Characterizing hybrids using genome-wide single nucleotide polymorphisms across the Papilio machaon species group of swallowtail butterflies

The reticulate nature of hybridization violates the basic assumption of tree-like evolution in phylogenetics. From an analytical perspective, differential introgression often creates incongruence between datasets, thus complicating the inference of species phylogenies from gene phylogenies. Despite these difficulties, hybrid systems offer unique opportunities to study the nature of species boundaries. Here we characterize phylogenetic relationships between members of the Papilio machaon species complex of swallowtail butterflies. Hybridization is common in this group, and several recognized species and subspecies across North America are thought to be of hybrid origin. We focus on these hybrid lineages, and characterize them using mitochondrial and nuclear DNA sequences, microsatellite markers, and genome-wide single nucleotide polymorphisms generated with genotyping-by-sequencing. Despite broad geographic separation, hybrid lineages share mitochondrial DNA, indicating similar maternal influences during initial hybridization. Microsatellites, on the other hand, suggest more recent differential introgression from the paternal species, which matches broad morphological pattern in the group. Finally, single nucleotide polymorphisms provide unprecedented resolution of the phylogenetic relationships of the entire complex, and show that hybrid taxa are genetically distinctive from both parental taxa at the genome-wide scale. These results demonstrate the utility of genome-wide datasets for resolving complex phylogenies involving hybridization.