Genomic landscape of the global oak phylogeny

Andrew L. Hipp, Paul S. Manos, Marlene Hahn, Michael Avishai, Cathérine Bodénès, Jeannine Cavender-Bares, Andrew A. Crowl, Min Deng, Thomas Denk, Sorel Fitz-Gibbon, Oliver Gailing, M. Socorro González-Elizondo, Antonio González-Rodríguez, Guido W. Grimm, Xiao Long Jiang, Antoine Kremer, Isabelle Lesur, John D. McVay, Christophe Plomion, Hernando Rodríguez-CorreaErnst Detlef Schulze, Marco C. Simeone, Victoria L. Sork, Susana Valencia-Avalos

Research output: Contribution to journalArticlepeer-review

177 Scopus citations


The 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.

Original languageEnglish (US)
Pages (from-to)1198-1212
Number of pages15
JournalNew Phytologist
Issue number4
StatePublished - May 1 2020

Bibliographical note

Funding Information:
Funding for this project was provided by US National Science Foundation Awards 1146488 to ALH, 1146102 to PSM and 1146380 to JCB; Swedish Research Grant 2015-03986 to TD and 2009-00000 to GWG; support of the German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig funded by the German Research Foundation (FZT 118) to E-DS and GWG; and The Morton Arboretum Center for Tree Science. The authors gratefully acknowledge the contributions of associate editor Susana Magallon and two anonymous reviewers.

Publisher Copyright:
© 2019 The Authors. New Phytologist © 2019 New Phytologist Trust


  • Quercus
  • diversification rates
  • genomic mosaicism
  • introgression
  • oaks
  • phylogenomics
  • restriction-site associated DNA sequencing (RAD-seq)
  • tree diversity


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