Genomic scan for single nucleotide polymorphisms reveals patterns of divergence and gene flow between ecologically divergent species.
Identifieur interne : 002665 ( Main/Exploration ); précédent : 002664; suivant : 002666Genomic scan for single nucleotide polymorphisms reveals patterns of divergence and gene flow between ecologically divergent species.
Auteurs : Kai N. Stölting [Suisse] ; Rick Nipper ; Dorothea Lindtke ; Celine Caseys ; Stephan Waeber ; Stefano Castiglione ; Christian LexerSource :
- Molecular ecology [ 1365-294X ] ; 2013.
Descripteurs français
- KwdFr :
- ADN des plantes (génétique), Analyse de séquence d'ADN (MeSH), Chromosomes de plante (MeSH), Flux des gènes (MeSH), Génome végétal (MeSH), Génomique (méthodes), Hybridation génétique (MeSH), Polymorphisme de nucléotide simple (MeSH), Populus (classification), Populus (génétique), Répétitions microsatellites (MeSH).
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : DNA, Plant.
- classification : Populus.
- genetics : Populus.
- methods : Genomics.
- Chromosomes, Plant, Gene Flow, Genome, Plant, Hybridization, Genetic, Microsatellite Repeats, Polymorphism, Single Nucleotide, Sequence Analysis, DNA.
Abstract
Recent advances in population genomics have triggered great interest in the genomic landscape of divergence in taxa with 'porous' species boundaries. One important obstable of previous studies of this topic was the low genomic coverage achieved. This issue can now be overcome by the use of 'next generation' or short-read DNA-sequencing approaches capable of assaying many thousands of single nucleotide polymorphisms (SNPs) in divergent species. We have scanned the 'porous' genomes of Populus alba and Populus tremula, two ecologically divergent hybridizing forest trees, using >38,000 SNPs assayed by restriction site associated DNA (RAD) sequencing. Windowed analyses indicate great variation in genetic divergence (e.g. the proportion of fixed SNPs) between species, and these results are unlikely to be strongly biased by genomic features of the Populus trichocarpa reference genome used for SNP calling. Divergence estimates were significantly autocorrelated (P < 0.01; Moran's I up to 0.6) along 11 of 19 chromosomes. Many of these autocorrelations involved low divergence blocks, thus suggesting that allele sharing was caused by recurrent gene flow rather than shared ancestral polymorphism. A conspicuous low divergence block of three megabases was detected on chromosome XIX, recently put forward as an incipient sex chromosome in Populus, and was largely congruent with introgression of mapped microsatellites in two natural hybrid zones (N > 400). Our results help explain the origin of the 'genomic mosaic' seen in these taxa with 'porous' genomes and suggest rampant introgression or extensive among-species conservation of an incipient plant sex chromosome. RAD sequencing holds great promise for detecting patterns of divergence and gene flow in highly divergent hybridizing species.
DOI: 10.1111/mec.12011
PubMed: 22967258
Affiliations:
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Stölting</name><affiliation wicri:level="4"><nlm:affiliation>Department of Biology, Unit of Ecology & Evolution, University of Fribourg, Fribourg, Switzerland.</nlm:affiliation><country xml:lang="fr">Suisse</country><wicri:regionArea>Department of Biology, Unit of Ecology & Evolution, University of Fribourg, Fribourg</wicri:regionArea><orgName type="university">Université de Fribourg</orgName><placeName><settlement type="city">Fribourg</settlement><region nuts="3" type="region">Canton de Fribourg</region></placeName></affiliation></author><author><name sortKey="Nipper, Rick" sort="Nipper, Rick" uniqKey="Nipper R" first="Rick" last="Nipper">Rick Nipper</name></author><author><name sortKey="Lindtke, Dorothea" sort="Lindtke, Dorothea" uniqKey="Lindtke D" first="Dorothea" last="Lindtke">Dorothea Lindtke</name></author><author><name sortKey="Caseys, Celine" sort="Caseys, Celine" uniqKey="Caseys C" first="Celine" last="Caseys">Celine Caseys</name></author><author><name sortKey="Waeber, Stephan" sort="Waeber, Stephan" uniqKey="Waeber S" first="Stephan" last="Waeber">Stephan Waeber</name></author><author><name sortKey="Castiglione, Stefano" sort="Castiglione, Stefano" uniqKey="Castiglione S" first="Stefano" last="Castiglione">Stefano Castiglione</name></author><author><name sortKey="Lexer, Christian" sort="Lexer, Christian" uniqKey="Lexer C" first="Christian" last="Lexer">Christian Lexer</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2013">2013</date><idno type="RBID">pubmed:22967258</idno><idno type="pmid">22967258</idno><idno type="doi">10.1111/mec.12011</idno><idno type="wicri:Area/Main/Corpus">002885</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">002885</idno><idno type="wicri:Area/Main/Curation">002885</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">002885</idno><idno type="wicri:Area/Main/Exploration">002885</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Genomic scan for single nucleotide polymorphisms reveals patterns of divergence and gene flow between ecologically divergent species.</title><author><name sortKey="Stolting, Kai N" sort="Stolting, Kai N" uniqKey="Stolting K" first="Kai N" last="Stölting">Kai N. Stölting</name><affiliation wicri:level="4"><nlm:affiliation>Department of Biology, Unit of Ecology & Evolution, University of Fribourg, Fribourg, Switzerland.</nlm:affiliation><country xml:lang="fr">Suisse</country><wicri:regionArea>Department of Biology, Unit of Ecology & Evolution, University of Fribourg, Fribourg</wicri:regionArea><orgName type="university">Université de Fribourg</orgName><placeName><settlement type="city">Fribourg</settlement><region nuts="3" type="region">Canton de Fribourg</region></placeName></affiliation></author><author><name sortKey="Nipper, Rick" sort="Nipper, Rick" uniqKey="Nipper R" first="Rick" last="Nipper">Rick Nipper</name></author><author><name sortKey="Lindtke, Dorothea" sort="Lindtke, Dorothea" uniqKey="Lindtke D" first="Dorothea" last="Lindtke">Dorothea Lindtke</name></author><author><name sortKey="Caseys, Celine" sort="Caseys, Celine" uniqKey="Caseys C" first="Celine" last="Caseys">Celine Caseys</name></author><author><name sortKey="Waeber, Stephan" sort="Waeber, Stephan" uniqKey="Waeber S" first="Stephan" last="Waeber">Stephan Waeber</name></author><author><name sortKey="Castiglione, Stefano" sort="Castiglione, Stefano" uniqKey="Castiglione S" first="Stefano" last="Castiglione">Stefano Castiglione</name></author><author><name sortKey="Lexer, Christian" sort="Lexer, Christian" uniqKey="Lexer C" first="Christian" last="Lexer">Christian Lexer</name></author></analytic><series><title level="j">Molecular ecology</title><idno type="eISSN">1365-294X</idno><imprint><date when="2013" type="published">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Chromosomes, Plant (MeSH)</term><term>DNA, Plant (genetics)</term><term>Gene Flow (MeSH)</term><term>Genome, Plant (MeSH)</term><term>Genomics (methods)</term><term>Hybridization, Genetic (MeSH)</term><term>Microsatellite Repeats (MeSH)</term><term>Polymorphism, Single Nucleotide (MeSH)</term><term>Populus (classification)</term><term>Populus (genetics)</term><term>Sequence Analysis, DNA (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN des plantes (génétique)</term><term>Analyse de séquence d'ADN (MeSH)</term><term>Chromosomes de plante (MeSH)</term><term>Flux des gènes (MeSH)</term><term>Génome végétal (MeSH)</term><term>Génomique (méthodes)</term><term>Hybridation génétique (MeSH)</term><term>Polymorphisme de nucléotide simple (MeSH)</term><term>Populus (classification)</term><term>Populus (génétique)</term><term>Répétitions microsatellites (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA, Plant</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>ADN des plantes</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Genomics</term></keywords><keywords scheme="MESH" qualifier="méthodes" xml:lang="fr"><term>Génomique</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Chromosomes, Plant</term><term>Gene Flow</term><term>Genome, Plant</term><term>Hybridization, Genetic</term><term>Microsatellite Repeats</term><term>Polymorphism, Single Nucleotide</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de séquence d'ADN</term><term>Chromosomes de plante</term><term>Flux des gènes</term><term>Génome végétal</term><term>Hybridation génétique</term><term>Polymorphisme de nucléotide simple</term><term>Répétitions microsatellites</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Recent advances in population genomics have triggered great interest in the genomic landscape of divergence in taxa with 'porous' species boundaries. One important obstable of previous studies of this topic was the low genomic coverage achieved. This issue can now be overcome by the use of 'next generation' or short-read DNA-sequencing approaches capable of assaying many thousands of single nucleotide polymorphisms (SNPs) in divergent species. We have scanned the 'porous' genomes of Populus alba and Populus tremula, two ecologically divergent hybridizing forest trees, using >38,000 SNPs assayed by restriction site associated DNA (RAD) sequencing. Windowed analyses indicate great variation in genetic divergence (e.g. the proportion of fixed SNPs) between species, and these results are unlikely to be strongly biased by genomic features of the Populus trichocarpa reference genome used for SNP calling. Divergence estimates were significantly autocorrelated (P < 0.01; Moran's I up to 0.6) along 11 of 19 chromosomes. Many of these autocorrelations involved low divergence blocks, thus suggesting that allele sharing was caused by recurrent gene flow rather than shared ancestral polymorphism. A conspicuous low divergence block of three megabases was detected on chromosome XIX, recently put forward as an incipient sex chromosome in Populus, and was largely congruent with introgression of mapped microsatellites in two natural hybrid zones (N > 400). Our results help explain the origin of the 'genomic mosaic' seen in these taxa with 'porous' genomes and suggest rampant introgression or extensive among-species conservation of an incipient plant sex chromosome. RAD sequencing holds great promise for detecting patterns of divergence and gene flow in highly divergent hybridizing species.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">22967258</PMID><DateCompleted><Year>2013</Year><Month>06</Month><Day>05</Day></DateCompleted><DateRevised><Year>2013</Year><Month>01</Month><Day>16</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1365-294X</ISSN><JournalIssue CitedMedium="Internet"><Volume>22</Volume><Issue>3</Issue><PubDate><Year>2013</Year><Month>Feb</Month></PubDate></JournalIssue><Title>Molecular ecology</Title><ISOAbbreviation>Mol Ecol</ISOAbbreviation></Journal><ArticleTitle>Genomic scan for single nucleotide polymorphisms reveals patterns of divergence and gene flow between ecologically divergent species.</ArticleTitle><Pagination><MedlinePgn>842-55</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1111/mec.12011</ELocationID><Abstract><AbstractText>Recent advances in population genomics have triggered great interest in the genomic landscape of divergence in taxa with 'porous' species boundaries. One important obstable of previous studies of this topic was the low genomic coverage achieved. This issue can now be overcome by the use of 'next generation' or short-read DNA-sequencing approaches capable of assaying many thousands of single nucleotide polymorphisms (SNPs) in divergent species. We have scanned the 'porous' genomes of Populus alba and Populus tremula, two ecologically divergent hybridizing forest trees, using >38,000 SNPs assayed by restriction site associated DNA (RAD) sequencing. Windowed analyses indicate great variation in genetic divergence (e.g. the proportion of fixed SNPs) between species, and these results are unlikely to be strongly biased by genomic features of the Populus trichocarpa reference genome used for SNP calling. Divergence estimates were significantly autocorrelated (P < 0.01; Moran's I up to 0.6) along 11 of 19 chromosomes. Many of these autocorrelations involved low divergence blocks, thus suggesting that allele sharing was caused by recurrent gene flow rather than shared ancestral polymorphism. A conspicuous low divergence block of three megabases was detected on chromosome XIX, recently put forward as an incipient sex chromosome in Populus, and was largely congruent with introgression of mapped microsatellites in two natural hybrid zones (N > 400). Our results help explain the origin of the 'genomic mosaic' seen in these taxa with 'porous' genomes and suggest rampant introgression or extensive among-species conservation of an incipient plant sex chromosome. RAD sequencing holds great promise for detecting patterns of divergence and gene flow in highly divergent hybridizing species.</AbstractText><CopyrightInformation>© 2012 Blackwell Publishing Ltd.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Stölting</LastName><ForeName>Kai N</ForeName><Initials>KN</Initials><AffiliationInfo><Affiliation>Department of Biology, Unit of Ecology & Evolution, University of Fribourg, Fribourg, Switzerland.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Nipper</LastName><ForeName>Rick</ForeName><Initials>R</Initials></Author><Author ValidYN="Y"><LastName>Lindtke</LastName><ForeName>Dorothea</ForeName><Initials>D</Initials></Author><Author ValidYN="Y"><LastName>Caseys</LastName><ForeName>Celine</ForeName><Initials>C</Initials></Author><Author ValidYN="Y"><LastName>Waeber</LastName><ForeName>Stephan</ForeName><Initials>S</Initials></Author><Author ValidYN="Y"><LastName>Castiglione</LastName><ForeName>Stefano</ForeName><Initials>S</Initials></Author><Author ValidYN="Y"><LastName>Lexer</LastName><ForeName>Christian</ForeName><Initials>C</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>2012</Year><Month>09</Month><Day>11</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Mol Ecol</MedlineTA><NlmUniqueID>9214478</NlmUniqueID><ISSNLinking>0962-1083</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D018744">DNA, Plant</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D032461" MajorTopicYN="N">Chromosomes, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018744" MajorTopicYN="N">DNA, Plant</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D051456" MajorTopicYN="Y">Gene Flow</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018745" MajorTopicYN="N">Genome, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D023281" MajorTopicYN="N">Genomics</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D006824" MajorTopicYN="N">Hybridization, Genetic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018895" MajorTopicYN="N">Microsatellite Repeats</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020641" MajorTopicYN="Y">Polymorphism, Single Nucleotide</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000145" MajorTopicYN="N">classification</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017422" MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2012</Year><Month>01</Month><Day>14</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2012</Year><Month>07</Month><Day>17</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2012</Year><Month>07</Month><Day>27</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2012</Year><Month>9</Month><Day>13</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2012</Year><Month>9</Month><Day>13</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2013</Year><Month>6</Month><Day>6</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">22967258</ArticleId><ArticleId IdType="doi">10.1111/mec.12011</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Suisse</li></country><region><li>Canton de Fribourg</li></region><settlement><li>Fribourg</li></settlement><orgName><li>Université de Fribourg</li></orgName></list><tree><noCountry><name sortKey="Caseys, Celine" sort="Caseys, Celine" uniqKey="Caseys C" first="Celine" last="Caseys">Celine Caseys</name><name sortKey="Castiglione, Stefano" sort="Castiglione, Stefano" uniqKey="Castiglione S" first="Stefano" last="Castiglione">Stefano Castiglione</name><name sortKey="Lexer, Christian" sort="Lexer, Christian" uniqKey="Lexer C" first="Christian" last="Lexer">Christian Lexer</name><name sortKey="Lindtke, Dorothea" sort="Lindtke, Dorothea" uniqKey="Lindtke D" first="Dorothea" last="Lindtke">Dorothea Lindtke</name><name sortKey="Nipper, Rick" sort="Nipper, Rick" uniqKey="Nipper R" first="Rick" last="Nipper">Rick Nipper</name><name sortKey="Waeber, Stephan" sort="Waeber, Stephan" uniqKey="Waeber S" first="Stephan" last="Waeber">Stephan Waeber</name></noCountry><country name="Suisse"><region name="Canton de Fribourg"><name sortKey="Stolting, Kai N" sort="Stolting, Kai N" uniqKey="Stolting K" first="Kai N" last="Stölting">Kai N. 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