Exome Resequencing Reveals Evolutionary History, Genomic Diversity, and Targets of Selection in the Conifers Pinus taeda and Pinus elliottii

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dc.contributor.authorAcosta, Juan J.en
dc.contributor.authorFahrenkrog, Annette M.en
dc.contributor.authorNeves, Leandro G.en
dc.contributor.authorResende, Marcio FR R.en
dc.contributor.authorDervinis, Christopheren
dc.contributor.authorDavis, John M.en
dc.contributor.authorHolliday, Jason A.en
dc.contributor.authorKirst, Matiasen
dc.date.accessioned2021-10-15T12:31:48Zen
dc.date.available2021-10-15T12:31:48Zen
dc.date.issued2019-02-01en
dc.date.updated2021-10-15T12:31:45Zen
dc.description.abstractLoblolly pine (Pinus taeda) and slash pine (Pinus elliottii) are ecologically and economically important pine species that dominate many forest ecosystems in the southern United States, but like all conifers, the study of their genetic diversity and demographic history has been hampered by their large genome size. A small number of studies mainly based on candidate-gene sequencing have been reported for P. taeda to date, whereas none are available for P. elliottii. Targeted exome resequencing has recently enabled population genomics studies for conifers, approach used here to assess genomic diversity, signatures of selection, population structure, and demographic history of P. elliottii and P. taeda. Extensive similarities were revealed between these species: both species feature rapid linkage disequilibrium decay and high levels of genetic diversity. Moreover, genome-wide positive correlations for measures of genetic diversity between the species were also observed, likely due to shared structural genomic constraints. Also, positive selection appears to be targeting a common set of genes in both pines. Demographic history differs between both species, with only P. taeda being affected by a dramatic bottleneck during the last glacial period. The ability of P. taeda to recover from a dramatic reduction in population size while still retaining high levels of genetic diversity shows promise for other pines facing environmental stressors associated with climate change, indicating that these too may be able to adapt successfully to new future conditions even after a drastic population size contraction.en
dc.description.versionPublished versionen
dc.format.extentPages 508-520en
dc.format.extent13 page(s)en
dc.format.mimetypeapplication/pdfen
dc.identifier.doihttps://doi.org/10.1093/gbe/evz016en
dc.identifier.eissn1759-6653en
dc.identifier.issn1759-6653en
dc.identifier.issue2en
dc.identifier.other5303544 (PII)en
dc.identifier.pmid30689841en
dc.identifier.urihttp://hdl.handle.net/10919/105394en
dc.identifier.volume11en
dc.language.isoenen
dc.publisherOxford University Pressen
dc.relation.urihttp://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000467953500014&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=930d57c9ac61a043676db62af60056c1en
dc.rightsCreative Commons Attribution-NonCommercial 4.0 Internationalen
dc.rights.urihttp://creativecommons.org/licenses/by-nc/4.0/en
dc.subjectLife Sciences & Biomedicineen
dc.subjectEvolutionary Biologyen
dc.subjectGenetics & Heredityen
dc.subjectPinus taedaen
dc.subjectPinus elliottiien
dc.subjectdemographyen
dc.subjectgenetic diversityen
dc.subjectnatural selectionen
dc.subjectexomeen
dc.subjectAPPROXIMATE BAYESIAN COMPUTATIONen
dc.subjectLINKAGE DISEQUILIBRIUMen
dc.subjectNUCLEOTIDE DIVERSITYen
dc.subjectDEMOGRAPHIC HISTORYen
dc.subjectGENETIC DIVERSITYen
dc.subjectLOBLOLLY-PINEen
dc.subjectPOPULATION-STRUCTUREen
dc.subjectMULTILOCUS PATTERNSen
dc.subjectSTATISTICAL TESTSen
dc.subjectBALSAM POPLARen
dc.subjectDevelopmental Biologyen
dc.subject0601 Biochemistry and Cell Biologyen
dc.subject0603 Evolutionary Biologyen
dc.subject0604 Geneticsen
dc.subject.meshPinus taedaen
dc.subject.meshPopulation Dynamicsen
dc.subject.meshLinkage Disequilibriumen
dc.subject.meshComputer Simulationen
dc.subject.meshGenetic Variationen
dc.subject.meshSelection, Geneticen
dc.subject.meshOvuleen
dc.subject.meshBiological Evolutionen
dc.titleExome Resequencing Reveals Evolutionary History, Genomic Diversity, and Targets of Selection in the Conifers Pinus taeda and Pinus elliottiien
dc.title.serialGenome Biology and Evolutionen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten
dc.type.otherArticleen
dc.type.otherJournalen
dcterms.dateAccepted2019-01-22en
pubs.organisational-group/Virginia Techen
pubs.organisational-group/Virginia Tech/Natural Resources & Environmenten
pubs.organisational-group/Virginia Tech/Natural Resources & Environment/Forest Resources and Environmental Conservationen
pubs.organisational-group/Virginia Tech/University Research Institutesen
pubs.organisational-group/Virginia Tech/University Research Institutes/Fralin Life Sciencesen
pubs.organisational-group/Virginia Tech/All T&R Facultyen
pubs.organisational-group/Virginia Tech/Natural Resources & Environment/CNRE T&R Facultyen
pubs.organisational-group/Virginia Tech/University Research Institutes/Fralin Life Sciences/Durelle Scotten

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