Incomplete lineage sorting and hybridization in the Culicoides variipennis complex

Over time, changes in the genomes of closely related species caused by incomplete lineage sorting (ILS) or hybridization can produce gene trees that do not represent the true evolutionary history of a group. This ambiguity can lead to misidentifications and/or a lack of phylogenetic resolution, which are particularly serious problems when it occurs in a vector group. The Culicoides variipennis complex, currently contains three species, one of which (C. sonorensis) is a vector of bluetongue virus and epizootic hemorrhagic disease virus in North America. Species-level identification within this group has been difficult, and molecular and morphological tools remain inconclusive. Here, a whole-genome approach was used to investigate speciation within the C. variipennis complex. Single nucleotide polymorphism (SNP) data were generated for 206 individuals originating from 17 populations throughout the United States and Canada. Clustering analyses (STRUCTURE, PCA, and maximum likelihood) each inferred five distinct groups which we feel consist of the three current species, a no longer recognized subspecies (C. albertensis), and an undescribed cryptic species from southern California. Hybridization was found in three different species parings. Mitochondrial data was used to trace the parentage of these hybrids; however, this was impossible for certain pairings as three species were found to share closely related or identical haplotypes. Divergence within the C. variipennis complex appears to be ongoing and continued study of this group could lead to a better understanding of the role of hybridization on speciation.