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Understanding the genetic basis of reproductive isolation is a long-standing goal of speciation research. In recently diverged populations, genealogical discordance may reveal genes and genomic regions that contribute to the speciation process. Previous work has shown that conspecific colonies of Acropora that spawn in different seasons (spring and autumn) are associated with highly diverged lineages of the phylogenetic marker PaxC . Here, we used 10 034 single-nucleotide polymorphisms to generate a genome-wide phylogeny and compared it with gene genealogies from the PaxC intron and the mtDNA Control Region in 20 species of Acropora , including three species with spring- and autumn-spawning cohorts. The PaxC phylogeny separated conspecific autumn and spring spawners into different genetic clusters in all three species; however, this pattern was not supported in two of the three species at the genome level, suggesting a selective connection between PaxC and reproductive timing in Acropora corals. This genome-wide phylogeny provides an improved foundation for resolving phylogenetic relationships in Acropora and, combined with PaxC , provides a fascinating platform for future research into regions of the genome that influence reproductive isolation and speciation in corals.

A primary goal in evolutionary biology is to identify the historical events that have facilitated the origin and spread of adaptations. When these adaptations also lead to reproductive isolation, we can learn about the evolutionary mechanisms contributing to speciation. We reveal the complex history of the geneMaMyb2in shaping flower colour divergence within a recent radiation of monkeyflowers. In theMimulus aurantiacusspecies complex, red-floweredM. a.ssp. puniceusand yellow-floweredM. a.ssp.australisare partially isolated because of differences in pollinator preferences. Phylogenetic analyses based on genome-wide variation across the complex suggest two origins of red flowers from a yellow-flowered ancestor: one inM. a.ssp. puniceusand one inM. a.ssp.flemingii. However, in both cases, red flowers are caused bycis-regulatory mutations in the geneMaMyb2. Although this could be due to distinct mutations in each lineage, we show that the red allele inM. a.ssp.puniceusdid not evolvede novoor exist as standing variation in its yellow-flowered ancestor. Rather, our results suggest that a single redMaMyb2allele evolved during the radiation ofM. aurantiacusthat was subsequently transferred to the yellow-flowered ancestor ofM. a.ssp.puniceusvia introgressive hybridization. Because gene flow is still possible among taxa, we conclude that introgressive hybridization can be a potent driver of adaptation at the early stages of divergence that can contribute to the origins of biodiversity.