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Genomic landscape of the global oak phylogeny

hal.structure.identifierThe Morton Arboretum
dc.contributor.authorHIPP, Andrew
hal.structure.identifierDuke University [Durham]
dc.contributor.authorMANOS, Paul
hal.structure.identifierThe Morton Arboretum
dc.contributor.authorHAHN, Marlene
hal.structure.identifierThe Hebrew University of Jerusalem [HUJ]
dc.contributor.authorAVISHAI, Michael
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorBODÉNÈS, Catherine
hal.structure.identifierUniversity of Minnesota [Morris] [UMM]
dc.contributor.authorCAVENDER‐BARES, Jeannine
hal.structure.identifierDuke University [Durham]
dc.contributor.authorCROWL, Andrew
hal.structure.identifierChinese Academy of Sciences [Beijing] [CAS]
dc.contributor.authorDENG, Min
hal.structure.identifierSwedish Museum of Natural History [NRM]
dc.contributor.authorDENK, Thomas
hal.structure.identifierUniversity of California [Berkeley] [UC Berkeley]
dc.contributor.authorFITZ‐GIBBON, Sorel
hal.structure.identifierGeorg-August-University = Georg-August-Universität Göttingen
dc.contributor.authorGAILING, Oliver
hal.structure.identifierInstituto Politecnico Nacional [Mexico] [IPN]
dc.contributor.authorGONZÁLEZ‐ELIZONDO, M. Socorro
hal.structure.identifierUniversidad Nacional Autónoma de México = National Autonomous University of Mexico [UNAM]
dc.contributor.authorGONZÁLEZ‐RODRÍGUEZ, Antonio
dc.contributor.authorGRIMM, Guido
hal.structure.identifierChinese Academy of Sciences [Beijing] [CAS]
dc.contributor.authorJIANG, Xiao‐long
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorKREMER, Antoine
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorLESUR, Isabelle
hal.structure.identifierDuke University [Durham]
dc.contributor.authorMCVAY, John
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorPLOMION, Christophe
hal.structure.identifierUniversidad Nacional Autónoma de México = National Autonomous University of Mexico [UNAM]
dc.contributor.authorRODRÍGUEZ‐CORREA, Hernando
hal.structure.identifierMax Planck Institute for Biogeochemistry [MPI-BGC]
dc.contributor.authorSCHULZE, Ernst‐detlef
hal.structure.identifierUniversità degli studi della Tuscia [Viterbo]
dc.contributor.authorSIMEONE, Marco
hal.structure.identifierUniversity of California [Berkeley] [UC Berkeley]
dc.contributor.authorSORK, Victoria
hal.structure.identifierUniversidad Nacional Autónoma de México = National Autonomous University of Mexico [UNAM]
dc.contributor.authorVALENCIA‐AVALOS, Susana
dc.date.issued2020-05
dc.identifier.issn0028-646X
dc.description.abstractEnThe tree of life is highly reticulate, with the history of population divergence emerging from populations of gene phylogenies that reflect histories of introgression, lineage sorting and divergence. In this study, we investigate global patterns of oak diversity and test the hypothesis that there are regions of the oak genome that are broadly informative about phylogeny.We utilize fossil data and restriction-site associated DNA sequencing (RAD-seq) for 632 individuals representing nearly 250 Quercus species to infer a time-calibrated phylogeny of the world's oaks. We use a reversible-jump Markov chain Monte Carlo method to reconstruct shifts in lineage diversification rates, accounting for among-clade sampling biases. We then map the > 20 000 RAD-seq loci back to an annotated oak genome and investigate genomic distribution of introgression and phylogenetic support across the phylogeny.Oak lineages have diversified among geographic regions, followed by ecological divergence within regions, in the Americas and Eurasia. Roughly 60% of oak diversity traces back to four clades that experienced increases in net diversification, probably in response to climatic transitions or ecological opportunity.The strong support for the phylogeny contrasts with high genomic heterogeneity in phylogenetic signal and introgression. Oaks are phylogenomic mosaics, and their diversity may in fact depend on the gene flow that shapes the oak genome.
dc.language.isoen
dc.publisherWiley
dc.subject.endiversification rates
dc.subject.engenomic mosaicism
dc.subject.enintrogression
dc.subject.enoaks
dc.subject.enphylogenomics
dc.subject.enQuercus
dc.subject.enrestriction-site associated DNA sequencing (RAD-seq)
dc.subject.entree diversity
dc.title.enGenomic landscape of the global oak phylogeny
dc.typeArticle de revue
dc.identifier.doi10.1111/nph.16162
dc.subject.halSciences de l'environnement
bordeaux.journalNew Phytologist
bordeaux.page1198-1212
bordeaux.volume226
bordeaux.issue4
bordeaux.peerReviewedoui
hal.identifierhal-03162542
hal.version1
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-03162542v1
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