Fig. 2

Topological conflicts of gene trees in Causonis based on the 23taxa-810nu dataset. a Supernetwork constructed with SplitsTree based on 810 rooted ML gene trees (10% majority-rule consensus trees), where parallelograms indicate incongruences among gene trees. Branches in orange indicate the japonica-corniculata clade, green indicates other clades in Causonis, and black represents the outgroup. b MSC tree constructed with ML gene trees. The pie chart at each node represents the proportion of genes supporting congruent relationships (blue), the dominant alternative (red), the remaining conflicting alternatives (yellow), and genes with less than 75% BS value for that node (gray). The numbers beside the pie chart denote quartet scores (quartet concordance/quartet differential/quartet informativeness)