Skip to main content

Advertisement

Table 1 Summary of the four models analyzed

From: BEAST: Bayesian evolutionary analysis by sampling trees

Substitution Model Marginal Likelihood 50% credible set size Mean tree height (years)
(a) GTR + CP + strict -3656.13 ± 0.11 38 70.1 ± 0.09
(b) GTR + CP + relaxed -3655.33 ± 0.11 57 70.5 ± 0.2
(c) GTR + Γ + I + strict -3751.37 ± 0.11 289 71.7 ± 0.1
(d) GTR + Γ + I + relaxed -3750.23 ± 0.11 469 72.0 ± 0.2
  1. The marginal likelihoods, the number of distinct tree topologies in the 50% credible set and the mean tree height (± stderr) of the four substitution models that were analyzed in the example. The large improvement in marginal likelihood clearly indicates that the two codon-position substitution models (CP) are substantially superior to the models in which rate heterogeneity among sites is modeled by a 3-distribution and a proportion of invariant sites. In contrast, in this example there is little difference in fit to the data between the strict clock and the relaxed clock analyses, suggesting that this data is clock-like.