Table 1.
Summary of results for simulation analyses
| Number of loci: 2 | Number of loci: 10 | |||||||||||||||
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| Symmetrical tree | Asymmetrical tree | Symmetrical tree | Asymmetrical tree | |||||||||||||
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| Prior | LH | T | LH | T | LH | T | LH | T | LH | T | LH | T | LH | T | LH | T |
| Node | Proportion of datasets with true node present in consensus tree | |||||||||||||||
| 1 | 0.98 | 0.98 | 0.80 | 0.76 | 0.98 | 1.0 | 0.88 | 0.86 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 |
| 2 | 1.0 | 0.98 | 0.90 | 0.84 | 0.94 | 0.96 | 0.88 | 0.90 | 1.0 | 1.0 | 1.0 | 0.98 | 1.0 | 1.0 | 1.0 | 1.0 |
| 3 | 1.0 | 1.0 | 0.88 | 0.74 | 0.98 | 1.0 | 0.84 | 0.86 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 |
| 4 | 0.98 | 0.94 | 0.92 | 0.92 | 0.96 | 1.0 | 0.82 | 0.84 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 |
| 5 | 0.96 | 0.92 | 0.90 | 0.88 | 0.94 | 0.98 | 0.76 | 0.80 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 |
| 6 | 1.0 | 1.0 | 0.90 | 0.80 | 0.96 | 0.98 | 0.78 | 0.84 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 |
| 7 | 0.96 | 0.96 | 0.76 | 0.64 | 0.96 | 0.98 | 0.76 | 0.80 | 1.0 | 1.0 | 0.98 | 0.98 | 1.0 | 1.0 | 1.0 | 1.0 |
| 8 | 1.0 | 0.98 | 0.88 | 0.82 | 0.96 | 1.0 | 0.84 | 0.86 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 | 0.98 | 1.0 |
| 9 | 0.98 | 0.98 | 0.90 | 0.90 | 0.94 | 0.98 | 0.86 | 0.88 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 |
| 10 | 0.96 | 0.96 | 0.80 | 0.78 | 0.98 | 1.0 | 0.86 | 0.90 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 |
| 11 | 0.98 | 0.94 | 0.80 | 0.76 | 0.96 | 1.0 | 0.76 | 0.80 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 |
| 12 | 0.98 | 0.96 | 0.92 | 0.88 | 0.90 | 0.96 | 0.68 | 0.80 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 |
| 13 | 0.96 | 0.96 | 0.76 | 0.68 | 0.86 | 0.94 | 0.36 | 0.64 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 | 0.98 | 1.0 |
| 14 | 0.96 | 0.94 | 0.78 | 0.74 | 0.66 | 0.80 | 0.13 | 0.46 | 1.0 | 1.0 | 1.0 | 1.0 | 0.94 | 0.98 | 0.58 | 0.80 |
| CST | Empirical coverage | |||||||||||||||
| 95% | 1.0 | 1.0 | 1.0 | 0.98 | 1.0 | 1.0 | 0.92 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 |
| 99% | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 | 0.92 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 |
| CST | Mean number of trees in 99% CST | |||||||||||||||
| 243.5 | 372.8 | 4375.7 | 6297.3 | 443.9 | 200.9 | 6205.8 | 2711.7 | 1.1 | 1.1 | 15.6 | 19.1 | 3.7 | 3.0 | 46.9 | 26.3 | |
Notes: The upper matrix shows the proportion of simulated datasets for which each node of the true species tree is present in consensus tree. The empirical coverage of the 95% and 99% credible sets of trees (CSTs) tabulates the proportion of simulated datasets (across 50 simulated datasets for each set of simulation conditions) for which the true tree is contained within the credible set. The mean number of trees in the CST is the average number of trees in the 99% CST (averaging across 50 simulated datasets for each set of simulation conditions). Each dataset is analyzed using 2 species tree priors: the uniform prior for labeled histories (LH) and the uniform prior for rooted trees (T). Node numbers are shown in Figure 4.