Natural Selection and Recombination Rate Variation Shape Nucleotide Polymorphism Across the Genomes of Three Related Populus Species.
Identifieur interne : 001757 ( Main/Exploration ); précédent : 001756; suivant : 001758Natural Selection and Recombination Rate Variation Shape Nucleotide Polymorphism Across the Genomes of Three Related Populus Species.
Auteurs : Jing Wang [Suède] ; Nathaniel R. Street [Suède] ; Douglas G. Scofield [Suède] ; P R K. Ingvarsson [Suède]Source :
- Genetics [ 1943-2631 ] ; 2016.
Descripteurs français
- KwdFr :
- ADN des plantes (génétique), Analyse de séquence d'ADN (MeSH), Aptitude génétique (MeSH), Déséquilibre de liaison (MeSH), Fréquence d'allèle (MeSH), Génome végétal (MeSH), Génotype (MeSH), Génétique des populations (MeSH), Phylogenèse (MeSH), Polymorphisme de nucléotide simple (MeSH), Populus (classification), Populus (génétique), Recombinaison génétique (MeSH), Substitution d'acide aminé (MeSH), Sélection génétique (MeSH), Évolution moléculaire (MeSH).
- MESH :
- génétique : ADN des plantes, Populus.
- Analyse de séquence d'ADN, Aptitude génétique, Déséquilibre de liaison, Fréquence d'allèle, Génome végétal, Génotype, Génétique des populations, Phylogenèse, Polymorphisme de nucléotide simple, Recombinaison génétique, Substitution d'acide aminé, Sélection génétique, Évolution moléculaire.
English descriptors
- KwdEn :
- Amino Acid Substitution (MeSH), DNA, Plant (genetics), Evolution, Molecular (MeSH), Gene Frequency (MeSH), Genetic Fitness (MeSH), Genetics, Population (MeSH), Genome, Plant (MeSH), Genotype (MeSH), Linkage Disequilibrium (MeSH), Phylogeny (MeSH), Polymorphism, Single Nucleotide (MeSH), Populus (classification), Populus (genetics), Recombination, Genetic (MeSH), Selection, Genetic (MeSH), Sequence Analysis, DNA (MeSH).
- MESH :
- chemical , genetics : DNA, Plant.
- classification : Populus.
- genetics : Populus.
- Amino Acid Substitution, Evolution, Molecular, Gene Frequency, Genetic Fitness, Genetics, Population, Genome, Plant, Genotype, Linkage Disequilibrium, Phylogeny, Polymorphism, Single Nucleotide, Recombination, Genetic, Selection, Genetic, Sequence Analysis, DNA.
Abstract
A central aim of evolutionary genomics is to identify the relative roles that various evolutionary forces have played in generating and shaping genetic variation within and among species. Here we use whole-genome resequencing data to characterize and compare genome-wide patterns of nucleotide polymorphism, site frequency spectrum, and population-scaled recombination rates in three species of Populus: Populus tremula, P. tremuloides, and P. trichocarpa. We find that P. tremuloides has the highest level of genome-wide variation, skewed allele frequencies, and population-scaled recombination rates, whereas P. trichocarpa harbors the lowest. Our findings highlight multiple lines of evidence suggesting that natural selection, due to both purifying and positive selection, has widely shaped patterns of nucleotide polymorphism at linked neutral sites in all three species. Differences in effective population sizes and rates of recombination largely explain the disparate magnitudes and signatures of linked selection that we observe among species. The present work provides the first phylogenetic comparative study on a genome-wide scale in forest trees. This information will also improve our ability to understand how various evolutionary forces have interacted to influence genome evolution among related species.
DOI: 10.1534/genetics.115.183152
PubMed: 26721855
PubMed Central: PMC4788117
Affiliations:
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Here we use whole-genome resequencing data to characterize and compare genome-wide patterns of nucleotide polymorphism, site frequency spectrum, and population-scaled recombination rates in three species of Populus: Populus tremula, P. tremuloides, and P. trichocarpa. We find that P. tremuloides has the highest level of genome-wide variation, skewed allele frequencies, and population-scaled recombination rates, whereas P. trichocarpa harbors the lowest. Our findings highlight multiple lines of evidence suggesting that natural selection, due to both purifying and positive selection, has widely shaped patterns of nucleotide polymorphism at linked neutral sites in all three species. Differences in effective population sizes and rates of recombination largely explain the disparate magnitudes and signatures of linked selection that we observe among species. The present work provides the first phylogenetic comparative study on a genome-wide scale in forest trees. This information will also improve our ability to understand how various evolutionary forces have interacted to influence genome evolution among related species.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">26721855</PMID><DateCompleted><Year>2017</Year><Month>01</Month><Day>12</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1943-2631</ISSN><JournalIssue CitedMedium="Internet"><Volume>202</Volume><Issue>3</Issue><PubDate><Year>2016</Year><Month>Mar</Month></PubDate></JournalIssue><Title>Genetics</Title><ISOAbbreviation>Genetics</ISOAbbreviation></Journal><ArticleTitle>Natural Selection and Recombination Rate Variation Shape Nucleotide Polymorphism Across the Genomes of Three Related Populus Species.</ArticleTitle><Pagination><MedlinePgn>1185-200</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1534/genetics.115.183152</ELocationID><Abstract><AbstractText>A central aim of evolutionary genomics is to identify the relative roles that various evolutionary forces have played in generating and shaping genetic variation within and among species. Here we use whole-genome resequencing data to characterize and compare genome-wide patterns of nucleotide polymorphism, site frequency spectrum, and population-scaled recombination rates in three species of Populus: Populus tremula, P. tremuloides, and P. trichocarpa. We find that P. tremuloides has the highest level of genome-wide variation, skewed allele frequencies, and population-scaled recombination rates, whereas P. trichocarpa harbors the lowest. Our findings highlight multiple lines of evidence suggesting that natural selection, due to both purifying and positive selection, has widely shaped patterns of nucleotide polymorphism at linked neutral sites in all three species. Differences in effective population sizes and rates of recombination largely explain the disparate magnitudes and signatures of linked selection that we observe among species. The present work provides the first phylogenetic comparative study on a genome-wide scale in forest trees. This information will also improve our ability to understand how various evolutionary forces have interacted to influence genome evolution among related species.</AbstractText><CopyrightInformation>Copyright © 2016 by the Genetics Society of America.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Jing</ForeName><Initials>J</Initials><Identifier Source="ORCID">0000-0002-3793-3264</Identifier><AffiliationInfo><Affiliation>Department of Ecology and Environmental Science, Umeå University, Umeå SE 90187, Sweden.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Street</LastName><ForeName>Nathaniel R</ForeName><Initials>NR</Initials><Identifier Source="ORCID">0000-0001-6031-005X</Identifier><AffiliationInfo><Affiliation>Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå SE 90187, Sweden.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Scofield</LastName><ForeName>Douglas G</ForeName><Initials>DG</Initials><Identifier Source="ORCID">0000-0001-5235-6461</Identifier><AffiliationInfo><Affiliation>Department of Ecology and Environmental Science, Umeå University, Umeå SE 90187, Sweden Department of Ecology and Genetics: Evolutionary Biology, Uppsala University, Uppsala SE 75105, Sweden Uppsala Multidisciplinary Center for Advanced Computational Science, Uppsala University, Uppsala SE 75105, Sweden.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ingvarsson</LastName><ForeName>Pär K</ForeName><Initials>PK</Initials><Identifier Source="ORCID">0000-0001-9225-7521</Identifier><AffiliationInfo><Affiliation>Department of Ecology and Environmental Science, Umeå University, Umeå SE 90187, Sweden par.ingvarsson@umu.se.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2015</Year><Month>12</Month><Day>31</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Genetics</MedlineTA><NlmUniqueID>0374636</NlmUniqueID><ISSNLinking>0016-6731</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D018744">DNA, Plant</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D019943" MajorTopicYN="N">Amino Acid Substitution</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018744" MajorTopicYN="N">DNA, Plant</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D019143" MajorTopicYN="Y">Evolution, Molecular</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005787" MajorTopicYN="N">Gene Frequency</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D056084" MajorTopicYN="N">Genetic Fitness</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005828" MajorTopicYN="N">Genetics, Population</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018745" MajorTopicYN="N">Genome, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005838" MajorTopicYN="N">Genotype</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D015810" MajorTopicYN="N">Linkage Disequilibrium</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020641" MajorTopicYN="Y">Polymorphism, Single Nucleotide</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000145" MajorTopicYN="N">classification</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D011995" MajorTopicYN="Y">Recombination, Genetic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012641" MajorTopicYN="Y">Selection, Genetic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017422" MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Populus</Keyword><Keyword MajorTopicYN="N">natural selection</Keyword><Keyword MajorTopicYN="N">nucleotide polymorphism</Keyword><Keyword MajorTopicYN="N">recombination</Keyword><Keyword MajorTopicYN="N">whole-genome resequencing</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2015</Year><Month>09</Month><Day>25</Day></PubMedPubDate><PubMedPubDate 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sort="Ingvarsson, P R K" uniqKey="Ingvarsson P" first="P R K" last="Ingvarsson">P R K. Ingvarsson</name><name sortKey="Scofield, Douglas G" sort="Scofield, Douglas G" uniqKey="Scofield D" first="Douglas G" last="Scofield">Douglas G. Scofield</name><name sortKey="Street, Nathaniel R" sort="Street, Nathaniel R" uniqKey="Street N" first="Nathaniel R" last="Street">Nathaniel R. Street</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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