Dipteran Phylogeny. This figure shows two alternative topologies obtained from the phylogenetic analysis of 21 species, differing only on the position of C. albipunctata. Numbers above branches (in black) indicate the percentage of individual gene trees from the four reconstructed phylomes supporting each bipartition. (A) Hypothesis supported by most of the phylogenetic methods tested, including maximum likelihood analysis of 160 concatenated genes and one supertree approach (DupTree-tree). Branch lengths and bootstrap values (in red) correspond to the RAxML-tree (see Methods). Bootstrap values were calculated for all branch points. For clarity, we only show the one for the branch leading to C. albipunctata. (B) Alternative topology supported by one supertree approach (Clann-SFIT-tree). Branch information and bootstrap supports are not available with this methodology (C) Summary of all phylogenetic results: four methods supported topology A, while only one supported topology B. We also show results from CONSEL-based hypothesis testing (yellow background; Approximately Unbiased (AU) Test, see Methods). These results indicate significant p-values for the rejection of topology B both in the case of raw and BMGE-corrected alignment (p = 0.071 and 0.027 respectively).