Fig. 3

Best-scoring ASTRAL-II tree (displayed as a cladogram) based on 303 input best-scoring maximum likelihood gene trees from RAxML. Numbers above branches represent the number of gene trees in concordance with a particular clade in the species tree (blue in pie chart), whereas those below indicate gene trees in conflict (red/green in pie chart). Pie charts were constructed using 206 genes, and additionally represent the portion of conflicting gene trees that support the main alternative (green), those that support all remaining alternatives (red), and finally those with no information (gray), which could be due to bootstrap support < 50% for the branch in question or missing data (Fig. S1, Additional file 2). The ASTRAL tree and concatenated ML tree are represented with branch lengths (with the exception of tip branch lengths) in Figure S2 (Additional file 2) and individual tree files are provided in the Dryad repository that accompanies this study