RADseq data reveal ancient, but not pervasive, introgression between Californian tree and scrub oak species (Quercussect.Quercus: Fagaceae)

Abstract A long‐term debate in evolutionary biology is the extent to which reproductive isolation is a necessary element of speciation. Hybridizing plants in general are cited as evidence against this notion, and oaks specifically have been used as the classic example of species maintenance without reproductive isolation. Here, we use thousands of SNPs generated by RAD sequencing to describe the phylogeny of a set of sympatric white oak species in California and then test whether these species exhibit pervasive interspecific gene exchange. Using RAD sequencing, we first constructed a phylogeny of ten oak species found in California. Our phylogeny revealed that seven scrub oak taxa occur within one clade that diverged from a common ancestor with Q. lobata , that they comprise two subclades, and they are not monophyletic but include the widespread tree oak Q. douglasii . Next, we searched for genomic patterns of allele sharing consistent with gene flow between long‐divergent tree oaks with scrub oaks. Specifically, we utilized the D‐ statistic as well as model‐based inference to compare the signature of shared alleles between two focal tree species ( Q. lobata and Q. engelmannii ) with multiple scrub species within the two subclades. We found that introgression is not equally pervasive between sympatric tree and scrub oak species. Instead, gene flow commonly occurs from scrub oaks to recently sympatric Q. engelmannii , but less so from scrub oaks to long‐sympatric Q. lobata . This case study illustrates the influence of ancient introgression and impact of reproductive isolating mechanisms in preventing indiscriminate interspecific gene exchange.