Fig. 2

Combined ML (species tree) topology for Hymenoptera, with summary of conflicting and concordant homologs. For each branch, the top number indicates the number of homologs concordant with the species tree at that node, and the bottom number indicates the number of homologs in conflict with that clade in the species tree. The pie charts at each node present the proportion of homologs that support that clade (blue), the proportion that support the main alternative for that clade (green), the proportion that support the remaining alternatives (red), and the proportion that inform (conflict or support) this clade that have less than 50 % bootstrap support (grey). The histograms show, for three nodes, the proportion of the total homologs that support each conflicting alternative resolution for the clade in question, sorted from largest to smallest. Grey lines represent distributions of conflicting alternative resolutions based on coalescent simulations generated with three tree heights. The histograms for other nodes are presented in Additional file 2: Figure S5