Robber flies or assassin flies (Diptera: Asilidae) are a diverse family of venomous predators. The most recent classification organizes Asilidae into 14 subfamilies based on a comprehensive morphological phylogeny, but many of these have not been supported in a subsequent molecular study using traditional markers. To help address questions of monophyly in Asilidae, we leveraged the recently developed Diptera-wide UCE baitset to compile seven datasets consisting of 151 robber flies and 146-2508 loci varying in the extent of missing data. We also studied the behavior of different nodal support metrics, as the bootstrap is known to perform poorly with large datasets. We find that nodal support does not significantly vary with missing data. Furthermore, the bootstrap overestimates nodal support, as has been reported from many recent analyses. Gene concordance and site concordance factors perform better, but may actually underestimate support. We instead recommend quartet concordance as a replacement for the bootstrap, as it does not appear to over- or underestimate nodal support. Our phylogeny did not recover the subfamilies Brachyrhopalinae, Dasypogoninae, Dioctriinae, Stenopogoninae, Tillobromatinae, Trigonomiminae, and Willistonininae as monophyletic, consistent with a previous molecular study. This comprehensive phylogeny of Asildiae will allow for the long-needed revision of the subfamily classification as well as provide an evolutionary framework for studies in comparative biology.
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