Edited by Nina G. Jablonski, The Pennsylvania State University, University Park, Pennsylvania, and accepted by the Editorial Board February 1, 2014 (received for review September 4, 2013)
Probabilities of obtaining FST equal to or greater than that observed (0.00551) between 60 Eneolithic (ca. 6,500–5,000 y ago) and Bronze Age (ca. 5,000–4,000 y ago) samples from the Pontic–Caspian steppe, and a combined sample of 246 homologous modern sequences from the same geographic region, across a range of assumed ancestral population size combinations. Two phases of exponential growth were modeled, the first after the initial colonization of Europe 45,000 y ago, of assumed effective female population size NUP (y axis), and ending when farming began in the region considered 7,000 y ago, when the assumed effective female population size was NN (x axis), and the second leading up to the present, when the assumed effective female population size is 5,444,812. The initial colonizers of Europe were sampled from a constant ancestral African population of 5,000 effective females. Gray shaded areas indicate P values >0.05.
Two-tailed empirical P values for obtaining the observed (A) SLC45A2 G allele, (B) TYR A allele, and (C) HERC2 G allele frequency increase. P values were obtained by forward simulation of drift and natural selection across a range of assumed ancestral population sizes and selection coefficients, assuming exponential growth to a modern Ne of 4,845,710. The SLC45A2 rs16891982 G allele and the TYR rs1042602 A allele were assumed to be codominant. The HERC2 rs12913832 G allele was assumed to be recessive (values less than 0.01 are shaded gray).
Allele frequencies of three functional SNPs associated with pigmentation in ancient and modern populations
| Derived allele frequency | |||||||
| Gene | SNP | Polymorphism | Europe | Asia | Africa | Modern Ukrainian sample | Ancient sample |
| HERC2 | rs12913832 regulatory element (OCA2) | A > G | 0.710 [758] | 0.002 [572] | 0.000 [370] | 0.651 (0.546–0.744) [86] | 0.160 (0.099–0.247) [94] |
| SLC45A2 (MATP) | rs16891982 Leu374Phe | C > G | 0.970 [758] | 0.007 [572] | 0.000 [370] | 0.927 (0.849–0.965) [82] | 0.432 (0.296–0.578) [44] |
| TYR | rs1042602 Ser192Tyr | C > A | 0.368 [758] | 0.002 [572] | 0.000 [370] | 0.367 (0.279–0.466) [98] | 0.043 (0.018–0.106) [92] |
Modern allele frequencies are from 1000 Genomes (http://browser.1000genomes.org) (65). Range in parentheses indicates the equal-tailed 95% confidence interval calculated as described using the qbeta function in R (66). Numbers in square brackets indicate 2N individuals. The African American (ASW) data from 1000 Genomes were excluded because this population is admixed to an unknown extent.
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