The tree of life is highly reticulate, with the history of population divergence emerging frompopulations of gene phylogenies that reflect histories of introgression, lineage sorting anddivergence. In this study, we investigate global patterns of oak diversity and test the hypothesisthat 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 ofthe world’s oaks. We use a reversible-jump Markov chain Monte Carlo method to reconstructshifts in lineage diversification rates, accounting for among-clade sampling biases. We thenmap the > 20 000 RAD-seq loci back to an annotated oak genome and investigate genomicdistribution of introgression and phylogenetic support across the phylogeny.

 Oak lineages have diversified among geographic regions, followed by ecological divergencewithin regions, in the Americas and Eurasia. Roughly 60% of oak diversity traces back to fourclades that experienced increases in net diversification, probably in response to climatic transitionsor ecological opportunity.

 The strong support for the phylogeny contrasts with high genomic heterogeneity in phylogeneticsignal and introgression. Oaks are phylogenomic mosaics, and their diversity may infact depend on the gene flow that shapes the oak genome.