Table 1.
Posterior Probability for Clades in the MAP Tree under Different Priors for the Frogs Dataset
| Prior | (HL) | (HLC) | Tree | Pjump | |
|---|---|---|---|---|---|
| θ ∼ IG(3, 0.0002) | τ0 ∼ IG(3, 0.004) | 0.69 | 0.35 | 0.28 | 6.6% |
| θ ∼ IG(3, 0.002) | τ0 ∼ IG(3, 0.004) | 0.72 | 0.38 | 0.32 | 5.6% |
| θ ∼ IG(3, 0.02) | τ0 ∼ IG(3, 0.004) | 0.45 | 0.30 | 0.19 | 10.0% |
| θ ∼ IG(21, 0.002) | τ0 ∼ IG(3, 0.004) | 0.41 | 0.34 | 0.20 | 12.3% |
| θ ∼ IG(21, 0.02) | τ0 ∼ IG(3, 0.004) | 0.47 | 0.36 | 0.24 | 10.0% |
| θ ∼ IG(21, 0.2) | τ0 ∼ IG(3, 0.004) | 0.39 | 0.35 | 0.19 | 14.1% |
| θ ∼ IG(3, 0.002) | τ0 ∼ IG(3, 0.0004) | 0.69 | 0.33 | 0.28 | 6.3% |
| θ ∼ IG(3, 0.002) | τ0 ∼ IG(3, 0.004) | 0.72 | 0.38 | 0.32 | 5.6% |
| θ ∼ IG(3, 0.002) | τ0 ∼ IG(3, 0.04) | 0.69 | 0.53 | 0.44 | 4.6% |
| θ ∼ IG(3, 0.002) | τ0 ∼ IG(21, 0.004) | 0.70 | 0.41 | 0.30 | 7.5% |
| θ ∼ IG(3, 0.002) | τ0 ∼ IG(21, 0.04) | 0.69 | 0.34 | 0.29 | 6.2% |
| θ ∼ IG(3, 0.002) | τ0 ∼ IG(21, 0.4) | 0.87 | 1.00 | 0.87 | 0.7% |
Note.—The MAP tree is (((HL)C)K), shown in figure 5. Pjump is the acceptance proportion of the SPR move across species trees recorded during the MCMC run. The same analysis was run three times (with burnin = 8000, sampfreq = 2 and nsample = 105) to check for consistency between runs, and the combined sample was then summarized. There were mixing problems for the last analysis, with priors θ ∼ IG(3, 0.002) and τ0 ∼ IG(21, 0.4), in which case we used burnin = 4 × 104 and nsample = 5 × 105.