Table 4.
Summary Statistics of the HPV16 E6 Gene Sequences (n = 1,123) with Geographic Origin of the Sample.
| Metapopulation | n | bp | S | h | Hd | (95% CI)a | (95% CI)b | MPD | (95% CI)a | (95% CI)b | WIMP | Tajima’s D | P-valuec | (95% CI)b | P-valueb | Fu’s-Li’s D* | (95% CI)b | P-valueb | R2 | (95% CI)b | P-valueb |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| sub-Saharan Africa | 213 | 456 | 34 | 32 | 0.754 | (0.712 –0.796) | (0.439 –0.892) | 3.049 | (2.739 –3.359) | (0.815 –7.389) | 1.459 | –1.427 | >0.1 | (–1.642 to 2.053) | 0.047 | –3.459 | (–2.178 to 1.523) | 0.003 | 0.044 | (0.033 –0.148) | 0.100 |
| North Africa | 221 | 456 | 30 | 26 | 0.861 | (0.839 –0.883) | (0.653 –0.918) | 4.985 | (4.52 –5.45) | (1.543 –12.592) | 0.969 | –0.196 | >0.1 | (–1.598 to 2.097) | 0.519 | –3.288 | (–1.959 to 1.311) | 0.466 | 0.081 | (0.035 –0.14) | 0.533 |
| Europe | 161 | 456 | 31 | 25 | 0.734 | (0.688 –0.78) | (0.16 –0.838) | 1.62 | (1.401 –1.839) | (0.194 –4.219) | 1.187 | –2.043 | <0.05 | (–1.62 to 2.05) | 0.001 | –3.825 | (–1.958 to 1.447) | 0.002 | 0.026 | (0.028 –0.164) | 0.017 |
| South Asia | 139 | 456 | 8 | 6 | 0.523 | (0.455 –0.591) | (0.056 –0.797) | 0.998 | (0.831 –1.165) | (0.043 –2.744) | 0.464 | –0.724 | >0.1 | (–1.509 to 2.026) | 0.253 | –0.454 | (–2.302 to 1.297) | 0.281 | 0.062 | (0.026 –0.193) | 0.302 |
| East Asia | 207 | 456 | 31 | 37 | 0.643 | (0.567 –0.719) | (0.495 –0.894) | 3.425 | (3.079 –3.771) | (0.853 –8.014) | 1.712 | 1.211 | >0.1 | (–1.593 to 2.11) | 0.091 | –2.848 | (–2.415 to 1.606) | 0.014 | 0.054 | (0.032 –0.146) | 0.180 |
| Central America | 50 | 456 | 21 | 14 | 0.889 | (0.851 –0.927) | (0.589 –0.925) | 4.551 | (3.641 –5.461) | (1.197 –10.979) | 1.803 | –0.237 | >0.1 | (–1.683 to 2.033) | 0.475 | –1.027 | (–2.568 to 1.511) | 0.167 | 0.103 | (0.052 –0.177) | 0.503 |
| South America | 132 | 402 | 18 | 17 | 0.78 | (0.744 –0.816) | (0.486 –0.893) | 3.184 | (2.774 –3.594) | (0.772 –7.859) | 0.947 | –0.096 | >0.1 | (–1.613 to 1.896) | 0.526 | –0.850 | (–2.371 to 1.543) | 0.185 | 0.087 | (0.035 –0.156) | 0.542 |
Note.—Number of samples (n), base pair (bp), Segregating sites (S), haplotypes (h), haplotype diversity (Hd), mean pairwise difference (MPD), weighted intralineage mean pairwise difference (WIMP) (Hurles et al. 2002), Tajima’s D, Fu’s and Li’s D* and R2 statistics were calculated using DnaSP (Librado and Rozas 2009).
a
Calculcated from empirical distribution.
b
Calculated from a coalescent simulation with 1,000 replications and no recombination.
c
Calculated assuming beta distribution.