An evaluation of alternative models for the the Netherlands populationa
Mean πb | Mean HKA χ2 | Mean D | Mean Var(D) | Mean H | Mean Var(H) | Mean #IL | |
|---|---|---|---|---|---|---|---|
| Observedc | 2.00 | 192.87 | −0.06 | 1.55 | −1.58 | 6.46 | 14 |
| Model | |||||||
| SNMd | 1.97 | 75.9 (<10−4) | −0.02 (0.250) | 0.66 (<10−4) | −0.00 (<10−4) | 1.49 (<10−4) | 2.7 (<10−4) |
| BN1d | 2.08 | 157.7 (0.029) | 0.39 (0.000) | 1.41 (0.163) | −1.26 (0.071) | 4.73 (0.101) | 13 (0.470) |
| BN2d | 2.09 | 135.6 (<10−3) | −0.01 (0.315) | 1.25 (0.007) | −0.96 (0.002) | 4.03 (0.030) | 7.6 (0.015) |
| BN3d | 2.01 | 165.4 (0.078) | 0.08 (0.125) | 1.63 (0.700) | −1.20 (0.050)e | 5.08 (0.157) | 14 (0.549) |
| HHd | 2.06 | (n.d.) | −0.60 (<10−3) | 0.57 (<10−3) | 0.24 (<10−3) | 2.24 (<10−3) | 6.6 (0.006) |
a Combining the 10 loci surveyed here and 106 loci surveyed in Glinka et al. (2003).
b Average π per locus across loci, the average number of sites surveyed is 477 base pairs.
c Mean of the observed values. Var(D): the variance of D; Var(H): the variance of H; #IL: the number of invariant loci out of 115 surveyed.
d Mean simulated values are given for π, HKA χ2 and #IL; the mean of mean simulated values are given for Tajima's D, Var(D), and Fay and Wu's H, and Var(H). P-values of the observed means under the model simulated are given in parentheses. See Methods for descriptions of the models. SNM: the standard neutral model, mean Θ = 5.43. BN1: a bottleneck started 0.12Ne generations ago (duration = 0.106Ne generations, between ∼4000 and 30,000 years ago; f = 0.05; mean Θ = 5.43); BN2: a bottleneck started 0.192Ne generations ago (duration = 0.112Ne generations, between ∼20,000 and 50,000 years ago; f = 0.05; mean Θ = 5.43); BN3: a bottleneck started 0.06Ne generations ago (duration = 0.000021Ne generations, about 16,000 years ago; f = 0.00001; mean Θ = 5.43); HH: recurrent hitchhiking (Ne = 2.5 million; s = 0.005; λ = 0.000052; mean Θ = 5.43). P-values are based on 1000 replicates for models HH and 10,000 replicates for the models SNM, BN1, BN2, and BN3. p/Θ = 7 for all models. (n.d.): the HKA test was not performed for the hitchhiking model.
e P = 0.060 under a finite-sites model (see Supplemental Results).