Elamo-Dravidian and the Koraga

Novel 4,400-year-old ancestral component in a tribe speaking a Dravidian language:

Research has shown that the present-day population on the Indian subcontinent derives its ancestry from at least three components identified with pre-Indo-Iranian agriculturalists once inhabiting the Iranian plateau, pastoralists originating from the Pontic-Caspian steppe and ancient hunter-gatherer related to the Andamanese Islanders. The present-day Indian gene pool represents a gradient of mixtures from these three sources. However, with more sequences of ancient and modern genomes and fine structure analyses, we can expect a more complex picture of ancestry to emerge. In this study, we focus on Dravidian linguistic groups to propose a fourth putative source which may have branched out from the basal Middle Eastern component that gave rise to the Iranian plateau farmer related ancestry. The Elamo-Dravidian theory and the linguistic phylogeny of the Dravidian family tree provide chronological fits for the genetic findings presented here. Our findings show a correlation between the linguistic and genetic lineages in language communities speaking Dravidian languages when they are modelled together. We suggest that this source, which we shall call ‘Proto-Dravidian’ ancestry, emerged around the dawn of the Indus Valley civilisation. This ancestry is distinct from all other sources described so far, and its plausible origin not later than 4,400 years ago on the region between the Iranian plateau and the Indus valley supports a Dravidian heartland before the arrival of Indo-European languages on the Indian subcontinent. Admixture analysis shows that this Proto-Dravidian ancestry is still carried by most modern inhabitants of the Indian subcontinent other than the tribal populations. This momentous finding underscores the importance of population-specific fine structure studies. We also recommend informed sampling strategies for biobanks and to avoid oversimplification of ancestral reconstruction. Achieving this requires interdisciplinary collaboration.

Not definitive, but I think this shows the value of greater sampling in Indian subcontinental populations.

Bengalis are all basically very similar (except for Brahmins)

The new paper, 50,000 years of Evolutionary History of India: Insights from ~2,700 Whole Genome Sequences, is very good. It also answers a question that comes up sometimes: how different are West Bengalis from Bangladeshis? We haven’t had a apples to apples comparison until this paper that’s easy to understand.

There are figures in the paper that make the overlap clearer. The main difference is more variance in the West Bengalis, and a greater East Asian shift among Bangladeshis. But the latter is clearly just geography; those whose ancestry is from the east of the Padma (like me) always have more East Asian ancestry than those from the west, while those in the north also seem to have more.

The variance in West Bengal is probably driven by caste. You can see Brahmins, and probably what are Bengali-speaking scheduled castes and tribes. In the Bangladesh Muslim population everyone eventually intermarried.

The Assamese are even more East Asian shifted than the Bangaldeshis. As I said in a previous post, these Indo-Aryan groups look like they mixed with a Khasi-like population at some point.

Finally, the West Bengal population had admixture from an East Asian group between 500 and 600 AD. This is the same date as for the Bangladeshis, meaning they are both the same population with the same origin. The major difference seems likely to be the proportion of East Asian ancestry and lack of caste structure within eastern Bengal.

Sri Lanka Genetics

Reconstructing the population history of Sinhalese, the major ethnic group in Śrī Laṅkā:

Interestingly, we found an unexpected excess of smaller chunks sharing between Marāṭhā and Sinhala (>16%) than the Marāṭhā and STU, thus supporting the linguistic hypothesis of Geiger, Turner and van Driem. To confirm the excess sharing, we looked for the population which was sharing maximum IBD with Sinhala and STU.

Looks like confirmation of Sinhala western Indian origins rather than eastern Indian origins.

Population structure in South Asian – Genomes Asian 1K paper

The full version of this paper is out, South Asian medical cohorts reveal strong founder effects and high rates of homozygosity. It’s not the best for understanding population structure because they focus on within South Asia variation, but it does seem to confirm that among Bengalis there is a cline from west to east, irrespective of religion (see the discussion where they note that Muslims in the west cluster with westerners). I found a PCA in the supplements where I added some explanatory notes. It’s really hard to parse their figures because they really didn’t care, and the Genomes Asia Consortium doesn’t release their data… (their browser sucks)

Perhaps the Indus Valley Civilization did descend from Zagrosian farmers?

On the limits of fitting complex models of population history to f-statistics:

These results show that at least with regard to the AG analysis, a key historical conclusion of the study (that the predominant genetic component in the Indus Periphery lineage diverged from the Iranian clade prior to the date of the Ganj Dareh Neolithic group at ca. 10 kya and thus prior to the arrival of West Asian crops and Anatolian genetics in Iran) depends on the parsimony assumption, but the
preference for three admixture events instead of four is hard to justify based on archaeological or other arguments.

Why did the Shinde et al. 2019 AG analysis find support for the IP Iranian-related lineage being the first to split, while our findGraphs analysis did not? The Shinde et al. 2019 study sought to carry out a systematic exploration of the AG space in the same spirit as findGraphs—one of only a few papers in the literature where there has been an attempt to do so—and thus this qualitative difference in findings is notable. We hypothesize that the inconsistency reflects the fact that the deeply-diverging WSHG-related ancestry (Narasimhan et al. 2019) present in the IP genetic grouping at a level of ca. 10% was not taken into account explicitly neither in the AG analysis nor in the admixture-corrected f4-symmetry tests also reported in Shinde et al. (2019).

Cousin marriage in Bangladesh

This piece arguing for the end to cousin marriage in the UK in The Times (driven by Pakistanis) took me to a paper in PLOS One, Genetic and reproductive consequences of consanguineous marriage in Bangladesh:

The mean prevalence of CM in our studied population was 6.64%. Gross fertility was higher among CM families, as compared to the non-CM families (p < 0.05). The rate of under-5 child (U5) mortality was significantly higher among CM families (16.6%) in comparison with the non-CM families (5.8%) (p < 0.01). We observed a persuasive rise of abortion/miscarriage and U5 mortality rates with the increasing level of inbreeding. The value of lethal equivalents per gamete found elevated for autosomal inheritances as compared to sex-linked inheritance. CM was associated with the incidence of several single-gene and multifactorial diseases, and congenital malformations, including bronchial asthma, hearing defect, heart diseases, sickle cell anemia (p < 0.05). The general attitude and perception toward CM were rather indifferent, and very few people were concerned about its genetic burden.

A rate around 5% is in line with my intuition and what I’ve seen elsewhere, though there is wide variance by locality. The best thing about the paper is the chart above, the offspring of first cousin marriage have mortality rates 3 times greater than non-cousin marriages. There are other numbers relating to disease, etc. The paper is good because it’s from a developing country without world-class healthcare (though no longer a total basketcase) so you can see disease risk plainly.

More generally in relation to “cousin marriage”

– I have seen “outbred” Pakistani genomes that look like the product of cousin marriage due to the practice’s frequently earlier on in the pedigree

– This is comparable to some Indian caste groups that practice exogamy (North Indian) on the jati level. The jati has been endogamous so long that everyone has become a second cousin…

Merry Christmas!

I got a sample from someone where one parent was a West Bengal Sadgop, and another parent a Baidya with family origins in East Bengal. One hypothesis that I’ve see is that Baidya are basically Brahmins who lost their caste. Genetically this does not seem to be the case. Bengali Brahmins shift considerably toward the steppe samples compared to average Bangladeshis, and this individual does not. Rather, their uniqueness is that they have very little East Asian ancestry compared to the median. This is typical of non-Bramin West Bengalis. It is plausible to me that this individual’s Baidya parent, from East Bengal (Bangal), had more East Asian ancestry than their West Bengali (Ghoti) parent, so you see an average.

Though there are some exceptions, it seems that the non-Brahmnin bhadralok castes did undergo ritual uplift from that of conventional peasant cultivators at some point in Bengal. This seems similar with regard to Kayasthas in UP, but not in Maharashtra, where CKPs seem to have an affinity with Brahmins distinct from the Maratha cultivators.

Update: I found a preprint that pretty much answers all the questions re: Bengalis.

Here is a panel with a UMAP representation of genetic distance, and you see West Bengal is adjacent to Bangladesh. But there is a “tail” of individuals that are parallel to South Indians.

This UMAP makes clear Bengali Brahmins are distinct from Kayasthas and Sadgop. These populations seem roughly similar to most Bangladeshis except they are shift over, and I assume this means less East Asian ancestry, as PCA seems to how:

Brown Pundits