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We leveraged our data to examine the change in frequency of SNP alleles known to be related to metabolism, pigmentation, disease susceptibility, immunity, and inflammation in the Levant_ChL population, considered in relation to allele frequencies in the Levant_N, Levant_BA_North, Levant_BA_South, Anatolia_N and Iran_ChL populations and present-day pools of African (AFR), East Asian (EAS), and European (EUR) ancestry in the 1000 Genomes Project Phase 3 dataset39 (Supplementary Data 7).
We highlight three findings of interest. First, an allele (G) at rs12913832 near the OCA2 gene, with a proven association to blue eye color in individuals of European descent40, has an estimated alternative allele frequency of 49% in the Levant_ChL population, suggesting that the blue-eyed phenotype was common in the Levant_ChL.
Second, an allele at rs1426654 in the SLC24A5 gene which is one of the most important determinants of light pigmentation in West Eurasians41 is fixed for the derived allele (A) in the Levant_ChL population suggesting that a light skinned phenotype may have been common in this population, although any inferences about skin pigmentation based on allele frequencies observed at a single site need to be viewed with caution42.
Third, an allele (G) at rs6903823 in the ZKSCAN3 and ZSCAN31 genes which is absent in all early agriculturalists reported to date (Levant_N, Anatolia_N, Iran_N) and that has been argued to have been under positive selection by Mathieson et al.31, occurs with an estimated frequency of 20% in the Levant_ChL, 17% in the Levant_BA_South, and 15% in the Iran_ChL populations, while it is absent in all other populations. This suggests that the allele was rising in frequency in Chalcolithic and Bronze Age Near Eastern populations at the same time as it was rising in frequency in Europe.
We highlight three findings of interest. First, an allele (G) at rs12913832 near the OCA2 gene, with a proven association to blue eye color in individuals of European descent40, has an estimated alternative allele frequency of 49% in the Levant_ChL population, suggesting that the blue-eyed phenotype was common in the Levant_ChL.
Second, an allele at rs1426654 in the SLC24A5 gene which is one of the most important determinants of light pigmentation in West Eurasians41 is fixed for the derived allele (A) in the Levant_ChL population suggesting that a light skinned phenotype may have been common in this population, although any inferences about skin pigmentation based on allele frequencies observed at a single site need to be viewed with caution42.
Third, an allele (G) at rs6903823 in the ZKSCAN3 and ZSCAN31 genes which is absent in all early agriculturalists reported to date (Levant_N, Anatolia_N, Iran_N) and that has been argued to have been under positive selection by Mathieson et al.31, occurs with an estimated frequency of 20% in the Levant_ChL, 17% in the Levant_BA_South, and 15% in the Iran_ChL populations, while it is absent in all other populations. This suggests that the allele was rising in frequency in Chalcolithic and Bronze Age Near Eastern populations at the same time as it was rising in frequency in Europe.