Demographically idiosyncratic responses to climate change and rapid Pleistocene diversification of the walnut genus Juglans (Juglandaceae) revealed by whole-genome sequences.
Identifieur interne : 000F67 ( Main/Exploration ); précédent : 000F66; suivant : 000F68Demographically idiosyncratic responses to climate change and rapid Pleistocene diversification of the walnut genus Juglans (Juglandaceae) revealed by whole-genome sequences.
Auteurs : Wei-Ning Bai [République populaire de Chine] ; Peng-Cheng Yan [République populaire de Chine] ; Bo-Wen Zhang [République populaire de Chine] ; Keith E. Woeste [États-Unis] ; Kui Lin [République populaire de Chine] ; Da-Yong Zhang [République populaire de Chine]Source :
- The New phytologist [ 1469-8137 ] ; 2018.
Descripteurs français
- KwdFr :
- Chaines de Markov (MeSH), Changement climatique (MeSH), Densité de population (MeSH), Facteurs temps (MeSH), Fraxinus (génétique), Génome végétal (MeSH), Juglans (génétique), Phylogenèse (MeSH), Populus (génétique), Spécificité d'espèce (MeSH), Séquence nucléotidique (MeSH), Séquençage du génome entier (MeSH), Variation génétique (MeSH).
- MESH :
English descriptors
- KwdEn :
- Base Sequence (MeSH), Climate Change (MeSH), Fraxinus (genetics), Genetic Variation (MeSH), Genome, Plant (MeSH), Juglans (genetics), Markov Chains (MeSH), Phylogeny (MeSH), Population Density (MeSH), Populus (genetics), Species Specificity (MeSH), Time Factors (MeSH), Whole Genome Sequencing (MeSH).
- MESH :
Abstract
Whether species demography and diversification are driven primarily by extrinsic environmental changes such as climatic oscillations in the Quaternary or by intrinsic biological interactions like coevolution between antagonists is a matter of active debate. In fact, their relative importance can be assessed by tracking past population fluctuations over considerable time periods. We applied the pairwise sequentially Markovian coalescent approach on the genomes of 11 temperate Juglans species to estimate trajectories of changes in effective population size (Ne ) and used a Bayesian-coalescent based approach that simultaneously considers multiple genomes (G-PhoCS) to estimate divergence times between lineages. Ne curves of all study species converged 1.0 million yr ago, probably reflecting the time when the walnut genus last shared a common ancestor. This estimate was confirmed by the G-PhoCS estimates of divergence times. But all species did not react similarly to the dramatic climatic oscillations following early Pleistocene cooling, so the timing and amplitude of changes in Ne differed among species and even among conspecific lineages. The population histories of temperate walnut species were not driven by extrinsic environmental changes alone, and a key role was probably played by species-specific factors such as coevolutionary interactions with specialized pathogens.
DOI: 10.1111/nph.14917
PubMed: 29178135
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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sequences.</title><author><name sortKey="Bai, Wei Ning" sort="Bai, Wei Ning" uniqKey="Bai W" first="Wei-Ning" last="Bai">Wei-Ning Bai</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875</wicri:regionArea><wicri:noRegion>100875</wicri:noRegion></affiliation></author><author><name sortKey="Yan, Peng Cheng" sort="Yan, Peng Cheng" uniqKey="Yan P" first="Peng-Cheng" last="Yan">Peng-Cheng Yan</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875</wicri:regionArea><wicri:noRegion>100875</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Beijing Key Laboratory of Cloud Computing Key Technology and Application, Beijing Computing Center, Beijing, 100094, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Beijing Key Laboratory of Cloud Computing Key Technology and Application, Beijing Computing Center, Beijing, 100094</wicri:regionArea><wicri:noRegion>100094</wicri:noRegion></affiliation></author><author><name sortKey="Zhang, Bo Wen" sort="Zhang, Bo Wen" uniqKey="Zhang B" first="Bo-Wen" last="Zhang">Bo-Wen Zhang</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875</wicri:regionArea><wicri:noRegion>100875</wicri:noRegion></affiliation></author><author><name sortKey="Woeste, Keith E" sort="Woeste, Keith E" uniqKey="Woeste K" first="Keith E" last="Woeste">Keith E. Woeste</name><affiliation wicri:level="1"><nlm:affiliation>USDA Forest Service Hardwood Tree Improvement and Regeneration Center (HTIRC), Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN, 47907, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>USDA Forest Service Hardwood Tree Improvement and Regeneration Center (HTIRC), Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN, 47907</wicri:regionArea><wicri:noRegion>47907</wicri:noRegion></affiliation></author><author><name sortKey="Lin, Kui" sort="Lin, Kui" uniqKey="Lin K" first="Kui" last="Lin">Kui Lin</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875</wicri:regionArea><wicri:noRegion>100875</wicri:noRegion></affiliation></author><author><name sortKey="Zhang, Da Yong" sort="Zhang, Da Yong" uniqKey="Zhang D" first="Da-Yong" last="Zhang">Da-Yong Zhang</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875</wicri:regionArea><wicri:noRegion>100875</wicri:noRegion></affiliation></author></analytic><series><title level="j">The New phytologist</title><idno type="eISSN">1469-8137</idno><imprint><date when="2018" type="published">2018</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Base Sequence (MeSH)</term><term>Climate Change (MeSH)</term><term>Fraxinus (genetics)</term><term>Genetic Variation (MeSH)</term><term>Genome, Plant (MeSH)</term><term>Juglans (genetics)</term><term>Markov Chains (MeSH)</term><term>Phylogeny (MeSH)</term><term>Population Density (MeSH)</term><term>Populus (genetics)</term><term>Species Specificity (MeSH)</term><term>Time Factors (MeSH)</term><term>Whole Genome Sequencing (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Chaines de Markov (MeSH)</term><term>Changement climatique (MeSH)</term><term>Densité de population (MeSH)</term><term>Facteurs temps (MeSH)</term><term>Fraxinus (génétique)</term><term>Génome végétal (MeSH)</term><term>Juglans (génétique)</term><term>Phylogenèse (MeSH)</term><term>Populus (génétique)</term><term>Spécificité d'espèce (MeSH)</term><term>Séquence nucléotidique (MeSH)</term><term>Séquençage du génome entier (MeSH)</term><term>Variation génétique (MeSH)</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Fraxinus</term><term>Juglans</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Fraxinus</term><term>Juglans</term><term>Populus</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Base Sequence</term><term>Climate Change</term><term>Genetic Variation</term><term>Genome, Plant</term><term>Markov Chains</term><term>Phylogeny</term><term>Population Density</term><term>Species Specificity</term><term>Time Factors</term><term>Whole Genome Sequencing</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Chaines de Markov</term><term>Changement climatique</term><term>Densité de population</term><term>Facteurs temps</term><term>Génome végétal</term><term>Phylogenèse</term><term>Spécificité d'espèce</term><term>Séquence nucléotidique</term><term>Séquençage du génome entier</term><term>Variation génétique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Whether species demography and diversification are driven primarily by extrinsic environmental changes such as climatic oscillations in the Quaternary or by intrinsic biological interactions like coevolution between antagonists is a matter of active debate. In fact, their relative importance can be assessed by tracking past population fluctuations over considerable time periods. We applied the pairwise sequentially Markovian coalescent approach on the genomes of 11 temperate Juglans species to estimate trajectories of changes in effective population size (N<sub>e</sub> ) and used a Bayesian-coalescent based approach that simultaneously considers multiple genomes (G-PhoCS) to estimate divergence times between lineages. N<sub>e</sub> curves of all study species converged 1.0 million yr ago, probably reflecting the time when the walnut genus last shared a common ancestor. This estimate was confirmed by the G-PhoCS estimates of divergence times. But all species did not react similarly to the dramatic climatic oscillations following early Pleistocene cooling, so the timing and amplitude of changes in N<sub>e</sub> differed among species and even among conspecific lineages. The population histories of temperate walnut species were not driven by extrinsic environmental changes alone, and a key role was probably played by species-specific factors such as coevolutionary interactions with specialized pathogens.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">29178135</PMID><DateCompleted><Year>2019</Year><Month>09</Month><Day>13</Day></DateCompleted><DateRevised><Year>2020</Year><Month>09</Month><Day>30</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1469-8137</ISSN><JournalIssue CitedMedium="Internet"><Volume>217</Volume><Issue>4</Issue><PubDate><Year>2018</Year><Month>03</Month></PubDate></JournalIssue><Title>The New phytologist</Title><ISOAbbreviation>New Phytol</ISOAbbreviation></Journal><ArticleTitle>Demographically idiosyncratic responses to climate change and rapid Pleistocene diversification of the walnut genus Juglans (Juglandaceae) revealed by whole-genome sequences.</ArticleTitle><Pagination><MedlinePgn>1726-1736</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1111/nph.14917</ELocationID><Abstract><AbstractText>Whether species demography and diversification are driven primarily by extrinsic environmental changes such as climatic oscillations in the Quaternary or by intrinsic biological interactions like coevolution between antagonists is a matter of active debate. In fact, their relative importance can be assessed by tracking past population fluctuations over considerable time periods. We applied the pairwise sequentially Markovian coalescent approach on the genomes of 11 temperate Juglans species to estimate trajectories of changes in effective population size (N<sub>e</sub> ) and used a Bayesian-coalescent based approach that simultaneously considers multiple genomes (G-PhoCS) to estimate divergence times between lineages. N<sub>e</sub> curves of all study species converged 1.0 million yr ago, probably reflecting the time when the walnut genus last shared a common ancestor. This estimate was confirmed by the G-PhoCS estimates of divergence times. But all species did not react similarly to the dramatic climatic oscillations following early Pleistocene cooling, so the timing and amplitude of changes in N<sub>e</sub> differed among species and even among conspecific lineages. The population histories of temperate walnut species were not driven by extrinsic environmental changes alone, and a key role was probably played by species-specific factors such as coevolutionary interactions with specialized pathogens.</AbstractText><CopyrightInformation>© 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Bai</LastName><ForeName>Wei-Ning</ForeName><Initials>WN</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Yan</LastName><ForeName>Peng-Cheng</ForeName><Initials>PC</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Beijing Key Laboratory of Cloud Computing Key Technology and Application, Beijing Computing Center, Beijing, 100094, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Bo-Wen</ForeName><Initials>BW</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Woeste</LastName><ForeName>Keith E</ForeName><Initials>KE</Initials><AffiliationInfo><Affiliation>USDA Forest Service Hardwood Tree Improvement and Regeneration Center (HTIRC), Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN, 47907, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lin</LastName><ForeName>Kui</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Da-Yong</ForeName><Initials>DY</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><DataBankList CompleteYN="Y"><DataBank><DataBankName>GENBANK</DataBankName><AccessionNumberList><AccessionNumber>GCA_000002775</AccessionNumber><AccessionNumber>GCA_900149125</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>2017</Year><Month>11</Month><Day>27</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>New Phytol</MedlineTA><NlmUniqueID>9882884</NlmUniqueID><ISSNLinking>0028-646X</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D001483" MajorTopicYN="N">Base Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D057231" MajorTopicYN="Y">Climate Change</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D031661" MajorTopicYN="N">Fraxinus</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D014644" MajorTopicYN="Y">Genetic Variation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018745" MajorTopicYN="Y">Genome, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D031324" MajorTopicYN="N">Juglans</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D008390" MajorTopicYN="N">Markov Chains</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D011156" MajorTopicYN="N">Population Density</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D013045" MajorTopicYN="N">Species Specificity</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D013997" MajorTopicYN="N">Time Factors</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D000073336" MajorTopicYN="Y">Whole Genome Sequencing</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="Y">Juglans
</Keyword><Keyword MajorTopicYN="Y">diversification</Keyword><Keyword MajorTopicYN="Y">effective population size</Keyword><Keyword MajorTopicYN="Y">pairwise sequentially Markovian coalescent (PSMC)</Keyword><Keyword MajorTopicYN="Y">temperate forests</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2017</Year><Month>09</Month><Day>04</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2017</Year><Month>10</Month><Day>24</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2017</Year><Month>11</Month><Day>28</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2019</Year><Month>9</Month><Day>14</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2017</Year><Month>11</Month><Day>28</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">29178135</ArticleId><ArticleId IdType="doi">10.1111/nph.14917</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>République populaire de Chine</li><li>États-Unis</li></country></list><tree><country name="République populaire de Chine"><noRegion><name sortKey="Bai, Wei Ning" sort="Bai, Wei Ning" uniqKey="Bai W" first="Wei-Ning" last="Bai">Wei-Ning Bai</name></noRegion><name sortKey="Lin, Kui" sort="Lin, Kui" uniqKey="Lin K" first="Kui" last="Lin">Kui Lin</name><name sortKey="Yan, Peng Cheng" sort="Yan, Peng Cheng" uniqKey="Yan P" first="Peng-Cheng" last="Yan">Peng-Cheng Yan</name><name sortKey="Yan, Peng Cheng" sort="Yan, Peng Cheng" uniqKey="Yan P" first="Peng-Cheng" last="Yan">Peng-Cheng Yan</name><name sortKey="Zhang, Bo Wen" sort="Zhang, Bo Wen" uniqKey="Zhang B" first="Bo-Wen" last="Zhang">Bo-Wen Zhang</name><name sortKey="Zhang, Da Yong" sort="Zhang, Da Yong" uniqKey="Zhang D" first="Da-Yong" last="Zhang">Da-Yong Zhang</name></country><country name="États-Unis"><noRegion><name sortKey="Woeste, Keith E" sort="Woeste, Keith E" uniqKey="Woeste K" first="Keith E" last="Woeste">Keith E. Woeste</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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