Fig. 4.

Different evolutionary dynamics of genes within the accessory genome. (a) Inferred probability of transfer using species-tree gene-tree reconciliation for the entire accessory genome (i.e. all 12 distribution classes which make up the accessory genome), only the ‘multi-lineage core’ genes, and only ‘intermediate and rare’ genes (Wilcoxon rank sum test, ***P<0.001). (b,c) Number of gain events estimated to have occurred on each branch using ancestral state reconstruction when considering the ‘multi-lineage core’ genes (b) or all the ‘intermediate and rare’ genes (c). Darker colours indicate that more gain events were estimated to have occurred on a branch.