Subtle introgression footprints at the end of the speciation continuum in a clade of Heliconius butterflies

Quantifying gene flow between lineages at different stages of the speciation continuum is central to understanding speciation. Heliconius butterflies have undergone an adaptive radiation in wing colour patterns driven partly by natural selection for local mimicry. They are also known for assortative mating based on wing pattern. Therefore, wing patterns may facilitate speciation. Here, we take a multifaceted approach to explore speciation and species boundaries between closely-related species H. hecale and H. ismenius. We focus our research in geographic regions where the two are mimetic and contrast this with geographic regions where they do not mimic each other. To examine population history and patterns of gene flow, we developed a four population model accounting for linked selection. This model suggests that the two species have remained isolated for the majority of their history, yet with a small amount of gene exchange. Accordingly, signatures of genomic introgression were small except at a major wing pattern allele. Additionally, behavioural assays suggest that other cues determine strong sexual isolation. Tests for chemical differentiation between species identified major differences in putative pheromones which likely mediate mate choice and the maintenance of species differences. Our results show that strong divergence and adaptive introgression at wing pattern loci may not reveal the whole Heliconius speciation history. In a clade where assortative mating is readily triggered by wing pattern differences, we show that this alone may not lead to speciation and that the accumulation of other barriers to gene flow are important in the completion of speciation.