Table 2.
Haplotype frequency tests
| n | S | θ | K | M | Haplotype configuration | |
|---|---|---|---|---|---|---|
| Arabiensisa | 19 | 79 | 22.6 | 7* | 7* | (4,1,0,0,0,1,1,0,0,0,0,0,0,0,0,0,0,..)*** |
| TEP1s | 9 | 10 | 3.7 | 5 | 3 | (3,0,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,..) |
| TEP1r | 12 | 8 | 2.6 | 4 | 6 | (2,0,0,1,0,1,0,0,0,0,0,0,0,0,0,0,0,..) |
| Mbita | 17 | 85 | 25.1 | 3*** | 9*** | (0,0,0,2,0,0,0,0,1,0,0,0,0,0,0,0,0,..)*** |
| TEP1s | 24 | 10 | 2.7 | 4 | 16 | (0,0,1,1,0,0,0,0,0,0,0,0,0,0,0,1,0,..) |
| TEP1r | 10 | 2 | 0.7 | 2 | 6 | (0,0,0,1,0,1,0,0,0,0,0,0,0,0,0,0,0,..) |
| Cameroon | 24 | 20 | 5.4 | 4* | 15* | (0,1,1,1,0,0,0,0,0,0,0,0,0,0,1,0,0,..)*** |
| TEP1s | 9 | 8 | 2.9 | 3 | 4 | (0,1,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,..) |
| TEP1s/r | 15 | 0 | 0.0 | 1b | 15b | (0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,..)b |
n is the number of haplotypes sequenced, S the number of segregating sites, θ Watterson's estimate of 4 Nμ per gene, K the number of haplotypes, M the frequency of the commonest haplotype. The 'Haplotype Configuration' is a vector (n1, n2, n3, ..., ni) giving the number of distinct haplotypes that appeared i times in the sample (see Innan et al 2005). For example, the first haplotype configuration (4,1,0,0,0,1,1,...) has four haplotypes that appeared once each, one that appear twice, none that appeared three, four or five times, one that appeared six times and one that appeared seven times. aSampling was not at random with respect to s/r state, bsignificance not tested. Significance assessed through coalescent simulation is indicated as *p < 0.05, ***p < 0.001.