Pigmentation SNP genotypes for Mal’ta 1 and Afontova Gora 2

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
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One comment on “Pigmentation SNP genotypes for Mal’ta 1 and Afontova Gora 2
  1. […] SLC24A5 mutation started 19,000–11,000 years ago. It’s also consistent with my finding in this post that Afontova Gora 2, an Upper Paleolithic hunter-gatherer who lived 17,000 years ago in Siberia, […]

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