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Runs of homozygosity in North Indian Punjabi Brahmins, non-Brahmin Tamils, and Northwest Europeans (left to right)

Runs of homozygosity in North Indian Punjabi Brahmins, non-Brahmin Tamils, and Northwest Europeans (left to right)

The above figure is from Population and genomic lessons from genetic analysis of two Indian populations. What you see here is that two Indian Hindu populations from the north and south of the subcontinent have clearly elevated stretches of genomic homozygosity in comparison to the classic Northwest European population of whites from Utah. This is interesting because the social practices of the two groups here are quite different. Some South Indian Hindus practice consanguineous marriage; e.g., first cousins or uncle-niece. This is evident in some individuals in the data set. But North Indian Hindus traditionally enforce significant exogamy among relations via the gotra system and seeking partners outside natal villages. And yet the genomic evidence indicates a relatively small effective population. That’s because though North Indian Hindus practice exogamy on the scale of families, they nevertheless usually marry within a local caste. The effect of this genomically was one of the less trumpeted findings of the 2009 paper Reconstructing Indian Population History. India may have a very large population, but the genealogical history of many of its people is sharply delimited. This recent paper uses exomes, and I think clinches the finding.

Second, two data sets that I stumbled upon in case you don’t know which are in VCF and phased Beagle format (though the newest release of Beagle uses VCF anyhow):

Singapore Sequencing Malay, 100 Malays.

Singapore Sequencing Indian. 36 individuals. Mostly South Indian Tamil.

• Category: Science • Tags: Inbreeding 
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  1. A question. All I know is ROH is associated with parental relatedness. What does the various parts of the box and whiskers in the above plot signify? Larger box size means more intermarriage? intermarriage among first cousins?

  2. The significant thing for me was the following from the abstract of the paper, “tagSNPs show a high level of portability between the two Indian populations, in contrast to the common belief that North and South Indian populations are genetically very different”. This indicates that variation due to geography and caste in India is clinal rather than discontinuous. The fact that “there is limited genetic marker portability from available genetic resources such as HapMap or the 1,000 Genomes Project to Indian populations” indicates that Indians are quite distinct from Europeans, Middle Easterners and East Asians and much more like each other.

  3. #1, wide distribution of ROH

    #2, geography is pretty bad predicting gen var in south asia. caste is a huge confound. much of what you say is true. OTOH, Fst across castes in s asia is HUGE in comparison to europe (last i checked by a factor of . so let’s not overdue how ‘natural’ a cluster s a3-5 vs. europeans) e asians are.

  4. What I would be very interested in would be comparisons of the ROH of the comparatively cosmipolitan coastal areas with the more clannish, mountainous interior.

    Same thing with China. I think that the regions of China wherein there is a similar pattern of elevated ROH is likely to be concentrated in the South and the interior, while the North East and the coast is likely to be (comparatively) more outbred, though probably still a little less so than the CEU.

    I suspect that looking at “India” and “China” is a bit like looking at “Europe”, even if we in India can further subdivide into Caste. We probably overlook a lot of substructure.

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