Evidence for widespread selection in shaping the genomic landscape during speciation of Populus.
Identifieur interne : 000416 ( Main/Exploration ); précédent : 000415; suivant : 000417Evidence for widespread selection in shaping the genomic landscape during speciation of Populus.
Auteurs : Jing Wang [République populaire de Chine] ; Nathaniel R. Street [Suède] ; Eung-Jun Park [Corée du Sud] ; Jianquan Liu [République populaire de Chine] ; P R K. Ingvarsson [Suède]Source :
- Molecular ecology [ 1365-294X ] ; 2020.
Abstract
Increasing our understanding of how evolutionary processes drive the genomic landscape of variation is fundamental to a better understanding of the genomic consequences of speciation. However, genome-wide patterns of within- and between- species variation have not been fully investigated in most forest tree species despite their global ecological and economic importance. Here, we use whole-genome resequencing data from four Populus species spanning the speciation continuum to reconstruct their demographic histories and investigate patterns of diversity and divergence within and between species. Using Populus trichocarpa as an outgroup species, we further infer the genealogical relationships and estimate the extent of ancient introgression among the three aspen species (Populus tremula, Populus davidiana and Populus tremuloides) throughout the genome. Our results show substantial variation in these patterns along the genomes with this variation being strongly predicted by local recombination rates and the density of functional elements. This implies that the interaction between recurrent selection and intrinsic genomic features has dramatically sculpted the genomic landscape over long periods of time. In addition, our findings provide evidence that, apart from background selection, recent positive selection and long-term balancing selection have also been crucial components in shaping patterns of genome-wide variation during the speciation process.
DOI: 10.1111/mec.15388
PubMed: 32068935
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Street</name><affiliation wicri:level="1"><nlm:affiliation>Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden.</nlm:affiliation><country xml:lang="fr">Suède</country><wicri:regionArea>Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå</wicri:regionArea><wicri:noRegion>Umeå</wicri:noRegion></affiliation></author><author><name sortKey="Park, Eung Jun" sort="Park, Eung Jun" uniqKey="Park E" first="Eung-Jun" last="Park">Eung-Jun Park</name><affiliation wicri:level="1"><nlm:affiliation>Department of Bioresources, National Institute of Forest Science, Suwon, Korea.</nlm:affiliation><country xml:lang="fr">Corée du Sud</country><wicri:regionArea>Department of Bioresources, National Institute of Forest Science, Suwon</wicri:regionArea><wicri:noRegion>Suwon</wicri:noRegion></affiliation></author><author><name sortKey="Liu, Jianquan" sort="Liu, Jianquan" uniqKey="Liu J" first="Jianquan" last="Liu">Jianquan Liu</name><affiliation wicri:level="1"><nlm:affiliation>Key Laboratory for Bio-Resources and Eco-Environment, College of Life Science, Sichuan University, Chengdu, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory for Bio-Resources and Eco-Environment, College of Life Science, Sichuan University, Chengdu</wicri:regionArea><wicri:noRegion>Chengdu</wicri:noRegion></affiliation></author><author><name sortKey="Ingvarsson, P R K" sort="Ingvarsson, P R K" uniqKey="Ingvarsson P" first="P R K" last="Ingvarsson">P R K. Ingvarsson</name><affiliation wicri:level="1"><nlm:affiliation>Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden.</nlm:affiliation><country xml:lang="fr">Suède</country><wicri:regionArea>Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala</wicri:regionArea><wicri:noRegion>Uppsala</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2020">2020</date><idno type="RBID">pubmed:32068935</idno><idno type="pmid">32068935</idno><idno type="doi">10.1111/mec.15388</idno><idno type="wicri:Area/Main/Corpus">000451</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">000451</idno><idno type="wicri:Area/Main/Curation">000451</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">000451</idno><idno type="wicri:Area/Main/Exploration">000451</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Evidence for widespread selection in shaping the genomic landscape during speciation of Populus.</title><author><name sortKey="Wang, Jing" sort="Wang, Jing" uniqKey="Wang J" first="Jing" last="Wang">Jing Wang</name><affiliation wicri:level="1"><nlm:affiliation>Key Laboratory for Bio-Resources and Eco-Environment, College of Life Science, Sichuan University, Chengdu, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory for Bio-Resources and Eco-Environment, College of Life Science, Sichuan University, Chengdu</wicri:regionArea><wicri:noRegion>Chengdu</wicri:noRegion></affiliation></author><author><name sortKey="Street, Nathaniel R" sort="Street, Nathaniel R" uniqKey="Street N" first="Nathaniel R" last="Street">Nathaniel R. Street</name><affiliation wicri:level="1"><nlm:affiliation>Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden.</nlm:affiliation><country xml:lang="fr">Suède</country><wicri:regionArea>Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå</wicri:regionArea><wicri:noRegion>Umeå</wicri:noRegion></affiliation></author><author><name sortKey="Park, Eung Jun" sort="Park, Eung Jun" uniqKey="Park E" first="Eung-Jun" last="Park">Eung-Jun Park</name><affiliation wicri:level="1"><nlm:affiliation>Department of Bioresources, National Institute of Forest Science, Suwon, Korea.</nlm:affiliation><country xml:lang="fr">Corée du Sud</country><wicri:regionArea>Department of Bioresources, National Institute of Forest Science, Suwon</wicri:regionArea><wicri:noRegion>Suwon</wicri:noRegion></affiliation></author><author><name sortKey="Liu, Jianquan" sort="Liu, Jianquan" uniqKey="Liu J" first="Jianquan" last="Liu">Jianquan Liu</name><affiliation wicri:level="1"><nlm:affiliation>Key Laboratory for Bio-Resources and Eco-Environment, College of Life Science, Sichuan University, Chengdu, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory for Bio-Resources and Eco-Environment, College of Life Science, Sichuan University, Chengdu</wicri:regionArea><wicri:noRegion>Chengdu</wicri:noRegion></affiliation></author><author><name sortKey="Ingvarsson, P R K" sort="Ingvarsson, P R K" uniqKey="Ingvarsson P" first="P R K" last="Ingvarsson">P R K. Ingvarsson</name><affiliation wicri:level="1"><nlm:affiliation>Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden.</nlm:affiliation><country xml:lang="fr">Suède</country><wicri:regionArea>Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala</wicri:regionArea><wicri:noRegion>Uppsala</wicri:noRegion></affiliation></author></analytic><series><title level="j">Molecular ecology</title><idno type="eISSN">1365-294X</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Increasing our understanding of how evolutionary processes drive the genomic landscape of variation is fundamental to a better understanding of the genomic consequences of speciation. However, genome-wide patterns of within- and between- species variation have not been fully investigated in most forest tree species despite their global ecological and economic importance. Here, we use whole-genome resequencing data from four Populus species spanning the speciation continuum to reconstruct their demographic histories and investigate patterns of diversity and divergence within and between species. Using Populus trichocarpa as an outgroup species, we further infer the genealogical relationships and estimate the extent of ancient introgression among the three aspen species (Populus tremula, Populus davidiana and Populus tremuloides) throughout the genome. Our results show substantial variation in these patterns along the genomes with this variation being strongly predicted by local recombination rates and the density of functional elements. This implies that the interaction between recurrent selection and intrinsic genomic features has dramatically sculpted the genomic landscape over long periods of time. In addition, our findings provide evidence that, apart from background selection, recent positive selection and long-term balancing selection have also been crucial components in shaping patterns of genome-wide variation during the speciation process.</div></front></TEI><pubmed><MedlineCitation Status="In-Process" Owner="NLM"><PMID Version="1">32068935</PMID><DateRevised><Year>2020</Year><Month>07</Month><Day>01</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1365-294X</ISSN><JournalIssue CitedMedium="Internet"><Volume>29</Volume><Issue>6</Issue><PubDate><Year>2020</Year><Month>03</Month></PubDate></JournalIssue><Title>Molecular ecology</Title><ISOAbbreviation>Mol Ecol</ISOAbbreviation></Journal><ArticleTitle>Evidence for widespread selection in shaping the genomic landscape during speciation of Populus.</ArticleTitle><Pagination><MedlinePgn>1120-1136</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1111/mec.15388</ELocationID><Abstract><AbstractText>Increasing our understanding of how evolutionary processes drive the genomic landscape of variation is fundamental to a better understanding of the genomic consequences of speciation. However, genome-wide patterns of within- and between- species variation have not been fully investigated in most forest tree species despite their global ecological and economic importance. Here, we use whole-genome resequencing data from four Populus species spanning the speciation continuum to reconstruct their demographic histories and investigate patterns of diversity and divergence within and between species. Using Populus trichocarpa as an outgroup species, we further infer the genealogical relationships and estimate the extent of ancient introgression among the three aspen species (Populus tremula, Populus davidiana and Populus tremuloides) throughout the genome. Our results show substantial variation in these patterns along the genomes with this variation being strongly predicted by local recombination rates and the density of functional elements. This implies that the interaction between recurrent selection and intrinsic genomic features has dramatically sculpted the genomic landscape over long periods of time. In addition, our findings provide evidence that, apart from background selection, recent positive selection and long-term balancing selection have also been crucial components in shaping patterns of genome-wide variation during the speciation process.</AbstractText><CopyrightInformation>© 2020 John Wiley & Sons Ltd.</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>Key Laboratory for Bio-Resources and Eco-Environment, College of Life Science, Sichuan University, Chengdu, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Street</LastName><ForeName>Nathaniel R</ForeName><Initials>NR</Initials><AffiliationInfo><Affiliation>Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Park</LastName><ForeName>Eung-Jun</ForeName><Initials>EJ</Initials><AffiliationInfo><Affiliation>Department of Bioresources, National Institute of Forest Science, Suwon, Korea.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Liu</LastName><ForeName>Jianquan</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Key Laboratory for Bio-Resources and Eco-Environment, College of Life Science, Sichuan University, Chengdu, China.</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 Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><DataBankList CompleteYN="Y"><DataBank><DataBankName>GENBANK</DataBankName><AccessionNumberList><AccessionNumber>PRJNA576115</AccessionNumber></AccessionNumberList></DataBank></DataBankList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>03</Month><Day>09</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Mol Ecol</MedlineTA><NlmUniqueID>9214478</NlmUniqueID><ISSNLinking>0962-1083</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="Y">Populus
</Keyword><Keyword MajorTopicYN="Y">ancient introgression</Keyword><Keyword MajorTopicYN="Y">incomplete lineage sorting</Keyword><Keyword MajorTopicYN="Y">linked selection</Keyword><Keyword MajorTopicYN="Y">phylogenetic relationship</Keyword><Keyword MajorTopicYN="Y">recombination</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2019</Year><Month>10</Month><Day>15</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2020</Year><Month>02</Month><Day>13</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2020</Year><Month>02</Month><Day>14</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>2</Month><Day>19</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>2</Month><Day>19</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>2</Month><Day>19</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">32068935</ArticleId><ArticleId IdType="doi">10.1111/mec.15388</ArticleId></ArticleIdList><ReferenceList><Title>REFERENCES</Title><Reference><Citation>Abbott, R., Albach, D., Ansell, S., Arntzen, J. 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Ingvarsson</name></country><country name="Corée du Sud"><noRegion><name sortKey="Park, Eung Jun" sort="Park, Eung Jun" uniqKey="Park E" first="Eung-Jun" last="Park">Eung-Jun Park</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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