Figure 2.

Pervasive topology discordance, prevalent hybridization, and introgression in Brassicaceae.

(A) Cloudogram inferred from 1463 SCOGs (Orthofinder). Scale in mya.

(B) Extensive conflicts between plastome-based (right panel) and nuclear-genome-based (left panel) species ML trees using concatenated data. Introgression events are shown as broken red lines on the nuclear tree.

(C) Gene-tree compatibility as revealed by the portion of gene trees that are highly (weakly) supported or rejected. Weakly rejected refers to those not in the tree but compatible if low support branches (<75%) are contracted.

(D) Tests for introgression with D statistics (upper right panel) and QulBL analysis (lower left panel). Heatmaps of mean pairwise D per species pair and the mean total proportion of introgressed loci per species pair inferred with QuIBL.

(E) Test for introgression, with identification of excess sharing of derived alleles via the branch-specific statistic f_b(C) approach. The branch-specific statistic f_b(C) value indicates excess sharing of derived alleles between a given branch (b) on the y-axis, relative to its sister branch, and species C on the x-axis.