Figure 13
Underestimate of ML branch lengths using empirical parameters. Percentage that branch lengths were underestimated for data simulated using empirical parameters for the mitochondrial genes atp6, cob, and cox3, as well as the 3rd codon positions for the 13 mitochondrial protein coding genes on the plethodontid salamander phylogeny of Mueller et al. (2004). Data were analyzed in an ML framework using PAUP* to determine the effects of biologically realistic, unequal branch lengths on branch length estimation. For clarity, only the mean underestimate for each branch across simulations is shown. This analysis is equivalent to that of Figure 7, but conducted using an ML framework.