Table 2. Parameters of positive selection assumed in simulations and the proportion of polyDFE runs for which modeling positive selection gave a significantly better fit to the data.
| γa | pa | γa pa | Proportion of likelihood ratio tests significant | Proportion of analyses with gradient < 0.01 | ||
|---|---|---|---|---|---|---|
| With divergence | Without divergence | With divergence | Without divergence | |||
| 10 | 0.0001 | 0.001 | 0.02 | 0.07 | 0.11 | 0.71 |
| 50 | 0.005 | 0.98 | 0.86 | 0.10 | 0.77 | |
| 100 | 0.01 | 0.98 | 0.02 | 0.03 | 0.58 | |
| 500 | 0.05 | 1.00 | 0.39 | 0.00 | 0.99 | |
| 1,000 | 0.10 | 1.00 | 1.00 | 0.00 | 0.71 | |
| 10 | 0.001 | 0.01 | 0.99 | 0.96 | 0.15 | 0.71 |
| 50 | 0.05 | 1.00 | 1.00 | 0.06 | 0.98 | |
| 100 | 0.10 | 1.00 | 1.00 | 0.00 | 0.97 | |
| 500 | 0.50 | 1.00 | 1.00 | 0.00 | 0.94 | |
| 1,000 | 1.00 | 1.00 | 1.00 | 0.00 | 0.71 | |
| 10 | 0.01 | 0.10 | 1.00 | 1.00 | 0.03 | 0.80 |
| 50 | 0.50 | 1.00 | 1.00 | 0.02 | 0.99 | |
| 100 | 1.00 | 1.00 | 1.00 | 0.02 | 0.95 | |
| 500 | 5.00 | 1.00 | 1.00 | 0.00 | 0.72 | |
| 1,000 | 10.0 | 1.00 | 1.00 | 0.00 | 0.41 | |