An evaluation of alternative models for the Zimbabwe populationa
|
|
Mean πb |
Mean HKA χ2 |
Mean D |
Mean He |
|---|---|---|---|---|
| Observedc | 4.82 | 80.3 | −0.56 | −0.44 |
| Model | ||||
| SNMd | 5.42 | 43.6 (<10−4) | −0.01 (<10−4) | 0.00 (0.012) |
| G1d | 4.78 | 43.3 (<10−4) | −0.35 (0.003) | 0.39 (<10−4) |
| G2d | 4.78 | 40.4 (<10−4) | −0.59 (0.766) | 0.93 (<10−4) |
| HH1d | 4.78 | n.d. | −0.62 (0.854) | 0.49 (<10−3) |
| HH2d | 4.86 | n.d. | −0.62 (0.830) | 0.50 (<10−3) |
| BNd
|
4.82
|
75.07 (0.286)
|
−0.48 (0.148)
|
−0.23 (0.172)
|
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↵a Combining the 10 loci surveyed here and 105 loci surveyed in Glinka et al. (2003).
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↵b Average π per locus across loci, the average number of sites surveyed is 477 base pairs.
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↵c The mean of the observed values.
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↵d The mean simulated values are given for π and HKA χ2; the mean of mean simulated values are given for Tajima's D and Fay and Wu's 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. G1: exponential growth started 0.023Ne generations ago (∼50,000 years ago; rate of growth = 100; growth factor = 10; mean θ = 43.5). G2: exponential growth started 0.161Ne generations ago (∼150,000 years ago; rate of growth = 10; growth factor = 5; mean θ = 18.5). BN: a bottleneck started 0.5Ne generations ago (about 200,000 years ago; duration = 0.00002Ne generations; f = 0.00001; mean θ = 9.5). See Methods for assumptions underlying estimates of timing in years. HH1: recurrent hitchhiking (Ne = 5 million; s = 0.005; λ = 0.000045; mean θ = 10.85). HH2: recurrent hitchhiking (Ne = 5 million; s = 0.01; λ = 0.000023; mean θ = 10.85). P-values are based on 1000 replicates for models HH1 and HH2 and 10,000 replicates for the models SNM, G1, G2, and BN. ρ/θ = 7 for all models. (n.d.): the HKA test was not performed for the hitchhiking models.
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↵e These P-values are based on infinite-sites simulations. We also implemented a correction for finite-sites (see Supplemental Results). Under the finite-sites model, the mean H under model SNM was −0.14 (P = 0.065). P-values under G and HH models were ≤10−3. The P-value under the BN model was 0.405. Thus, the conclusion that the mean H is incompatible with growth or hitchhiking is robust to the infinite-sites assumption.
