Fig. 5.

Relationships between taxon occupancy and proportion of gene trees that were identified as concordant or discordant with the species tree shown in figure 2. (a) High-taxon-occupancy data sets have a greater proportion of gene trees that are concordant with the species tree. (b) The proportion of gene trees in conflict with the species tree is relatively invariable across varying levels of taxon occupancy. For both panels, each line corresponds to a split in the species tree at different levels of taxon occupancy. The four focal nodes identified in figure 2 are likewise identified in panel (b), but all of them have uniformly low gene-tree support and so fall below the dashed line in panel (a). A split in a gene tree was considered concordant if it was shared with the species tree and had ≥70% bootstrap support in the gene tree. Splits in a gene tree were considered discordant if they had ≥70% bootstrap support and were not shared with the species tree. Shared numbers above whiskers indicate no significant difference in mean values at P < 0.05.