Recombination Rate Variation, Hitchhiking, and Demographic History Shape Deleterious Load in Poplar.
Identifieur interne : 001691 ( Main/Exploration ); précédent : 001690; suivant : 001692Recombination Rate Variation, Hitchhiking, and Demographic History Shape Deleterious Load in Poplar.
Auteurs : M. Zhang ; L. Zhou ; R. Bawa ; H. Suren [États-Unis] ; J A Holliday [États-Unis]Source :
- Molecular biology and evolution [ 1537-1719 ] ; 2016.
Descripteurs français
- KwdFr :
- Allèles (MeSH), Bases de données d'acides nucléiques (MeSH), Densité de population (MeSH), Démographie (méthodes), Fardeau génétique (MeSH), Fréquence d'allèle (MeSH), Génome végétal (MeSH), Génomique (MeSH), Homozygote (MeSH), Populus (génétique), Recombinaison génétique (MeSH), Sélection génétique (MeSH), Variation génétique (MeSH), Évolution moléculaire (MeSH).
- MESH :
English descriptors
- KwdEn :
- Alleles (MeSH), Databases, Nucleic Acid (MeSH), Demography (methods), Evolution, Molecular (MeSH), Gene Frequency (MeSH), Genetic Load (MeSH), Genetic Variation (MeSH), Genome, Plant (MeSH), Genomics (MeSH), Homozygote (MeSH), Population Density (MeSH), Populus (genetics), Recombination, Genetic (MeSH), Selection, Genetic (MeSH).
- MESH :
Abstract
Deleterious alleles are expected to be purged by purifying selection or maintained at low frequency. However, many additional evolutionary forces may shape the pattern of deleterious mutations across the genome and among populations, including selection, hitchhiking, recombination, and demographic history. We used exome capture data to estimate the genome-wide distribution of deleterious alleles across natural populations of the model tree black cottonwood (Populus trichocarpa). Although deleterious alleles were on average present at low frequency suggesting purifying selection, they were preferentially enriched both within genomic regions of low-recombination and in regions showing evidence of positive selection. The demographic history of this species also appeared to play a role in the distribution of deleterious alleles among populations, with peripheral populations having higher rates of deleterious homozygosity. This be due to less efficient selection arising from smaller effective population sizes at the edges of the range, and possibly also due to recent bottlenecks associated with postglacial recolonization. Finally, correlations between deleterious homozygosity and plant growth suggest a significant effect of deleterious load on fitness. Our results show that both genomic context and historical demography play a role in shaping the distribution of deleterious alleles across the genome and range of P. trichocarpa.
DOI: 10.1093/molbev/msw169
PubMed: 27512114
Affiliations:
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Zhang</name><affiliation><nlm:affiliation>Department of Forest Resources and Environmental Conservation, Virginia Polytechnic Institute and State University.</nlm:affiliation><wicri:noCountry code="subField">Virginia Polytechnic Institute and State University</wicri:noCountry></affiliation></author><author><name sortKey="Zhou, L" sort="Zhou, L" uniqKey="Zhou L" first="L" last="Zhou">L. Zhou</name><affiliation><nlm:affiliation>Department of Forest Resources and Environmental Conservation, Virginia Polytechnic Institute and State University.</nlm:affiliation><wicri:noCountry code="subField">Virginia Polytechnic Institute and State University</wicri:noCountry></affiliation></author><author><name sortKey="Bawa, R" sort="Bawa, R" uniqKey="Bawa R" first="R" last="Bawa">R. 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Suren</name><affiliation wicri:level="2"><nlm:affiliation>Department of Forest Resources and Environmental Conservation, Virginia Polytechnic Institute and State University Genetics, Bioinformatics and Computational Biology Program, Virginia Tech, Blacksburg, VA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><placeName><region type="state">Virginie</region></placeName><wicri:cityArea>Department of Forest Resources and Environmental Conservation, Virginia Polytechnic Institute and State University Genetics, Bioinformatics and Computational Biology Program, Virginia Tech, Blacksburg</wicri:cityArea></affiliation></author><author><name sortKey="Holliday, J A" sort="Holliday, J A" uniqKey="Holliday J" first="J A" last="Holliday">J A Holliday</name><affiliation wicri:level="1"><nlm:affiliation>Department of Forest Resources and Environmental Conservation, Virginia Polytechnic Institute and State University jah1@vt.edu.</nlm:affiliation><country wicri:rule="url">États-Unis</country><wicri:regionArea>Department of Forest Resources and Environmental Conservation</wicri:regionArea></affiliation></author></analytic><series><title level="j">Molecular biology and evolution</title><idno type="eISSN">1537-1719</idno><imprint><date when="2016" type="published">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Alleles (MeSH)</term><term>Databases, Nucleic Acid (MeSH)</term><term>Demography (methods)</term><term>Evolution, Molecular (MeSH)</term><term>Gene Frequency (MeSH)</term><term>Genetic Load (MeSH)</term><term>Genetic Variation (MeSH)</term><term>Genome, Plant (MeSH)</term><term>Genomics (MeSH)</term><term>Homozygote (MeSH)</term><term>Population Density (MeSH)</term><term>Populus (genetics)</term><term>Recombination, Genetic (MeSH)</term><term>Selection, Genetic (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Allèles (MeSH)</term><term>Bases de données d'acides nucléiques (MeSH)</term><term>Densité de population (MeSH)</term><term>Démographie (méthodes)</term><term>Fardeau génétique (MeSH)</term><term>Fréquence d'allèle (MeSH)</term><term>Génome végétal (MeSH)</term><term>Génomique (MeSH)</term><term>Homozygote (MeSH)</term><term>Populus (génétique)</term><term>Recombinaison génétique (MeSH)</term><term>Sélection génétique (MeSH)</term><term>Variation génétique (MeSH)</term><term>Évolution moléculaire (MeSH)</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Populus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Populus</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Demography</term></keywords><keywords scheme="MESH" qualifier="méthodes" xml:lang="fr"><term>Démographie</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Alleles</term><term>Databases, Nucleic Acid</term><term>Evolution, Molecular</term><term>Gene Frequency</term><term>Genetic Load</term><term>Genetic Variation</term><term>Genome, Plant</term><term>Genomics</term><term>Homozygote</term><term>Population Density</term><term>Recombination, Genetic</term><term>Selection, Genetic</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Allèles</term><term>Bases de données d'acides nucléiques</term><term>Densité de population</term><term>Fardeau génétique</term><term>Fréquence d'allèle</term><term>Génome végétal</term><term>Génomique</term><term>Homozygote</term><term>Recombinaison génétique</term><term>Sélection génétique</term><term>Variation génétique</term><term>Évolution moléculaire</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Deleterious alleles are expected to be purged by purifying selection or maintained at low frequency. However, many additional evolutionary forces may shape the pattern of deleterious mutations across the genome and among populations, including selection, hitchhiking, recombination, and demographic history. We used exome capture data to estimate the genome-wide distribution of deleterious alleles across natural populations of the model tree black cottonwood (Populus trichocarpa). Although deleterious alleles were on average present at low frequency suggesting purifying selection, they were preferentially enriched both within genomic regions of low-recombination and in regions showing evidence of positive selection. The demographic history of this species also appeared to play a role in the distribution of deleterious alleles among populations, with peripheral populations having higher rates of deleterious homozygosity. This be due to less efficient selection arising from smaller effective population sizes at the edges of the range, and possibly also due to recent bottlenecks associated with postglacial recolonization. Finally, correlations between deleterious homozygosity and plant growth suggest a significant effect of deleterious load on fitness. Our results show that both genomic context and historical demography play a role in shaping the distribution of deleterious alleles across the genome and range of P. trichocarpa.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">27512114</PMID><DateCompleted><Year>2017</Year><Month>06</Month><Day>21</Day></DateCompleted><DateRevised><Year>2018</Year><Month>03</Month><Day>05</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1537-1719</ISSN><JournalIssue CitedMedium="Internet"><Volume>33</Volume><Issue>11</Issue><PubDate><Year>2016</Year><Month>11</Month></PubDate></JournalIssue><Title>Molecular biology and evolution</Title><ISOAbbreviation>Mol Biol Evol</ISOAbbreviation></Journal><ArticleTitle>Recombination Rate Variation, Hitchhiking, and Demographic History Shape Deleterious Load in Poplar.</ArticleTitle><Pagination><MedlinePgn>2899-2910</MedlinePgn></Pagination><Abstract><AbstractText>Deleterious alleles are expected to be purged by purifying selection or maintained at low frequency. However, many additional evolutionary forces may shape the pattern of deleterious mutations across the genome and among populations, including selection, hitchhiking, recombination, and demographic history. We used exome capture data to estimate the genome-wide distribution of deleterious alleles across natural populations of the model tree black cottonwood (Populus trichocarpa). Although deleterious alleles were on average present at low frequency suggesting purifying selection, they were preferentially enriched both within genomic regions of low-recombination and in regions showing evidence of positive selection. The demographic history of this species also appeared to play a role in the distribution of deleterious alleles among populations, with peripheral populations having higher rates of deleterious homozygosity. This be due to less efficient selection arising from smaller effective population sizes at the edges of the range, and possibly also due to recent bottlenecks associated with postglacial recolonization. Finally, correlations between deleterious homozygosity and plant growth suggest a significant effect of deleterious load on fitness. Our results show that both genomic context and historical demography play a role in shaping the distribution of deleterious alleles across the genome and range of P. trichocarpa.</AbstractText><CopyrightInformation>© The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>M</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Department of Forest Resources and Environmental Conservation, Virginia Polytechnic Institute and State University.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhou</LastName><ForeName>L</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>Department of Forest Resources and Environmental Conservation, Virginia Polytechnic Institute and State University.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Bawa</LastName><ForeName>R</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>Department of Forest Resources and Environmental Conservation, Virginia Polytechnic Institute and State University.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Suren</LastName><ForeName>H</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Department of Forest Resources and Environmental Conservation, Virginia Polytechnic Institute and State University Genetics, Bioinformatics and Computational Biology Program, Virginia Tech, Blacksburg, VA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Holliday</LastName><ForeName>J A</ForeName><Initials>JA</Initials><AffiliationInfo><Affiliation>Department of Forest Resources and Environmental Conservation, Virginia Polytechnic Institute and State University jah1@vt.edu.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013486">Research Support, U.S. Gov't, Non-P.H.S.</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2016</Year><Month>08</Month><Day>10</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Mol Biol Evol</MedlineTA><NlmUniqueID>8501455</NlmUniqueID><ISSNLinking>0737-4038</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000483" MajorTopicYN="N">Alleles</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D030561" MajorTopicYN="N">Databases, Nucleic Acid</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D003710" MajorTopicYN="N">Demography</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="N">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D019143" MajorTopicYN="N">Evolution, Molecular</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005787" MajorTopicYN="N">Gene Frequency</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D040741" MajorTopicYN="N">Genetic Load</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014644" MajorTopicYN="N">Genetic Variation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018745" MajorTopicYN="N">Genome, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D023281" MajorTopicYN="N">Genomics</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D006720" MajorTopicYN="N">Homozygote</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D011156" MajorTopicYN="N">Population Density</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D011995" MajorTopicYN="N">Recombination, Genetic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012641" MajorTopicYN="N">Selection, Genetic</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="Y">deleterious alleles</Keyword><Keyword MajorTopicYN="Y">genetic hitchhiking</Keyword><Keyword MajorTopicYN="Y">genetic load</Keyword><Keyword MajorTopicYN="Y">populus trichocarpa</Keyword><Keyword MajorTopicYN="Y">selective sweep</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2016</Year><Month>8</Month><Day>12</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2017</Year><Month>6</Month><Day>22</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2016</Year><Month>8</Month><Day>12</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">27512114</ArticleId><ArticleId IdType="pii">msw169</ArticleId><ArticleId IdType="doi">10.1093/molbev/msw169</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>États-Unis</li></country><region><li>Virginie</li></region></list><tree><noCountry><name sortKey="Bawa, R" sort="Bawa, R" uniqKey="Bawa R" first="R" last="Bawa">R. Bawa</name><name sortKey="Zhang, M" sort="Zhang, M" uniqKey="Zhang M" first="M" last="Zhang">M. Zhang</name><name sortKey="Zhou, L" sort="Zhou, L" uniqKey="Zhou L" first="L" last="Zhou">L. Zhou</name></noCountry><country name="États-Unis"><region name="Virginie"><name sortKey="Suren, H" sort="Suren, H" uniqKey="Suren H" first="H" last="Suren">H. Suren</name></region><name sortKey="Holliday, J A" sort="Holliday, J A" uniqKey="Holliday J" first="J A" last="Holliday">J A Holliday</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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