The assumed tree topologies for the vertebrate, insect, worm, and yeast data sets (top to bottom) and the branch lengths estimated for the conserved (left) and nonconserved (right) states of the phylo-HMM. The conserved and nonconserved phylogenies are identical, except for the scaling constant ρ, which was estimated at 0.33, 0.24, 0.36, and 0.32 (top to bottom). Horizontal lines indicate branch lengths and are drawn to scale, both within and between species groups. The estimated trees were unrooted; arbitrary roots were chosen for display purposes. Note that some distortions in the branch lengths occur due to alignment-related ascertainment biases (see text and Supplemental material).
