A Combined Transcriptome and Anchored Hybrid Phylogenomic Approach to Address Acalyptrate Fly Phylogeny (Diptera: Cyclorrhapha)

Many major genetic models and economically important species of flies are members of Schizophora. Taxa including Drosophila, tephritid fruit flies, and calyptrate flies such as house flies and blow flies have been the subject of intense research however their relationships remain controversial. Rapid cladogenesis has made attempts to deduce the phylogeny of this group incredibly challenging, particularly in terms of the relationships among families and the monophyly of superfamilies. Previous studies that include robust sampling of genes and taxa yield unresolved or contradictory phylogenetic hypotheses. This study uses new approaches with unprecedented gene coverage from transcriptome data to provide an evidence- based, robustly supported phylogeny of the acalyptrate flies. A dataset including three thousand genes and an alignment of over one million amino acid positions was assembled to address this question. This was complemented by an anchored hybrid enrichment exome capture approach where genomic DNA was hybridized to probes yielding 60-300 gene markers. Data collected by these two approaches was combined to provide a thorough sampling regime. Although support values continue to be low for the relationships between many families, insight can be gained into several previously intractable problems in the evolution of higher flies.