Fig. 5

Reconciliation infeasibility due to poorly supported branches. a Bootstrap support among conflicting and non-conflicting branches. A branch is said to conflict if its labels are part of a connected component that contains multiple loci from a single species (weak conflict) or if its labels map to multiple loci from a single species (strong conflict). For both types of conflict, the distribution of bootstrap support for conflicting branches was significantly lower than the distribution for non-conflicting branches (mean denoted as ‘ ×’, statistics in Additional file 1: Table S1). b Reconciliation infeasibility after collapsing poorly supported branches. For each gene tree, we collapsed branches with bootstrap support below the threshold, generated LEGs for the resulting multifurcating gene trees, and evaluated the feasibility of the LEGs. Non-binary trees with a reconcilable LEG have unknown reconciliation feasibility and are not shown but constitute the remainder of the 6298 gene trees. As the threshold increases, the numbers of feasible (blue) and infeasible (red) gene trees decrease while the number of trees with unknown feasibility increases