Below are all of the available genotypes from Mal’ta 1 and Afontova Gora 2 for the pigmentation SNPs included in the 8-plex and HIrisPlex systems.
Mal’ta 1 and Afontova Gora 2 both had two copies of the ancestral allele of rs1545397, which is used in the 8-plex system for the prediction of both skin color and eye color.
Mal’ta 1 and Afontova Gora 2 also both had two copies of the ancestral allele of rs1800407, the derived allele of which is associated with green or hazel eyes.
Mal’ta 1 had two copies of the ancestral allele of rs1426654, but Afontova Gora 2 had two copies of the derived allele. This SNP is located in the gene SLC24A5, and its derived allele is one of the two major Caucasoid depigmentation mutations. The other major Caucasoid depigmentation mutation is the derived allele of rs16891982, in the gene SLC45A2.
So we now know that Stora Förvar 11, who lived 7,500 years ago in Sweden, had the SLC45A2 mutation, and that Motala 12, who lived 8,000 years ago in Sweden, and Afontova Gora 2, who lived 17,000 years ago in Siberia, had the SLC24A5 mutation. This means that the simplistic picture that some people have been advancing of light-skinned farmers and dark-skinned hunter-gatherers is not correct.
This paper from last year dated the coalescence of the SLC24A5 mutation at 28,000–22,000 years ago, and this paper from 2012 estimated that the selective sweep for the SLC24A5 mutation started 19,000–11,000 years ago. These estimates are consistent with the Afontova Gora 2 finding.
Gene SNP Sample Genotype ASIP rs6119471 Mal'ta 1 CC IRF4 rs12203592 Mal'ta 1 CC MC1R rs1110400 Mal'ta 1 TT MC1R rs11547464 Mal'ta 1 GG MC1R rs1805005 Mal'ta 1 GG MC1R rs1805006 Mal'ta 1 CC MC1R rs1805007 Mal'ta 1 CC MC1R rs2228479 Mal'ta 1 GG OCA2/HERC2 rs12913832 Mal'ta 1 AA OCA2 rs1545397 Afontova Gora 2 AA OCA2 rs1545397 Mal'ta 1 AA OCA2 rs1800407 Afontova Gora 2 CC OCA2 rs1800407 Mal'ta 1 CC PIGU/ASIP rs2378249 Mal'ta 1 AA SLC24A4 rs12896399 Mal'ta 1 GG SLC24A4 rs2402130 Mal'ta 1 AA SLC24A5 rs1426654 Afontova Gora 2 AA SLC24A5 rs1426654 Mal'ta 1 GG SLC45A2 rs28777 Mal'ta 1 CC TYR rs1042602 Mal'ta 1 CC