Phylogenomic analyses of Diptera to resolve long-standing questions in fly classification

Advances in DNA sequencing technology and phylogenomic methods are providing new opportunities to resolve major phylogenetic questions in flies. Previous studies have use only a few genes to address questions regarding the evolutionary history of major fly groups, the age of diversification of fly lineages, and the origin of key life history traits in flies. To begin to sample the genome more widely for nuclear gene markers useful for fly phylogeny, we sequenced and assembled adult stage transcriptomes for three fly species, one species each in the families Tabanidae, Empididae and Apystomyiidae. Single-read sequences from Illumina GAIIX pyrosequencing were assembled and used to compare to other published fly sequences to evaluate information content and evolutionary rate in diverse orthologous genes from across the family-level diversity of flies (Diptera).