Patterns of major divergence between the internal transcribed spacers of ribosomal DNA in Xenopus borealis and Xenopus laevis, and of minimal divergence within ribosomal coding regions.

    OpenAIRE

    Furlong, J C; Maden, B E

    1983-01-01

    We have determined the nucleotide sequences of the two internal transcribed spacers, the adjacent ribosomal coding sequences and the boundary between the external transcribed spacer and the 18S coding sequence in a cloned ribosomal transcription unit from Xenopus borealis. The transcribed spacers differ very extensively from those of X. laevis. Nevertheless, embedded in the internal transcribed spacers are several short sequence elements which are identical between the two species. These cons...

  10. Test technology on divergence angle of laser range finder based on CCD imaging fusion

    Science.gov (United States)

    Shi, Sheng-bing; Chen, Zhen-xing; Lv, Yao

    2016-09-01

    Laser range finder has been equipped with all kinds of weapons, such as tank, ship, plane and so on, is important component of fire control system. Divergence angle is important performance and incarnation of horizontal resolving power for laser range finder, is necessary appraised test item in appraisal test. In this paper, based on high accuracy test on divergence angle of laser range finder, divergence angle test system is designed based on CCD imaging, divergence angle of laser range finder is acquired through fusion technology for different attenuation imaging, problem that CCD characteristic influences divergence angle test is solved.

  11. Genetic structuring of European anchovy (Engraulis encrasicolus) populations through mitochondrial DNA sequences.

    Science.gov (United States)

    Keskin, Emre; Atar, Hasan Huseyin

    2012-04-01

    Mitochondrial DNA sequence variation in 655 bpfragments of the cytochrome oxidase c subunit I gene, known as the DNA barcode, of European anchovy (Engraulis encrasicolus) was evaluated by analyzing 1529 individuals representing 16 populations from the Black Sea, through the Marmara Sea and the Aegean Sea to the Mediterranean Sea. A total of 19 (2.9%) variable sites were found among individuals, and these defined 10 genetically diverged populations with an overall mean distance of 1.2%. The highest nucleotide divergence was found between samples of eastern Mediterranean and northern Aegean (2.2%). Evolutionary history analysis among 16 populations clustered the Mediterranean Sea clades in one main branch and the other clades in another branch. Diverging pattern of the European anchovy populations correlated with geographic dispersion supports the genetic structuring through the Black Sea-Marmara Sea-Aegean Sea-Mediterranean Sea quad.

  12. Astonishing 35S rDNA diversity in the gymnosperm species Cycas revoluta Thunb.

    Science.gov (United States)

    Wang, Wencai; Ma, Lu; Becher, Hannes; Garcia, Sònia; Kovarikova, Alena; Leitch, Ilia J; Leitch, Andrew R; Kovarik, Ales

    2016-09-01

    In all eukaryotes, the highly repeated 35S ribosomal DNA (rDNA) sequences encoding 18S-5.8S-26S ribosomal RNA (rRNA) typically show high levels of intragenomic uniformity due to homogenisation processes, leading to concerted evolution of 35S rDNA repeats. Here, we compared 35S rDNA divergence in several seed plants using next generation sequencing and a range of molecular and cytogenetic approaches. Most species showed similar 35S rDNA homogeneity indicating concerted evolution. However, Cycas revoluta exhibits an extraordinary diversity of rDNA repeats (nucleotide sequence divergence of different copies averaging 12 %), influencing both the coding and non-coding rDNA regions nearly equally. In contrast, its rRNA transcriptome was highly homogeneous suggesting that only a minority of genes ( T substitutions located in symmetrical CG and CHG contexts which were also highly methylated. Both functional genes and pseudogenes appear to cluster on chromosomes. The extraordinary high levels of 35S rDNA diversity in C. revoluta, and probably other species of cycads, indicate that the frequency of repeat homogenisation has been much lower in this lineage, compared with all other land plant lineages studied. This has led to the accumulation of methylation-driven mutations and pseudogenisation. Potentially, the reduced homology between paralogs prevented their elimination by homologous recombination, resulting in long-term retention of rDNA pseudogenes in the genome.

  13. Distribution of DTHS3 satellite DNA across 12 bivalve species Eva ...

    Indian Academy of Sciences (India)

    Windows User

    Long-term conservation vs high sequence divergence: the case of an extraordinarily old satellite DNA in bivalve mollusks. Heredity. 104, 543–551. Salser W., Bowen S., Browne D., el-Adli F., Fedoroff N., Fry K., Heindell H., Paddock G.,. Poon R., Wallace B., Whitcome P. 1976 Investigation of the organization of mammalian.

  14. Evolution of vocal patterns: tuning hindbrain circuits during species divergence.

    Science.gov (United States)

    Barkan, Charlotte L; Zornik, Erik; Kelley, Darcy B

    2017-03-01

    The neural circuits underlying divergent courtship behaviors of closely related species provide a framework for insight into the evolution of motor patterns. In frogs, male advertisement calls serve as unique species identifiers and females prefer conspecific to heterospecific calls. Advertisement calls of three relatively recently (∼8.5 Mya) diverged species - Xenopus laevis , X. petersii and X. victorianus - include rapid trains of sound pulses (fast trills). We show that while fast trills are similar in pulse rate (∼60 pulses s -1 ) across the three species, they differ in call duration and period (time from the onset of one call to the onset of the following call). Previous studies of call production in X. laevis used an isolated brain preparation in which the laryngeal nerve produces compound action potentials that correspond to the advertisement call pattern (fictive calling). Here, we show that serotonin evokes fictive calling in X. petersii and X. victorianus as it does in X. laevis As in X. laevis , fictive fast trill in X. petersii and X. victorianus is accompanied by an N -methyl-d-aspartate receptor-dependent local field potential wave in a rostral hindbrain nucleus, DTAM. Across the three species, wave duration and period are strongly correlated with species-specific fast trill duration and period, respectively. When DTAM is isolated from the more rostral forebrain and midbrain and/or more caudal laryngeal motor nucleus, the wave persists at species-typical durations and periods. Thus, intrinsic differences within DTAM could be responsible for the evolutionary divergence of call patterns across these related species. © 2017. Published by The Company of Biologists Ltd.

  15. Rethinking conformity and imitation: divergence, convergence, and social understanding

    Directory of Open Access Journals (Sweden)

    Bert eHodges

    2014-07-01

    Full Text Available Social and developmental psychologists have stressed the pervasiveness and strength of humans’ tendencies to conform and to imitate, and social anthropologists have argued that these tendencies are crucial to the formation of cultures. Research from four domains is reviewed and elaborated to show that divergence is also pervasive and potent, and is interwoven with convergence in a complex set of dynamics that is often unnoticed or minimized. First, classic research in social conformity is reinterpreted in terms of truth, trust, and social solidarity, revealing that dissent is its most salient feature. Second, recent studies of children’s use of testimony to guide action reveal a surprisingly sophisticated balance of trust and prudence, and a concern for truth and charity. Third, new experiments indicate that people diverge from others even under conditions where conformity seems assured. Fourth, current studies of imitation provide strong evidence that children are both selective and faithful in who, what, and why they follow others. All of the evidence reviewed points toward children and adults as being engaged, embodied partners with others, motivated to learn and understand the world, others, and themselves in ways that go beyond goals and rules, prediction and control. Even young children act as if they are in a dialogical relationship with others and the world, rather than acting as if they are solo explorers or blind followers. Overall, the evidence supports the hypothesis that social understanding cannot be reduced to convergence or divergence, but includes ongoing activities that seek greater comprehensiveness and complexity in the ability to act and interact effectively, appropriately, and with integrity.

  16. Evolution of cichlid vision via trans-regulatory divergence

    Directory of Open Access Journals (Sweden)

    O’Quin Kelly E

    2012-12-01

    Full Text Available Abstract Background Phenotypic evolution may occur through mutations that affect either the structure or expression of protein-coding genes. Although the evolution of color vision has historically been attributed to structural mutations within the opsin genes, recent research has shown that opsin regulatory mutations can also tune photoreceptor sensitivity and color vision. Visual sensitivity in African cichlid fishes varies as a result of the differential expression of seven opsin genes. We crossed cichlid species that express different opsin gene sets and scanned their genome for expression Quantitative Trait Loci (eQTL responsible for these differences. Our results shed light on the role that different structural, cis-, and trans-regulatory mutations play in the evolution of color vision. Results We identified 11 eQTL that contribute to the divergent expression of five opsin genes. On three linkage groups, several eQTL formed regulatory “hotspots” associated with the expression of multiple opsins. Importantly, however, the majority of the eQTL we identified (8/11 or 73% occur on linkage groups located trans to the opsin genes, suggesting that cichlid color vision has evolved primarily via trans-regulatory divergence. By modeling the impact of just two of these trans-regulatory eQTL, we show that opsin regulatory mutations can alter cichlid photoreceptor sensitivity and color vision at least as much as opsin structural mutations can. Conclusions Combined with previous work, we demonstrate that the evolution of cichlid color vision results from the interplay of structural, cis-, and especially trans-regulatory loci. Although there are numerous examples of structural and cis-regulatory mutations that contribute to phenotypic evolution, our results suggest that trans-regulatory mutations could contribute to phenotypic divergence more commonly than previously expected, especially in systems like color vision, where compensatory changes in the

  17. On the Critical Role of Divergent Selection in Evolvability

    Directory of Open Access Journals (Sweden)

    Joel Lehman

    2016-08-01

    Full Text Available An ambitious goal in evolutionary robotics is to evolve increasingly complex robotic behaviors with minimal human design effort. Reaching this goal requires evolutionary algorithms that can unlock from genetic encodings their latent potential for evolvability. One issue clouding this goal is conceptual confusion about evolvability, which often obscures the aspects of evolvability that are important or desirable. The danger from such confusion is that it may establish unrealistic goals for evolvability that prove unproductive in practice. An important issue separate from conceptual confusion is the common misalignment between selection and evolvability in evolutionary robotics. While more expressive encodings can represent higher-level adaptations (e.g. sexual reproduction or developmental systems that increase long-term evolutionary potential (i.e. evolvability, realizing such potential requires gradients of fitness and evolvability to align. In other words, selection is often a critical factor limiting increasing evolvability. Thus, drawing from a series of recent papers, this article seeks to both (1 clarify and focus the ways in which the term evolvability is used within artificial evolution, and (2 argue for the importance of one type of selection, i.e. divergent selection, for enabling evolvability. The main argument is that there is a fundamental connection between divergent selection and evolvability (on both the individual and population level that does not hold for typical goal-oriented selection. The conclusion is that selection pressure plays a critical role in realizing the potential for evolvability, and that divergent selection in particular provides a principled mechanism for encouraging evolvability in artificial evolution.

  18. Rethinking conformity and imitation: divergence, convergence, and social understanding.

    Science.gov (United States)

    Hodges, Bert H

    2014-01-01

    Social and developmental psychologists have stressed the pervasiveness and strength of humans' tendencies to conform and to imitate, and social anthropologists have argued that these tendencies are crucial to the formation of cultures. Research from four domains is reviewed and elaborated to show that divergence is also pervasive and potent, and it is interwoven with convergence in a complex set of dynamics that is often unnoticed or minimized. First, classic research in social conformity is reinterpreted in terms of truth, trust, and social solidarity, revealing that dissent is its most salient feature. Second, recent studies of children's use of testimony to guide action reveal a surprisingly sophisticated balance of trust and prudence, and a concern for truth and charity. Third, new experiments indicate that people diverge from others even under conditions where conformity seems assured. Fourth, current studies of imitation provide strong evidence that children are both selective and faithful in who, what, and why they follow others. All of the evidence reviewed points toward children and adults as being engaged, embodied partners with others, motivated to learn and understand the world, others, and themselves in ways that go beyond goals and rules, prediction and control. Even young children act as if they are in a dialogical relationship with others and the world, rather than acting as if they are solo explorers or blind followers. Overall, the evidence supports the hypothesis that social understanding cannot be reduced to convergence or divergence, but includes ongoing activities that seek greater comprehensiveness and complexity in the ability to act and interact effectively, appropriately, and with integrity.

  19. Symbolic interactionism and critical perspective: divergent or synergistic?

    Science.gov (United States)

    Burbank, Patricia M; Martins, Diane C

    2010-01-01

    Throughout their history, symbolic interactionism and critical perspective have been viewed as divergent theoretical perspectives with different philosophical underpinnings. A review of their historical and philosophical origins reveals both points of divergence and areas of convergence. Their underlying philosophies of science and views of human freedom are different as is their level of focus with symbolic interactionism having a micro perspective and critical perspective using a macro perspective. This micro/macro difference is reflected in the divergence of their major concepts, goals and basic tenets. While their underlying philosophies are different, however, they are not necessarily contradictory and areas of convergence may include the concepts of reference groups and looking glass self within symbolic interactionism and ideological hegemony within critical perspective. By using a pragmatic approach and combining symbolic interactionism and critical perspectives, both micro and macro levels come into focus and strategies for change across individual and societal levels can be developed and applied. Application of both symbolic interactionism and critical perspective to nursing research and scholarship offers exciting new opportunities for theory development and research methodologies. In nursing education, these two perspectives can give students added insight into patients' and families' problems at the micro level while, at the same time, giving them a lens to see and tools to apply to problems at the macro level in health care. In nursing practice, a combined symbolic interactionism/critical perspective approach assists nurses to give high-quality care at the individual level while also working at the macro level to address the manufacturers of illness. New research questions emerge from this combination of perspectives with new possibilities for theory development, a transformation in nursing education, and the potential for new practice strategies that

  20. Wiring visual systems: common and divergent mechanisms and principles.

    Science.gov (United States)

    Kolodkin, Alex L; Hiesinger, P Robin

    2017-02-01

    The study of visual systems has a rich history, leading to the discovery and understanding of basic principles underlying the elaboration of neuronal connectivity. Recent work in model organisms such as fly, fish and mouse has yielded a wealth of new insights into visual system wiring. Here, we consider how axonal and dendritic patterning in columns and laminae influence synaptic partner selection in these model organisms. We highlight similarities and differences among disparate visual systems with the goal of identifying common and divergent principles for visual system wiring. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

  1. Distributions of the Kullback-Leibler divergence with applications.

    Science.gov (United States)

    Belov, Dmitry I; Armstrong, Ronald D

    2011-05-01

    The Kullback-Leibler divergence (KLD) is a widely used method for measuring the fit of two distributions. In general, the distribution of the KLD is unknown. Under reasonable assumptions, common in psychometrics, the distribution of the KLD is shown to be asymptotically distributed as a scaled (non-central) chi-square with one degree of freedom or a scaled (doubly non-central) F. Applications of the KLD for detecting heterogeneous response data are discussed with particular emphasis on test security. © The British Psychological Society.

  2. Scattering theory of infrared divergent Pauli-Fierz Hamiltonians

    CERN Document Server

    Derezinski, J

    2003-01-01

    We consider in this paper the scattering theory of infrared divergent massless Pauli-Fierz Hamiltonians. We show that the CCR representations obtained from the asymptotic field contain so-called {\\em coherent sectors} describing an infinite number of asymptotically free bosons. We formulate some conjectures leading to mathematically well defined notion of {\\em inclusive and non-inclusive scattering cross-sections} for Pauli-Fierz Hamiltonians. Finally we give a general description of the scattering theory of QFT models in the presence of coherent sectors for the asymptotic CCR representations.

  3. Demographic transitions and children's resources: growth or divergence?

    Directory of Open Access Journals (Sweden)

    C. Shannon Stokes

    2007-03-01

    Full Text Available How do fertility transitions affect children's resource endowments? Existing perspectives provide two seemingly different answers: Dilution arguments focusing on family size predict an average gain, while divergence arguments focusing on family structure predict increased inequality. We attempt to integrate these two perspectives, to show how changes in family size and structure additively and interactively shape the levels and inequality in children's resource endowments. Failure to consider these interactions can severely bias estimates of the magnitude or even direction of the influences of fertility transitions. An empirical illustration is provided with Cameroon data.

  4. Juvenile skeletogenesis in anciently diverged sea urchin clades.

    Science.gov (United States)

    Gao, Feng; Thompson, Jeffrey R; Petsios, Elizabeth; Erkenbrack, Eric; Moats, Rex A; Bottjer, David J; Davidson, Eric H

    2015-04-01

    Mechanistic understanding of evolutionary divergence in animal body plans devolves from analysis of those developmental processes that, in forms descendant from a common ancestor, are responsible for their morphological differences. The last common ancestor of the two extant subclasses of sea urchins, i.e., euechinoids and cidaroids, existed well before the Permian/Triassic extinction (252 mya). Subsequent evolutionary divergence of these clades offers in principle a rare opportunity to solve the developmental regulatory events underlying a defined evolutionary divergence process. Thus (i) there is an excellent and fairly dense (if yet incompletely analyzed) fossil record; (ii) cladistically confined features of the skeletal structures of modern euechinoid and cidaroid sea urchins are preserved in fossils of ancestral forms; (iii) euechinoids and cidaroids are among current laboratory model systems in molecular developmental biology (here Strongylocentrotus purpuratus [Sp] and Eucidaris tribuloides [Et]); (iv) skeletogenic specification in sea urchins is uncommonly well understood at the causal level of interactions of regulatory genes with one another, and with known skeletogenic effector genes, providing a ready arsenal of available molecular tools. Here we focus on differences in test and perignathic girdle skeletal morphology that distinguish all modern euechinoid from all modern cidaroid sea urchins. We demonstrate distinct canonical test and girdle morphologies in juveniles of both species by use of SEM and X-ray microtomography. Among the sharply distinct morphological features of these clades are the internal skeletal structures of the perignathic girdle to which attach homologous muscles utilized for retraction and protraction of Aristotles׳ lantern and its teeth. We demonstrate that these structures develop de novo between one and four weeks after metamorphosis. In order to study the underlying developmental processes, a method of section whole mount in

  5. Beam divergence and ion current in multiaperture ion sources

    International Nuclear Information System (INIS)

    Ott, W.; Penningsfeld, F.P.

    1992-03-01

    Two different measurements of the divergence of high-current ion beams formed in a multiaperture ion source have been made. The current dependence of both measurements shows characteristic differences which are explained as a result of an inhomogeneity of the current density across the emission area. The model of Coupland et al. with a spherical beam geometry in the acceleration gap is reexamined. It is shown that a rigorous application of this model gives a beamlet defocusing in the decel electrode which is stronger by a factor of 1.35 than assumed hitherto. The implications on offset steering are discussed. (orig.)

  6. Evolutionary expansion and divergence in a large family of primate-specific zinc finger transcription factor genes

    Energy Technology Data Exchange (ETDEWEB)

    Hamilton, A T; Huntley, S; Tran-Gyamfi, M; Baggott, D; Gordon, L; Stubbs, L

    2005-09-28

    Although most genes are conserved as one-to-one orthologs in different mammalian orders, certain gene families have evolved to comprise different numbers and types of protein-coding genes through independent series of gene duplications, divergence and gene loss in each evolutionary lineage. One such family encodes KRAB-zinc finger (KRAB-ZNF) genes, which are likely to function as transcriptional repressors. One KRAB-ZNF subfamily, the ZNF91 clade, has expanded specifically in primates to comprise more than 110 loci in the human genome, yielding large gene clusters in human chromosomes 19 and 7 and smaller clusters or isolated copies at other chromosomal locations. Although phylogenetic analysis indicates that many of these genes arose before the split between old world monkeys and new world monkeys, the ZNF91 subfamily has continued to expand and diversify throughout the evolution of apes and humans. The paralogous loci are distinguished by sequence divergence within their zinc finger arrays indicating a selection for proteins with different DNA binding specificities. RT-PCR and in situ hybridization data show that some of these ZNF genes can have tissue-specific expression patterns, however many KRAB-ZNFs that are near-ubiquitous could also be playing very specific roles in halting target pathways in all tissues except for a few, where the target is released by the absence of its repressor. The number of variant KRAB-ZNF proteins is increased not only because of the large number of loci, but also because many loci can produce multiple splice variants, which because of the modular structure of these genes may have separate and perhaps even conflicting regulatory roles. The lineage-specific duplication and rapid divergence of this family of transcription factor genes suggests a role in determining species-specific biological differences and the evolution of novel primate traits.

  7. Four new bat species (Rhinolophus hildebrandtii complex reflect Plio-Pleistocene divergence of dwarfs and giants across an Afromontane archipelago.

    Directory of Open Access Journals (Sweden)

    Peter J Taylor

    Full Text Available Gigantism and dwarfism evolve in vertebrates restricted to islands. We describe four new species in the Rhinolophus hildebrandtii species-complex of horseshoe bats, whose evolution has entailed adaptive shifts in body size. We postulate that vicissitudes of palaeoenvironments resulted in gigantism and dwarfism in habitat islands fragmented across eastern and southern Africa. Mitochondrial and nuclear DNA sequences recovered two clades of R. hildebrandtii senso lato which are paraphyletic with respect to a third lineage (R. eloquens. Lineages differ by 7.7 to 9.0% in cytochrome b sequences. Clade 1 includes R. hildebrandtii sensu stricto from the east African highlands and three additional vicariants that speciated across an Afromontane archipelago through the Plio-Pleistocene, extending from the Kenyan Highlands through the Eastern Arc, northern Mozambique and the Zambezi Escarpment to the eastern Great Escarpment of South Africa. Clade 2 comprises one species confined to lowland savanna habitats (Mozambique and Zimbabwe. A third clade comprises R. eloquens from East Africa. Speciation within Clade 1 is associated with fixed differences in echolocation call frequency, and cranial shape and size in populations isolated since the late Pliocene (ca 3.74 Mya. Relative to the intermediate-sized savanna population (Clade 2, these island-populations within Clade 1 are characterised by either gigantism (South African eastern Great Escarpment and Mts Mabu and Inago in Mozambique or dwarfism (Lutope-Ngolangola Gorge, Zimbabwe and Soutpansberg Mountains, South Africa. Sympatry between divergent clades (Clade 1 and Clade 2 at Lutope-Ngolangola Gorge (NW Zimbabwe is attributed to recent range expansions. We propose an "Allometric Speciation Hypothesis", which attributes the evolution of this species complex of bats to divergence in constant frequency (CF sonar calls. The origin of species-specific peak frequencies (overall range = 32 to 46 kHz represents the

  8. Genomic Landscape of Atypical Adenomatous Hyperplasia Reveals Divergent Modes to Lung Adenocarcinoma.

    Science.gov (United States)

    Sivakumar, Smruthy; Lucas, F Anthony San; McDowell, Tina L; Lang, Wenhua; Xu, Li; Fujimoto, Junya; Zhang, Jianjun; Futreal, P Andrew; Fukuoka, Junya; Yatabe, Yasushi; Dubinett, Steven M; Spira, Avrum E; Fowler, Jerry; Hawk, Ernest T; Wistuba, Ignacio I; Scheet, Paul; Kadara, Humam

    2017-11-15

    There is a dearth of knowledge about the pathogenesis of premalignant lung lesions, especially for atypical adenomatous hyperplasia (AAH), the only known precursor for the major lung cancer subtype adenocarcinoma (LUAD). In this study, we performed deep DNA and RNA sequencing analyses of a set of AAH, LUAD, and normal tissues. Somatic BRAF variants were found in AAHs from 5 of 22 (23%) patients, 4 of 5 of whom had matched LUAD with driver EGFR mutations. KRAS mutations were present in AAHs from 4 of 22 (18%) of patients. KRAS mutations in AAH were only found in ever-smokers and were exclusive to BRAF -mutant cases. Integrative analysis revealed profiles expressed in KRAS -mutant cases ( UBE2C, REL ) and BRAF -mutant cases ( MAX ) of AAH, or common to both sets of cases (suppressed AXL ). Gene sets associated with suppressed antitumor (Th1; IL12A, GZMB ) and elevated protumor ( CCR2, CTLA-4 ) immune signaling were enriched in AAH development and progression. Our results reveal potentially divergent BRAF or KRAS pathways in AAH as well as immune dysregulation in the pathogenesis of this premalignant lung lesion. Cancer Res; 77(22); 6119-30. ©2017 AACR . ©2017 American Association for Cancer Research.

  9. Genetic divergence across habitats in the widespread coral Seriatopora hystrix and its associated Symbiodinium.

    Directory of Open Access Journals (Sweden)

    Pim Bongaerts

    2010-05-01

    Full Text Available Coral reefs are hotspots of biodiversity, yet processes of diversification in these ecosystems are poorly understood. The environmental heterogeneity of coral reef environments could be an important contributor to diversification, however, evidence supporting ecological speciation in corals is sparse. Here, we present data from a widespread coral species that reveals a strong association of host and symbiont lineages with specific habitats, consistent with distinct, sympatric gene pools that are maintained through ecologically-based selection.Populations of a common brooding coral, Seriatopora hystrix, were sampled from three adjacent reef habitats (spanning a approximately 30 m depth range at three locations on the Great Barrier Reef (n = 336. The populations were assessed for genetic structure using a combination of mitochondrial (putative control region and nuclear (three microsatellites markers for the coral host, and the ITS2 region of the ribosomal DNA for the algal symbionts (Symbiodinium. Our results show concordant genetic partitioning of both the coral host and its symbionts across the different habitats, independent of sampling location.This study demonstrates that coral populations and their associated symbionts can be highly structured across habitats on a single reef. Coral populations from adjacent habitats were found to be genetically isolated from each other, whereas genetic similarity was maintained across similar habitat types at different locations. The most parsimonious explanation for the observed genetic partitioning across habitats is that adaptation to the local environment has caused ecological divergence of distinct genetic groups within S. hystrix.

  10. Strong genome-wide divergence between sympatric European river and brook lampreys.

    Science.gov (United States)

    Mateus, Catarina S; Stange, Madlen; Berner, Daniel; Roesti, Marius; Quintella, Bernardo R; Alves, M Judite; Almeida, Pedro R; Salzburger, Walter

    2013-08-05

    Lampreys, together with hagfishes, are the only extant representatives of jawless vertebrates and thus of prime interest for the study of vertebrate evolution [1]. Most lamprey genera occur in two forms with divergent life histories: a parasitic, anadromous and a non-parasitic, freshwater resident form [2-8]. The taxonomic status of such 'paired species' is disputed, however. While indistinguishable at larval stages, but clearly distinct as adults, they cannot be differentiated with available genetic data [6,7], which has fuelled speculations that the two forms may in fact represent products of phenotypic plasticity within a single species. Here, we use restriction site-associated DNA sequencing (RADseq) to examine the genetic population structure of sympatric European river (Lampetra fluviatilis L., 1758) and brook (Lampetra planeri Bloch, 1784) lampreys. We find strong genetic differentiation and identify numerous fixed and diagnostic single nucleotide polymorphisms (SNPs) between the two species, 12 of which can be unequivocally assigned to specific genes. Copyright © 2013 Elsevier Ltd. All rights reserved.

  11. Characterization of the carrot beta-tubulin gene coding a divergent isotype, beta-2.

    Science.gov (United States)

    Okamura, S; Naito, K; Sonehara, S; Ohkawa, H; Kuramori, S; Tatsuta, M; Minamizono, M; Kataoka, T

    1997-04-01

    Four different beta-tubulin clones were isolated from carrot genomic and cDNA libraries. Their nucleotide sequences were determined 1 and their predicted amino acids were compared with each other. The predicted amino acid composition of the C-terminal region of three of them (beta-1, 3, 4) resembled one another, but that of one isotype (beta-2) was divergent. The beta-2 tubulin included two hydroxyl amino acids, serine and threonine, and consisted of a lower number of negatively charged amino acids than the others in the C-terminal region. The predicted hydrophobicity profile of the beta-2 tubulin around the residue 200 is less hydrophobic than beta-1, but it is still more hydrophobic than those of animal and fungal beta-tubulins. The beta-2 gene was transcribed in cultured cells and flowers, while the beta-1 gene was ubiquitously transcribed in cultured cells, roots, shoots and flowers. When the predicted amino acids of plant tubulin were compared with those of other organisms, substitutions from non-polar amino acids to those with hydroxyl group were conspicuous in the region corresponding to the third exon in the plant genes.

  12. Rapid adaptive divergence in new world achillea, an autopolyploid complex of ecological races.

    Science.gov (United States)

    Ramsey, Justin; Robertson, Alexander; Husband, Brian

    2008-03-01

    Adaptive evolution is often associated with speciation. In plants, however, ecotypic differentiation is common within widespread species, suggesting that climatic and edaphic specialization can outpace cladogenesis and the evolution of postzygotic reproductive isolation. We used cpDNA sequence (5 noncoding regions, 3.5 kb) and amplified fragment length polymorphisms (AFLPs: 4 primer pairs, 1,013 loci) to evaluate the history of ecological differentiation in the North American Achillea millefolium, an autopolyploid complex of "ecological races" exhibiting morphological, physiological, and life-history adaptations to diverse environments. Phylogenetic analyses reveal North American A. millefolium to be a monophyletic group distinct from its European and Asian relatives. Based on patterns of sequence divergence, as well as fossil and paleoecological data, colonization of North America appears to have occurred via the Bering Land Bridge during the Pleistocene (1.8 MYA to 11,500 years ago). Population genetic analyses indicate negligible structure within North American A. millefolium associated with varietal identity, geographic distribution, or ploidy level. North American populations, moreover, exhibit the signature of demographic expansion. These results affirm the "ecotype" concept of the North American Achillea advocated by classical research and demonstrate the rapid rate of ecological differentiation that sometimes occurs in plants.

  13. Comparative performance of double-digest RAD sequencing across divergent arachnid lineages.

    Science.gov (United States)

    Burns, Mercedes; Starrett, James; Derkarabetian, Shahan; Richart, Casey H; Cabrero, Allan; Hedin, Marshal

    2017-05-01

    Next-generation sequencing technologies now allow researchers of non-model systems to perform genome-based studies without the requirement of a (often unavailable) closely related genomic reference. We evaluated the role of restriction endonuclease (RE) selection in double-digest restriction-site-associated DNA sequencing (ddRADseq) by generating reduced representation genome-wide data using four different RE combinations. Our expectation was that RE selections targeting longer, more complex restriction sites would recover fewer loci than RE with shorter, less complex sites. We sequenced a diverse sample of non-model arachnids, including five congeneric pairs of harvestmen (Opiliones) and four pairs of spiders (Araneae). Sample pairs consisted of either conspecifics or closely related congeneric taxa, and in total 26 sample pair analyses were tested. Sequence demultiplexing, read clustering and variant calling were performed in the pyRAD program. The 6-base pair cutter EcoRI combined with methylated site-specific 4-base pair cutter MspI produced, on average, the greatest numbers of intra-individual loci and shared loci per sample pair. As expected, the number of shared loci recovered for a sample pair covaried with the degree of genetic divergence, estimated with cytochrome oxidase I sequences, although this relationship was non-linear. Our comparative results will prove useful in guiding protocol selection for ddRADseq experiments on many arachnid taxa where reference genomes, even from closely related species, are unavailable. © 2016 John Wiley & Sons Ltd.

  14. Divergent evolution of CHD3 proteins resulted in MOM1 refining epigenetic control in vascular plants.

    Directory of Open Access Journals (Sweden)

    Marian Caikovski

    2008-08-01

    Full Text Available Arabidopsis MOM1 is required for the heritable maintenance of transcriptional gene silencing (TGS. Unlike many other silencing factors, depletion of MOM1 evokes transcription at selected loci without major changes in DNA methylation or histone modification. These loci retain unusual, bivalent chromatin properties, intermediate to both euchromatin and heterochromatin. The structure of MOM1 previously suggested an integral nuclear membrane protein with chromatin-remodeling and actin-binding activities. Unexpected results presented here challenge these presumed MOM1 activities and demonstrate that less than 13% of MOM1 sequence is necessary and sufficient for TGS maintenance. This active sequence encompasses a novel Conserved MOM1 Motif 2 (CMM2. The high conservation suggests that CMM2 has been the subject of strong evolutionary pressure. The replacement of Arabidopsis CMM2 by a poplar motif reveals its functional conservation. Interspecies comparison suggests that MOM1 proteins emerged at the origin of vascular plants through neo-functionalization of the ubiquitous eukaryotic CHD3 chromatin remodeling factors. Interestingly, despite the divergent evolution of CHD3 and MOM1, we observed functional cooperation in epigenetic control involving unrelated protein motifs and thus probably diverse mechanisms.

  15. Genetic Divergent of Tomato Lines Based on AFLP Molecular Markers and Relationship with Heterosis

    Directory of Open Access Journals (Sweden)

    M Nabipoor

    2012-10-01

    Full Text Available Tomato as a highly nutritious vegetable crop is widely grown in the world. Hybrid seed is preferably used for tomato production. Identification of superior hybrid combination is one of the most important steps in the hybrid breeding programs. Breeding of high yielding hybrids is expensive and involves testing large numbers of hybrid combinations in multi-environment trials. Successful prediction of heterosis from the genetic similarity of their parents based on molecular markers has been reported in several crops and can be very helpful in hybrid breeding. The present study was carried out to evaluate genetic divergent among tomato lines and to assess the relationship between genetic distance and heterosis among them. Thirty genotypes were examined for DNA polymorphism, using amplified fragment length polymorphisms (AFLPs. A total of 165 polymorphic variants were generated and genetic distances ranged from 0.04 to 0.23. Our result indicated that AFLP markers were successful in identification of polymorphism and genetic distances among tomato lines, but correlation of genetic distance based on AFLPs with mid-parent heterosis of yield, fruit weight, fruit number and fruit durability time was low and not useful for predicting heterosis in tomato genotypes.

  16. Genetic divergence among elephantgrass cultivars assessed by RAPD markers in composit samples Divergência genética entre cultivares de capim-elefante avaliada por marcadores RAPD em amostras compostas

    Directory of Open Access Journals (Sweden)

    Rogério Figueiredo Daher

    2002-12-01

    Full Text Available Elephantgrass (Pennisetum purpureum Schum. is native to regions of tropical Africa and was introduced in Brazil around 1920 through plantings imported from Cuba. It is currently one of the most widespread forage plants throughout the country. At first, there were two cultivars, Napier and Mercker, with well defined characteristics. New genotypes arose and it is believed that the large number of cultivars existing today in germplasm bank is due to duplicates. DNA markers for cultivar characterization are a very valuable tool, especially in situations where morphological and isoenzymatic markers have already been used as in the case of elephantgrass. Thus RAPD markers were used to estimate the genetic divergence among the Napier group elephantgrass cultivars from the elephantgrass Active Germplasm Bank at EMBRAPA Dairy Cattle. The polymerase chain reaction with 37 arbitrary primers from the OPERON Technologies series supplied 94 polymorphic and 73 monomorphic bands. From the matrix of complement of the Nei index, cluster analysis by the Tocher optimization method formed three clusters. Pearson correlation among genetic distance estimates obtained from the DNA markers and the isoenzymatic markers showed the consistency of both the methods in assessing genetic divergence among elephantgrass cultivars. No duplicates were found in the treatments assessed.O capim-elefante (Pennisetum purpureum Schum. é nativo de regiões da África Tropical e foi introduzido no Brasil por volta de 1920, por meio de mudas provenientes de Cuba, e é, atualmente, uma das forrageiras mais difundidas em todo o país. No início de sua utilização, existiam praticamente dois cultivares com características bem definidas, Napier e Mercker. Com o decorrer do tempo, surgiram novos genótipos e acredita-se que o grande número de cultivares existentes atualmente no Banco de Germoplasma da espécie se deva à ocorrência de duplicatas. O uso de marcadores de DNA na caracteriza

  17. 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

  18. Coherence and Divergence of Megatrends in Science and Engineering

    International Nuclear Information System (INIS)

    Roco, M.C.

    2002-01-01

    Scientific discoveries and technological innovations are at the core of human endeavor, and it is estimated that their role will only increase in time. Such advancements evolve in coherence, with areas of confluence and temporary divergences, which bring synergism and that stimulate further developments following in average an exponential growth. Six increasingly interconnected megatrends are perceived as dominating the scene for the next decades: (a) information and computing, (b) nanoscale science and engineering (S and E), (c) biology and bio-environmental approaches, (d) medical sciences and enhancing human physical capabilities, (e) cognitive sciences and enhancing intellectual abilities, and (f) collective behavior and system approach.This paper presents a perspective on the process of identification, planning and program implementation of S and E megatrends, with illustration for the US research initiative on nanoscale science, engineering, and technology. The interplay between coherence and divergence, leading to unifying science and converging technologies, does not develop only among simultaneous scientific trends but also along time and across geopolitical boundaries. There is no single way of development of S and E, and here is the role of taking visionary measures. Societal implication scientists need to be involved from the conceptual phase of a program responding to a S and E megatrend

  19. A highly divergent Puumala virus lineage in southern Poland.

    Science.gov (United States)

    Rosenfeld, Ulrike M; Drewes, Stephan; Ali, Hanan Sheikh; Sadowska, Edyta T; Mikowska, Magdalena; Heckel, Gerald; Koteja, Paweł; Ulrich, Rainer G

    2017-05-01

    Puumala virus (PUUV) represents one of the most important hantaviruses in Central Europe. Phylogenetic analyses of PUUV strains indicate a strong genetic structuring of this hantavirus. Recently, PUUV sequences were identified in the natural reservoir, the bank vole (Myodes glareolus), collected in the northern part of Poland. The objective of this study was to evaluate the presence of PUUV in bank voles from southern Poland. A total of 72 bank voles were trapped in 2009 at six sites in this part of Poland. RT-PCR and IgG-ELISA analyses detected three PUUV positive voles at one trapping site. The PUUV-infected animals were identified by cytochrome b gene analysis to belong to the Carpathian and Eastern evolutionary lineages of bank vole. The novel PUUV S, M and L segment nucleotide sequences showed the closest similarity to sequences of the Russian PUUV lineage from Latvia, but were highly divergent to those previously found in northern Poland, Slovakia and Austria. In conclusion, the detection of a highly divergent PUUV lineage in southern Poland indicates the necessity of further bank vole monitoring in this region allowing rational public health measures to prevent human infections.

  20. Quantum networks in divergence-free circuit QED

    Science.gov (United States)

    Parra-Rodriguez, A.; Rico, E.; Solano, E.; Egusquiza, I. L.

    2018-04-01

    Superconducting circuits are one of the leading quantum platforms for quantum technologies. With growing system complexity, it is of crucial importance to develop scalable circuit models that contain the minimum information required to predict the behaviour of the physical system. Based on microwave engineering methods, divergent and non-divergent Hamiltonian models in circuit quantum electrodynamics have been proposed to explain the dynamics of superconducting quantum networks coupled to infinite-dimensional systems, such as transmission lines and general impedance environments. Here, we study systematically common linear coupling configurations between networks and infinite-dimensional systems. The main result is that the simple Lagrangian models for these configurations present an intrinsic natural length that provides a natural ultraviolet cutoff. This length is due to the unavoidable dressing of the environment modes by the network. In this manner, the coupling parameters between their components correctly manifest their natural decoupling at high frequencies. Furthermore, we show the requirements to correctly separate infinite-dimensional coupled systems in local bases. We also compare our analytical results with other analytical and approximate methods available in the literature. Finally, we propose several applications of these general methods to analogue quantum simulation of multi-spin-boson models in non-perturbative coupling regimes.

  1. Happy creativity: Listening to happy music facilitates divergent thinking

    Science.gov (United States)

    Ferguson, Sam

    2017-01-01

    Creativity can be considered one of the key competencies for the twenty-first century. It provides us with the capacity to deal with the opportunities and challenges that are part of our complex and fast-changing world. The question as to what facilitates creative cognition—the ability to come up with creative ideas, problem solutions and products—is as old as the human sciences, and various means to enhance creative cognition have been studied. Despite earlier scientific studies demonstrating a beneficial effect of music on cognition, the effect of music listening on creative cognition has remained largely unexplored. The current study experimentally tests whether listening to specific types of music (four classical music excerpts systematically varying on valance and arousal), as compared to a silence control condition, facilitates divergent and convergent creativity. Creativity was higher for participants who listened to ‘happy music’ (i.e., classical music high on arousal and positive mood) while performing the divergent creativity task, than for participants who performed the task in silence. No effect of music was found for convergent creativity. In addition to the scientific contribution, the current findings may have important practical implications. Music listening can be easily integrated into daily life and may provide an innovative means to facilitate creative cognition in an efficient way in various scientific, educational and organizational settings when creative thinking is needed. PMID:28877176

  2. Expression divergence measured by transcriptome sequencing of four yeast species

    Directory of Open Access Journals (Sweden)

    Busby Michele A

    2011-12-01

    Full Text Available Abstract Background The evolution of gene expression is a challenging problem in evolutionary biology, for which accurate, well-calibrated measurements and methods are crucial. Results We quantified gene expression with whole-transcriptome sequencing in four diploid, prototrophic strains of Saccharomyces species grown under the same condition to investigate the evolution of gene expression. We found that variation in expression is gene-dependent with large variations in each gene's expression between replicates of the same species. This confounds the identification of genes differentially expressed across species. To address this, we developed a statistical approach to establish significance bounds for inter-species differential expression in RNA-Seq data based on the variance measured across biological replicates. This metric estimates the combined effects of technical and environmental variance, as well as Poisson sampling noise by isolating each component. Despite a paucity of large expression changes, we found a strong correlation between the variance of gene expression change and species divergence (R2 = 0.90. Conclusion We provide an improved methodology for measuring gene expression changes in evolutionary diverged species using RNA Seq, where experimental artifacts can mimic evolutionary effects. GEO Accession Number: GSE32679

  3. Genome-nutrition divergence: evolving understanding of the malnutrition spectrum.

    Science.gov (United States)

    Eaton, Jacob C; Iannotti, Lora L

    2017-11-01

    Humans adapted over a period of 2.3 million years to a diet high in quality and diversity. Genome-nutrition divergence describes the misalignment between modern global diets and the genome formed through evolution. A survey of hominin diets over time shows that humans have thrived on a broad range of foods. Earlier diets were highly diverse and nutrient dense, in contrast to modern food systems in which monotonous diets of staple cereals and ultraprocessed foods play a more prominent role. Applying the lens of genome-nutrition divergence to malnutrition reveals shared risk factors for undernutrition and overnutrition at nutrient, food, and environmental levels. Mechanisms for food system shifts, such as crop-neutral agricultural policy, agroecology, and social policy, are explored as a means to realign modern diets with the nutritional patterns to which humans may be better adapted to thrive. © The Author(s) 2017. Published by Oxford University Press on behalf of the International Life Sciences Institute. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  4. Distributed Vector Quantization Based on Kullback-Leibler Divergence

    Directory of Open Access Journals (Sweden)

    Pengcheng Shen

    2015-11-01

    Full Text Available The goal of vector quantization is to use a few reproduction vectors to represent original vectors/data while maintaining the necessary fidelity of the data. Distributed signal processing has received much attention in recent years, since in many applications data are dispersedly collected/stored in distributed nodes over networks, but centralizing all these data to one processing center is sometimes impractical. In this paper, we develop a distributed vector quantization (VQ algorithm based on Kullback-Leibler (K-L divergence. We start from the centralized case and propose to minimize the K-L divergence between the distribution of global original data and the distribution of global reproduction vectors, and then obtain an online iterative solution to this optimization problem based on the Robbins-Monro stochastic approximation. Afterwards, we extend the solution to apply to distributed cases by introducing diffusion cooperation among nodes. Numerical simulations show that the performances of the distributed K-L–based VQ algorithm are very close to the corresponding centralized algorithm. Besides, both the centralized and distributed K-L–based VQ show more robustness to outliers than the (centralized Linde-Buzo-Gray (LBG algorithm and the (centralized self-organization map (SOM algorithm.

  5. Adaptive divergence in resistance to herbivores in Datura stramonium

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    Guillermo Castillo

    2015-11-01

    Full Text Available Defensive traits exhibited by plants vary widely across populations. Heritable phenotypic differentiation is likely to be produced by genetic drift and spatially restricted gene flow between populations. However, spatially variable selection exerted by herbivores may also give rise to differences among populations. To explore to what extent these factors promote the among-population differentiation of plant resistance of 13 populations of Datura stramonium, we compared the degree of phenotypic differentiation (PST of leaf resistance traits (trichome density, atropine and scopolamine concentration against neutral genetic differentiation (FST at microsatellite loci. Results showed that phenotypic differentiation in defensive traits among-population is not consistent with divergence promoted by genetic drift and restricted gene flow alone. Phenotypic differentiation in scopolamine concentration was significantly higher than FST across the range of trait heritability values. In contrast, genetic differentiation in trichome density was different from FST only when heritability was very low. On the other hand, differentiation in atropine concentration differed from the neutral expectation when heritability was less than or equal to 0.3. In addition, we did not find a significant correlation between pair-wise neutral genetic distances and distances of phenotypic resistance traits. Our findings reinforce previous evidence that divergent natural selection exerted by herbivores has promoted the among-population phenotypic differentiation of defensive traits in D. stramonium.

  6. Adaptive divergence in resistance to herbivores in Datura stramonium.

    Science.gov (United States)

    Castillo, Guillermo; Valverde, Pedro L; Cruz, Laura L; Hernández-Cumplido, Johnattan; Andraca-Gómez, Guadalupe; Fornoni, Juan; Sandoval-Castellanos, Edson; Olmedo-Vicente, Erika; Flores-Ortiz, César M; Núñez-Farfán, Juan

    2015-01-01

    Defensive traits exhibited by plants vary widely across populations. Heritable phenotypic differentiation is likely to be produced by genetic drift and spatially restricted gene flow between populations. However, spatially variable selection exerted by herbivores may also give rise to differences among populations. To explore to what extent these factors promote the among-population differentiation of plant resistance of 13 populations of Datura stramonium, we compared the degree of phenotypic differentiation (P ST) of leaf resistance traits (trichome density, atropine and scopolamine concentration) against neutral genetic differentiation (F ST) at microsatellite loci. Results showed that phenotypic differentiation in defensive traits among-population is not consistent with divergence promoted by genetic drift and restricted gene flow alone. Phenotypic differentiation in scopolamine concentration was significantly higher than F ST across the range of trait heritability values. In contrast, genetic differentiation in trichome density was different from F ST only when heritability was very low. On the other hand, differentiation in atropine concentration differed from the neutral expectation when heritability was less than or equal to 0.3. In addition, we did not find a significant correlation between pair-wise neutral genetic distances and distances of phenotypic resistance traits. Our findings reinforce previous evidence that divergent natural selection exerted by herbivores has promoted the among-population phenotypic differentiation of defensive traits in D. stramonium.

  7. WORMHOLE: Novel Least Diverged Ortholog Prediction through Machine Learning.

    Science.gov (United States)

    Sutphin, George L; Mahoney, J Matthew; Sheppard, Keith; Walton, David O; Korstanje, Ron

    2016-11-01

    The rapid advancement of technology in genomics and targeted genetic manipulation has made comparative biology an increasingly prominent strategy to model human disease processes. Predicting orthology relationships between species is a vital component of comparative biology. Dozens of strategies for predicting orthologs have been developed using combinations of gene and protein sequence, phylogenetic history, and functional interaction with progressively increasing accuracy. A relatively new class of orthology prediction strategies combines aspects of multiple methods into meta-tools, resulting in improved prediction performance. Here we present WORMHOLE, a novel ortholog prediction meta-tool that applies machine learning to integrate 17 distinct ortholog prediction algorithms to identify novel least diverged orthologs (LDOs) between 6 eukaryotic species-humans, mice, zebrafish, fruit flies, nematodes, and budding yeast. Machine learning allows WORMHOLE to intelligently incorporate predictions from a wide-spectrum of strategies in order to form aggregate predictions of LDOs with high confidence. In this study we demonstrate the performance of WORMHOLE across each combination of query and target species. We show that WORMHOLE is particularly adept at improving LDO prediction performance between distantly related species, expanding the pool of LDOs while maintaining low evolutionary distance and a high level of functional relatedness between genes in LDO pairs. We present extensive validation, including cross-validated prediction of PANTHER LDOs and evaluation of evolutionary divergence and functional similarity, and discuss future applications of machine learning in ortholog prediction. A WORMHOLE web tool has been developed and is available at http://wormhole.jax.org/.

  8. WORMHOLE: Novel Least Diverged Ortholog Prediction through Machine Learning.

    Directory of Open Access Journals (Sweden)

    George L Sutphin

    2016-11-01

    Full Text Available The rapid advancement of technology in genomics and targeted genetic manipulation has made comparative biology an increasingly prominent strategy to model human disease processes. Predicting orthology relationships between species is a vital component of comparative biology. Dozens of strategies for predicting orthologs have been developed using combinations of gene and protein sequence, phylogenetic history, and functional interaction with progressively increasing accuracy. A relatively new class of orthology prediction strategies combines aspects of multiple methods into meta-tools, resulting in improved prediction performance. Here we present WORMHOLE, a novel ortholog prediction meta-tool that applies machine learning to integrate 17 distinct ortholog prediction algorithms to identify novel least diverged orthologs (LDOs between 6 eukaryotic species-humans, mice, zebrafish, fruit flies, nematodes, and budding yeast. Machine learning allows WORMHOLE to intelligently incorporate predictions from a wide-spectrum of strategies in order to form aggregate predictions of LDOs with high confidence. In this study we demonstrate the performance of WORMHOLE across each combination of query and target species. We show that WORMHOLE is particularly adept at improving LDO prediction performance between distantly related species, expanding the pool of LDOs while maintaining low evolutionary distance and a high level of functional relatedness between genes in LDO pairs. We present extensive validation, including cross-validated prediction of PANTHER LDOs and evaluation of evolutionary divergence and functional similarity, and discuss future applications of machine learning in ortholog prediction. A WORMHOLE web tool has been developed and is available at http://wormhole.jax.org/.

  9. Fossils, molecules, divergence times, and the origin of lissamphibians.

    Science.gov (United States)

    Marjanović, David; Laurin, Michel

    2007-06-01

    A review of the paleontological literature shows that the early dates of appearance of Lissamphibia recently inferred from molecular data do not favor an origin of extant amphibians from temnospondyls, contrary to recent claims. A supertree is assembled using new Mesquite modules that allow extinct taxa to be incorporated into a time-calibrated phylogeny with a user-defined geological time scale. The supertree incorporates 223 extinct species of lissamphibians and has a highly significant stratigraphic fit. Some divergences can even be dated with sufficient precision to serve as calibration points in molecular divergence date analyses. Fourteen combinations of minimal branch length settings and 10 random resolutions for each polytomy give much more recent minimal origination times of lissamphibian taxa than recent studies based on a phylogenetic analyses of molecular sequences. Attempts to replicate recent molecular date estimates show that these estimates depend strongly on the choice of calibration points, on the dating method, and on the chosen model of evolution; for instance, the estimate for the date of the origin of Lissamphibia can lie between 351 and 266 Mya. This range of values is generally compatible with our time-calibrated supertree and indicates that there is no unbridgeable gap between dates obtained using the fossil record and those using molecular evidence, contrary to previous suggestions.

  10. Happy creativity: Listening to happy music facilitates divergent thinking.

    Directory of Open Access Journals (Sweden)

    Simone M Ritter

    Full Text Available Creativity can be considered one of the key competencies for the twenty-first century. It provides us with the capacity to deal with the opportunities and challenges that are part of our complex and fast-changing world. The question as to what facilitates creative cognition-the ability to come up with creative ideas, problem solutions and products-is as old as the human sciences, and various means to enhance creative cognition have been studied. Despite earlier scientific studies demonstrating a beneficial effect of music on cognition, the effect of music listening on creative cognition has remained largely unexplored. The current study experimentally tests whether listening to specific types of music (four classical music excerpts systematically varying on valance and arousal, as compared to a silence control condition, facilitates divergent and convergent creativity. Creativity was higher for participants who listened to 'happy music' (i.e., classical music high on arousal and positive mood while performing the divergent creativity task, than for participants who performed the task in silence. No effect of music was found for convergent creativity. In addition to the scientific contribution, the current findings may have important practical implications. Music listening can be easily integrated into daily life and may provide an innovative means to facilitate creative cognition in an efficient way in various scientific, educational and organizational settings when creative thinking is needed.

  11. Happy creativity: Listening to happy music facilitates divergent thinking.

    Science.gov (United States)

    Ritter, Simone M; Ferguson, Sam

    2017-01-01

    Creativity can be considered one of the key competencies for the twenty-first century. It provides us with the capacity to deal with the opportunities and challenges that are part of our complex and fast-changing world. The question as to what facilitates creative cognition-the ability to come up with creative ideas, problem solutions and products-is as old as the human sciences, and various means to enhance creative cognition have been studied. Despite earlier scientific studies demonstrating a beneficial effect of music on cognition, the effect of music listening on creative cognition has remained largely unexplored. The current study experimentally tests whether listening to specific types of music (four classical music excerpts systematically varying on valance and arousal), as compared to a silence control condition, facilitates divergent and convergent creativity. Creativity was higher for participants who listened to 'happy music' (i.e., classical music high on arousal and positive mood) while performing the divergent creativity task, than for participants who performed the task in silence. No effect of music was found for convergent creativity. In addition to the scientific contribution, the current findings may have important practical implications. Music listening can be easily integrated into daily life and may provide an innovative means to facilitate creative cognition in an efficient way in various scientific, educational and organizational settings when creative thinking is needed.

  12. Gene duplication and divergence affecting drug content in Cannabis sativa.

    Science.gov (United States)

    Weiblen, George D; Wenger, Jonathan P; Craft, Kathleen J; ElSohly, Mahmoud A; Mehmedic, Zlatko; Treiber, Erin L; Marks, M David

    2015-12-01

    Cannabis sativa is an economically important source of durable fibers, nutritious seeds, and psychoactive drugs but few economic plants are so poorly understood genetically. Marijuana and hemp were crossed to evaluate competing models of cannabinoid inheritance and to explain the predominance of tetrahydrocannabinolic acid (THCA) in marijuana compared with cannabidiolic acid (CBDA) in hemp. Individuals in the resulting F2 population were assessed for differential expression of cannabinoid synthase genes and were used in linkage mapping. Genetic markers associated with divergent cannabinoid phenotypes were identified. Although phenotypic segregation and a major quantitative trait locus (QTL) for the THCA/CBDA ratio were consistent with a simple model of codominant alleles at a single locus, the diversity of THCA and CBDA synthase sequences observed in the mapping population, the position of enzyme coding loci on the map, and patterns of expression suggest multiple linked loci. Phylogenetic analysis further suggests a history of duplication and divergence affecting drug content. Marijuana is distinguished from hemp by a nonfunctional CBDA synthase that appears to have been positively selected to enhance psychoactivity. An unlinked QTL for cannabinoid quantity may also have played a role in the recent escalation of drug potency. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

  13. Vertical divergence of fogwater fluxes above a spruce forest

    Science.gov (United States)

    Burkard, R.; Eugster, W.; Wrzesinsky, T.; Klemm, O.

    Two almost identical eddy covariance measurement setups were used to measure the fogwater fluxes to a forest ecosystem in the "Fichtelgebirge" mountains (Waldstein research site, 786 m a.s.l.) in Germany. During the first experiment, an intercomparison was carried out with both setups running simultaneously at the same measuring height on a meteorological tower, 12.5 m above the forest canopy. The results confirmed a close agreement of the turbulent fluxes between the two setups, and allowed to intercalibrate liquid water content (LWC) and gravitational fluxes. During the second experiment, the setups were mounted at a height of 12.5 and 3 m above the canopy, respectively. For the 22 fog events, a persistent negative flux divergence was observed with a greater downward flux at the upper level. To extrapolate the turbulent liquid water fluxes measured at height z to the canopy of height hc, a conversion factor 1/[1+0.116( z- hc)] was determined. For the fluxes of nonvolatile ions, no such correction is necessary since the net evaporation of the fog droplets appears to be the primary cause of the vertical flux divergence. Although the net evaporation reduces the liquid water flux reaching the canopy, it is not expected to change the absolute amount of ions dissolved in fogwater.

  14. The taxonomic placement of three fossil Fundulus species and the timing of divergence within the North American topminnows (Teleostei: Fundulidae).

    Science.gov (United States)

    Ghedotti, Michael J; Davis, Matthew P

    2017-04-10

    The fossils species †Fundulus detillae, †F. lariversi, and †F. nevadensis from localities in the western United States are represented by well-preserved material with date estimations. We combined morphological data for these fossil taxa with morphological and DNA-sequence data to conduct a phylogenetic analysis and a tip-based divergence-time estimation for the family Fundulidae. The resultant phylogeny is largely concordant with the prior total-evidence phylogeny. The fossil species do not form a monophyletic group, and do not represent a discrete western radiation of Fundulus as previously proposed. The genus Fundulus diverged into subgeneric clades likely in the Eocene or Oligocene (mean age 34.6 mya, 53-23 mya), and all subgeneric and most species-group clades had evolved by the middle Miocene. †Fundulus lariversi is a member of subgenus Fundulus in which all extant species are found only in eastern North America, demonstrating that fundulids had a complicated biogeographic history. We confirmed †Fundulus detillae as a member of the subgenus Plancterus. †F. nevadensis is not classified in a subgenus but likely is related to the subgenera Plancterus and Wileyichthys.

  15. DNA barcoding Bromeliaceae: achievements and pitfalls.

    Directory of Open Access Journals (Sweden)

    Vitor Hugo Maia

    Full Text Available BACKGROUND: DNA barcoding has been successfully established in animals as a tool for organismal identification and taxonomic clarification. Slower nucleotide substitution rates in plant genomes have made the selection of a DNA barcode for land plants a much more difficult task. The Plant Working Group of the Consortium for the Barcode of Life (CBOL recommended the two-marker combination rbcL/matK as a pragmatic solution to a complex trade-off between universality, sequence quality, discrimination, and cost. METHODOLOGY/PRINCIPAL FINDINGS: It is expected that a system based on any one, or a small number of plastid genes will fail within certain taxonomic groups with low amounts of plastid variation, while performing well in others. We tested the effectiveness of the proposed CBOL Plant Working Group barcoding markers for land plants in identifying 46 bromeliad species, a group rich in endemic species from the endangered Brazilian Atlantic Rainforest. Although we obtained high quality sequences with the suggested primers, species discrimination in our data set was only 43.48%. Addition of a third marker, trnH-psbA, did not show significant improvement. This species identification failure in Bromeliaceaecould also be seen in the analysis of the GenBank's matK data set. Bromeliaceae's sequence divergence was almost three times lower than the observed for Asteraceae and Orchidaceae. This low variation rate also resulted in poorly resolved tree topologies. Among the three Bromeliaceae subfamilies sampled, Tillandsioideae was the only one recovered as a monophyletic group with high bootstrap value (98.6%. Species paraphyly was a common feature in our sampling. CONCLUSIONS/SIGNIFICANCE: Our results show that although DNA barcoding is an important tool for biodiversity assessment, it tends to fail in taxonomy complicated and recently diverged plant groups, such as Bromeliaceae. Additional research might be needed to develop markers capable to

  16. DNA barcoding Bromeliaceae: achievements and pitfalls.

    Science.gov (United States)

    Maia, Vitor Hugo; Mata, Camila Souza da; Franco, Luciana Ozório; Cardoso, Mônica Aires; Cardoso, Sérgio Ricardo Sodré; Hemerly, Adriana Silva; Ferreira, Paulo Cavalcanti Gomes

    2012-01-01

    DNA barcoding has been successfully established in animals as a tool for organismal identification and taxonomic clarification. Slower nucleotide substitution rates in plant genomes have made the selection of a DNA barcode for land plants a much more difficult task. The Plant Working Group of the Consortium for the Barcode of Life (CBOL) recommended the two-marker combination rbcL/matK as a pragmatic solution to a complex trade-off between universality, sequence quality, discrimination, and cost. It is expected that a system based on any one, or a small number of plastid genes will fail within certain taxonomic groups with low amounts of plastid variation, while performing well in others. We tested the effectiveness of the proposed CBOL Plant Working Group barcoding markers for land plants in identifying 46 bromeliad species, a group rich in endemic species from the endangered Brazilian Atlantic Rainforest. Although we obtained high quality sequences with the suggested primers, species discrimination in our data set was only 43.48%. Addition of a third marker, trnH-psbA, did not show significant improvement. This species identification failure in Bromeliaceaecould also be seen in the analysis of the GenBank's matK data set. Bromeliaceae's sequence divergence was almost three times lower than the observed for Asteraceae and Orchidaceae. This low variation rate also resulted in poorly resolved tree topologies. Among the three Bromeliaceae subfamilies sampled, Tillandsioideae was the only one recovered as a monophyletic group with high bootstrap value (98.6%). Species paraphyly was a common feature in our sampling. Our results show that although DNA barcoding is an important tool for biodiversity assessment, it tends to fail in taxonomy complicated and recently diverged plant groups, such as Bromeliaceae. Additional research might be needed to develop markers capable to discriminate species in these complex botanical groups.

  17. DNA Damage, DNA Repair, Aging, and Neurodegeneration

    Science.gov (United States)

    Maynard, Scott; Fang, Evandro Fei; Scheibye-Knudsen, Morten; Croteau, Deborah L.; Bohr, Vilhelm A.

    2015-01-01

    Aging in mammals is accompanied by a progressive atrophy of tissues and organs, and stochastic damage accumulation to the macromolecules DNA, RNA, proteins, and lipids. The sequence of the human genome represents our genetic blueprint, and accumulating evidence suggests that loss of genomic maintenance may causally contribute to aging. Distinct evidence for a role of imperfect DNA repair in aging is that several premature aging syndromes have underlying genetic DNA repair defects. Accumulation of DNA damage may be particularly prevalent in the central nervous system owing to the low DNA repair capacity in postmitotic brain tissue. It is generally believed that the cumulative effects of the deleterious changes that occur in aging, mostly after the reproductive phase, contribute to species-specific rates of aging. In addition to nuclear DNA damage contributions to aging, there is also abundant evidence for a causative link between mitochondrial DNA damage and the major phenotypes associated with aging. Understanding the mechanistic basis for the association of DNA damage and DNA repair with aging and age-related diseases, such as neurodegeneration, would give insight into contravening age-related diseases and promoting a healthy life span. PMID:26385091

  18. Phylogeography, genetic structure and population divergence time of cheetahs in Africa and Asia: evidence for long-term geographic isolates

    Science.gov (United States)

    Charruau, P; Fernandes, C; Orozco-terWengel, P; Peters, J; Hunter, L; Ziaie, H; Jourabchian, A; Jowkar, H; Schaller, G; Ostrowski, S; Vercammen, P; Grange, T; Schlötterer, C; Kotze, A; Geigl, E-M; Walzer, C; Burger, P A

    2011-01-01

    The cheetah (Acinonyx jubatus) has been described as a species with low levels of genetic variation. This has been suggested to be the consequence of a demographic bottleneck 10 000–12 000 years ago (ya) and also led to the assumption that only small genetic differences exist between the described subspecies. However, analysing mitochondrial DNA and microsatellites in cheetah samples from most of the historic range of the species we found relatively deep phylogeographic breaks between some of the investigated populations, and most of the methods assessed divergence time estimates predating the postulated bottleneck. Mitochondrial DNA monophyly and overall levels of genetic differentiation support the distinctiveness of Northern-East African cheetahs (Acinonyx jubatus soemmeringii). Moreover, combining archaeozoological and contemporary samples, we show that Asiatic cheetahs (Acinonyx jubatus venaticus) are unambiguously separated from African subspecies. Divergence time estimates from mitochondrial and nuclear data place the split between Asiatic and Southern African cheetahs (Acinonyx jubatus jubatus) at 32 000–67 000 ya using an average mammalian microsatellite mutation rate and at 4700–44 000 ya employing human microsatellite mutation rates. Cheetahs are vulnerable to extinction globally and critically endangered in their Asiatic range, where the last 70–110 individuals survive only in Iran. We demonstrate that these extant Iranian cheetahs are an autochthonous monophyletic population and the last representatives of the Asiatic subspecies A. j. venaticus. We advocate that conservation strategies should consider the uncovered independent evolutionary histories of Asiatic and African cheetahs, as well as among some African subspecies. This would facilitate the dual conservation priorities of maintaining locally adapted ecotypes and genetic diversity. PMID:21214655

  19. Divergência genética entre cultivares de caupi Genetic divergence among cultivars of cowpea

    Directory of Open Access Journals (Sweden)

    Francisco José de Oliveira

    2003-05-01

    Full Text Available O objetivo deste trabalho foi quantificar a divergência genética de cultivares de caupi, agrupadas por análise multivariada visando à seleção de parentais superiores. Foram utilizadas 16 cultivares de caupi [Vigna unguiculata (L. Walp.] do banco de germoplasma do Centro de Ciências Agrárias da Universidade Federal do Ceará. As observações fenotípicas foram realizadas num ensaio com delineamento experimental em blocos completos casualizados, com seis blocos e 16 tratamentos, incluindo três testemunhas, com parcela experimental de 24 m² e área útil de 16 m², sendo quatro fileiras de plantas, com espaços de 1,0 x 0,5 m, contendo duas plantas por cova. Para mensurar os caracteres fenotípicos, cinco plantas competitivas, localizadas nas duas fileiras centrais da parcela, foram tomadas ao acaso. Os cruzamentos entre os grupos I [TVx-337-3F e Vita-4 (TVu 1977-OD] e II (Bengala e V-4 Alagoas podem resultar em produção de novas combinações gênicas, por serem divergentes e reunirem maior número de caracteres agronomicamente desejáveis. Os caracteres que mais contribuem para divergência genética são o comprimento da vagem (36,80% e o peso de 100 sementes (19,21%.This work aimed to determine the genetic divergence among cowpea cultivars [Vigna unguiculata (L. Walp.] when grouped in a multivariate analysis concerning to select superior parents. So 16 cowpea cultivars were used from the germplasm bank of the Centro de Ciências Agrárias of the Universidade Federal do Ceará, in Brazil. The data were accomplished in complete randomized blocks, with six blocks, 16 treatments and three cultivar checks. The total area of experimental plots was 24 m² and the net area was 16 m², displayed in four rows, plants were spaced about 1.0 x 0.5 m with two plants in each plot. The phenotypic data were estimated from five competitive plants as casual samples on two central rows of each replicate. Breeding among the groups I [TVx-337-3F and

  20. Quantifying the roles of ecology and geography in spatial genetic divergence.

    Science.gov (United States)

    Wang, Ian J; Glor, Richard E; Losos, Jonathan B

    2013-02-01

    Investigating the properties of ecological landscapes that influence gene flow among populations can provide key insights into the earliest stages of biological divergence. Both ecological and geographical factors can reduce gene flow, which can lead to population divergence, but we know little of the relative strengths of these phenomena in nature. Here, we use a novel application of structural equation modelling to quantify the contributions of ecological and geographical isolation to spatial genetic divergence in 17 species of Anolis lizards. Our comparative analysis shows that although both processes contributed significantly, geographical isolation explained substantially more genetic divergence than ecological isolation (36.3 vs. 17.9% of variance respectively), suggesting that despite the proposed ubiquity of ecological divergence, non-ecological factors play the dominant role in the evolution of spatial genetic divergence. © 2012 Blackwell Publishing Ltd/CNRS.

  1. Genomic islands of divergence are not affected by geography of speciation in sunflowers.

    Science.gov (United States)

    Renaut, S; Grassa, C J; Yeaman, S; Moyers, B T; Lai, Z; Kane, N C; Bowers, J E; Burke, J M; Rieseberg, L H

    2013-01-01

    Genomic studies of speciation often report the presence of highly differentiated genomic regions interspersed within a milieu of weakly diverged loci. The formation of these speciation islands is generally attributed to reduced inter-population gene flow near loci under divergent selection, but few studies have critically evaluated this hypothesis. Here, we report on transcriptome scans among four recently diverged pairs of sunflower (Helianthus) species that vary in the geographical context of speciation. We find that genetic divergence is lower in sympatric and parapatric comparisons, consistent with a role for gene flow in eroding neutral differences. However, genomic islands of divergence are numerous and small in all comparisons, and contrary to expectations, island number and size are not significantly affected by levels of interspecific gene flow. Rather, island formation is strongly associated with reduced recombination rates. Overall, our results indicate that the functional architecture of genomes plays a larger role in shaping genomic divergence than does the geography of speciation.

  2. Understanding creative cultural divergence: a Bakhtinian reflection from a culture-crossing scholar

    Science.gov (United States)

    Hsu, Pei-Ling

    2012-03-01

    I respond to Baron and Chen's article on creative cultural divergence, which they describe as the novel pedagogy of diverging from culturally generated educational expectations. Their article provides an analysis on how an experienced Taiwanese teacher drew on different forms of creative cultural divergence to facilitate students' critical thinking and science inquiry. To better understand the phenomenon of creative cultural divergence, I draw on Bakhtin's concepts of outsideness, novelization, and internally persuasive discourse to analyze how these divergences are produced. These concepts not only help us to understand the phenomenon of creative cultural divergence, they also help me to reflect on my own culture-crossing experience. The implications of these concepts for culture and education are further discussed.

  3. Two distinct mtDNA lineages among captive African penguins in Japan.

    Science.gov (United States)

    Murata, Michiko; Murakami, Masaru

    2014-04-01

    The African penguin (Spheniscus demersus) is one of the world's most endangered seabirds. In Japan, although the number of African penguins in captivity continues to increase, genetic data have not been collected for either wild or captive populations. To reveal genetic diversity and characterization in captive African penguins, we analyzed the nucleotide sequences of mitochondrial DNA (mtDNA) from a sample of 236 African penguins. Analysis of 433 bp of the control region and 1,140 bp of cytochrome b sequences revealed the existence of two mtDNA clades. Control region haplotypes were much more divergent (d=3.39%) between the two clades than within each clade. The divergence of these clades may reflect differences at the subspecies or geographical population level in African penguins. These findings suggest that at least two distinct maternal lineages exist in the wild populations of the African penguin.

  4. Out of Borneo: biogeography, phylogeny and divergence date estimates of Artocarpus (Moraceae).

    Science.gov (United States)

    Williams, Evelyn W; Gardner, Elliot M; Harris, Robert; Chaveerach, Arunrat; Pereira, Joan T; Zerega, Nyree J C

    2017-03-01

    The breadfruit genus ( Artocarpus , Moraceae) includes valuable underutilized fruit tree crops with a centre of diversity in Southeast Asia. It belongs to the monophyletic tribe Artocarpeae, whose only other members include two small neotropical genera. This study aimed to reconstruct the phylogeny, estimate divergence dates and infer ancestral ranges of Artocarpeae, especially Artocarpus , to better understand spatial and temporal evolutionary relationships and dispersal patterns in a geologically complex region. To investigate the phylogeny and biogeography of Artocarpeae, this study used Bayesian and maximum likelihood approaches to analyze DNA sequences from six plastid and two nuclear regions from 75% of Artocarpus species, both neotropical Artocarpeae genera, and members of all other Moraceae tribes. Six fossil-based calibrations within the Moraceae family were used to infer divergence times. Ancestral areas and estimated dispersal events were also inferred. Artocarpeae, Artocarpus and four monophyletic Artocarpus subgenera were well supported. A late Cretaceous origin of the Artocarpeae tribe in the Americas is inferred, followed by Eocene radiation of Artocarpus in Asia, with the greatest diversification occurring during the Miocene. Borneo is reconstructed as the ancestral range of Artocarpus , with dozens of independent in situ diversification events inferred there, as well as dispersal events to other regions of Southeast Asia. Dispersal pathways of Artocarpus and its ancestors are proposed. Borneo was central in the diversification of the genus Artocarpus and probably served as the centre from which species dispersed and diversified in several directions. The greatest amount of diversification is inferred to have occurred during the Miocene, when sea levels fluctuated and land connections frequently existed between Borneo, mainland Asia, Sumatra and Java. Many species found in these areas have extant overlapping ranges, suggesting that sympatric

  5. ex vivo DNA assembly

    Directory of Open Access Journals (Sweden)

    Adam B Fisher

    2013-10-01

    Full Text Available Even with decreasing DNA synthesis costs there remains a need for inexpensive, rapid and reliable methods for assembling synthetic DNA into larger constructs or combinatorial libraries. Advances in cloning techniques have resulted in powerful in vitro and in vivo assembly of DNA. However, monetary and time costs have limited these approaches. Here, we report an ex vivo DNA assembly method that uses cellular lysates derived from a commonly used laboratory strain of Escherichia coli for joining double-stranded DNA with short end homologies embedded within inexpensive primers. This method concurrently shortens the time and decreases costs associated with current DNA assembly methods.

  6. Characterization of a variant vlhA gene of Mycoplasma synoviae, strain WVU 1853, with a highly divergent haemagglutinin region

    Directory of Open Access Journals (Sweden)

    Ben Abdelmoumen Mardassi Boutheina

    2010-01-01

    Full Text Available Abstract Background In Mycoplasma synoviae, type strain WVU 1853, a single member of the haemaglutinin vlhA gene family has been previously shown to be expressed. Variants of vlhA are expressed from the same unique vlhA promoter by recruiting pseudogene sequences via site-specific recombination events, thus generating antigenic variability. Using a bacterial stock of M. synoviae WVU 1853 that had been colony purified thrice and maintained in our laboratory at low passage level, we previously identified a vlhA gene-related partial coding sequence, referred to as MS2/28.1. The E. coli-expressed product of this partial coding sequence was found to be immunodominant, suggesting that it might be expressed. Results Reverse transcription-PCR amplification (RT-PCR, using a sense primer located at the 5'-end region of the expected vlhA transcript and a reverse primer located at the 3' end of MS2/28.1 coding sequence, yielded a consistent amplification product showing that MS2/28.1 was indeed transcribed. Nucleotide sequence analysis of the RT-PCR product identified an 1815-nucleotide full-length open reading frame (ORF, immediately preceded by a nucleotide sequence identical to that previously reported for expressed vlhA genes. PCR amplifications using genomic DNA isolated from single colonies further confirmed that the full-length ORF of MS2/28.1 was located downstream of the unique vlhA promoter sequence. The deduced 604-amino acid (aa sequence showed a perfect sequence identity to the previously reported vlhA expressed genes along the first 224 residues, then highly diverged with only 37.6% aa identity. Despite the fact that this M. synoviae clone expressed a highly divergent and considerably shorter C-terminal haemagglutinin product, it was found to be expressed at the surface of the bacterium and was able to haemagglutinate chicken erythrocytes. Importantly, the E. coli-expressed C-terminal highly divergent 60 residues of MS2/28.1 proved

  7. Identification of species Leucochloridium paradoxum and L. perturbatum (Trematoda) based on rDNA sequences.

    Science.gov (United States)

    Zhukova, A; Prokhorova, E E; Tokmakova, A S; Tsymbalenko, N V; Ataev, G L

    2014-01-01

    The full nucleotide sequences of DNA ribosome cluster of Leucochloridium paradoxum Carus, 1835 and L. perturbatum Pojmanska, 1967 were obtained. rDNA was extracted from 40 isolates of Leucochloridium sp. and analyzed using specific primers. The intraspecific genetically identity of morphologically detected L. paradoxum and L. perturbatum sporocysts was proven. A noticeable interspecific divergence between L. paradoxum and L. perturbatum was indicated. Using rDNA genotyping a case of double infection of snail Succinea sp. with L. paradoxum and L. perturbatum sporocysts was detected.

  8. Arachidonic and oleic acid exert distinct effects on the DNA methylome

    DEFF Research Database (Denmark)

    Silva-Martínez, Guillermo A.; Rodríguez-Ríos, Dalia; Alvarado-Caudillo, Yolanda

    2016-01-01

    ABSTRACT: Abnormal fatty acid metabolism and availability are landmarks of metabolic diseases, which in turn are associated with aberrant DNA methylation profiles. To understand the role of fatty acids in disease epigenetics, we sought DNA methylation profiles specifically induced by arachidonic....... The divergent response to AA and OA was prominent within the gene body of target genes, where it correlated positively with transcription. AA-induced DNA methylation profiles were similar to the corresponding profiles described for palmitic acid, atherosclerosis, diabetes, obesity, and autism, but relatively...

  9. Kullback-Leibler divergence and the Pareto-Exponential approximation.

    Science.gov (United States)

    Weinberg, G V

    2016-01-01

    Recent radar research interests in the Pareto distribution as a model for X-band maritime surveillance radar clutter returns have resulted in analysis of the asymptotic behaviour of this clutter model. In particular, it is of interest to understand when the Pareto distribution is well approximated by an Exponential distribution. The justification for this is that under the latter clutter model assumption, simpler radar detection schemes can be applied. An information theory approach is introduced to investigate the Pareto-Exponential approximation. By analysing the Kullback-Leibler divergence between the two distributions it is possible to not only assess when the approximation is valid, but to determine, for a given Pareto model, the optimal Exponential approximation.

  10. Divergent series, summability and resurgence I monodromy and resurgence

    CERN Document Server

    Mitschi, Claude

    2016-01-01

    Providing an elementary introduction to analytic continuation and monodromy, the first part of this volume applies these notions to the local and global study of complex linear differential equations, their formal solutions at singular points, their monodromy and their differential Galois groups. The Riemann-Hilbert problem is discussed from Bolibrukh’s point of view. The second part expounds 1-summability and Ecalle’s theory of resurgence under fairly general conditions. It contains numerous examples and presents an analysis of the singularities in the Borel plane via “alien calculus”, which provides a full description of the Stokes phenomenon for linear or non-linear differential or difference equations. The first of a series of three, entitled Divergent Series, Summability and Resurgence, this volume is aimed at graduate students, mathematicians and theoretical physicists interested in geometric, algebraic or local analytic properties of dynamical systems. It includes useful exercises with solution...

  11. Entangled inequalities, divergent struggles: migration and the Argentine textile industry

    Directory of Open Access Journals (Sweden)

    Sergio Caggiano

    2014-09-01

    Full Text Available Despite the economic recovery that followed the 2001-2002 crisis in Argentina, sectors that rely on a significant migrant worker presence, such as textiles, have maintained and consolidated previously-existing forms of exploitation and discrimination. In this context, trade unions and other civil society actors are fighting against the inequalities that affect Bolivian migrant workers in the textile industry in Buenos Aires and La Plata. This article seeks to understand some of the limitations of that struggle. Such limitations relate to the difficulty of acting on entangled inequalities, and respond to the seemingly irreconcilable forms of association in terms of class, nationality or ethnicity of these organisations, which generate divergent characterisations of the inequalities and of the actors involved.

  12. Regularized κ-distributions with non-diverging moments

    Science.gov (United States)

    Scherer, K.; Fichtner, H.; Lazar, M.

    2017-12-01

    For various plasma applications the so-called (non-relativistic) κ-distribution is widely used to reproduce and interpret the suprathermal particle populations exhibiting a power-law distribution in velocity or energy. Despite its reputation the standard κ-distribution as a concept is still disputable, mainly due to the velocity moments M l which make a macroscopic characterization possible, but whose existence is restricted only to low orders l definition of the κ-distribution itself is conditioned by the existence of the moment of order l = 2 (i.e., kinetic temperature) satisfied only for κ > 3/2 . In order to resolve these critical limitations we introduce the regularized κ-distribution with non-diverging moments. For the evaluation of all velocity moments a general analytical expression is provided enabling a significant step towards a macroscopic (fluid-like) description of space plasmas, and, in general, any system of κ-distributed particles.

  13. A detector for localizing diverging beams of ionizing radiations

    International Nuclear Information System (INIS)

    Allemand, Robert.

    1974-01-01

    Description is given of a detector for localizing diverging radiation beams, adapted to provide the angular distribution of nuclear events. That detector comprises a casing filled with a fluid adapted to produce electric charges under radiations and provided with a front-side and a rear-side, means for generating an electric field at right angles to portions of parallel surfaces of revolution having in common an axis of revolution contained in the place of symmetry, and a plane unit for localizing electric charges mounted at the rear of said means, the initial portion of the beam being on the axis of revolution. This can be applied to X-ray diffraction and to neutron diffraction [fr

  14. Research Performance Progress Report: Diverging Supernova Explosion Experiments on NIF

    Energy Technology Data Exchange (ETDEWEB)

    Plewa, Tomasz [Florida State Univ., Tallahassee, FL (United States)

    2016-10-25

    The aim of this project was to design a series of blast-wave driven Rayleigh-Taylor (RT) experiments on the National Ignition Facility (NIF). The experiments of this kind are relevant to mixing in core-collapse supernovae (ccSNe) and have the potential to address previously unanswered questions in high-energy density physics (HEDP) and astrophysics. The unmatched laser power of the NIF laser offers a unique chance to observe and study “new physics” like the mass extensions observed in HEDP RT experiments performed on the Omega laser [1], which might be linked to self-generated magnetic fields [2] and so far could not be reproduced by numerical simulations. Moreover, NIF is currently the only facility that offers the possibility to execute a diverging RT experiment, which would allow to observe processes such as inter-shell penetration via turbulent mixing and shock-proximity effects (distortion of the shock by RT spikes).

  15. Activation Detection in fMRI Using Jeffrey Divergence

    Science.gov (United States)

    Seghouane, Abd-Krim

    2009-12-01

    A statistical test for detecting activated pixels in functional MRI (fMRI) data is proposed. For the derivation of this test, the fMRI time series measured at each voxel is modeled as the sum of a response signal which arises due to the experimentally controlled activation-baseline pattern, a nuisance component representing effects of no interest, and Gaussian white noise. The test is based on comparing the dimension of the voxels fMRI time series fitted data models with and without controlled activation-baseline pattern. The Jeffrey divergence is used for this comparison. The test has the advantage of not requiring a level of significance or a threshold to be provided.

  16. Agreements and Divergences in German Idealism: Regarding the Publication

    Directory of Open Access Journals (Sweden)

    Hugo Ochoa

    2011-12-01

    Full Text Available The history of German Idealism is marked by points of agreement and divergence among those who attempted to complete a task that might have remained unfinished in terms of its first formulations and that would lead to the definitive constitution of philosophy. In this sense, the correspondence among Kant, Fichte, Schelling, and Hegel makes it possible to unravel, to some extent, the non-explicitassumptions underlying the systems of these thinkers, since it reveals the questions,objectives, initial formulations, discussions, and differences that would later acquire a systematic structure. This article attempts to show how despite the intention of these philosophers to remain faithful to an original impulse, that allegedfidelity was based on essential misunderstandings.

  17. The Global Monsoon as Seen through the Divergent Atmospheric Circulation.

    Science.gov (United States)

    Trenberth, Kevin E.; Stepaniak, David P.; Caron, Julie M.

    2000-11-01

    A comprehensive description is given of the global monsoon as seen through the large-scale overturning in the atmosphere that changes with the seasons, and it provides a basis for delimiting the monsoon regions of the world. The analysis focuses on the mean annual cycle of the divergent winds and associated vertical motions, as given by the monthly mean fields for 1979-93 reanalyses from the National Centers for Environmental Prediction-National Center for Atmospheric Research (NCEP-NCAR) and European Centre for Medium-Range Weather Forecasts (ECMWF), which are able to reproduce the dominant modes. A complex empirical orthogonal function analysis of the divergent circulation brings out two dominant modes with essentially the same vertical structures in all months of the year. The first mode, which depicts the global monsoon, has a simple vertical structure with a maximum in vertical motion at about 400 mb, divergence in the upper troposphere that is strongest at 150 mb and decays to zero amplitude above 70 mb, and convergence in the lower troposphere with a maximum at 925 mb (ECMWF) or 850 mb (NCEP). However, this mode has a rich three-dimensional spatial structure that evolves with the seasons. It accounts for 60% of the annual cycle variance of the divergent mass circulation and dominates the Hadley circulation as well as three overturning transverse cells. These include the Pacific Walker circulation; an Americas-Atlantic Walker circulation, both of which comprise rising motion in the west and sinking in the east; and a transverse cell over Asia, the Middle East, North Africa, and the Indian Ocean that has rising motion in the east and sinking toward the west. These exist year-round but migrate and evolve considerably with the seasons and have about a third to half of the mass flux of the peak Hadley cell. The annual cycle of the two Hadley cells reveals peak strength in early February and early August in both reanalyses.A second monsoon mode, which accounts for

  18. A Divergence Statistics Extension to VTK for Performance Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Pebay, Philippe Pierre [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Bennett, Janine Camille [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2015-02-01

    This report follows the series of previous documents ([PT08, BPRT09b, PT09, BPT09, PT10, PB13], where we presented the parallel descriptive, correlative, multi-correlative, principal component analysis, contingency, k -means, order and auto-correlative statistics engines which we developed within the Visualization Tool Kit ( VTK ) as a scalable, parallel and versatile statistics package. We now report on a new engine which we developed for the calculation of divergence statistics, a concept which we hereafter explain and whose main goal is to quantify the discrepancy, in a stasticial manner akin to measuring a distance, between an observed empirical distribution and a theoretical, "ideal" one. The ease of use of the new diverence statistics engine is illustrated by the means of C++ code snippets. Although this new engine does not yet have a parallel implementation, it has already been applied to HPC performance analysis, of which we provide an example.

  19. Kullback-Leibler divergence measure of intermittency: Application to turbulence

    Science.gov (United States)

    Granero-Belinchón, Carlos; Roux, Stéphane G.; Garnier, Nicolas B.

    2018-01-01

    For generic systems exhibiting power law behaviors, and hence multiscale dependencies, we propose a simple tool to analyze multifractality and intermittency, after noticing that these concepts are directly related to the deformation of a probability density function from Gaussian at large scales to non-Gaussian at smaller scales. Our framework is based on information theory and uses Shannon entropy and Kullback-Leibler divergence. We provide an extensive application to three-dimensional fully developed turbulence, seen here as a paradigmatic complex system where intermittency was historically defined and the concepts of scale invariance and multifractality were extensively studied and benchmarked. We compute our quantity on experimental Eulerian velocity measurements, as well as on synthetic processes and phenomenological models of fluid turbulence. Our approach is very general and does not require any underlying model of the system, although it can probe the relevance of such a model.

  20. The constancy of gene conservation across divergent bacterial orders

    Directory of Open Access Journals (Sweden)

    Ackermann Martin

    2009-01-01

    Full Text Available Abstract Background Orthologous genes are frequently presumed to perform similar functions. However, outside of model organisms, this is rarely tested. One means of inferring changes in function is if there are changes in the level of gene conservation and selective constraint. Here we compare levels of gene conservation across three bacterial groups to test for changes in gene functionality. Findings The level of gene conservation for different orthologous genes is highly correlated across clades, even for highly divergent groups of bacteria. These correlations do not arise from broad differences in gene functionality (e.g. informational genes vs. metabolic genes, but instead seem to result from very specific differences in gene function. Furthermore, these functional differences appear to be maintained over very long periods of time. Conclusion These results suggest that even over broad time scales, most bacterial genes are under a nearly constant level of purifying selection, and that bacterial evolution is thus dominated by selective and functional stasis.

  1. Creative Cognition in Secondary Science: An exploration of divergent thinking in science among adolescents

    Science.gov (United States)

    Antink-Meyer, Allison; Lederman, Norman G.

    2015-07-01

    The divergent thinking skills in science of 282 US high school students were investigated across 16 weeks of instruction in order to determine whether typical academic time periods can significantly influence changes in thinking skills. Students' from 6 high school science classrooms completed the Scientific Structures Creativity Measure (SSCM) before and after a semester of instruction. Even the short time frame of a typical academic term was found to be sufficient to promote both improvements in divergent thinking skills as well as declining divergent thinking. Declining divergent thinking skills were more common in this time frame than were improvements. The nature of student performance on the SSCM and implications are discussed.

  2. Ecological selection as the cause and sexual differentiation as the consequence of species divergence?

    Science.gov (United States)

    Oneal, Elen; Knowles, L Lacey

    2013-01-07

    Key conceptual issues about speciation go unanswered without consideration of non-mutually exclusive factors. With tests based on speciation theory, we exploit the island distribution and habitat differences exhibited by the Caribbean cricket Amphiacusta sanctaecrucis, and with an analysis of divergent ecological selection, sexually selected differentiation and geographical isolation, address how these different factors interact. After testing for divergent selection by comparing neutral genetic and morphological divergence in one ecological (mandible shape) and one sexual (male genitalia shape) trait, we examine whether ecological or sexual selection is the primary mechanism driving population divergence. We find that all three factors--isolation, ecological and sexual selection--contribute to divergence, and that their interaction determines the stage of completeness achieved during the speciation process, as measured by patterns of genetic differentiation. Moreover, despite the striking diversity in genitalic shapes across the genus Amphiacusta, which suggests that sexual selection drives speciation, the significant differences in genitalia shape between forest habitats revealed here implies that ecological divergence may be the primary axis of divergence. Our work highlights critical unstudied aspects in speciation-differentiating the cause from the consequence of divergence-and suggests avenues for further disentangling the roles of natural and sexual selection in driving divergence in Amphiacusta.

  3. Evidence for stabilizing selection and slow divergent evolution of male genitalia in a millipede (Antichiropus variabilis).

    Science.gov (United States)

    Wojcieszek, Janine M; Simmons, Leigh W

    2012-04-01

    It is generally accepted that postcopulatory sexual selection drives rapid divergence of genital morphology among isolated populations. The mode of selection operating upon genitalia can be explored by comparing patterns of population divergence in genetic and genitalic traits. We collected Antichiropus variabilis millipedes from eight localities across the species range. Levels of among-population genetic divergence, at microsatellite loci, and the mitochondrial COI gene were very high. Following geometric morphometric analyses, genital morphology was also found to be highly divergent among the populations surveyed, whereas head morphology had not diverged as markedly. However, pairwise comparisons of F(ST) and P(ST) showed that among-population divergence in both genital and head shape was significantly lower than that experienced by neutral genetic markers. Our results suggest that the genitalia of A. variabilis are currently experiencing a period of stabilizing selection, the mode of selection expected for genitalia that function in species recognition via a "lock-and-key" mechanism. Our results demonstrate that although genital morphology can clearly diverge among genetically isolated populations, divergence is not necessarily as rapid as commonly argued, and continuous directional sexual selection may not always underpin the evolutionary divergence of male genitalia. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.

  4. Divergent selection and the evolution of signal traits and mating preferences.

    Directory of Open Access Journals (Sweden)

    2005-11-01

    Full Text Available Mating preferences are common in natural populations, and their divergence among populations is considered an important source of reproductive isolation during speciation. Although mechanisms for the divergence of mating preferences have received substantial theoretical treatment, complementary experimental tests are lacking. We conducted a laboratory evolution experiment, using the fruit fly Drosophila serrata, to explore the role of divergent selection between environments in the evolution of female mating preferences. Replicate populations of D. serrata were derived from a common ancestor and propagated in one of three resource environments: two novel environments and the ancestral laboratory environment. Adaptation to both novel environments involved changes in cuticular hydrocarbons, traits that predict mating success in these populations. Furthermore, female mating preferences for these cuticular hydrocarbons also diverged among populations. A component of this divergence occurred among treatment environments, accounting for at least 17.4% of the among-population divergence in linear mating preferences and 17.2% of the among-population divergence in nonlinear mating preferences. The divergence of mating preferences in correlation with environment is consistent with the classic by-product model of speciation in which premating isolation evolves as a side effect of divergent selection adapting populations to their different environments.

  5. Acidic ribosomal proteins and histone H3 from Leishmania present a high rate of divergence

    Directory of Open Access Journals (Sweden)

    Ysabel Montoya

    2000-08-01

    Full Text Available Another additional peculiarity in Leishmania will be discussed about of the amino acid divergence rate of three structural proteins: acidic ribosomal P1 and P2b proteins, and histone H3 by using multiple sequence alignment and dendrograms. These structural proteins present a high rate of divergence regarding to their homologous protein in Trypanosoma cruzi. At this regard, L. (V. peruviana P1 and T. cruzi P1 showed 57.4% of divergence rate. Likewise, L. (V. braziliensis histone H3 and acidic ribosomal P2 protein exhibited 31.8% and 41.7% respectively of rate of divergence in comparison with their homologous in T. cruzi.

  6. Consequences of Secondary Calibrations on Divergence Time Estimates.

    Directory of Open Access Journals (Sweden)

    John J Schenk

    Full Text Available Secondary calibrations (calibrations based on the results of previous molecular dating studies are commonly applied in divergence time analyses in groups that lack fossil data; however, the consequences of applying secondary calibrations in a relaxed-clock approach are not fully understood. I tested whether applying the posterior estimate from a primary study as a prior distribution in a secondary study results in consistent age and uncertainty estimates. I compared age estimates from simulations with 100 randomly replicated secondary trees. On average, the 95% credible intervals of node ages for secondary estimates were significantly younger and narrower than primary estimates. The primary and secondary age estimates were significantly different in 97% of the replicates after Bonferroni corrections. Greater error in magnitude was associated with deeper than shallower nodes, but the opposite was found when standardized by median node age, and a significant positive relationship was determined between the number of tips/age of secondary trees and the total amount of error. When two secondary calibrated nodes were analyzed, estimates remained significantly different, and although the minimum and median estimates were associated with less error, maximum age estimates and credible interval widths had greater error. The shape of the prior also influenced error, in which applying a normal, rather than uniform, prior distribution resulted in greater error. Secondary calibrations, in summary, lead to a false impression of precision and the distribution of age estimates shift away from those that would be inferred by the primary analysis. These results suggest that secondary calibrations should not be applied as the only source of calibration in divergence time analyses that test time-dependent hypotheses until the additional error associated with secondary calibrations is more properly modeled to take into account increased uncertainty in age estimates.

  7. Extensive genetic divergence among Diptychus maculatus populations in northwest China

    Science.gov (United States)

    Meng, Wei; Yang, Tianyan; Hai, Sa; Ma, Yanwu; Cai, Lingang; Ma, Xufa; Gao, Tianxiang; Guo, Yan

    2015-05-01

    D. maculates is a kind of specialized Schizothoracinae fish has been locally listed as a protected animal in Xinjiang Province, China. Ili River located in north of Tianshan Mountain and Tarim River located in north of Qinghai-Tibetan Plateau were two main distribution areas of this fish. To investigate the genetic diversity and genetic structure of D. maculates, four populations from Tarim River system and two populations from Ili River system were collected in this study. A 570-bp sequence of the control region was obtained for 105 specimens. Twenty-four haplotypes were detected from six populations, only Kunes River population and Kashi River population shared haplotypes with each other. For all the populations examined, the haplotype diversity ( h) was 0.904 8±0.012 6, nucleotide diversity (π) was 0.027 9±0.013 9, and the average number of pairwise nucleotide differences ( k) was 15.878 3±7.139 1. The analysis of molecular variance (AMOVA) showed that 86.31% of the total genetic variation was apportioned among populations, and the variation within sampled populations was 13.69%. Genetic differences among sampled populations were highly significant. F st statistical test indicated that all populations were significantly divergent from each other ( P<0.01). The largest F st value was between Yurungkash River population and Muzat River population, while the smallest F st value was between Kunes River population and Kashi River population. NJ phylogenetic tree of D-loop haplotypes revealed two main clades. The neutrality test and mismatch distribution analysis suggested that the fish had went through a recent population expansion. The uplift of Tianshan Mountain and movement of Qinghai-Tibetan Plateau might contribute to the wide genetic divergence of D. maculates in northwest China.

  8. Worldwide Patterns of Ancestry, Divergence, and Admixture in Domesticated Cattle

    Science.gov (United States)

    Decker, Jared E.; McKay, Stephanie D.; Rolf, Megan M.; Kim, JaeWoo; Molina Alcalá, Antonio; Sonstegard, Tad S.; Hanotte, Olivier; Götherström, Anders; Seabury, Christopher M.; Praharani, Lisa; Babar, Masroor Ellahi; Correia de Almeida Regitano, Luciana; Yildiz, Mehmet Ali; Heaton, Michael P.; Liu, Wan-Sheng; Lei, Chu-Zhao; Reecy, James M.; Saif-Ur-Rehman, Muhammad; Schnabel, Robert D.; Taylor, Jeremy F.

    2014-01-01

    The domestication and development of cattle has considerably impacted human societies, but the histories of cattle breeds and populations have been poorly understood especially for African, Asian, and American breeds. Using genotypes from 43,043 autosomal single nucleotide polymorphism markers scored in 1,543 animals, we evaluate the population structure of 134 domesticated bovid breeds. Regardless of the analytical method or sample subset, the three major groups of Asian indicine, Eurasian taurine, and African taurine were consistently observed. Patterns of geographic dispersal resulting from co-migration with humans and exportation are recognizable in phylogenetic networks. All analytical methods reveal patterns of hybridization which occurred after divergence. Using 19 breeds, we map the cline of indicine introgression into Africa. We infer that African taurine possess a large portion of wild African auroch ancestry, causing their divergence from Eurasian taurine. We detect exportation patterns in Asia and identify a cline of Eurasian taurine/indicine hybridization in Asia. We also identify the influence of species other than Bos taurus taurus and B. t. indicus in the formation of Asian breeds. We detect the pronounced influence of Shorthorn cattle in the formation of European breeds. Iberian and Italian cattle possess introgression from African taurine. American Criollo cattle originate from Iberia, and not directly from Africa with African ancestry inherited via Iberian ancestors. Indicine introgression into American cattle occurred in the Americas, and not Europe. We argue that cattle migration, movement and trading followed by admixture have been important forces in shaping modern bovine genomic variation. PMID:24675901

  9. Divergence and Conservative Evolution of XTNX Genes in Land Plants

    Directory of Open Access Journals (Sweden)

    Yan-Mei Zhang

    2017-10-01

    Full Text Available The Toll-interleukin-1 receptor (TIR and Nucleotide-binding site (NBS domains are two major components of the TIR-NBS-leucine-rich repeat family plant disease resistance genes. Extensive functional and evolutionary studies have been performed on these genes; however, the characterization of a small group of genes that are composed of atypical TIR and NBS domains, namely XTNX genes, is limited. The present study investigated this specific gene family by conducting genome-wide analyses of 59 green plant genomes. A total of 143 XTNX genes were identified in 51 of the 52 land plant genomes, whereas no XTNX gene was detected in any green algae genomes, which indicated that XTNX genes originated upon emergence of land plants. Phylogenetic analysis revealed that the ancestral XTNX gene underwent two rounds of ancient duplications in land plants, which resulted in the formation of clades I/II and clades IIa/IIb successively. Although clades I and IIb have evolved conservatively in angiosperms, the motif composition difference and sequence divergence at the amino acid level suggest that functional divergence may have occurred since the separation of the two clades. In contrast, several features of the clade IIa genes, including the absence in the majority of dicots, the long branches in the tree, the frequent loss of ancestral motifs, and the loss of expression in all detected tissues of Zea mays, all suggest that the genes in this lineage might have undergone pseudogenization. This study highlights that XTNX genes are a gene family originated anciently in land plants and underwent specific conservative pattern in evolution.

  10. Ecological and genetic divergence between two lineages of Middle American túngara frogs Physalaemus (= Engystomops pustulosus

    Directory of Open Access Journals (Sweden)

    Ron Santiago R

    2010-05-01

    Full Text Available Abstract Background Uncovering how populations of a species differ genetically and ecologically is important for understanding evolutionary processes. Here we combine population genetic methods (microsatellites with phylogenetic information (mtDNA to define genetic population clusters of the wide-spread Neotropical túngara frog (Physalaemus pustulosus. We measure gene flow and migration within and between population clusters and compare genetic diversity between population clusters. By applying ecological niche modeling we determine whether the two most divergent genetic groups of the túngara frog (1 inhabit different habitats, and (2 are separated geographically by unsuitable habitat across a gap in the distribution. Results Most population structure is captured by dividing all sample localities into two allopatric genetic lineages. The Northern genetic lineage (NW Costa Rica is genetically homogenous while the Southern lineage (SW Costa Rica and Panama is sub-divided into three population clusters by both microsatellite and mtDNA analyses. Gene flow is higher within the Northern lineage than within the Southern lineage, perhaps due to increased landscape heterogeneity in the South. Niche modeling reveals differences in suitable habitat between the Northern and Southern lineages: the Northern lineage inhabits dry/pine-oak forests, while the Southern lineage is confined to tropical moist forests. Both lineages seem to have had little movement across the distribution gap, which persisted during the last glacial maximum. The lack of movement was more pronounced for the Southern lineage than for the Northern lineage. Conclusions This study confirms the finding of previous studies that túngara frogs diverged into two allopatric genetic lineages north and south of the gap in the distribution in central Costa Rica several million years ago. The allopatric distribution is attributed to unsuitable habitat and probably other unknown ecological factors

  11. DNA damage and autophagy

    International Nuclear Information System (INIS)

    Rodriguez-Rocha, Humberto; Garcia-Garcia, Aracely; Panayiotidis, Mihalis I.; Franco, Rodrigo

    2011-01-01

    Both exogenous and endogenous agents are a threat to DNA integrity. Exogenous environmental agents such as ultraviolet (UV) and ionizing radiation, genotoxic chemicals and endogenous byproducts of metabolism including reactive oxygen species can cause alterations in DNA structure (DNA damage). Unrepaired DNA damage has been linked to a variety of human disorders including cancer and neurodegenerative disease. Thus, efficient mechanisms to detect DNA lesions, signal their presence and promote their repair have been evolved in cells. If DNA is effectively repaired, DNA damage response is inactivated and normal cell functioning resumes. In contrast, when DNA lesions cannot be removed, chronic DNA damage triggers specific cell responses such as cell death and senescence. Recently, DNA damage has been shown to induce autophagy, a cellular catabolic process that maintains a balance between synthesis, degradation, and recycling of cellular components. But the exact mechanisms by which DNA damage triggers autophagy are unclear. More importantly, the role of autophagy in the DNA damage response and cellular fate is unknown. In this review we analyze evidence that supports a role for autophagy as an integral part of the DNA damage response.

  12. DNA qualification workflow for next generation sequencing of histopathological samples.

    Directory of Open Access Journals (Sweden)

    Michele Simbolo

    Full Text Available Histopathological samples are a treasure-trove of DNA for clinical research. However, the quality of DNA can vary depending on the source or extraction method applied. Thus a standardized and cost-effective workflow for the qualification of DNA preparations is essential to guarantee interlaboratory reproducible results. The qualification process consists of the quantification of double strand DNA (dsDNA and the assessment of its suitability for downstream applications, such as high-throughput next-generation sequencing. We tested the two most frequently used instrumentations to define their role in this process: NanoDrop, based on UV spectroscopy, and Qubit 2.0, which uses fluorochromes specifically binding dsDNA. Quantitative PCR (qPCR was used as the reference technique as it simultaneously assesses DNA concentration and suitability for PCR amplification. We used 17 genomic DNAs from 6 fresh-frozen (FF tissues, 6 formalin-fixed paraffin-embedded (FFPE tissues, 3 cell lines, and 2 commercial preparations. Intra- and inter-operator variability was negligible, and intra-methodology variability was minimal, while consistent inter-methodology divergences were observed. In fact, NanoDrop measured DNA concentrations higher than Qubit and its consistency with dsDNA quantification by qPCR was limited to high molecular weight DNA from FF samples and cell lines, where total DNA and dsDNA quantity virtually coincide. In partially degraded DNA from FFPE samples, only Qubit proved highly reproducible and consistent with qPCR measurements. Multiplex PCR amplifying 191 regions of 46 cancer-related genes was designated the downstream application, using 40 ng dsDNA from FFPE samples calculated by Qubit. All but one sample produced amplicon libraries suitable for next-generation sequencing. NanoDrop UV-spectrum verified contamination of the unsuccessful sample. In conclusion, as qPCR has high costs and is labor intensive, an alternative effective standard

  13. DNA Qualification Workflow for Next Generation Sequencing of Histopathological Samples

    Science.gov (United States)

    Simbolo, Michele; Gottardi, Marisa; Corbo, Vincenzo; Fassan, Matteo; Mafficini, Andrea; Malpeli, Giorgio; Lawlor, Rita T.; Scarpa, Aldo

    2013-01-01

    Histopathological samples are a treasure-trove of DNA for clinical research. However, the quality of DNA can vary depending on the source or extraction method applied. Thus a standardized and cost-effective workflow for the qualification of DNA preparations is essential to guarantee interlaboratory reproducible results. The qualification process consists of the quantification of double strand DNA (dsDNA) and the assessment of its suitability for downstream applications, such as high-throughput next-generation sequencing. We tested the two most frequently used instrumentations to define their role in this process: NanoDrop, based on UV spectroscopy, and Qubit 2.0, which uses fluorochromes specifically binding dsDNA. Quantitative PCR (qPCR) was used as the reference technique as it simultaneously assesses DNA concentration and suitability for PCR amplification. We used 17 genomic DNAs from 6 fresh-frozen (FF) tissues, 6 formalin-fixed paraffin-embedded (FFPE) tissues, 3 cell lines, and 2 commercial preparations. Intra- and inter-operator variability was negligible, and intra-methodology variability was minimal, while consistent inter-methodology divergences were observed. In fact, NanoDrop measured DNA concentrations higher than Qubit and its consistency with dsDNA quantification by qPCR was limited to high molecular weight DNA from FF samples and cell lines, where total DNA and dsDNA quantity virtually coincide. In partially degraded DNA from FFPE samples, only Qubit proved highly reproducible and consistent with qPCR measurements. Multiplex PCR amplifying 191 regions of 46 cancer-related genes was designated the downstream application, using 40 ng dsDNA from FFPE samples calculated by Qubit. All but one sample produced amplicon libraries suitable for next-generation sequencing. NanoDrop UV-spectrum verified contamination of the unsuccessful sample. In conclusion, as qPCR has high costs and is labor intensive, an alternative effective standard workflow for

  14. Genetic divergence between Pseudoplatystoma corruscans and Pseudoplatystoma reticulatum (Siluriformes: Pimelodidae in the Paraná River Basin

    Directory of Open Access Journals (Sweden)

    TS. Bignotto

    Full Text Available Pseudoplatystoma corruscans (Spix and Agassiz, 1829 and Pseudoplatystoma reticulatum (Eingenmann and Eigenmann, 1889 are large migratory catfishes of high biological importance and great commercial value in South America. Because fertile crossbreeds can be artificially produced in hatcheries, a high genetic proximity between these two Pimelodidae species is conceivable. Possible escape of crossbred specimens from pisciculture stations is a serious environmental concern. Despite their importance, knowledge of P. corruscans and P. reticulatum biology, ecology, population diversity and genetics is limited. In the present work, the genetic divergence between P. corruscans and P. reticulatum populations from the Paraná River Basin was analyzed on the basis of polymorphisms in ISSR fragments and in the hypervariable sequence of the mitochondrial DNA (mtDNA control region. Estimates of intraspecific haplotype (h > 0.5 and nucleotide diversities (π < 0.01 indicate that P. corruscans and P. reticulatum have survived a historical population decline, followed by a demographic expansion. The interspecific polymorphisms within the mtDNA control region and ISSR fragments were suitable as diagnostic molecular markers and could be used to discriminate the two species. A unique Pseudoplatystoma specimen, captured in the Upper Paraná River Floodplain, was identified by these DNA diagnostic markers as a hybrid P. reticulatum x P. corruscans, which possibly escaped from pisciculture. The integrity of the natural population of P. corruscans in the Upper Paraná River is at risk of genetic introgression or homogenization due to the presence of hybrids and the transposition of P. reticulatum upstream through the Canal da Piracema at Itaipu Dam. Data presented herein improve the understanding of the genetic relatedness between P. corruscans and P. reticulatum and represent potential tools for future programs of conservation and surveillance of genetic introgression

  15. Brain feminization requires active repression of masculinization via DNA methylation

    Science.gov (United States)

    Nugent, Bridget M.; Wright, Christopher L.; Shetty, Amol C.; Hodes, Georgia E.; Lenz, Kathryn M.; Mahurkar, Anup; Russo, Scott J.; Devine, Scott E.; McCarthy, Margaret M.

    2015-01-01

    The developing mammalian brain is destined for a female phenotype unless exposed to gonadal hormones during a perinatal sensitive period. It has been assumed that the undifferentiated brain is masculinized by direct induction of transcription by ligand-activated nuclear steroid receptors. We found that a primary effect of gonadal steroids in the highly sexually-dimorphic preoptic area (POA) is to reduce activity of DNA methyltransferase (Dnmt) enzymes, thereby decreasing DNA methylation and releasing masculinizing genes from epigenetic repression. Pharmacological inhibition of Dnmts mimicked gonadal steroids, resulting in masculinized neuronal markers and male sexual behavior in females. Conditional knockout of the de novo Dnmt isoform, Dnmt3a, also masculinized sexual behavior in female mice. RNA sequencing revealed gene and isoform variants modulated by methylation that may underlie the divergent reproductive behaviors of males versus females. Our data show that brain feminization is maintained by the active suppression of masculinization via DNA methylation. PMID:25821913

  16. Mitochondrial DNA differentiation in the Japanese brown frog Rana japonica as revealed by restriction endonuclease analysis.

    Science.gov (United States)

    Sumida, M

    1997-04-01

    To elucidate mtDNA differentiation in the Japanese brown frog Rana japonica, and compare it with results from allozyme analysis and crossing experiments, RFLP analysis was conducted on 78 frogs from 16 populations in Honshu. Purified mtDNA was digested with eight six-base recognizing restriction enzymes and analyzed by 1% agarose-slab gel electrophoresis. Cleavage patterns of the mtDNA showed three distinct genome size classes: small (18.5 kb), middle (20.0 kb) and large (21.5 kb). Ten haplotypes (I approximately X) were observed among the 16 populations. The expected nucleotide divergences within populations ranged from 0 to 0.47% with a mean of 0.08%. The net nucleotide divergences among 16 populations ranged from 0 to 7.74% with a mean of 3.49%. The UPGMA dendrogram and NJ tree, which were constructed based on the net nucleotide divergences, showed that R. japonica diverged first into the eastern and western groups. The eastern group subsequently differentiated into a subgroup containing six populations and the Akita population, and the western group divided into several subgroups. These results, as well as the results of allozyme analysis and crossing experiments, suggest the the eastern and western groups have experienced secondary contact, and introgression has occurred in the Akita population.

  17. Phylogenetic relationship and time of divergence of Mus terricolor ...

    Indian Academy of Sciences (India)

    Mitochondrial DNA control region ofMus terricolor. , three aboriginal speciesM. spretus. ,M. macedonicus. ,M. spicilegus. ;the Asian lineageM. caroli. ,M. cervicolor. ,M. cookii. ; and the two house mice,M. musculus domesticusandM. m. castaneuswere analysed to estimate the substitution rate, phylogenetic relationship and ...

  18. Subcloning of DNA fragments.

    Science.gov (United States)

    Struhl, K

    2001-05-01

    The essence of recombinant DNA technology is the joining of two or more separate segments of DNA to generate a single DNA molecule that is capable of autonomous replication in a given host. The simplest constructions of hybrid DNA molecules involve the cloning of insert sequences into plasmid or bacteriophage cloning vectors. The insert sequences can derive from essentially any organism, and they may be isolated directly from the genome, from mRNA, or from previously cloned DNA segments (in which case, the procedure is termed subcloning). Alternatively, insert DNAs can be created directly by DNA synthesis. This unit provides protocols for the subcloning of DNA fragments and ligation of DNA fragments in gels.

  19. DNA tagged microparticles

    Science.gov (United States)

    Farquar, George Roy; Leif, Roald N; Wheeler, Elizabeth

    2015-05-05

    A simulant that includes a carrier and DNA encapsulated in the carrier. Also a method of making a simulant including the steps of providing a carrier and encapsulating DNA in the carrier to produce the simulant.

  20. DNA computing models

    CERN Document Server

    Ignatova, Zoya; Zimmermann, Karl-Heinz

    2008-01-01

    In this excellent text, the reader is given a comprehensive introduction to the field of DNA computing. The book emphasizes computational methods to tackle central problems of DNA computing, such as controlling living cells, building patterns, and generating nanomachines.

  1. DNA Repair Systems

    Indian Academy of Sciences (India)

    exogenous damage). Endogenous damage ... of spontaneous DNA-damage due to endogenous factors. He es- timated that around 10,000 potentially mutagenic .... 3 –5 direction is defined as. 'upstream'. A single DNA strand is synthesized in a.

  2. Highlighting Astyanax Species Diversity through DNA Barcoding

    Science.gov (United States)

    Oliveira, Carlos Alexandre Miranda; de Melo, Filipe Augusto Gonçalves; Bertaco, Vinicius de Araújo; de Astarloa, Juan M. Díaz; Rosso, Juan J.; Foresti, Fausto; Oliveira, Claudio

    2016-01-01

    DNA barcoding has been used extensively to solve taxonomic questions and identify new species. Neotropical fishes are found in a wide variety of shapes and sizes, with a large number of species yet to be described, many of which are very difficult to identify. Characidae is the most species-rich family of the Characiformes, and many of its genera are affected by taxonomic uncertainties, including the widely-distributed, species-rich genus Astyanax. In this study, we present an extensive analysis of Astyanax covering almost its entire area of occurrence, based on DNA barcoding. The use of different approaches (ABGD, GMYC and BIN) to the clustering of the sequences revealed ample consistency in the results obtained by the initial cutoff value of 2% divergence for putative species in the Neighbor-Joining analysis using the Kimura-2-parameter model. The results indicate the existence of five Astyanax lineages. Some groups, such as that composed by the trans-Andean forms, are mostly composed of well-defined species, and in others a number of nominal species are clustered together, hampering the delimitation of species, which in many cases proved impossible. The results confirm the extreme complexity of the systematics of the genus Astyanax and show that DNA barcoding can be an useful tool to address these complexes questions. PMID:27992537

  3. Amplification of a Zygosaccharomyces bailii DNA segment in wine yeast genomes by extrachromosomal circular DNA formation.

    Science.gov (United States)

    Galeote, Virginie; Bigey, Frédéric; Beyne, Emmanuelle; Novo, Maite; Legras, Jean-Luc; Casaregola, Serge; Dequin, Sylvie

    2011-03-10

    We recently described the presence of large chromosomal segments resulting from independent horizontal gene transfer (HGT) events in the genome of Saccharomyces cerevisiae strains, mostly of wine origin. We report here evidence for the amplification of one of these segments, a 17 kb DNA segment from Zygosaccharomyces bailii, in the genome of S. cerevisiae strains. The copy number, organization and location of this region differ considerably between strains, indicating that the insertions are independent and that they are post-HGT events. We identified eight different forms in 28 S. cerevisiae strains, mostly of wine origin, with up to four different copies in a single strain. The organization of these forms and the identification of an autonomously replicating sequence functional in S. cerevisiae, strongly suggest that an extrachromosomal circular DNA (eccDNA) molecule serves as an intermediate in the amplification of the Z. bailii region in yeast genomes. We found little or no sequence similarity at the breakpoint regions, suggesting that the insertions may be mediated by nonhomologous recombination. The diversity between these regions in S. cerevisiae represents roughly one third the divergence among the genomes of wine strains, which confirms the recent origin of this event, posterior to the start of wine strain expansion. This is the first report of a circle-based mechanism for the expansion of a DNA segment, mediated by nonhomologous recombination, in natural yeast populations.

  4. Amplification of a Zygosaccharomyces bailii DNA segment in wine yeast genomes by extrachromosomal circular DNA formation.

    Directory of Open Access Journals (Sweden)

    Virginie Galeote

    Full Text Available We recently described the presence of large chromosomal segments resulting from independent horizontal gene transfer (HGT events in the genome of Saccharomyces cerevisiae strains, mostly of wine origin. We report here evidence for the amplification of one of these segments, a 17 kb DNA segment from Zygosaccharomyces bailii, in the genome of S. cerevisiae strains. The copy number, organization and location of this region differ considerably between strains, indicating that the insertions are independent and that they are post-HGT events. We identified eight different forms in 28 S. cerevisiae strains, mostly of wine origin, with up to four different copies in a single strain. The organization of these forms and the identification of an autonomously replicating sequence functional in S. cerevisiae, strongly suggest that an extrachromosomal circular DNA (eccDNA molecule serves as an intermediate in the amplification of the Z. bailii region in yeast genomes. We found little or no sequence similarity at the breakpoint regions, suggesting that the insertions may be mediated by nonhomologous recombination. The diversity between these regions in S. cerevisiae represents roughly one third the divergence among the genomes of wine strains, which confirms the recent origin of this event, posterior to the start of wine strain expansion. This is the first report of a circle-based mechanism for the expansion of a DNA segment, mediated by nonhomologous recombination, in natural yeast populations.

  5. Whole genome investigation of a divergent clade of the pathogen Streptococcus suis

    Directory of Open Access Journals (Sweden)

    Abiyad eBaig

    2015-11-01

    Full Text Available Streptococcus suis is a major porcine and zoonotic pathogen responsible for significant economic losses in the pig industry and an increasing number of human cases. Multiple isolates of S. suis show marked genomic diversity. Here we report the analysis of whole genome sequences of nine pig isolates that caused disease typical of S. suis and had phenotypic characteristics of S. suis, but their genomes were divergent from those of many other S. suis isolates. Comparison of protein sequences predicted from divergent genomes with those from normal S. suis reduced the size of core genome from 793 to only 397 genes. Divergence was clear if phylogenetic analysis was performed on reduced core genes and MLST alleles. Phylogenies based on certain other genes (16S rRNA, sodA, recN and cpn60 did not show divergence for all isolates, suggesting recombination between some divergent isolates with normal S. suis for these genes. Indeed, there is evidence of recent recombination between the divergent and normal S. suis genomes for 249 of 397 core genes. In addition, phylogenetic analysis based on the 16S rRNA gene and 132 genes that were conserved between the divergent isolates and representatives of the broader Streptococcus genus showed that divergent isolates were more closely related to S. suis. Six out of nine divergent isolates possessed a S. suis-like capsule region with variation in capsular gene sequences but the remaining three did not have a discrete capsule locus. The majority (40/70, of virulence-associated genes in normal S. suis were present in the divergent genomes. Overall, the divergent isolates extend the current diversity of S. suis species but the phenotypic similarities and the large amount of gene exchange with normal S. suis gives insufficient evidence to assign these isolates to a new species or subspecies. Further sampling and whole genome analysis of more isolates is warranted to understand the diversity of the species.

  6. Animal Mitochondrial DNA Replication

    Science.gov (United States)

    Ciesielski, Grzegorz L.; Oliveira, Marcos T.; Kaguni, Laurie S.

    2016-01-01

    Recent advances in the field of mitochondrial DNA (mtDNA) replication highlight the diversity of both the mechanisms utilized and the structural and functional organization of the proteins at mtDNA replication fork, despite the simplicity of the animal mtDNA genome. DNA polymerase γ, mtDNA helicase and mitochondrial single-stranded DNA-binding protein- the key replisome proteins, have evolved distinct structural features and biochemical properties. These appear to be correlated with mtDNA genomic features in different metazoan taxa and with their modes of DNA replication, although a substantial integrative research is warranted to establish firmly these links. To date, several modes of mtDNA replication have been described for animals: rolling circle, theta, strand-displacement, and RITOLS/bootlace. Resolution of a continuing controversy relevant to mtDNA replication in mammals/vertebrates will have a direct impact on the mechanistic interpretation of mtDNA-related human diseases. Here we review these subjects, integrating earlier and recent data to provide a perspective on the major challenges for future research. PMID:27241933

  7. Replicating animal mitochondrial DNA

    Directory of Open Access Journals (Sweden)

    Emily A. McKinney

    2013-01-01

    Full Text Available The field of mitochondrial DNA (mtDNA replication has been experiencing incredible progress in recent years, and yet little is certain about the mechanism(s used by animal cells to replicate this plasmid-like genome. The long-standing strand-displacement model of mammalian mtDNA replication (for which single-stranded DNA intermediates are a hallmark has been intensively challenged by a new set of data, which suggests that replication proceeds via coupled leading-and lagging-strand synthesis (resembling bacterial genome replication and/or via long stretches of RNA intermediates laid on the mtDNA lagging-strand (the so called RITOLS. The set of proteins required for mtDNA replication is small and includes the catalytic and accessory subunits of DNA polymerase y, the mtDNA helicase Twinkle, the mitochondrial single-stranded DNA-binding protein, and the mitochondrial RNA polymerase (which most likely functions as the mtDNA primase. Mutations in the genes coding for the first three proteins are associated with human diseases and premature aging, justifying the research interest in the genetic, biochemical and structural properties of the mtDNA replication machinery. Here we summarize these properties and discuss the current models of mtDNA replication in animal cells.

  8. Bisulfite sequencing reveals that Aspergillus flavus holds a hollow in DNA methylation.

    Directory of Open Access Journals (Sweden)

    Si-Yang Liu

    Full Text Available Aspergillus flavus first gained scientific attention for its production of aflatoxin. The underlying regulation of aflatoxin biosynthesis has been serving as a theoretical model for biosynthesis of other microbial secondary metabolites. Nevertheless, for several decades, the DNA methylation status, one of the important epigenomic modifications involved in gene regulation, in A. flavus remains to be controversial. Here, we applied bisulfite sequencing in conjunction with a biological replicate strategy to investigate the DNA methylation profiling of A. flavus genome. Both the bisulfite sequencing data and the methylome comparisons with other fungi confirm that the DNA methylation level of this fungus is negligible. Further investigation into the DNA methyltransferase of Aspergillus uncovers its close relationship with RID-like enzymes as well as its divergence with the methyltransferase of species with validated DNA methylation. The lack of repeat contents of the A. flavus' genome and the high RIP-index of the small amount of remanent repeat potentially support our speculation that DNA methylation may be absent in A. flavus or that it may possess de novo DNA methylation which occurs very transiently during the obscure sexual stage of this fungal species. This work contributes to our understanding on the DNA methylation status of A. flavus, as well as reinforces our views on the DNA methylation in fungal species. In addition, our strategy of applying bisulfite sequencing to DNA methylation detection in species with low DNA methylation may serve as a reference for later scientific investigations in other hypomethylated species.

  9. Carboxyl terminal domain basic amino acids of mycobacterial topoisomerase I bind DNA to promote strand passage.

    Science.gov (United States)

    Ahmed, Wareed; Bhat, Anuradha Gopal; Leelaram, Majety Naga; Menon, Shruti; Nagaraja, Valakunja

    2013-08-01

    Bacterial DNA topoisomerase I (topoI) carries out relaxation of negatively supercoiled DNA through a series of orchestrated steps, DNA binding, cleavage, strand passage and religation. The N-terminal domain (NTD) of the type IA topoisomerases harbor DNA cleavage and religation activities, but the carboxyl terminal domain (CTD) is highly diverse. Most of these enzymes contain a varied number of Zn(2+) finger motifs in the CTD. The Zn(2+) finger motifs were found to be essential in Escherichia coli topoI but dispensable in the Thermotoga maritima enzyme. Although, the CTD of mycobacterial topoI lacks Zn(2+) fingers, it is indispensable for the DNA relaxation activity of the enzyme. The divergent CTD harbors three stretches of basic amino acids needed for the strand passage step of the reaction as demonstrated by a new assay. We also show that the basic amino acids constitute an independent DNA-binding site apart from the NTD and assist the simultaneous binding of two molecules of DNA to the enzyme, as required during the catalytic step. Although the NTD binds to DNA in a site-specific fashion to carry out DNA cleavage and religation, the basic residues in CTD bind to non-scissile DNA in a sequence-independent manner to promote the crucial strand passage step during DNA relaxation. The loss of Zn(2+) fingers from the mycobacterial topoI could be associated with Zn(2+) export and homeostasis.

  10. Close relatedness of Acanthamoeba pustulosa with Acanthamoeba palestinensis based on isoenzyme profiles and rDNA PCR-RFLP patterns.

    Science.gov (United States)

    Kim, Y H; Ock, M S; Yun, H C; Hwang, M Y; Yu, H S; Kong, H H; Chung, D I

    1996-12-01

    The taxonomic validity of morphological group III Acanthamoeba spp. is uncertain. In the present study, six type strains of group III Acanthamoeba spp., A. culbertsoni, A. healyi, A. pustulosa, A. palestinensis, A. royreba and A. lenticulata were subjected for the evaluation of their taxonomic validity by comparison of the isoenzyme patterns by isoelectic focusing on polyacrylamide gels, mitochondrial DNA (Mt DNA) restriction fragment length polymorphism (RFLP), and small subunit ribosomal DNA (ssu rDNA) PCR-RFLP patterns. The Mt DNA RFLP patterns were heterogeneous between the species. The type strains of A. palestinensis and A. pustulosa showed almost identical patterns of isoenzymes and rDNA PCR RFLP with an estimated sequence divergence of 2.6%. The other species showed heterogeneous patterns of isoenzymes and rDNA PCR-RFLP. It is likely that A. pustulosa is closely related with A. palestinensis and that the former may be regarded as a junior synonym of the latter.

  11. Transposable Elements: No More 'Junk DNA'

    Directory of Open Access Journals (Sweden)

    Yun-Ji Kim

    2012-12-01

    Full Text Available Since the advent of whole-genome sequencing, transposable elements (TEs, just thought to be 'junk' DNA, have been noticed because of their numerous copies in various eukaryotic genomes. Many studies about TEs have been conducted to discover their functions in their host genomes. Based on the results of those studies, it has been generally accepted that they have a function to cause genomic and genetic variations. However, their infinite functions are not fully elucidated. Through various mechanisms, including de novo TE insertions, TE insertion-mediated deletions, and recombination events, they manipulate their host genomes. In this review, we focus on Alu, L1, human endogenous retrovirus, and short interspersed element/variable number of tandem repeats/Alu (SVA elements and discuss how they have affected primate genomes, especially the human and chimpanzee genomes, since their divergence.

  12. Unexpected Functional Divergence of Bat Influenza Virus NS1 Proteins.

    Science.gov (United States)

    Turkington, Hannah L; Juozapaitis, Mindaugas; Tsolakos, Nikos; Corrales-Aguilar, Eugenia; Schwemmle, Martin; Hale, Benjamin G

    2018-03-01

    Recently, two influenza A virus (FLUAV) genomes were identified in Central and South American bats. These sequences exhibit notable divergence from classical FLUAV counterparts, and functionally, bat FLUAV glycoproteins lack canonical receptor binding and destroying activity. Nevertheless, other features that distinguish these viruses from classical FLUAVs have yet to be explored. Here, we studied the viral nonstructural protein NS1, a virulence factor that modulates host signaling to promote efficient propagation. Like all FLUAV NS1 proteins, bat FLUAV NS1s bind double-stranded RNA and act as interferon antagonists. Unexpectedly, we found that bat FLUAV NS1s are unique in being unable to bind host p85β, a regulatory subunit of the cellular metabolism-regulating enzyme, phosphoinositide 3-kinase (PI3K). Furthermore, neither bat FLUAV NS1 alone nor infection with a chimeric bat FLUAV efficiently activates Akt, a PI3K effector. Structure-guided mutagenesis revealed that the bat FLUAV NS1-p85β interaction can be reengineered (in a strain-specific manner) by changing two to four NS1 residues (96L, 99M, 100I, and 145T), thereby creating a hydrophobic patch. Notably, ameliorated p85β-binding is insufficient for bat FLUAV NS1 to activate PI3K, and a chimeric bat FLUAV expressing NS1 with engineered hydrophobic patch mutations exhibits cell-type-dependent, but species-independent, propagation phenotypes. We hypothesize that bat FLUAV hijacking of PI3K in the natural bat host has been selected against, perhaps because genes in this metabolic pathway were differentially shaped by evolution to suit the unique energy use strategies of this flying mammal. These data expand our understanding of the enigmatic functional divergence between bat FLUAVs and classical mammalian and avian FLUAVs. IMPORTANCE The potential for novel influenza A viruses to establish infections in humans from animals is a source of continuous concern due to possible severe outbreaks or pandemics. The

  13. Proterozoic microfossils revealing the time of algal divergences

    Science.gov (United States)

    Moczydlowska-Vidal, Malgorzata

    2010-05-01

    Proterozoic microfossils revealing the time of algal divergences Małgorzata Moczydłowska-Vidal Uppsala University, Department of Earth Sciences, Palaeobiology, Villavägen 16, SE 752 36 Uppsala, Sweden (malgo.vidal@pal.uu.se) Morphological and reproductive features and cell wall ultrastructure and biochemistry of Proterozoic acritarchs are used to determine their affinity to modern algae. The first appearance datum of these microbiota is traced to infer a minimum age of the divergence of the algal classes to which they may belong. The chronological appearance of microfossils that represent phycoma-like and zygotic cysts and vegetative cells and/or aplanospores, respectively interpreted as prasinophyceaen and chlorophyceaen microalgae, is related to the Viridiplantae phylogeny. These divergence times differ from molecular clock estimates, and the palaeontological evidence suggests that they are older. The best examples of unicellular, organic-walled microfossils (acritarchs) from the Mesoproterozoic to Early Ordovician are reviewed to demonstrate features, which are indicative of their affinity to photosynthetic microalgae. The first indication that a microfossil may be algal is a decay- and acid-resistant cell wall, which reflects its biochemistry and ultrastructure, and probably indicates the ability to protect a resting/reproductive cyst. The biopolymers synthesized in the cell walls of algae and in land plants ("plant cells"), such as sporopollenin/algaenan, are diagnostic for photosynthetic taxa and were inherited from early unicellular ancestors. These preservable cell walls are resistant to acetolysis, hydrolysis and acids, and show diagnostic ultrastructures such as the trilaminar sheath structure (TLS). "Plant cell" walls differ in terms of chemical compounds, which give high preservation potential, from fungal and animal cell walls. Fungal and animal cells are fossilized only by syngenetic permineralization, whereas "plant cells" are fossilized as body

  14. DNA: Structure and function

    DEFF Research Database (Denmark)

    Sinden, Richard R.; E. Pearson, Christopher; N. Potaman, Vladimir

    1998-01-01

    This chapter discusses the structure and function of DNA. DNA occupies a critical role in cells, because it is the source of all intrinsic genetic information. Chemically, DNA is a very stable molecule, a characteristic important for a macromolecule that may have to persist in an intact form...... for a long period of time before its information is accessed by the cell. Although DNA plays a critical role as an informational storage molecule, it is by no means as unexciting as a computer tape or disk drive. The structure of the DNA described by Watson and Crick in 1953 is a right handed helix of two...

  15. Fast phylogenetic DNA barcoding

    DEFF Research Database (Denmark)

    Terkelsen, Kasper Munch; Boomsma, Wouter Krogh; Willerslev, Eske

    2008-01-01

    We present a heuristic approach to the DNA assignment problem based on phylogenetic inferences using constrained neighbour joining and non-parametric bootstrapping. We show that this method performs as well as the more computationally intensive full Bayesian approach in an analysis of 500 insect...... DNA sequences obtained from GenBank. We also analyse a previously published dataset of environmental DNA sequences from soil from New Zealand and Siberia, and use these data to illustrate the fact that statistical approaches to the DNA assignment problem allow for more appropriate criteria...... for determining the taxonomic level at which a particular DNA sequence can be assigned....

  16. DNA Sequencing apparatus

    Science.gov (United States)

    Tabor, Stanley; Richardson, Charles C.

    1992-01-01

    An automated DNA sequencing apparatus having a reactor for providing at least two series of DNA products formed from a single primer and a DNA strand, each DNA product of a series differing in molecular weight and having a chain terminating agent at one end; separating means for separating the DNA products to form a series bands, the intensity of substantially all nearby bands in a different series being different, band reading means for determining the position an This invention was made with government support including a grant from the U.S. Public Health Service, contract number AI-06045. The U.S. government has certain rights in the invention.

  17. Divergent Task Performance in Older Adults: Declarative Memory or Creative Potential?

    Science.gov (United States)

    Leon, Susan A.; Altmann, Lori J. P.; Abrams, Lise; Gonzalez Rothi, Leslie J.; Heilman, Kenneth M.

    2014-01-01

    Divergent thinking is a process or method used to generate creative ideas by exploring many possible solutions or responses, and is a critical element of creativity. Lesion and imaging studies have shown that the frontal lobes are important in mediating divergent thinking, and frontal lobe function is highly dependent on white matter connections…

  18. Typing Speed as a Confounding Variable and the Measurement of Quality in Divergent Thinking

    Science.gov (United States)

    Forthmann, Boris; Holling, Heinz; Çelik, Pinar; Storme, Martin; Lubart, Todd

    2017-01-01

    The need to control for writing or typing speed when assessing divergent-thinking performance has been recognized since the early '90s. An even longer tradition in divergent-thinking research has the issue of scoring the responses for quality. This research addressed both issues within structural equation modeling. Three dimensions of…

  19. Parasite-mediated sexual selection and species divergence in Lake Victoria cichlid fish

    NARCIS (Netherlands)

    Maan, Martine E.; Van Rooijen, Anne M. C.; Van Alphen, Jacques J. M.; Seehausen, Ole

    We investigate the role of parasite-mediated sexual selection in the divergence of two species of Lake Victoria cichlids. Pundamilia pundamilia and Pundamilia nyererei represent a common pattern of male nuptial colour divergence between haplochromine sister species: metallic grey-blue in P.

  20. Cycles and diamonds: how management consultants diverge and converge in organization design processes.

    NARCIS (Netherlands)

    Visscher, Klaasjan; Fisscher, O.A.M.

    2009-01-01

    Divergence and convergence are both important elements of organizational design processes. This is often stated in the normative design literature, but it has hardly been studied empirically. How do designers of organizations diverge and converge in practice? Do they first develop alternatives and