Data from: Protein-encoding ultraconserved elements provide a new phylogenomic perspective of Oestroidea flies (Diptera, Calyptratae)

The diverse superfamily Oestroidea with more than 15,000 known species
includes among others, blow flies, flesh flies, bot flies, and the diverse
tachinid flies. Oestroidea exhibit strikingly divergent morphological and
ecological traits, but even with a variety of data sources and inferences
there is no consensus on the relationships among major Oestroidea
lineages. Phylogenomic inferences derived from targeted enrichment of
ultraconserved elements or UCEs have emerged as a promising method for
resolving difficult phylogenetic problems at varying timescales. To
reconstruct phylogenetic relationships among families of Oestroidea, we
obtained UCE loci exclusively derived from the transcribed portion of the
genome making them suitable for larger and more integrative phylogenomic
studies using other genomic and transcriptomic resources. We analysed
datasets containing 37–2,077 UCE loci from 98 representatives of all
oestroid families (except Ulurumyiidae and Mystacinobiidae) and seven
calyptrate outgroups, with a total concatenated aligned length between
10–550 Mb. About 35% of the sampled taxa consisted of museum specimens
(2–92 years old), of which 85% resulted in successful UCE enrichment. Our
maximum likelihood and coalescent-based analyses produced well-resolved
and highly supported topologies. With the exception of Calliphoridae and
Oestridae, all included families were recovered as monophyletic with the
following conclusions: Oestroidea is monophyletic with Mesembrinellidae as
sister to the remaining oestroid families; Oestridae is paraphyletic with
respect to Sarcophagidae; Polleniidae is sister to Tachinidae;
Rhinophoridae sister to (Luciliinae (Toxotarsinae (Melanomyinae +
Calliphorinae))); Phumosiinae is sister to Chrysomyinae and Bengaliinae is
sister to Rhiniidae. These results support the ranking of most calliphorid
subfamilies as separate families.