SNPs within and between populations

A recent paper informs us that we have now found a small number of SNPs that explain skin color in European samples.

In the International Visible Trait Genetics (VisiGen) Consortium, we investigated the genetics of human skin color by combining a series of genome-wide association studies (GWAS) in a total of 17,262 Europeans with functional follow-up of discovered loci. Our GWAS provide the first genome-wide significant evidence for chromosome 20q11.22 harboring the ASIP gene being explicitly associated with skin color in Europeans. In addition, genomic loci at 5p13.2 (SLC45A2), 6p25.3 (IRF4), 15q13.1 (HERC2/OCA2), and 16q24.3 (MC1R) were confirmed to be involved in skin coloration in Europeans. In follow-up gene expression and regulation studies of 22 genes in 20q11.22, we highlighted two novel genes EIF2S2 and GSS, serving as competing functional candidates in this region and providing future research lines. A genetically inferred skin color score obtained from the 9 top-associated SNPs from 9 genes in 940 worldwide samples (HGDP-CEPH) showed a clear gradual pattern in Western Eurasians similar to the distribution of physical skin color, suggesting the used 9 SNPs as suitable markers for DNA prediction of skin color in Europeans and neighboring populations, relevant in future forensic and anthropological investigations.

However:

All 9 SNPs listed in Table 1 were used to construct a genetically inferred skin color score in 940 samples from 54 worldwide populations (HGDP-CEPH samples), which showed a spatial distribution with a clear gradual increase in skin darkness from Northern Europe to Southern Europe to Northern Africa, the Middle East and Western Asia (Figure S2); in agreement with the known distribution of skin color across these geographic regions. Outside of these geographic regions, the inferred skin color score appeared rather similar (i.e., failing to discriminate), despite the known phenotypic skin color difference between generally lighter Asians/Native Americans and darker Africans. This demonstrates that although these 9 SNPs can explain skin color variation among Europeans, they cannot explain existing skin color differences between Asians/Native Americans and Africans. Therefore, these differences in skin color variation may partly be due to different DNA variants not identifiable by this European study with restricted genetic origin.

The same general problem may apply to the Piffer results. Perhaps the SNPs found only affect cognitive ability within European samples (or Euroasian, because there is one Chinese replication). This sounds like a case of epistasis, where the other necessary gene(s) for the identified SNPs to have an effect on cognitive ability have substantial frequencies in European populations, but don't exist or are very rare in non-European populations. As far as I know, this is a possible but unlikely scenario. It will perhaps serve as one of the remaining areas where non-hereditarians can point to and say that there is still reasonable doubt. The solution is to perform GWAS on African subjects. Luckily, a large number of such subjects live in or near (relatively) affluent countries in the Americas.