Table 1.
Sensitivity of the popGenHMM to Violations of Independence among Sites
| 4Nr | popGenHMM | PRF |
| 1 | 0.20 | 0.33 |
| 5 | 0.16 | 0.26 |
| 10 | 0.15 | 0.22 |
| 25 | 0.11 | 0.13 |
| 50 | 0.09 | 0.09 |
| 75 | 0.08 | 0.09 |
| 100 | 0.08 | 0.08 |
| 200 | 0.06 | 0.06 |
| 500 | 0.05 | 0.05 |
| 1,000 | 0.05 | 0.05 |
NOTE.—Here, we show the proportion of simulations that show a significant element at the 5% level when data are generated under a SNM with varying levels of recombination. Results labeled “popGenGMM” are from a two-state HMM; those labeled “poisson random field (PRF)” are from Bustamante et al. (2001) LRT shown for comparison.