A 2015 Nicole Murray et al., study has intriguing findings that two genes not found in Africa or the Middle East may have been responsible for lighter skin. These genetic adaptations for lighter skin were found to have occurred in East Asia. One of the two genes (rs1800414 G allele) is found among the Japanese population with the highest frequencies (See excerpt immediately below, and open access source article also linked below):
The derived rs1800414 G allele has a broad distribution in East Asia, with the highest frequencies observed in the Japanese population (79%) and several populations from China (Dai, Miaozu, Han, Hezhen, Tujia and Xibo, with frequencies between 65 and 50%). In contrast, the distribution of the derived rs74653330 A allele is more restricted, with the highest frequencies found in Altaic speaking populations from northern East Asia and Mongolia
Distribution of two OCA2 polymorphisms associated with pigmentation in East-Asian populations 2015 Murray, Nicole, et al., Human Genome Variation volume2, Article number: 15058 (2015) Open access
Fig 1 Distribution of allele frequencies for SNPs rs1800414 (blue) and rs74653330 (orange) in East-Asian populations: (1) Dia; (2) Daur; (3) Han; (4) Hezhen; (5) Japanese; (6) Lahu; (7) Miaozu; (8) Mongola; (9) Naxi; (10) Oroqen; (11) She; (12) Tu; (13) Tujia; (14) Uyghur; (15) Xibo; (16) Yakut; (17) Yizu; and (18) Cambodia.
Abstract
Two OCA2 polymorphisms (rs1800414 and rs74653330) have been associated with pigmentation in East Asians. We explored the distribution of these markers in a panel of samples from populations around the world. The derived allele of rs1800414 has high frequencies in a broad East-Asian region, whereas the derived allele of rs74653330 is primarily restricted to northern East Asia. Our data suggest that these polymorphisms may have been selected independently in different regions of East Asia.
Although pigmentation varies globally, it has been more thoroughly studied and is therefore better understood in European populations. This has led to a research gap, especially in East-Asian populations. The OCA2 gene, which is thought to be responsible for maintaining pH levels within melanosomes,1 has been shown to be under positive selection in both European and East-Asian populations.2,3 However, the variants and haplotypes favored by selection are different in each population.2,4,5,6 For example, a variant located within the HERC2 gene is known to affect the expression of the nearby OCA2 gene, and it is strongly associated with blue eyes in European populations.7,8,9 The HERC2 rs12913832 allele associated with blue eyes has a high frequency in Europe but is not present in East-Asian populations.7,8,9
In addition, two non-synonymous polymorphisms, rs1800414 and rs74653330, have been associated with pigmentation in East Asians5,10,11 and are not found at high frequencies in any population outside of East Asia.12 It has been suggested that the phenotype of lighter skin is a result of convergent evolution in Europe and East Asia.2,6,13
Available population data indicate that the rs1800414 and rs74653330 polymorphisms show a distinct geographical distribution. The highest frequencies of the derived rs1800414 G allele are found in Japan, China and Korea, whereas the derived rs74653330 A allele has the highest frequencies in northern East Asia, including Mongolia.
… both polymorphisms are primarily restricted to East-Asian populations. The derived rs1800414 G allele has a broad distribution in East Asia, with the highest frequencies observed in the Japanese population (79%) and several populations from China (Dai, Miaozu, Han, Hezhen, Tujia and Xibo, with frequencies between 65 and 50%). In contrast, the distribution of the derived rs74653330 A allele is more restricted, with the highest frequencies found in Altaic speaking populations from northern East Asia and Mongolia, such as the Yakut from Siberia (36%), the Daur (33%), the Oroqen (28%), the Hezhen (22%) and the Mongola (20%). Figure 1 shows a map of East Asia with the frequencies of both polymorphisms. The derived rs1800414 G and rs74653330 A alleles are not present in any of the samples from Africa, the Middle East or Oceania. In the Americas, the rs1800414 G allele is also absent, and one Maya individual is heterozygous for rs74653330. Both derived alleles are present at very low frequencies in Central–South Asia (rs1800414 G: 4.4%; rs74653330 A: 2.1%) and Europe (rs1800414 G: 0.3%; rs74653330 A: 1%). Within Central–South Asia, the derived alleles are primarily present in the Hazara (Pakistan) and Uygur (China). Within Europe, the derived alleles are observed only in Russia. The presence of the two derived alleles in some of the populations from Central–South Asia and Europe seems to be the consequence of gene flow from East-Asian groups.
It is interesting to note that the frequency distribution of the rs74653330 A allele reflects the present genetic structure at a genome-wide level in East Asia. … There is a clear geographic pattern with the northern populations (Yakut, Oroqen, Mongola, Daur and Hezhen) present on the left side of the plot. As described above, it is precisely in these populations in which the highest frequencies of the derived rs74653330 A allele are observed.
***
Note1: The earlier 2012 study (Michael P. Donnelly et al., A global view of the OCA2-HERC2 region and pigmentation) found that” a missense mutation (rs1800414) is a candidate for light skin pigmentation in East Asia” (Yuasa et al. in Biochem Genet 45:535–542, 2007) and that the derived allele of rs1800414 is an East Asian skin pigmentation allele.. .the article also stated
We have shown that the C allele of the missense SNP rs1800414 is found almost exclusively in East Asia (Fig. 4). Within East Asia there is a general cline in the frequency of the C allele with the lowest frequencies in Western China, midrange frequencies in Southeast Asia,
and high frequencies in Eastern East Asia. …
In East Asia, we show that the C allele of the missense
SNP rs1800414 is also under selection (Fig. 10). Again this
result is not completely unexpected since this allele has
been associated with lighter skin pigmentation in East
Asians, and variants affecting skin pigmentation have
previously been shown to be targets of selection …
We have also shown that the C allele of rs1800414 is both restricted to East Asia and under selection in that region. This research provides
further evidence for lighter pigmentation evolving by means of selection at least partly independently in Europeans and East Asians but at some genes in common
Heritage of Japan 