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Indian genomics explained by four-way population structure, not two way population structure
Like to the study:
https://www.ncbi.nlm.nih.gov/pmc/art...60789/#s2title
Summary:
Ever since the proposing of the ANI-ASI model in 2009 by David Reich, most people have assumed that most Indian populations can be modeled as a two way mixture between ANI (a fully West Eurasian component related to Europeans/Middle Easterners/Central Asians), and ASI (a component indigenous to the Indian-subcontinent, which is yet to be fully understood). However, as Reich pointed out this year, even though this model can work well for many Indian groups, upper caste groups tend to be poor fits for this model due to elevated steppe ancestry. Additionally, his study over-looked many tribal ethnic groups in the study, missing an important piece to the genetic story of India.
Instead, Indian populations are better modeled by four ancestral components. ANI, ASI, AAA, and ATB. AAA being a component/cluster that represents the Austro-Asiatic speaking peoples of India. ATB representing a component/cline genetically similar to modern day East Asians. There are populations within India and South Asia that represent nearly unmixed forms of all four components, contrary to popular belief.
The study had a sample size of 367 individuals from 18 mainland and 2 island (Andaman and Nicobar Islands) populations. High-quality genotype data was generated using a DNA micro-array at over 800,000 SNPs.
Key Points
The diverse population of India was overlooked in Reich's 2009 study. Instead of a single ANI-ASI cline forming, geneticists see mainland Indians break up into four distinct genetic clines and clusters. Island populations such as the Andamanese and Nicobar Islanders are not represented by any of the mainlander components, including ASI. They instead belong to a distinct fifth ancestral component that is also ancestral to Oceanic populations, specifically Papuan groups. This contradicts David Reich's popular 2009 statement that the Andamanese are and Nicobar Islanders are "unique in being ASI-related groups without any ANI ancestry."
Additionally, the study was able to provide genetic evidence that India's ethnic groups started practicing endogamy 70 generations ago, especially the Indo-European ethnic groups.
The study found that extant mainland populations:
They also report- admixed widely irrespective of ancestry, although admixtures between populations was not always symmetric.
- this practice was rapidly replaced by endogamy about 70 generations ago, among upper castes and Indo-European speakers predominately.
As for mainland Indian populations:We analyzed high-quality genotype data, generated using a DNA microarray (Methods) at 803,570 autosomal SNPs on 367 individuals drawn from 20 ethnic populations of India (Table 1 and SI Appendix, Fig. S1), to provide evidence that the ancestry of the hunter-gatherers of A&N is distinct from mainland Indian populations, but is coancestral to contemporary Pacific Islanders (PI).
Who are Indians genetically closest to on a global scale?In addition to the ANI and ASI, we identified two ancestral components in mainland India that are major for the AA-speaking tribals and the TB speakers, which we respectively denote as AAA (for “Ancestral Austro-Asiatic”) and ATB (for “Ancestral Tibeto-Burman”).
Further, when comparing Indian populations to the globe, varied affinities were found for different Indian populations. Indians as a whole aren't marginally closer to any single global population. Indians aren't even all necessarily closest to each other, either. Different pockets of Indian ethnic groups are genetically closest to different global populations. For example, ethnic groups who are very high in ANI ancestry, such as the Khatri (97%), are genetically closest to Europeans, Middle Easterners, and Central Asians, other West Eurasians. Populations from the ATB Indian cluster are genetically closest to East Asian populations in Southwestern China. Andamanese and Nicobar Island populations share more common ancestry with Oceanic Pacific Islanders than they do with anyone on India's mainland.
Other Important Things to Know About the Genomics of India
Some degree of early admixture occurred among the ancestral populations. Eventually, gene flow abruptly ended with the introduction of new social values and norms, especially in the regions of ardent Hindu bupta rulers.
Interestingly enough, and contrary to popular belief of this pattern being the other way around, the authors found that:
They also mention that The ANI and the ATB can clearly be rooted to the CS-Asians (such as the Kalash, Burusho, and Pathans) and E-Asians, respectively; they likely entered India through the northwest and northeast corridors, respectively. Ancestral populations seem to have occupied geographically separated habitats. However, there was some degree of early admixture among the ancestral populations as evidenced by extant populations possessing multiancestral components and some geographical displacements as wellThe asymmetry of admixture, with ANI populations providing genomic inputs to tribal populations (AA, Dravidian tribe, and TB) but not vice versa, is consistent with elite dominance and patriarchy. Males from dominant populations, possibly upper castes, with high ANI component, mated outside of their caste, but their offspring were not allowed to be inducted into the caste. This phenomenon has been previously observed as asymmetry in homogeneity of mtDNA and heterogeneity of Y-chromosomal haplotypes in tribal populations of India (6) as well as the African Americans in United States (34). In this study, we noted that, although there are subtle sex-specific differences in admixture proportions, there are no major differences in inferences about population relationships and peopling whether X-chromosomal or autosomal data are used. We have also found our inferences to become more robust when our data are jointly analyzed with HGDP data.
How did Reich and this study come to their very different conclusions?
We surmise that the number of ancestral components in the populations of India may have been underestimated by Reich et al. (9) because of (i) lack of inclusion of tribal populations, who are considered by anthropologists to be the autochthones of India, and (ii) inadequate representation of the geocultural diversity of India in the set of sampled populations, and (iii) selective removal of some populations based on deviance of their genomic profiles. Our study has corrected this deficiency and has provided a more robust explanation of the genomic diversities and affinities among extant populations of the Indian subcontinent, elucidating in finer detail the peopling of the region.
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Originally Posted by Mortimer
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