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  • 1
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    Comparative population genomics in animals uncovers the determinants of genetic diversity (2014)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2014-08-21
    Description: Genetic diversity is the amount of variation observed between DNA sequences from distinct individuals of a given species. This pivotal concept of population genetics has implications for species health, domestication, management and conservation. Levels of genetic diversity seem to vary greatly in natural populations and species, but the determinants of this variation, and particularly the relative influences of species biology and ecology versus population history, are still largely mysterious. Here we show that the diversity of a species is predictable, and is determined in the first place by its ecological strategy. We investigated the genome-wide diversity of 76 non-model animal species by sequencing the transcriptome of two to ten individuals in each species. The distribution of genetic diversity between species revealed no detectable influence of geographic range or invasive status but was accurately predicted by key species traits related to parental investment: long-lived or low-fecundity species with brooding ability were genetically less diverse than short-lived or highly fecund ones. Our analysis demonstrates the influence of long-term life-history strategies on species response to short-term environmental perturbations, a result with immediate implications for conservation policies.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Romiguier, J -- Gayral, P -- Ballenghien, M -- Bernard, A -- Cahais, V -- Chenuil, A -- Chiari, Y -- Dernat, R -- Duret, L -- Faivre, N -- Loire, E -- Lourenco, J M -- Nabholz, B -- Roux, C -- Tsagkogeorga, G -- Weber, A A-T -- Weinert, L A -- Belkhir, K -- Bierne, N -- Glemin, S -- Galtier, N -- England -- Nature. 2014 Nov 13;515(7526):261-3. doi: 10.1038/nature13685. Epub 2014 Aug 20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] UMR 5554, Institute of Evolutionary Sciences, University Montpellier 2, Centre national de la recherche scientifique, Place E. Bataillon, 34095 Montpellier, France [2] Department of Ecology and Evolution, Biophore, University of Lausanne, 1015 Lausanne, Switzerland. ; 1] UMR 5554, Institute of Evolutionary Sciences, University Montpellier 2, Centre national de la recherche scientifique, Place E. Bataillon, 34095 Montpellier, France [2] UMR 7261, Institut de Recherches sur la Biologie de l'Insecte, Centre national de la recherche scientifique, Universite Francois-Rabelais, 37200 Tours, France. ; UMR 5554, Institute of Evolutionary Sciences, University Montpellier 2, Centre national de la recherche scientifique, Place E. Bataillon, 34095 Montpellier, France. ; Aix-Marseille Universite, Institut Mediterraneen de Biodiversite et d'Ecologie marine et continentale (IMBE) - CNRS - IRD - UAPV, 13007 Marseille, France. ; Department of Biology, University of South Alabama, Mobile, Alabama 36688-0002, USA. ; UMR 5558, Laboratoire de Biometrie et Biologie Evolutive, Universite Lyon 1, CNRS, 69622 Lyon, France. ; 1] UMR 5554, Institute of Evolutionary Sciences, University Montpellier 2, Centre national de la recherche scientifique, Place E. Bataillon, 34095 Montpellier, France [2] The School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK. ; 1] UMR 5554, Institute of Evolutionary Sciences, University Montpellier 2, Centre national de la recherche scientifique, Place E. Bataillon, 34095 Montpellier, France [2] Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25141177" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Ecology ; *Evolution, Molecular ; Genetic Variation/*genetics ; *Genetics, Population ; Genome/*genetics ; *Genomics ; *Phylogeny
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 2
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    Population size does not influence mitochondrial genetic diversity in animals (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-04-29
    Description: Within-species genetic diversity is thought to reflect population size, history, ecology, and ability to adapt. Using a comprehensive collection of polymorphism data sets covering approximately 3000 animal species, we show that the widely used mitochondrial DNA (mtDNA) marker does not reflect species abundance or ecology: mtDNA diversity is not higher in invertebrates than in vertebrates, in marine than in terrestrial species, or in small than in large organisms. Nuclear loci, in contrast, fit these intuitive expectations. The unexpected mitochondrial diversity distribution is explained by recurrent adaptive evolution, challenging the neutral theory of molecular evolution and questioning the relevance of mtDNA in biodiversity and conservation studies.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bazin, Eric -- Glemin, Sylvain -- Galtier, Nicolas -- New York, N.Y. -- Science. 2006 Apr 28;312(5773):570-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉CNRS UMR 5171-Genome, Populations, Interactions, Adaptation-Universite Montpellier 2 34095 Montpellier Cedex 5, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16645093" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Biological ; Animals ; *Biological Evolution ; Body Size ; DNA/genetics ; DNA, Mitochondrial/*genetics ; Ecosystem ; Evolution, Molecular ; *Genes, Mitochondrial ; Genetic Markers ; *Genetic Variation ; Genetics, Population ; Invertebrates/*genetics ; Isoenzymes/genetics ; Mutation ; *Polymorphism, Genetic ; Population Density ; Recombination, Genetic ; Selection, Genetic ; Vertebrates/*genetics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 3
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    Molecular Evolution of Freshwater Snails with Contrasting Mating Systems (2015)
    Oxford University Press
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    Publication Date: 2015-08-20
    Description: Because mating systems affect population genetics and ecology, they are expected to impact the molecular evolution of species. Self-fertilizing species experience reduced effective population size, recombination rates, and heterozygosity, which in turn should decrease the efficacy of natural selection, both adaptive and purifying, and the strength of meiotic drive processes such as GC-biased gene conversion. The empirical evidence is only partly congruent with these predictions, depending on the analyzed species, some, but not all, of the expected effects have been observed. One possible reason is that self-fertilization is an evolutionary dead-end, so that most current selfers recently evolved self-fertilization, and their genome has not yet been strongly impacted by selfing. Here, we investigate the molecular evolution of two groups of freshwater snails in which mating systems have likely been stable for several millions of years. Analyzing coding sequence polymorphism, divergence, and expression levels, we report a strongly reduced genetic diversity, decreased efficacy of purifying selection, slower rate of adaptive evolution, and weakened codon usage bias/GC-biased gene conversion in the selfer Galba compared with the outcrosser Physa , in full agreement with theoretical expectations. Our results demonstrate that self-fertilization, when effective in the long run, is a major driver of population genomic and molecular evolutionary processes. Despite the genomic effects of selfing, Galba truncatula seems to escape the demographic consequences of the genetic load. We suggest that the particular ecology of the species may buffer the negative consequences of selfing, shedding new light on the dead-end hypothesis.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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  • 4
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    Inference of Purifying and Positive Selection in Three Subspecies of Chimpanzees (Pan troglodytes) from Exome Sequencing (2015)
    Oxford University Press
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    Publication Date: 2015-04-19
    Description: We study genome-wide nucleotide diversity in three subspecies of extant chimpanzees using exome capture. After strict filtering, Single Nucleotide Polymorphisms and indels were called and genotyped for greater than 50% of exons at a mean coverage of 35 x per individual. Central chimpanzees ( Pan troglodytes troglodytes ) are the most polymorphic (nucleotide diversity, w = 0.0023 per site) followed by Eastern ( P. t. schweinfurthii ) chimpanzees ( w = 0.0016) and Western ( P. t. verus ) chimpanzees ( w = 0.0008). A demographic scenario of divergence without gene flow fits the patterns of autosomal synonymous nucleotide diversity well except for a signal of recent gene flow from Western into Eastern chimpanzees. The striking contrast in X-linked versus autosomal polymorphism and divergence previously reported in Central chimpanzees is also found in Eastern and Western chimpanzees. We show that the direction of selection statistic exhibits a strong nonmonotonic relationship with the strength of purifying selection S , making it inappropriate for estimating S . We instead use counts in synonymous versus nonsynonymous frequency classes to infer the distribution of S coefficients acting on nonsynonymous mutations in each subspecies. The strength of purifying selection we infer is congruent with the differences in effective sizes of each subspecies: Central chimpanzees are undergoing the strongest purifying selection followed by Eastern and Western chimpanzees. Coding indels show stronger selection against indels changing the reading frame than observed in human populations.
    Electronic ISSN: 1759-6653
    Topics: Biology
    Published by Oxford University Press
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  • 5
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    The Bimodal Distribution of Genic GC Content Is Ancestral to Monocot Species (2015)
    Oxford University Press
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    Publication Date: 2015-02-02
    Description: In grasses such as rice or maize, the distribution of genic GC content is well known to be bimodal. It is mainly driven by GC content at third codon positions (GC3 for short). This feature is thought to be specific to grasses as closely related species like banana have a unimodal GC3 distribution. GC3 is associated with numerous genomics features and uncovering the origin of this peculiar distribution will help understanding the potential roles and consequences of GC3 variations within and between genomes. Until recently, the origin of the peculiar GC3 distribution in grasses has remained unknown. Thanks to the recent publication of several complete genomes and transcriptomes of nongrass monocots, we studied more than 1,000 groups of one-to-one orthologous genes in seven grasses and three outgroup species (banana, palm tree, and yam). Using a maximum likelihood-based method, we reconstructed GC3 at several ancestral nodes. We found that the bimodal GC3 distribution observed in extant grasses is ancestral to both grasses and most monocot species, and that other species studied here have lost this peculiar structure. We also found that GC3 in grass lineages is globally evolving very slowly and that the decreasing GC3 gradient observed from 5' to 3' along coding sequences is also conserved and ancestral to monocots. This result strongly challenges the previous views on the specificity of grass genomes and we discuss its implications for the possible causes of the evolution of GC content in monocots.
    Electronic ISSN: 1759-6653
    Topics: Biology
    Published by Oxford University Press
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  • 6
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    Introns Structure Patterns of Variation in Nucleotide Composition in Arabidopsis thaliana and Rice Protein-Coding Genes (2015)
    Oxford University Press
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    Publication Date: 2015-10-31
    Description: Plant genomes present a continuous range of variation in nucleotide composition ( G + C content). In coding regions, G + C -poor species tend to have unimodal distributions of G + C content among genes within genomes and slight 5'–3' gradients along genes. In contrast, G + C -rich species display bimodal distributions of G + C content among genes and steep 5'–3' decreasing gradients along genes. The causes of these peculiar patterns are still poorly understood. Within two species ( Arabidopsis thaliana and rice), each representative of one side of the continuum, we studied the consequences of intron presence on coding region and intron G + C content at different scales. By properly taking intron structure into account, we showed that, in both species, intron presence is associated with step changes in nucleotide, codon, and amino acid composition. This suggests that introns have a barrier effect structuring G + C content along genes and that previous continuous characterizations of the 5'–3' gradients were artifactual. In external gene regions (located upstream first or downstream last introns), species-specific factors, such as GC-biased gene conversion, are shaping G + C content whereas in internal gene regions (surrounded by introns), G + C content is likely constrained to remain within a range common to both species.
    Electronic ISSN: 1759-6653
    Topics: Biology
    Published by Oxford University Press
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  • 7
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    The Rate of Molecular Adaptation in a Changing Environment (2013)
    Oxford University Press
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    Publication Date: 2013-05-10
    Description: It is currently unclear whether the amino acid substitutions that occur during protein evolution are primarily driven by adaptation, or reflect the random accumulation of neutral changes. When estimated from genomic data, the proportion of adaptive amino acid substitutions, called α , was found to vary greatly across species, from nearly zero in humans to above 0.5 in Drosophila . These variations have been interpreted as reflecting differences in effective population size, adaptation being supposedly more efficient in large populations. Here, we investigate the influence of effective population size and other biological parameters on the rate of adaptive evolution by simulating the evolution of a coding sequence under Fisher’s geometric formalism. We explicitly model recurrent environmental changes and the subsequent adaptive walks, followed by periods of stasis during which purifying selection dominates. We show that, under a variety of conditions, the effective population size has only a moderate influence on α , and an even weaker influence on the per generation rate of selective sweeps, modifying the prevalent view in current literature. The rate of environmental change and, interestingly, the dimensionality of the phenotypic space (organismal complexity) affect the adaptive rate more deeply than does the effective population size. We discuss the reasons why verbal arguments have been misleading on that subject and revisit the empirical evidence. Our results question the relevance of the " α " parameter as an indicator of the efficiency of molecular adaptation.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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  • 8
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    Marker-based investigation of inbreeding depression in the endangered species Brassica insularis (2006)
    Springer Nature
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    Publication Date: 2006-07-19
    Print ISSN: 0018-067X
    Electronic ISSN: 1365-2540
    Topics: Biology
    Published by Springer Nature
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  • 9
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    Pervasive hybridizations in the history of wheat relatives (2019)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2019
    Description: 〈p〉Cultivated wheats are derived from an intricate history of three genomes, A, B, and D, present in both diploid and polyploid species. It was recently proposed that the D genome originated from an ancient hybridization between the A and B lineages. However, this result has been questioned, and a robust phylogeny of wheat relatives is still lacking. Using transcriptome data from all diploid species and a new methodological approach, our comprehensive phylogenomic analysis revealed that more than half of the species descend from an ancient hybridization event but with a more complex scenario involving a different parent than previously thought—〈i〉Aegilops mutica〈/i〉, an overlooked wild species—instead of the B genome. We also detected other extensive gene flow events that could explain long-standing controversies in the classification of wheat relatives.〈/p〉
    Electronic ISSN: 2375-2548
    Topics: Natural Sciences in General
    Published by American Association for the Advancement of Science (AAAS)
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  • 10
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    Strong Variations of Mitochondrial Mutation Rate across Mammals--the Longevity Hypothesis (2007)
    Oxford University Press
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    Publication Date: 2007-11-13
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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