Higher caste, lighter skin

The Journal of Investigative Dermatology has a new paper on the pigmentation genetics of populations from the Middle Gangetic Plain in northern India. Its main finding is that upper caste Indians are generally lighter skinned than other Indians, particularly those from tribal groups.

This shouldn't be surprising to most people, but now we have a clearer idea of the genetics behind this phenomenon, including a new marker (SNP rs2470102) that helps to better explain skin pigmentation differences within South Asia.

Those of you wondering how the ancient samples likely to be relevant to the population history of South Asia stack up in terms of the alleles at rs2470102, check out the spreadsheet HERE. See anything interesting? I reckon I can; in terms of this one SNP, pre-Neolithic Western Europeans were potentially darker skinned than most modern-day Indians, because they're all homozygous for the G allele.

Our understanding of genetics of skin pigmentation has been largely skewed towards populations of European ancestry imparting much less attention to South Asian populations, who behold huge pigmentation diversity. Here, we investigate the skin pigmentation variation in a cohort of 1167 individuals in Middle Gangetic Plain of Indian subcontinent. Our data confirms the association of rs1426654 with skin pigmentation among South Asians, consistent with previous studies and also reveals association for rs2470102 SNP. Our haplotype analyses further help us to delineate the haplotype distribution across the social categories and skin color. Taken together, our findings suggest that the social structure defined by the caste system in India has a profound influence on the skin pigmentation patterns of the subcontinent. In particular, social category and associated SNPs explain about 32% and 6.4%, respectively, of the total phenotypic variance. Phylogeography of the associated SNPs studied across 52 diverse populations of the Indian subcontinent, reveals wide presence of the derived alleles, albeit their frequencies vary across populations. Our results show that both of the polymorphisms (rs1426654 and rs2470102) play an important role in skin pigmentation diversity of South Asians.

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However, some tribes show exceptionally high frequency of rs1426654-A allele for example Gujjar (Jammu and Kashmir -1) and Meena (Rajasthan -0.91) (Supplementary Table S3 online). These tribes have been also known to be fair skinned (Joshua project, https://joshuaproject.net/). Interestingly, Brahmins belonging to higher castes in the social hierarchy of the caste system (Supplementary text online), irrespective of their geographical locations (North- Kashmiri Pandits, Pandits of Haryana, Brahmins of Uttar UPradesh), Havik (Karnataka, South) show similar frequencies of rs1426654-A variant (0.83–1) (Supplementary Table S3 online).

Mishra, Anshuman et al., Genotype-phenotype study of Middle Gangetic Plain in India reveals association of rs2470102 with skin pigmentation, Journal of Investigative Dermatology, article in press, DOI: http://dx.doi.org/10.1016/j.jid.2016.10.043