TABLE 2.
Estimated values for the speciation times, ancestral population sizes, and recombination rate with various methods
| Model | THC | THC + THCG | NHC | NHCG | r | BIC |
|---|---|---|---|---|---|---|
| Target 1 (1,255,492 sites, rp = 0.9, u = 0.090) | ||||||
| 09 | 3.4 | 6.69 | 108,000 | 34,000 | 0.528 | 4,098,983 |
| 09+RAS | 3.67 | 6.97 | 98,000 | 26,000 | 0.17 | 4,098,680 |
| 09+RASa | 4.45 | 6.87 | 54,000 | 28,000 | 0.559 | |
| Target 106 (257,420 sites, rp = 0.2, u = 0.094) | ||||||
| 09 | 2.93 | 6.81 | 120,000 | 43,000 | 0.28 | 850,185 |
| 09+RAS | 2.76 | 7.11 | 131,000 | 34,000 | 0.143 | 850,071 |
| 09+RASa | 3.8 | 7.02 | 70,000 | 37,000 | 0.414 | |
| Target 121 (230,666 sites, rp = 0.6, u = 0.100) | ||||||
| 09 | 1.97 | 5.95 | 401,000 | 46,000 | 1.064 | 774,799 |
| 09+RAS | 0.65 | 5.99 | 627,000 | 44,000 | 2.394 | 774,802 |
| 09a | 4.56 | 6.51 | 131,000 | 36,000 | 2.942 | |
| Target 122 (92,240 sites, rp = 1.9, u = 0.097) | ||||||
| 09 | 4.08 | 5.91 | 61,000 | 48,000 | 2.336 | 308,087 |
| 09+RAS | 3.76 | 6.15 | 79,000 | 42,000 | 2.366 | 308,090 |
| 09a | 4.46 | 5.92 | 42,000 | 50,000 | 8.008 | |
| Target X (263,100 sites, u = 0.108) | ||||||
| 09 | 3.49 | 6.16 | 40,000 | 47,000 | 2.282 | 877,589 |
| 09+RAS | 4.26 | 5.91 | 20,000 | 51,000 | 1.273 | 877,565 |
| 09+RASa | 4.41 | 5.99 | 21,000 | 51,000 | 4.282 | |
| Average (2,098,918 sites) | ||||||
| 4.38 | 6.69 | 59,000 | 34,000 | |||
BIC: Bayesian information criterion. The value of the best model according to the BIC is in boldface type for each target. Average estimates are taken as the mean of estimates of the best model over all targets, weighted by their respective numbers of sites. For each target, the number of sites used is reported, together with the broad recombination rates in centimorgans per megabase (rp), as estimated from pedigree data, and the mutation rate (u) estimated from this analysis (in percentage of change per million years).
a
The parameters after correction for the bias.