Tuesday, October 18, 2016

The Genetics Of India From ASHG 2016

Archaeological excavations revealed artefacts used by homo Erectus as long as 500-200ky. The moistening at the end of the last glacial period brought expanded subsistence; drying then spread agriculture from 8-5kya, marking some of the earliest migrations and expansions. Around 5ky, the Indus Valley civilization began with the much matured Harappan civilization, whose de-urbanization led to the initiation of the Vedic period. Following this, displacements followed as foreign rulers established dominance in the Indian subcontinent: from Greeks and Scythians, to the first seeds of Muslim invasions, followed by the Mughal Empire. In this phase, India had diverse rulers (including Afghans, Turks, and Mongols). 
The migrations led to widespread admixture of the Indian population, influencing language, culture, caste endogamy, metallurgical technologies, and more, resulting in a complex and differentiated structure. We set out to explore modern genetics correlating with migration routes into the subcontinent, and to study genomic variation in 48,570 SNPs genotyped in 1484 individuals, across 104 population groups. We propose, COGG (Correlation Optimization of Genetics and Geodemographics), a novel optimization method to model genetic relationships with social factors such as castes, languages, occupation, and maximize the correlation with geography. We calculated the shared ancestry between different caste groups in the subcontinent with other reference populations from Eurasia, using a novel approach. We tested different migration theories into the subcontinent using a Linear Discriminant Analysis of redescription clusters and study recombination events shaping the gene pool. 
Our results demonstrate that COGG gives us significantly higher correlations, with p-values lower than 10-8. Identification of significant components among caste, language and genetics simplifies the complex structure. We identify varnas (Brahmins and Kshatriyas) to be closely related to reference Eurasian populations, whereas tribal groups show no shared ancestry with them and conclude that they resided in India before migration from Eurasia happened. We identify probable migration routes from Mongolia through Central Asia, and another via Anatolia into the subcontinent. Tibeto-Burman speaking populations share some ancestry with populations from East Asia; on the other hand, Austro-Asiatic speakers did not share ancestry with other Mon-Khmer language speaking populations.
A. Bose; D.E. Platt; L. Parida; P. Paschou; P. Drineas, "Genetic variation reveals migrations into the Indian subcontinent and its influence on the Indian society." (October 2016).

Much of this clarifies what has already been strongly suspected and nothing her could overcome the impact of whatever ancient DNA results we expect to see from South Asia in the near future. But, the lack of recent Eurasian origins in South Asian tribal populations, while always believed to be indigenous according to conventional wisdoms, had shown early but not definitive genetic indicators of more recent origins followed by regression to a less advanced subsistence strategy. So, that result is notable.

Davidski at Eurogenes has a low opinion of the paper and in particular its Anatolian origin hypothesis, but I'm content to wait and see in this case.


capra internetensis said...

Intriguing that they didn't find a relationship among Austro-Asiatic speakers, even though the Indian ones definitely have an East Asian autosomal component, and they all certainly share O2a1-M95 as the dominant paternal lineage, most likely a relatively young subclade too.

Different source populations? Or a weakness in the methodology?

terryt said...

Capra, I found that interesting as well. It is just yet further proof that the expansion of a particular haploid DNA does not necessarily coincide closely with aDNA expansion. This is especially so in the case of male lines. Once the front of a moving male line has offspring from resident females their aDNA is reduced by half in the descendants. And a further half as the front continues.

But what I found most interesting is that Mesolithic South Asians are at opposite ends of a genetic cline from the Mesolithic/Neolithic Iranians. That is a pretty convincing argument against India having been a main route east from Africa. Mesolithic South Asians are indeed closest to Papuans but It looks as though the Mesolithic South Asians derive from some Papuan-like Population rather than the other way round.

I presume you've seen the first diagram here:


CoCo PuFf said...


We do not find an origin in the Anatolias. What we suspect though is that the fertile crescent might have played a role in arrival of agriculture (Laziridis et al.) in India. The paths we find is through "Silk Route", that is from Mongolia - North China/Uygurs - Central Asia - Iran - Afghanistan to Indian subcontinent. That is also to influence the genetics of the Indo European forward caste people. So, to say an Anatolian origin is probably not the correct phrase.

What we were more interested in is to comment on how genetically stratified India is across caste and languages and we support the indigenous origin hypothesis. Still working on the paper, looking forward to at least get it to preprint soon, for detailed discussion. Thank you, it's a great deal to see discussions on it, already.

capra internetensis said...

Thanks for clarifying CoCoPuFf, looking forward to the paper when it comes out