Figure 6

Estimates of parameters in Bayesian analysis. The estimated transition:transversion rate ratio (kappa) as a function of branch length. Kappa used for simulations was 4 (transition:transversion = 2, equal base frequencies, twice as many transitions as transversions). Kappa was estimated from the data in a Bayesian framework using MrBayes with the default exponential branch length prior (mean = 0.1) for 4-taxon, equal-branch-length, HKY 1 kb datasets (white boxes); with the default exponential branch length prior for 4-taxon, equal-branch-length, HKY 10 kb datasets (gray boxes); and with an exponential branch length prior of mean = 1 for 4-taxon, equal branch length, HKY 1 kb datasets (dark gray boxes).