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Linked selection shapes the landscape of genomic variation in three oak species

hal.structure.identifierKey Laboratory of Plant Resources Conservation and Sustainable Utilization [Chinese Academy of Sciences]
hal.structure.identifierUniversity of Chinese Academy of Sciences [Beijing] [UCAS]
dc.contributor.authorLIANG, Yi‐Ye
hal.structure.identifierResearch Center on Fictitious Economy & Data Science [FEDS]
dc.contributor.authorSHI, Yong
hal.structure.identifierKey Laboratory of Plant Resources Conservation and Sustainable Utilization [Chinese Academy of Sciences]
dc.contributor.authorYUAN, Shuai
hal.structure.identifierKey Laboratory of Plant Resources Conservation and Sustainable Utilization [Chinese Academy of Sciences]
dc.contributor.authorZHOU, Biao‐feng
hal.structure.identifierKey Laboratory of Plant Resources Conservation and Sustainable Utilization [Chinese Academy of Sciences]
dc.contributor.authorCHEN, Xue‐yan
hal.structure.identifierKey Laboratory of Plant Resources Conservation and Sustainable Utilization [Chinese Academy of Sciences]
dc.contributor.authorAN, Qing‐qing
hal.structure.identifierSwedish University of Agricultural Sciences = Sveriges lantbruksuniversitet [SLU]
dc.contributor.authorINGVARSSON, Pär
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorPLOMION, Christophe
hal.structure.identifierKey Laboratory of Plant Resources Conservation and Sustainable Utilization [Chinese Academy of Sciences]
hal.structure.identifierChinese Academy of Sciences [Beijing] [CAS]
dc.contributor.authorWANG, Baosheng
dc.date2021
dc.date.issued2021
dc.identifier.issn0028-646X
dc.description.abstractEnNatural selection shapes genome-wide patterns of diversity within species and divergence between species. However, quantifying the efficacy of selection and elucidating the relative importance of different types of selection in shaping genomic variation remain challenging. We sequenced whole genomes of 101 individuals of three closely related oak species to track the divergence history, and to dissect the impacts of selective sweeps and background selection on patterns of genomic variation. We estimated that the three species diverged around the late Neogene and experienced a bottleneck during the Pleistocene. We detected genomic regions with elevated relative differentiation ('F-ST-islands'). Population genetic inferences from the site frequency spectrum and ancestral recombination graph indicated that F-ST-islands were formed by selective sweeps. We also found extensive positive selection; the fixation of adaptive mutations and reduction neutral diversity around substitutions generated a signature of selective sweeps. Prevalent negative selection and background selection have reduced genetic diversity in both genic and intergenic regions, and contributed substantially to the baseline variation in genetic diversity. Our results demonstrate the importance of linked selection in shaping genomic variation, and illustrate how the extent and strength of different selection models vary across the genome.
dc.language.isoen
dc.publisherWiley
dc.subject.enancestral recombination graph
dc.subject.enbackground selection
dc.subject.engenomic variation
dc.subject.enlinked selection
dc.subject.enQuercus
dc.subject.enrecombination rate
dc.subject.enselective sweeps
dc.title.enLinked selection shapes the landscape of genomic variation in three oak species
dc.typeArticle de revue
dc.identifier.doi10.1111/nph.17793
dc.subject.halSciences de l'environnement
bordeaux.journalNew Phytologist
bordeaux.peerReviewedoui
hal.identifierhal-03423484
hal.version1
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-03423484v1
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