Selection for and against pigmentation alleles in South Asia

Deepika Padukone

Recently some British friends were asking about what we knew about South Asian historical genetics now. I explained that it does look like there was some migration in from the Central Asian steppe and West Asia into South Asia during the Holocene. To which one friend responded, “that’s obvious though, many Indians look like brown white people.” Setting aside the semantic paradox (if you are brown, you are literally not white), it is clear what he is getting at: due to shared ancestry the facial structure of many South Asians is not that different from West Eurasians.

The Bollywood actress Deepika Padukone is an example of someone who is rather brown-skinned (naturally), but whose facial features are such that if she went with 100% skin-bleaching she would pass as white without too much trouble. For the purposes of this post, I Googled Indian albino…and came up with this family. You can make your own judgments. I don’t know what to think of that!

The reason for this post is a newly accepted paper, Ancestry-specific analyses reveal differential demographic histories and opposite selective pressures in modern South Asian populations:

Genetic variation in contemporary South Asian populations follows a northwest to southeast decreasing cline of shared West Eurasian ancestry. A growing body of ancient DNA evidence is being used to build increasingly more realistic models of demographic changes in the last few thousand years. Through high quality modern genomes, these models can be tested for gene and genome level deviations. Using local ancestry deconvolution and masking, we reconstructed population-specific surrogates of the two main ancestral components for more than 500 samples from 25 South Asian populations, and showed our approach to be robust via coalescent simulations.

Our f3 and f4 statistics based estimates reveal that the reconstructed haplotypes are good proxies for the source populations that admixed in the area and point to complex inter-population relationships within the West Eurasian component, compatible with multiple waves of arrival, as opposed to a simpler one wave scenario. Our approach also provides reliable local haplotypes for future downstream analyses. As one such example, the local ancestry deconvolution in South Asians reveals opposite selective pressures on two pigmentation genes (SLC45A2 and SLC24A5) that are common or fixed in West Eurasians, suggesting post-admixture purifying and positive selection signals, respectively.

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