Genome-Wide Characterization of Adaptation and Speciation in Tiger Swallowtail Butterflies Using De Novo Transcriptome Assemblies

Hybrid speciation appears to be rare in animals, yet characterization of possible examples offers to shed light on the genomic consequences of this unique phenomenon, as well as more general processes such as the role of adaptation in speciation. Here, we first generate transcriptome assemblies for a putative hybrid butterfly species, Papilio appalachiensis, its parental species, P. glaucus and P. canadensis, and an outgroup, P. polytes. Then, we use these data to infer genome-wide patterns of introgression and genomic mosaicism using both phylogenetic and population genetic approaches. Our results reveal that there is little genetic divergence among all three of the focal species, but the subset of gene trees that strongly support a specific tree topology suggest widespreadsharingofgeneticvariationbetweenP.appalachiensisandbothparental species, likelyasa resultofhybrid speciation.We also find evidence for substantial shared genetic variation between P. glaucus and P. canadensis,which may be due to gene flow or ancestral variation.Consistentwithpreviouswork,weshowthatP.applachiensis ismoresimilar toP. canadensisatZ-linkedgenesand more similar to P. glaucus at mitochondrial genes. We also identify a variety of targets of adaptive evolution, which appear to be enriched for traits that are likely to be important in the evolution of this butterfly system, such as pigmentation, hormone sensitivity, developmental processes, and cuticle formation. Overall, our results provide a genome-wide portrait of divergence and introgression associated with adaptation and speciation in an iconic butterfly radiation