Disentangling Complex Histories of Hybridisation: The Genomic Consequences of Ancient and Recent Introgression in Channel Island Monkeyflowers.

Hybridisation is a common feature of evolutionary radiations, but its genomic consequences vary depending on when it occurs. Since reproductive isolation takes time to accumulate, hybridisation can occur at multiple points during divergence. Previous studies suggested that the taxonomic diversity in evolutionary radiations can help infer the timing of past gene flow events. Here, we assess the power of these approaches for revealing when gene flow occurred between two monkeyflower taxa (Mimulus aurantiacus) endemic to the Channel Islands of California. Coalescent simulations reveal that conventional four-taxon tests may not be capable of fully distinguishing between recent and ancient introgression, but genome-wide patterns of phylogenetic discordance vary predictably with different histories of hybridisation. Using whole-genome sequencing and phylogenetic tests for introgression across the M. aurantiacus radiation, we identify signals of both ancient and recent hybridisation that occurred between the island taxa and their ancestors. In addition, we find widespread selection against introgressed ancestry, consistent with polygenic barriers to gene flow. However, we also identify localised signals across the genome that may indicate adaptive introgression. This study highlights the power and challenges of trying to disentangle complex histories of hybridisation. More broadly, our results illustrate the multiple roles that gene flow can play in evolutionary radiations: hybridisation can expose genetic incompatibilities that contribute to reproductive isolation while also likely facilitating adaptation by transferring beneficial alleles between taxa. These findings underscore the dynamic interplay between the timing of hybridisation and natural selection in shaping evolutionary trajectories within radiations.