Extended Data Table 5.
Allele counts at SNPs thought to be affected by selection in samples that have at least 1.0-fold coverage.rs4988235 is responsible for lactase persistence in Europe59,60. The SNPs at SLC24A5 and SLC45A2 are responsible for light skin pigmentation. The SNP at EDAR61,62 affects tooth morphology and hair thickness. The SNP at HERC263,64 is the primary determinant of light eye color in present-day Europeans. We present the fraction of fragments overlapping each SNP that are derived; the observation of a low rate of derived alleles does not prove that the individual carried the allele, and instead may reflect sequencing error or ancient DNA damage. We highlight in light gray sites that we judge (based on the derived allele count) are likely to be heterozygous for the derived allele, and in dark gray sites that are likely to be homozygous.
| LCT | SLC45A2 | SLC24A5 | EDAR | HERC2 | ||
|---|---|---|---|---|---|---|
| SNP | rs4988235 | rs16891982 | rs1426654 | rs3827760 | rs12913832 | |
| Ancestral | G | C | G | A | A | |
| Derived | A | G | A | G | G | |
| UstIshim | Coverage | 31 | 46 | 52 | 42 | 50 |
| Derived allele frequency | 0% | 0% | 2% | 0% | 0% | |
|
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| Kostenki14 | Coverage | 140 | 113 | 6 | 45 | 52 |
| Derived allele frequency | 0% | 2% | 17% | 0% | 0% | |
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| GoyetQ116-1 | Coverage | 8 | 6 | 0 | 9 | 1 |
| Derived allele frequency | 0% | 0% | n/a | 0% | 0% | |
|
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| Vestonice16 | Coverage | 13 | 18 | 0 | 4 | 5 |
| Derived allele frequency | 0% | 6% | 0% | 0% | ||
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| Malta1 | Coverage | 1 | 0 | 2 | 2 | 2 |
| Derived allele frequency | 0% | 0% | 0% | 0% | ||
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| ElMiron | Coverage | 2 | 10 | 0 | 7 | 5 |
| Derived allele frequency | 0% | 0% | 0% | 0% | ||
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| Villabruna | Coverage | 17 | 52 | 5 | 19 | 10 |
| Derived allele frequency | 0% | 0% | 0% | 0% | 100% | |
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| Bichon | Coverage | 11 | 4 | 25 | 16 | 9 |
| Derived allele frequency | 0% | 0% | 0% | 0% | 33% | |
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| Satsurblia | Coverage | 1 | 2 | 4 | 1 | 4 |
| Derived allele frequency | 0% | 0% | 100% | 0% | 50% | |
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| Kotias | Coverage | 16 | 22 | 13 | 20 | 15 |
| Derived allele frequency | 0% | 0% | 100% | 0% | 0% | |
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| Loschbour | Coverage | 19 | 18 | 20 | 17 | 21 |
| Derived allele frequency | 0% | 0% | 0% | 0% | 100% | |
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| LaBrana1 | Coverage | 8 | 6 | 2 | 11 | 3 |
| Derived allele frequency | 12% | 0% | 0% | 0% | 100% | |
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| Hungarian.KO1 | Coverage | 1 | 2 | 2 | 1 | 2 |
| Derived allele frequency | 0% | 0% | 50% | 0% | 100% | |
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| Motala12 | Coverage | 2 | 0 | 3 | 3 | 1 |
| Derived allele frequency | 0% | 0% | 33% | 100% | ||
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| Karelia | Coverage | 1 | 9 | 4 | 0 | 1 |
| Derived allele frequency | 0% | 67% | 0% | 0% | ||
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| Stuttgart | Coverage | 25 | 21 | 15 | 29 | 21 |
| Derived allele frequency | 0% | 0% | 100% | 0% | 0% | |