Table 3. Summary of sequence variation in the promoter and coding regions of the MC1R gene in four population groups composed of autochthonous populations from the 1000 Genomes project and results of three neutrality tests based on sequence data: Tajima’s D test, Fu’s F S test, and synonymous and non-synonymous nucleotide substitution test (dN - dS) of positive and purifying selection for analysis averaging MC1R coding haplotypes. Significant p-values are marked in boldface.
| Tajima’s D test | Fu’s F S test | dN / dS nucleotide substitution test | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 2n a | Number of nucleotide sites | K b | S c | θW ± SD | π ± SD (%)d | D | p-valuee | F S | p-valuef | Number of codons | HA = Positive Selection | HA = Purifying Selection | |
| (dN > dS) | (dN < dS) | ||||||||||||
| Promoter region | |||||||||||||
| AFR | 1008 | 3001 | 78 | 55 | 6.140 ± 1.367 | 0.224 ± 0.117 | -0.991 | 0.152 | -24.074 | 0.003 | - | - | - |
| EAS | 1008 | 3001 | 42 | 45 | 4.805 ± 1.131 | 0.188 ± 0.100 | -1.024 | 0.136 | -4.521 | 0.210 | - | - | - |
| EUR | 1006 | 3001 | 36 | 42 | 4.272 ± 1.036 | 0.164 ± 0.089 | -0.808 | 0.227 | -3.360 | 0.291 | - | - | - |
| SAS | 978 | 3001 | 64 | 56 | 6.298 ± 1.399 | 0.213 ± 0.112 | -1.030 | 0.157 | -17.287 | 0.017 | - | - | - |
| Coding region | |||||||||||||
| AFR | 1008 | 954 | 33 | 31 | 4.138 ± 1.012 | 0.093 ± 0.072 | -1.964 | 0.000 | -27.698 | 0.000 | 316 | -1,426; p = 1,000 | 1,453; p = 0,074 |
| EAS | 1008 | 954 | 26 | 20 | 2.669 ± 0.741 | 0.150 ± 0.102 | -1.078 | 0.128 | -13.226 | 0.006 | 317 | -0,142; p = 1,000 | 0,141; p = 0,444 |
| EUR | 1006 | 954 | 22 | 22 | 2.937 ± 0.792 | 0.103 ± 0.077 | -1.578 | 0.021 | -13.894 | 0.001 | 317 | 0,444; p = 0,329 | -0,439; p = 1,000 |
| SAS | 978 | 954 | 24 | 23 | 3.082 ± 0.821 | 0.062 ± 0.055 | -1.939 | 0.001 | -26.733 | 0.000 | 317 | -1,034; p = 1,000 | 1,055; p = 0,147 |
2n: number of chromosomes analyzed
Number of different haplotypes
Number of segregating sites
Average nucleotide diversity and its standard deviation
A p-value was computed by the comparison of the estimated statistic to a distribution of estimates computed for 99,999 random samples of the same sample size and level of polymorphism as the observed data, and represents the proportion of the simulated D statistics less or equal to the observed value.
A p-value was computed by the comparison of the estimated statistic to a distribution of estimates computed for 99,999 random samples of the same sample size and level of polymorphism as the observed data, and represents the proportion of the simulated F S statistics less or equal to the observed value. The 2% percentile of the distribution corresponded to the 5% cutoff value. Therefore, a F S statistic should be considered as significant at the 5% level, if its p-value is below 0.02, and not below 0.05.