Phylogenomics not supporting monophyly of Syrphoidea

The recent study from 1KITE using more than 3000 genes from 19 taxa concluded a phylogeny where Pipunculidae is the sister taxon to Schizophora, the largest group of flies. This finding leaves "Syrphoidea" paraphyletic.

Pauli, T., T. O. Burt, K. Meusemann, K. Bayless, A. Donath, L. Podsiadlowski, C. Mayer, A. Kozlov, A. Vasilikopoulos, S. Liu, X. Zhou, D. Yeates, B. Misof, R. S. Peters, and X. Mengual. 2018. New data, same story: phylogenomics does not support Syrphoidea (Diptera: Syrphidae, Pipunculidae). Systematic Entomology 33:445–13. PDF

Abstract: The Syrphoidea (families Pipunculidae and Syrphidae) has been suggested to be the sister group of the Schizophora, the largest species radiation of true ies. A major challenge in dipterology is inferring the phylogenetic relationship between Syr- phoidea and Schizophora in order to understand the evolutionary history of ies. Using newly sequenced transcriptomic data of Syrphidae, Pipunculidae and closely related lineages, we were able to fully resolve phylogenetic relationships of Syrphoidea using a supermatrix approach with more than 1 million amino acid positions derived from 3145 genes, including 19 taxa across nine families. Platypezoidea were inferred as a sister group to Eumuscomorpha, which was recovered monophyletic. While Syrphidae were also found to be monophyletic, the superfamily Syrphoidea was not recovered as a mono- phyletic group, as Pipunculidae were inferred as sister group to Schizophora. Within Syrphidae, the subfamily Microdontinae was resolved as sister group to the remaining taxa, Syrphinae and Pipizinae were placed as sister groups, and the monophyly of Eristalinae was not recovered. Although our results are consistent with previously established hypotheses on Eumuscomorphan evolution, our approach is new to dipteran phylogeny, using larger-scale transcriptomic data for the rst time for this insect group.