SLC24A5 has probably been under selection in India

Citation: Mallick, Chandana Basu, et al. "The Light Skin Allele of SLC24A5 in South Asians and Europeans Shares Identity by Descent." PLoS genetics 9.11 (2013): e1003912.
Citation: Mallick, Chandana Basu, et al. “The Light Skin Allele of SLC24A5 in South Asians and Europeans Shares Identity by Descent.” PLoS genetics 9.11 (2013): e1003912.

Greg Cochran has a few posts up on the phylogeography of SLC24A5. A quick refresher: this gene has been under very strong selection across Western Eurasia, and seems to correlate with lighter skin. One of Cochran’s points is that though it is fixed (100%) for the new variant in Europe, it persists at very high frequencies in the Middle East. Much of the sub-100% value in the Middle East can probably be attributed to recent Sub-Saharan African admixture. A paper from last fall, Molecular Phylogeography of a Human Autosomal Skin Color Locus Under Natural Selection, has convinced me that the derived variant so common across the world today probably spread from the Middle East least than 10,000 years ago. In any case, Cochran asks:

As for those who assume that sexual selection must be driving that increase – show me the time machine. I don’t know if there was any such preference over the past three thousand years in Ethiopia and neither do you. This is used as an excuse to avoid looking at the biochemical details and trying to find out what’s actually happening. If I hear it again, I may have to call the elephants.

Next, someone should do the same for the Deccan plateau, which ought to be easy.

Prompted by another paper I had stumbled upon data to answer this question a few months back. The results below are from Polymorphisms of four pigmentation genes (SLC45A2, SLC24A5, MC1R and TYRP1) among eleven endogamous populations of India (except for the HapMap samples).

Population State Linguistic Status SLC24A5 N
Konkanastha Brahmin Maharashtra Indo-European Caste 0.9789 71
Gujarati Gujarat Indo-European Diverse 0.955 100
Kanyakubja Brahmin Madhya Pradesh Indo-European Caste 0.8846 78
Sakaldwipi Brahmin Jharkhand Indo-European Caste 0.7692 65
Iyengar Brahmin Tamil Nadu Dravidian Caste 0.7463 66
Mahadev Maharashtra Indo-European Tribe 0.7231 65
Balmiki Punjab Indo-European Caste 0.6694 62
Kurumans Tamil Nadu Dravidian Tribe 0.4104 67
Gond Madhya Pradesh Dravidian Tribe 0.2333 75
Riang Tripura Tibeto-Burman Tribe 0.1119 67
Munda Jharkhand Austro-Asiatic Tribe 0.0956 68
Tripuri Tripura Tibeto-Burman Tribe 0.0923 65

If you look at the latest research it seems pretty obvious that the proportion of derived SLC24A5 in all the italicized populations is higher than their “Ancestral North Indian,” the West Eurasian element which arrived in the last 10,000 and almost certainly brought the derived variant. On the North Indian plain in Uttar Pradesh the ANI proportion for high castes like Brahmins is 60%, while for Dalit low castes like Chamars it is 40%.

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