The phylogenetic trees of fat (A), dachsous (B), hippo (C), and yorkie (D). Columns with < =2 amino acids were removed in all datasets. Trees were produced by PhyloBayes (after 2000 generations, maxdiff = 0.01 for fat, 0.036 for dachsous, 0.05 for hippo, and 0.04 for yorkie) based on the substitution model LG + G (gamma category = 4). Trees are shown in scale, except branches with an asterisk. Numbers indicate posterior probability. Red frames mark species correctly grouped; blue frames mark species grouped as in the RAxML trees (Additional file 1: Figure S6).