Northern Hemisphere forests changed drastically in the early Eocene with the diversification of the oak family (Fagaceae). Cooling climates over the next 20 million years fostered the spread of temperate biomes that became increasingly dominated by oaks and their chestnut relatives. Here we investigate the timing and pattern of major macroevolutionary events and ancient genome-wide signatures of hybridization across Fagaceae. An unparalleled transformation of forest dynamics began with the rapid diversification of major lineages within 15 million years following the K-Pg extinction. Innovations related to seed and pollen dispersal are implicated in triggering waves of continental radiations, while fungal symbioses fortified a competitive edge underground. We detected introgression at multiple time scales, including ancient events predating the origination of genus-level diversity. As oak lineages moved into newly available temperate habitats in the early Miocene, secondary contact between previously isolated species occurred. This resulted in adaptive introgression, further amplifying global proliferation.

To generate the nuclear DNA sequences, we sequenced whole genomes of 117 individuals to a coverage of 25-40× using the Illumina NovaSeq platform and called genotypes in SCGs regions. We trimmed and filtered raw reads using trimmomatic v0.39, mapped high quality reads to a reference genome using BWA, and called genotypes via HaplotypeCaller in GATK v4.2. We called all available sites (both variants and invariants).

For plasomes, raw reads from whole genome sequencing were used for de novo assembly of plastomes in NOVOPlasty v4.2. Assembled plastomes were annotated using the program PGA. The boundaries of inverted repeats and coding regions of each annotated gene were determined in Geneious 7.1.4 by using the Q. rubra plastome as a reference. Coding regions of 76 protein-coding genes present in all species were extracted from the assemblies, aligned using MAFFT 7.221, and manually adjusted using Bioedit v.7.2 (https://bioedit.software.informer.com).