Complex introgression history of the erato-sara clade of Heliconius butterflies

Introgression plays a key role in adaptive evolution and species diversification in many groups of species including Heliconius butterflies. However, frequent hybridization and subsequent gene flow between species makes estimation of the species phylogeny challenging. Here, we infer species phylogeny and introgression events from whole-genome sequence data of six members of the erato-sara clade of Heliconius using a multispecies coalescent model with introgression (MSci) and an isolation-with-migration (IM) model. These approaches probabilistically capture the genealogical heterogeneity across the genome due to introgression and incomplete lineage sorting in a full likelihood framework. We detect robust signals of introgression across the genome, and estimate the direction, timing and magnitude of each introgression event. The results clarify several processes of speciation and introgression in the erato-sara group. In particular, we confirm ancestral gene flow between the sara clade and an ancestral population of H. telesiphe, a hybrid origin of H. hecalesia, and gene flow between the sister species H. erato and H. himera. The ability to confidently infer the presence, timing and magnitude of introgression events using genomic sequence data is helpful for understanding speciation in the presence of gene flow and will be useful for understanding the adaptive consequences of introgressed regions of the genome. Our analysis serves to highlight the power of full likelihood methods under the MSci model to the history of species divergence and cross-species introgression from genome-scale data.