From: Complex signatures of selection for the melanogenic loci TYR, TYRP1 and DCT in humans
Pygmies | Senegal | Australian Ab. | Chinese | Europeans | Melanoma | |
---|---|---|---|---|---|---|
Number of segregating sites, S: | ||||||
DCT | 6 | 4 | 4 | 4 | 4 | 4 |
TYR | 5 | 8 | 5 | 7 | 6 | 7 |
TYRP1 | 11 | 21 | 5 | 3 | 6 | 4 |
Number of Haplotypes, h: | ||||||
DCT | 9 | 6 | 4 | 4 | 5 | 6 |
TYR | 9 | 7 | 7 | 7 | 8 | 10 |
TYRP1 | 13 | 12 | 4 | 4 | 7 | 5 |
Haplotype diversity, Hd (SD): | ||||||
DCT | 0.79 (0.09) | 0.82(0.05) | 0.66(0.12) | 0.28 (0.13) | 0.70 (0.07) | 0.74 (0.07) |
TYR | 0.89 (0.04) | 0.77 (0.06) | 0.88 (0.06) | 0.85 (0.06) | 0.70 (0.1) | 0.88 (0.05) |
TYRP1 | 0.93 (0.04) | 0.94 (0.03) | 0.71 (0.08) | 0.36 (0.13) | 0.71 (0.08) | 0.57 (0.12) |
Nucleotide diversity, Pi (SD) (*10 -4 ) | ||||||
DCT | 3.8 (0.7) | 3.1 (0.3) | 3 (0.7) | 1.2 (0.6) | 3.5 (0.4) | 3.5 (0.5) |
TYR | 5 (5) | 3.8 (0.8) | 4.9 (0.6) | 5.5 (0.7) | 3.8 (0.1) | 5.4 (0.8) |
TYRP1 | 7 (1) | 6 (1) | 4 (1) | 1 (0) | 4 (1) | 2 (1) |
Theta (per site) from S, Theta-W (SD a ) (*10 -4 ) | ||||||
DCT | 4.1 (1.7) | 2.7 (1.4) | 3.1 (1.5) | 2.8 (1.4) | 2.7 (1.3) | 2.7 (1.4) |
TYR | 3.8 (1.7) | 6.1 (2.2) | 4.3 (1.9) | 5.3 (2) | 4.5 (1.8) | 5.3 (2) |
TYRP1 | 6 (2) | 12 (3) | 3 (1) | 2 (1) | 3 (1) | 2 (1) |
Average number of nucleotide differences, k: | ||||||
DCT | 1.574 | 1.253 | 1.231 | 0.489 | 1.446 | 1.421 |
TYR | 1.832 | 1.4 | 1.802 | 2.032 | 1.403 | 1.989 |
TYRP1 | 3.268 | 2.963 | 1.890 | 0.389 | 1.827 | 1.289 |
Tajima's D value | ||||||
DCT | -0.221 | 0.321 | -0.071 | -1.638 | 0.892 | 0.754 |
TYR | 0.917 | -1.278 | 0.506 | 0.098 | -0.458 | 0.027 |
TYRP1 | 0.192 | -1.906 | 0.700 | -1.447 | 0.341 | 0.416 |
Tajima's D, p (D <= D obs) | ||||||
DCT | 0.39b(0.37)c | 0.67b(0.59)c | 0.52b(-)c | 0.04b(0.03)c | 0.84b(0.65)c | 0.8b(0.62)c |
TYR | 0.86b(0.79)c | 0.04b(0.02)c | 0.73b(-)c | 0.57b(0.39)c | 0.33b(0.21)c | 0.54b(0.38)c |
TYRP1 | 0.64b(0.49)c | 1e-3b,d(1e-3)c,d | 0.8b(-)c | 0.09b(0.04)c | 0.67b(0.44)c | 0.69b(0.5)c |
DHEW (HEW) p-values | ||||||
DCT | 0.19 (0.26) | 0.68 (0.73) | 0.20 (0.22) | 4e-3e (5e-3f) | 0.63 (0.32) | 0.57 (0.20) |
TYR | 0.75 (0.81) | 0.33 (0.43) | 0.62 (0.69) | 0.27 (0.12) | 0.1 (3e-3f) | 0.52 (0.63) |
TYRP1 | 0.87 (0.91) | 0.61 (0.72) | 0.76 (0.82) | 0.28 (0.33) | 0.4 (0.03) | 0.44 (0.03) |