Landscape genomics of Populus trichocarpa: the role of hybridization, limited gene flow, and natural selection in shaping patterns of population structure.
Identifieur interne : 002150 ( Main/Exploration ); précédent : 002149; suivant : 002151Landscape genomics of Populus trichocarpa: the role of hybridization, limited gene flow, and natural selection in shaping patterns of population structure.
Auteurs : Armando Geraldes [Canada] ; Nima Farzaneh ; Christopher J. Grassa ; Athena D. Mckown ; Robert D. Guy ; Shawn D. Mansfield ; Carl J. Douglas ; Quentin C B. CronkSource :
- Evolution; international journal of organic evolution [ 1558-5646 ] ; 2014.
Descripteurs français
- KwdFr :
- Flux des gènes (MeSH), Gènes de plante (MeSH), Génétique des populations (MeSH), Hybridation génétique (MeSH), Phylogéographie (MeSH), Phénotype (MeSH), Polymorphisme de nucléotide simple (MeSH), Populus (classification), Populus (génétique), Populus (physiologie), Sélection génétique (MeSH), Variation génétique (MeSH).
- MESH :
- génétique : Populus.
- physiologie : Populus.
- classification : Flux des gènes, Gènes de plante, Génétique des populations, Hybridation génétique, Phylogéographie, Phénotype, Polymorphisme de nucléotide simple, Populus, Sélection génétique, Variation génétique.
English descriptors
- KwdEn :
- Gene Flow (MeSH), Genes, Plant (MeSH), Genetic Variation (MeSH), Genetics, Population (MeSH), Hybridization, Genetic (MeSH), Phenotype (MeSH), Phylogeography (MeSH), Polymorphism, Single Nucleotide (MeSH), Populus (classification), Populus (genetics), Populus (physiology), Selection, Genetic (MeSH).
- MESH :
- classification : Populus.
- genetics : Populus.
- physiology : Populus.
- Gene Flow, Genes, Plant, Genetic Variation, Genetics, Population, Hybridization, Genetic, Phenotype, Phylogeography, Polymorphism, Single Nucleotide, Selection, Genetic.
Abstract
Populus trichocarpa is an ecologically important tree across western North America. We used a large population sample of 498 accessions over a wide geographical area genotyped with a 34K Populus SNP array to quantify geographical patterns of genetic variation in this species (landscape genomics). We present evidence that three processes contribute to the observed patterns: (1) introgression from the sister species P. balsamifera, (2) isolation by distance (IBD), and (3) natural selection. Introgression was detected only at the margins of the species' distribution. IBD was significant across the sampled area as a whole, but no evidence of restricted gene flow was detected in a core of drainages from southern British Columbia (BC). We identified a large number of FST outliers. Gene Ontology analyses revealed that FST outliers are overrepresented in genes involved in circadian rhythm and response to red/far-red light when the entire dataset is considered, whereas in southern BC heat response genes are overrepresented. We also identified strong correlations between geoclimate variables and allele frequencies at FST outlier loci that provide clues regarding the selective pressures acting at these loci.
DOI: 10.1111/evo.12497
PubMed: 25065449
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Landscape genomics of Populus trichocarpa: the role of hybridization, limited gene flow, and natural selection in shaping patterns of population structure.</title><author><name sortKey="Geraldes, Armando" sort="Geraldes, Armando" uniqKey="Geraldes A" first="Armando" last="Geraldes">Armando Geraldes</name><affiliation wicri:level="4"><nlm:affiliation>Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada. geraldes@mail.ubc.ca.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4</wicri:regionArea><orgName type="university">Université de la Colombie-Britannique</orgName><placeName><settlement type="city">Vancouver</settlement><region type="state">Colombie-Britannique </region></placeName></affiliation></author><author><name sortKey="Farzaneh, Nima" sort="Farzaneh, Nima" uniqKey="Farzaneh N" first="Nima" last="Farzaneh">Nima Farzaneh</name></author><author><name sortKey="Grassa, Christopher J" sort="Grassa, Christopher J" uniqKey="Grassa C" first="Christopher J" last="Grassa">Christopher J. Grassa</name></author><author><name sortKey="Mckown, Athena D" sort="Mckown, Athena D" uniqKey="Mckown A" first="Athena D" last="Mckown">Athena D. Mckown</name></author><author><name sortKey="Guy, Robert D" sort="Guy, Robert D" uniqKey="Guy R" first="Robert D" last="Guy">Robert D. Guy</name></author><author><name sortKey="Mansfield, Shawn D" sort="Mansfield, Shawn D" uniqKey="Mansfield S" first="Shawn D" last="Mansfield">Shawn D. Mansfield</name></author><author><name sortKey="Douglas, Carl J" sort="Douglas, Carl J" uniqKey="Douglas C" first="Carl J" last="Douglas">Carl J. Douglas</name></author><author><name sortKey="Cronk, Quentin C B" sort="Cronk, Quentin C B" uniqKey="Cronk Q" first="Quentin C B" last="Cronk">Quentin C B. Cronk</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2014">2014</date><idno type="RBID">pubmed:25065449</idno><idno type="pmid">25065449</idno><idno type="doi">10.1111/evo.12497</idno><idno type="wicri:Area/Main/Corpus">002075</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">002075</idno><idno type="wicri:Area/Main/Curation">002075</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">002075</idno><idno type="wicri:Area/Main/Exploration">002075</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Landscape genomics of Populus trichocarpa: the role of hybridization, limited gene flow, and natural selection in shaping patterns of population structure.</title><author><name sortKey="Geraldes, Armando" sort="Geraldes, Armando" uniqKey="Geraldes A" first="Armando" last="Geraldes">Armando Geraldes</name><affiliation wicri:level="4"><nlm:affiliation>Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada. geraldes@mail.ubc.ca.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4</wicri:regionArea><orgName type="university">Université de la Colombie-Britannique</orgName><placeName><settlement type="city">Vancouver</settlement><region type="state">Colombie-Britannique </region></placeName></affiliation></author><author><name sortKey="Farzaneh, Nima" sort="Farzaneh, Nima" uniqKey="Farzaneh N" first="Nima" last="Farzaneh">Nima Farzaneh</name></author><author><name sortKey="Grassa, Christopher J" sort="Grassa, Christopher J" uniqKey="Grassa C" first="Christopher J" last="Grassa">Christopher J. Grassa</name></author><author><name sortKey="Mckown, Athena D" sort="Mckown, Athena D" uniqKey="Mckown A" first="Athena D" last="Mckown">Athena D. Mckown</name></author><author><name sortKey="Guy, Robert D" sort="Guy, Robert D" uniqKey="Guy R" first="Robert D" last="Guy">Robert D. Guy</name></author><author><name sortKey="Mansfield, Shawn D" sort="Mansfield, Shawn D" uniqKey="Mansfield S" first="Shawn D" last="Mansfield">Shawn D. Mansfield</name></author><author><name sortKey="Douglas, Carl J" sort="Douglas, Carl J" uniqKey="Douglas C" first="Carl J" last="Douglas">Carl J. Douglas</name></author><author><name sortKey="Cronk, Quentin C B" sort="Cronk, Quentin C B" uniqKey="Cronk Q" first="Quentin C B" last="Cronk">Quentin C B. Cronk</name></author></analytic><series><title level="j">Evolution; international journal of organic evolution</title><idno type="eISSN">1558-5646</idno><imprint><date when="2014" type="published">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Gene Flow (MeSH)</term><term>Genes, Plant (MeSH)</term><term>Genetic Variation (MeSH)</term><term>Genetics, Population (MeSH)</term><term>Hybridization, Genetic (MeSH)</term><term>Phenotype (MeSH)</term><term>Phylogeography (MeSH)</term><term>Polymorphism, Single Nucleotide (MeSH)</term><term>Populus (classification)</term><term>Populus (genetics)</term><term>Populus (physiology)</term><term>Selection, Genetic (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Flux des gènes (MeSH)</term><term>Gènes de plante (MeSH)</term><term>Génétique des populations (MeSH)</term><term>Hybridation génétique (MeSH)</term><term>Phylogéographie (MeSH)</term><term>Phénotype (MeSH)</term><term>Polymorphisme de nucléotide simple (MeSH)</term><term>Populus (classification)</term><term>Populus (génétique)</term><term>Populus (physiologie)</term><term>Sélection génétique (MeSH)</term><term>Variation génétique (MeSH)</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Populus</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="physiologie" xml:lang="fr"><term>Populus</term></keywords><keywords scheme="MESH" qualifier="physiology" xml:lang="en"><term>Populus</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Gene Flow</term><term>Genes, Plant</term><term>Genetic Variation</term><term>Genetics, Population</term><term>Hybridization, Genetic</term><term>Phenotype</term><term>Phylogeography</term><term>Polymorphism, Single Nucleotide</term><term>Selection, Genetic</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="fr"><term>Flux des gènes</term><term>Gènes de plante</term><term>Génétique des populations</term><term>Hybridation génétique</term><term>Phylogéographie</term><term>Phénotype</term><term>Polymorphisme de nucléotide simple</term><term>Populus</term><term>Sélection génétique</term><term>Variation génétique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Populus trichocarpa is an ecologically important tree across western North America. We used a large population sample of 498 accessions over a wide geographical area genotyped with a 34K Populus SNP array to quantify geographical patterns of genetic variation in this species (landscape genomics). We present evidence that three processes contribute to the observed patterns: (1) introgression from the sister species P. balsamifera, (2) isolation by distance (IBD), and (3) natural selection. Introgression was detected only at the margins of the species' distribution. IBD was significant across the sampled area as a whole, but no evidence of restricted gene flow was detected in a core of drainages from southern British Columbia (BC). We identified a large number of FST outliers. Gene Ontology analyses revealed that FST outliers are overrepresented in genes involved in circadian rhythm and response to red/far-red light when the entire dataset is considered, whereas in southern BC heat response genes are overrepresented. We also identified strong correlations between geoclimate variables and allele frequencies at FST outlier loci that provide clues regarding the selective pressures acting at these loci. </div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">25065449</PMID><DateCompleted><Year>2015</Year><Month>06</Month><Day>04</Day></DateCompleted><DateRevised><Year>2014</Year><Month>10</Month><Day>29</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1558-5646</ISSN><JournalIssue CitedMedium="Internet"><Volume>68</Volume><Issue>11</Issue><PubDate><Year>2014</Year><Month>Nov</Month></PubDate></JournalIssue><Title>Evolution; international journal of organic evolution</Title><ISOAbbreviation>Evolution</ISOAbbreviation></Journal><ArticleTitle>Landscape genomics of Populus trichocarpa: the role of hybridization, limited gene flow, and natural selection in shaping patterns of population structure.</ArticleTitle><Pagination><MedlinePgn>3260-80</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1111/evo.12497</ELocationID><Abstract><AbstractText>Populus trichocarpa is an ecologically important tree across western North America. We used a large population sample of 498 accessions over a wide geographical area genotyped with a 34K Populus SNP array to quantify geographical patterns of genetic variation in this species (landscape genomics). We present evidence that three processes contribute to the observed patterns: (1) introgression from the sister species P. balsamifera, (2) isolation by distance (IBD), and (3) natural selection. Introgression was detected only at the margins of the species' distribution. IBD was significant across the sampled area as a whole, but no evidence of restricted gene flow was detected in a core of drainages from southern British Columbia (BC). We identified a large number of FST outliers. Gene Ontology analyses revealed that FST outliers are overrepresented in genes involved in circadian rhythm and response to red/far-red light when the entire dataset is considered, whereas in southern BC heat response genes are overrepresented. We also identified strong correlations between geoclimate variables and allele frequencies at FST outlier loci that provide clues regarding the selective pressures acting at these loci. </AbstractText><CopyrightInformation>© 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Geraldes</LastName><ForeName>Armando</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada. geraldes@mail.ubc.ca.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Farzaneh</LastName><ForeName>Nima</ForeName><Initials>N</Initials></Author><Author ValidYN="Y"><LastName>Grassa</LastName><ForeName>Christopher J</ForeName><Initials>CJ</Initials></Author><Author ValidYN="Y"><LastName>McKown</LastName><ForeName>Athena D</ForeName><Initials>AD</Initials></Author><Author ValidYN="Y"><LastName>Guy</LastName><ForeName>Robert D</ForeName><Initials>RD</Initials></Author><Author ValidYN="Y"><LastName>Mansfield</LastName><ForeName>Shawn D</ForeName><Initials>SD</Initials></Author><Author ValidYN="Y"><LastName>Douglas</LastName><ForeName>Carl J</ForeName><Initials>CJ</Initials></Author><Author ValidYN="Y"><LastName>Cronk</LastName><ForeName>Quentin C B</ForeName><Initials>QC</Initials></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>2014</Year><Month>09</Month><Day>04</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Evolution</MedlineTA><NlmUniqueID>0373224</NlmUniqueID><ISSNLinking>0014-3820</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D051456" MajorTopicYN="N">Gene Flow</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017343" MajorTopicYN="N">Genes, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014644" MajorTopicYN="N">Genetic Variation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005828" MajorTopicYN="N">Genetics, Population</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D006824" MajorTopicYN="N">Hybridization, Genetic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010641" MajorTopicYN="N">Phenotype</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D058974" MajorTopicYN="N">Phylogeography</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020641" MajorTopicYN="N">Polymorphism, Single Nucleotide</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000145" MajorTopicYN="Y">classification</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000502" MajorTopicYN="N">physiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012641" MajorTopicYN="N">Selection, Genetic</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Adaptation</Keyword><Keyword MajorTopicYN="N">FST outliers</Keyword><Keyword MajorTopicYN="N">Populus balsamifera</Keyword><Keyword MajorTopicYN="N">SNPs</Keyword><Keyword MajorTopicYN="N">isolation by distance</Keyword><Keyword MajorTopicYN="N">red/far-red</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2013</Year><Month>11</Month><Day>13</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2014</Year><Month>07</Month><Day>08</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2014</Year><Month>7</Month><Day>29</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2014</Year><Month>7</Month><Day>30</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2015</Year><Month>6</Month><Day>5</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">25065449</ArticleId><ArticleId IdType="doi">10.1111/evo.12497</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Canada</li></country><region><li>Colombie-Britannique </li></region><settlement><li>Vancouver</li></settlement><orgName><li>Université de la Colombie-Britannique</li></orgName></list><tree><noCountry><name sortKey="Cronk, Quentin C B" sort="Cronk, Quentin C B" uniqKey="Cronk Q" first="Quentin C B" last="Cronk">Quentin C B. Cronk</name><name sortKey="Douglas, Carl J" sort="Douglas, Carl J" uniqKey="Douglas C" first="Carl J" last="Douglas">Carl J. Douglas</name><name sortKey="Farzaneh, Nima" sort="Farzaneh, Nima" uniqKey="Farzaneh N" first="Nima" last="Farzaneh">Nima Farzaneh</name><name sortKey="Grassa, Christopher J" sort="Grassa, Christopher J" uniqKey="Grassa C" first="Christopher J" last="Grassa">Christopher J. Grassa</name><name sortKey="Guy, Robert D" sort="Guy, Robert D" uniqKey="Guy R" first="Robert D" last="Guy">Robert D. Guy</name><name sortKey="Mansfield, Shawn D" sort="Mansfield, Shawn D" uniqKey="Mansfield S" first="Shawn D" last="Mansfield">Shawn D. Mansfield</name><name sortKey="Mckown, Athena D" sort="Mckown, Athena D" uniqKey="Mckown A" first="Athena D" last="Mckown">Athena D. Mckown</name></noCountry><country name="Canada"><region name="Colombie-Britannique "><name sortKey="Geraldes, Armando" sort="Geraldes, Armando" uniqKey="Geraldes A" first="Armando" last="Geraldes">Armando Geraldes</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Bois/explor/PoplarV1/Data/Main/Exploration
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 002150 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 002150 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Bois
|area= PoplarV1
|flux= Main
|étape= Exploration
|type= RBID
|clé= pubmed:25065449
|texte= Landscape genomics of Populus trichocarpa: the role of hybridization, limited gene flow, and natural selection in shaping patterns of population structure.
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:25065449" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \
| NlmPubMed2Wicri -a PoplarV1
| This area was generated with Dilib version V0.6.37. |  |