Detection of nonneutral substitution rates on mammalian phylogenies

Subtree ROC curves. (Left) Phylogenetic tree used in this study, with branch lengths drawn in proportion to the values estimated from 4D sites. Three subtrees are highlighted: (maroon) primates, (gold) glires, and (blue) laurasiatherians. (Right) ROC curves for the LRT (red) and SCORE (green) subtree tests as applied to 3-bp and 10-bp elements under clade-specific selection in the primates (top) and laurasiatherians (bottom). (The SPH method did not perform as well, and the subtree test is not supported with the GERP method.) Results are shown for the case in which ρ = 1.0 and λ = 0.3, meaning that the clade of interest is evolving at approximately one-third the neutral rate, while the rest of the tree is neutrally evolving.