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Phylogenomics Reveals Three Sources of Adaptive Variation during a Rapid Radiation

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dc.contributor.authorPease, James B.en
dc.contributor.authorHaak, David C.en
dc.contributor.authorHahn, Matthew W.en
dc.contributor.authorMoyle, Leonie C.en
dc.contributor.departmentSchool of Plant and Environmental Sciencesen
dc.date.accessioned2017-01-16T18:18:54Zen
dc.date.available2017-01-16T18:18:54Zen
dc.date.issued2016-02-01en
dc.description.abstractSpeciation events often occur in rapid bursts of diversification, but the ecological and genetic factors that promote these radiations are still much debated. Using whole transcriptomes from all 13 species in the ecologically and reproductively diverse wild tomato clade (Solanum sect. Lycopersicon), we infer the species phylogeny and patterns of genetic diversity in this group. Despite widespread phylogenetic discordance due to the sorting of ancestral variation, we date the origin of this radiation to approximately 2.5 million years ago and find evidence for at least three sources of adaptive genetic variation that fuel diversification. First, we detect introgression both historically between early-branching lineages and recently between individual populations, at specific loci whose functions indicate likely adaptive benefits. Second, we find evidence of lineage-specific de novo evolution for many genes, including loci involved in the production of red fruit color. Finally, using a “PhyloGWAS” approach, we detect environment-specific sorting of ancestral variation among populations that come from different species but share common environmental conditions. Estimated across the whole clade, small but substantial and approximately equal fractions of the euchromatic portion of the genome are inferred to contribute to each of these three sources of adaptive genetic variation. These results indicate that multiple genetic sources can promote rapid diversification and speciation in response to new ecological opportunity, in agreement with our emerging phylogenomic understanding of the complexity of both ancient and recent species radiations.en
dc.description.versionPublished versionen
dc.format.extent? - ? (24) page(s)en
dc.format.mimetypeapplication/pdfen
dc.identifier.doihttps://doi.org/10.1371/journal.pbio.1002379en
dc.identifier.issn1545-7885en
dc.identifier.issue2en
dc.identifier.urihttp://hdl.handle.net/10919/74345en
dc.identifier.volume14en
dc.language.isoenen
dc.publisherPLOSen
dc.relation.urihttp://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000371883600011&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=930d57c9ac61a043676db62af60056c1en
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjectBiochemistry & Molecular Biologyen
dc.subjectBiologyen
dc.subjectLife Sciences & Biomedicine - Other Topicsen
dc.subjectSOLANUM SECTION LYCOPERSICONen
dc.subjectWILD TOMATOESen
dc.subjectMOLECULAR EVOLUTIONen
dc.subjectPHYLOGENETIC ANALYSISen
dc.subjectCLADOSPORIUM-FULVUMen
dc.subjectGENETIC-VARIATIONen
dc.subjectSPECIES TREESen
dc.subjectGENOMEen
dc.subjectSPECIATIONen
dc.subjectINTROGRESSIONen
dc.titlePhylogenomics Reveals Three Sources of Adaptive Variation during a Rapid Radiationen
dc.title.serialPLOS Biologyen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten
pubs.organisational-group/Virginia Techen
pubs.organisational-group/Virginia Tech/Agriculture & Life Sciencesen
pubs.organisational-group/Virginia Tech/Agriculture & Life Sciences/CALS T&R Facultyen
pubs.organisational-group/Virginia Tech/Agriculture & Life Sciences/Plant Pathology, Physiology, & Weed Scienceen
pubs.organisational-group/Virginia Tech/All T&R Facultyen

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