Divergent habitat selection across many loci maintains species boundaries during introgression

Evidence of introgression between well-defined species is abundant, begging the question, how are species boundaries maintained during introgression? Work on this question has largely focused on systems where divergence is controlled by a few large effect genetic loci. However, adaptive divergence is often highly polygenic, especially between young species that remain capable of gene exchange. Here, we use phylogeny based introgression statistics and local ancestry inference to characterize the genomic, spatial, and historical extent of introgression between two recently diverged Neotropical plant species. We then use QTL analysis to investigate the genetic basis of traits under divergent abiotic and biotic selection that are involved in habitat isolation. Finally, we combine these top-down and bottom-up approaches to clarify how species with polygenic reproductive isolation maintain cohesion in the face of gene flow. We find clear evidence of both recent and ancient introgression between Costus villosissimus and C. allenii, but overall genomic divergence remains relatively high (F_st :~0.27) in part due to strong divergent habitat selection. Traits involved in divergent habitat adaptation are polygenic, such that strong habitat selection is spread across many loci rather than concentrated on a few loci of large effect. In contrast to the 'islands of divergence' seen around large effect loci in other hybridizing species pairs, we see genomically widespread and moderate peaks of both differentiation and introgression. Our results indicate that strong selection spread across many loci contributing to reproductive isolation can maintain species differentiation despite introgression.