Genotyping-by-sequencing and ecological niche modeling illuminate phylogeography, admixture, and Pleistocene range dynamics in quaking aspen (Populus tremuloides).
Identifieur interne : 000367 ( Main/Exploration ); précédent : 000366; suivant : 000368Genotyping-by-sequencing and ecological niche modeling illuminate phylogeography, admixture, and Pleistocene range dynamics in quaking aspen (Populus tremuloides).
Auteurs : Justin C. Bagley ; Neander M. Heming ; Eliécer E. Gutiérrez ; Upendra K. Devisetty ; Karen E. Mock ; Andrew J. Eckert ; Steven H. StraussSource :
- Ecology and evolution [ 2045-7758 ] ; 2020.
Abstract
Populus tremuloides is the widest-ranging tree species in North America and an ecologically important component of mesic forest ecosystems displaced by the Pleistocene glaciations. Using phylogeographic analyses of genome-wide SNPs (34,796 SNPs, 183 individuals) and ecological niche modeling, we inferred population structure, ploidy levels, admixture, and Pleistocene range dynamics of P. tremuloides, and tested several historical biogeographical hypotheses. We found three genetic lineages located mainly in coastal-Cascades (cluster 1), east-slope Cascades-Sierra Nevadas-Northern Rockies (cluster 2), and U.S. Rocky Mountains through southern Canadian (cluster 3) regions of the P. tremuloides range, with tree graph relationships of the form ((cluster 1, cluster 2), cluster 3). Populations consisted mainly of diploids (86%) but also small numbers of triploids (12%) and tetraploids (1%), and ploidy did not adversely affect our genetic inferences. The main vector of admixture was from cluster 3 into cluster 2, with the admixture zone trending northwest through the Rocky Mountains along a recognized phenotypic cline (Utah to Idaho). Clusters 1 and 2 provided strong support for the "stable-edge hypothesis" that unglaciated southwestern populations persisted in situ since the last glaciation. By contrast, despite a lack of clinal genetic variation, cluster 3 exhibited "trailing-edge" dynamics from niche suitability predictions signifying complete northward postglacial expansion. Results were also consistent with the "inland dispersal hypothesis" predicting postglacial assembly of Pacific Northwestern forest ecosystems, but rejected the hypothesis that Pacific-coastal populations were colonized during outburst flooding from glacial Lake Missoula. Overall, congruent patterns between our phylogeographic and ecological niche modeling results and fossil pollen data demonstrate complex mixtures of stable-edge, refugial locations, and postglacial expansion within P. tremuloides. These findings confirm and refine previous genetic studies, while strongly supporting a distinct Pacific-coastal genetic lineage of quaking aspen.
DOI: 10.1002/ece3.6214
PubMed: 32551047
PubMed Central: PMC7297775
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Bagley</name><affiliation><nlm:affiliation>Plant Evolutionary Genomics Laboratory Department of Biology Virginia Commonwealth University Richmond VA USA.</nlm:affiliation><wicri:noCountry code="no comma">Plant Evolutionary Genomics Laboratory Department of Biology Virginia Commonwealth University Richmond VA USA.</wicri:noCountry></affiliation><affiliation><nlm:affiliation>Departamento de Zoologia Instituto de Ciências Biológicas Universidade de Brasília Brasília Brazil.</nlm:affiliation><wicri:noCountry code="no comma">Departamento de Zoologia Instituto de Ciências Biológicas Universidade de Brasília Brasília Brazil.</wicri:noCountry></affiliation></author><author><name sortKey="Heming, Neander M" sort="Heming, Neander M" uniqKey="Heming N" first="Neander M" last="Heming">Neander M. 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Bagley</name><affiliation><nlm:affiliation>Plant Evolutionary Genomics Laboratory Department of Biology Virginia Commonwealth University Richmond VA USA.</nlm:affiliation><wicri:noCountry code="no comma">Plant Evolutionary Genomics Laboratory Department of Biology Virginia Commonwealth University Richmond VA USA.</wicri:noCountry></affiliation><affiliation><nlm:affiliation>Departamento de Zoologia Instituto de Ciências Biológicas Universidade de Brasília Brasília Brazil.</nlm:affiliation><wicri:noCountry code="no comma">Departamento de Zoologia Instituto de Ciências Biológicas Universidade de Brasília Brasília Brazil.</wicri:noCountry></affiliation></author><author><name sortKey="Heming, Neander M" sort="Heming, Neander M" uniqKey="Heming N" first="Neander M" last="Heming">Neander M. Heming</name><affiliation><nlm:affiliation>Departamento de Zoologia Instituto de Ciências Biológicas Universidade de Brasília Brasília Brazil.</nlm:affiliation><wicri:noCountry code="no comma">Departamento de Zoologia Instituto de Ciências Biológicas Universidade de Brasília Brasília Brazil.</wicri:noCountry></affiliation></author><author><name sortKey="Gutierrez, Eliecer E" sort="Gutierrez, Eliecer E" uniqKey="Gutierrez E" first="Eliécer E" last="Gutiérrez">Eliécer E. Gutiérrez</name><affiliation><nlm:affiliation>Departamento de Zoologia Instituto de Ciências Biológicas Universidade de Brasília Brasília Brazil.</nlm:affiliation><wicri:noCountry code="no comma">Departamento de Zoologia Instituto de Ciências Biológicas Universidade de Brasília Brasília Brazil.</wicri:noCountry></affiliation><affiliation><nlm:affiliation>Programa de Pos-Graduação em Biodiversidade Animal Centro de Ciências Naturais e Exatas Universidade Federal de Santa Maria Santa Maria Brazil.</nlm:affiliation><wicri:noCountry code="no comma">Programa de Pos-Graduação em Biodiversidade Animal Centro de Ciências Naturais e Exatas Universidade Federal de Santa Maria Santa Maria Brazil.</wicri:noCountry></affiliation></author><author><name sortKey="Devisetty, Upendra K" sort="Devisetty, Upendra K" uniqKey="Devisetty U" first="Upendra K" last="Devisetty">Upendra K. Devisetty</name><affiliation><nlm:affiliation>CyVerse Bio5 University of Arizona Keating Bioresearch Building Tucson AZ USA.</nlm:affiliation><wicri:noCountry code="no comma">CyVerse Bio5 University of Arizona Keating Bioresearch Building Tucson AZ USA.</wicri:noCountry></affiliation></author><author><name sortKey="Mock, Karen E" sort="Mock, Karen E" uniqKey="Mock K" first="Karen E" last="Mock">Karen E. Mock</name><affiliation><nlm:affiliation>Department of Wildland Resources and Ecology Center Utah State University Logan UT USA.</nlm:affiliation><wicri:noCountry code="no comma">Department of Wildland Resources and Ecology Center Utah State University Logan UT USA.</wicri:noCountry></affiliation></author><author><name sortKey="Eckert, Andrew J" sort="Eckert, Andrew J" uniqKey="Eckert A" first="Andrew J" last="Eckert">Andrew J. Eckert</name><affiliation><nlm:affiliation>Plant Evolutionary Genomics Laboratory Department of Biology Virginia Commonwealth University Richmond VA USA.</nlm:affiliation><wicri:noCountry code="no comma">Plant Evolutionary Genomics Laboratory Department of Biology Virginia Commonwealth University Richmond VA USA.</wicri:noCountry></affiliation></author><author><name sortKey="Strauss, Steven H" sort="Strauss, Steven H" uniqKey="Strauss S" first="Steven H" last="Strauss">Steven H. Strauss</name><affiliation><nlm:affiliation>Department of Forest Ecosystems and Society Oregon State University Corvallis OR USA.</nlm:affiliation><wicri:noCountry code="no comma">Department of Forest Ecosystems and Society Oregon State University Corvallis OR USA.</wicri:noCountry></affiliation></author></analytic><series><title level="j">Ecology and evolution</title><idno type="ISSN">2045-7758</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"><i>Populus tremuloides</i> is the widest-ranging tree species in North America and an ecologically important component of mesic forest ecosystems displaced by the Pleistocene glaciations. Using phylogeographic analyses of genome-wide SNPs (34,796 SNPs, 183 individuals) and ecological niche modeling, we inferred population structure, ploidy levels, admixture, and Pleistocene range dynamics of <i>P. tremuloides</i>, and tested several historical biogeographical hypotheses. We found three genetic lineages located mainly in coastal-Cascades (cluster 1), east-slope Cascades-Sierra Nevadas-Northern Rockies (cluster 2), and U.S. Rocky Mountains through southern Canadian (cluster 3) regions of the <i>P. tremuloides</i> range, with tree graph relationships of the form ((cluster 1, cluster 2), cluster 3). Populations consisted mainly of diploids (86%) but also small numbers of triploids (12%) and tetraploids (1%), and ploidy did not adversely affect our genetic inferences. The main vector of admixture was from cluster 3 into cluster 2, with the admixture zone trending northwest through the Rocky Mountains along a recognized phenotypic cline (Utah to Idaho). Clusters 1 and 2 provided strong support for the "stable-edge hypothesis" that unglaciated southwestern populations persisted in situ since the last glaciation. By contrast, despite a lack of clinal genetic variation, cluster 3 exhibited "trailing-edge" dynamics from niche suitability predictions signifying complete northward postglacial expansion. Results were also consistent with the "inland dispersal hypothesis" predicting postglacial assembly of Pacific Northwestern forest ecosystems, but rejected the hypothesis that Pacific-coastal populations were colonized during outburst flooding from glacial Lake Missoula. Overall, congruent patterns between our phylogeographic and ecological niche modeling results and fossil pollen data demonstrate complex mixtures of stable-edge, refugial locations, and postglacial expansion within <i>P. tremuloides</i>. These findings confirm and refine previous genetic studies, while strongly supporting a distinct Pacific-coastal genetic lineage of quaking aspen.</div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">32551047</PMID><DateRevised><Year>2020</Year><Month>09</Month><Day>28</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Print">2045-7758</ISSN><JournalIssue CitedMedium="Print"><Volume>10</Volume><Issue>11</Issue><PubDate><Year>2020</Year><Month>Jun</Month></PubDate></JournalIssue><Title>Ecology and evolution</Title><ISOAbbreviation>Ecol Evol</ISOAbbreviation></Journal><ArticleTitle>Genotyping-by-sequencing and ecological niche modeling illuminate phylogeography, admixture, and Pleistocene range dynamics in quaking aspen (<i>Populus tremuloides</i>).</ArticleTitle><Pagination><MedlinePgn>4609-4629</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1002/ece3.6214</ELocationID><Abstract><AbstractText><i>Populus tremuloides</i> is the widest-ranging tree species in North America and an ecologically important component of mesic forest ecosystems displaced by the Pleistocene glaciations. Using phylogeographic analyses of genome-wide SNPs (34,796 SNPs, 183 individuals) and ecological niche modeling, we inferred population structure, ploidy levels, admixture, and Pleistocene range dynamics of <i>P. tremuloides</i>, and tested several historical biogeographical hypotheses. We found three genetic lineages located mainly in coastal-Cascades (cluster 1), east-slope Cascades-Sierra Nevadas-Northern Rockies (cluster 2), and U.S. Rocky Mountains through southern Canadian (cluster 3) regions of the <i>P. tremuloides</i> range, with tree graph relationships of the form ((cluster 1, cluster 2), cluster 3). Populations consisted mainly of diploids (86%) but also small numbers of triploids (12%) and tetraploids (1%), and ploidy did not adversely affect our genetic inferences. The main vector of admixture was from cluster 3 into cluster 2, with the admixture zone trending northwest through the Rocky Mountains along a recognized phenotypic cline (Utah to Idaho). Clusters 1 and 2 provided strong support for the "stable-edge hypothesis" that unglaciated southwestern populations persisted in situ since the last glaciation. By contrast, despite a lack of clinal genetic variation, cluster 3 exhibited "trailing-edge" dynamics from niche suitability predictions signifying complete northward postglacial expansion. Results were also consistent with the "inland dispersal hypothesis" predicting postglacial assembly of Pacific Northwestern forest ecosystems, but rejected the hypothesis that Pacific-coastal populations were colonized during outburst flooding from glacial Lake Missoula. Overall, congruent patterns between our phylogeographic and ecological niche modeling results and fossil pollen data demonstrate complex mixtures of stable-edge, refugial locations, and postglacial expansion within <i>P. tremuloides</i>. These findings confirm and refine previous genetic studies, while strongly supporting a distinct Pacific-coastal genetic lineage of quaking aspen.</AbstractText><CopyrightInformation>© 2020 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Bagley</LastName><ForeName>Justin C</ForeName><Initials>JC</Initials><Identifier Source="ORCID">https://orcid.org/0000-0001-6737-8380</Identifier><AffiliationInfo><Affiliation>Plant Evolutionary Genomics Laboratory Department of Biology Virginia Commonwealth University Richmond VA USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Departamento de Zoologia Instituto de Ciências Biológicas Universidade de Brasília Brasília Brazil.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Heming</LastName><ForeName>Neander M</ForeName><Initials>NM</Initials><Identifier Source="ORCID">https://orcid.org/0000-0003-2461-5045</Identifier><AffiliationInfo><Affiliation>Departamento de Zoologia Instituto de Ciências Biológicas Universidade de Brasília Brasília Brazil.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Gutiérrez</LastName><ForeName>Eliécer E</ForeName><Initials>EE</Initials><Identifier Source="ORCID">https://orcid.org/0000-0001-6790-8185</Identifier><AffiliationInfo><Affiliation>Departamento de Zoologia Instituto de Ciências Biológicas Universidade de Brasília Brasília Brazil.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Programa de Pos-Graduação em Biodiversidade Animal Centro de Ciências Naturais e Exatas Universidade Federal de Santa Maria Santa Maria Brazil.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Devisetty</LastName><ForeName>Upendra K</ForeName><Initials>UK</Initials><AffiliationInfo><Affiliation>CyVerse Bio5 University of Arizona Keating Bioresearch Building Tucson AZ USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Mock</LastName><ForeName>Karen E</ForeName><Initials>KE</Initials><AffiliationInfo><Affiliation>Department of Wildland Resources and Ecology Center Utah State University Logan UT USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Eckert</LastName><ForeName>Andrew J</ForeName><Initials>AJ</Initials><Identifier Source="ORCID">https://orcid.org/0000-0002-6522-2646</Identifier><AffiliationInfo><Affiliation>Plant Evolutionary Genomics Laboratory Department of Biology Virginia Commonwealth University Richmond VA USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Strauss</LastName><ForeName>Steven H</ForeName><Initials>SH</Initials><AffiliationInfo><Affiliation>Department of Forest Ecosystems and Society Oregon State University Corvallis OR USA.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>04</Month><Day>23</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Ecol Evol</MedlineTA><NlmUniqueID>101566408</NlmUniqueID><ISSNLinking>2045-7758</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">North America</Keyword><Keyword MajorTopicYN="N">admixture</Keyword><Keyword MajorTopicYN="N">phylogeography</Keyword><Keyword MajorTopicYN="N">population structure</Keyword><Keyword MajorTopicYN="N">quaking aspen</Keyword><Keyword MajorTopicYN="N">single nucleotide polymorphisms</Keyword></KeywordList><CoiStatement>None declared.</CoiStatement></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2020</Year><Month>01</Month><Day>27</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2020</Year><Month>02</Month><Day>23</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2020</Year><Month>02</Month><Day>24</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>6</Month><Day>20</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate 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Bagley</name><name sortKey="Devisetty, Upendra K" sort="Devisetty, Upendra K" uniqKey="Devisetty U" first="Upendra K" last="Devisetty">Upendra K. Devisetty</name><name sortKey="Eckert, Andrew J" sort="Eckert, Andrew J" uniqKey="Eckert A" first="Andrew J" last="Eckert">Andrew J. Eckert</name><name sortKey="Gutierrez, Eliecer E" sort="Gutierrez, Eliecer E" uniqKey="Gutierrez E" first="Eliécer E" last="Gutiérrez">Eliécer E. Gutiérrez</name><name sortKey="Heming, Neander M" sort="Heming, Neander M" uniqKey="Heming N" first="Neander M" last="Heming">Neander M. Heming</name><name sortKey="Mock, Karen E" sort="Mock, Karen E" uniqKey="Mock K" first="Karen E" last="Mock">Karen E. Mock</name><name sortKey="Strauss, Steven H" sort="Strauss, Steven H" uniqKey="Strauss S" first="Steven H" last="Strauss">Steven H. Strauss</name></noCountry></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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