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Reference: http://hpgl.stanford.edu/publications/AJHG_2006_v78_p202-221.pdf

Polarity and Temporality of High-Resolution Y-Chromosome Distributions in India Identify Both Indigenous and Exogenous Expansions and Reveal Minor Genetic Influence of Central Asian Pastoralists

by Sanghamitra Sengupta from Human Genetics Unit, Indian Statistical Institute, Kolkata, India;

Although considerable cultural impact on social hierarchy and language in South Asia is attributable to the arrival of nomadic Central Asian pastoralists, genetic data (mitochondrial and Y chromosomal) have yielded dramatically conflicting inferences on the genetic origins of tribes and castes of South Asia. We sought to resolve this conflict, using high-resolution data on 69 informative Y-chromosome binary markers and 10 microsatellite markers from a large set of geographically, socially, and linguistically representative ethnic groups of South Asia. We found that the influence of Central Asia on the pre-existing gene pool was minor. The ages of accumulated microsatellite variation in the majority of Indian haplogroups exceed 10,000–15,000 years, which attests to the antiquity of regional differentiation. Therefore, our data do not support models that invoke a pronounced recent genetic input from Central Asia to explain the observed genetic variation in South Asia. R1a1 and R2 haplogroups indicate demographic complexity that is inconsistent with a recent single history. Associated microsatellite analyses of the high-frequency R1a1 haplogroup chromosomes indicate independent recent histories of the Indus Valley and the peninsular Indian region. Our data are also more consistent with a peninsular origin of Dravidian speakers than a source with proximity to the Indus and with significant genetic input resulting from demic diffusion associated with agriculture. Our results underscore the importance of marker ascertainment for distinguishing phylogenetic terminal branches from basal nodes when attributing ancestral composition and temporality to either indigenous or exogenous sources. Our reappraisal indicates that pre-Holocene and Holocene-era—not Indo-European—expansions have shaped the distinctive South Asian Y-chromosome landscape.

The Phylogeny of South Asian Y-Chromosome Binary HGs

Eight HGs display frequencies 15% within India and account for 95.8% of the samples. They are, in descending frequency order, HGs H and its subclades H1*, H1c, H1a, and H2 (26.4%); R1a1-M17 (15.8%); O2a-M95 (14.6%); R2-M124 (9.3%); J2- M172 (9.1%); O3e-M134 (8.0%); L1-M76 (6.3%); and F*-M89 (5.2%). In Pakistan, nine HGs exceed 5% frequency and account for 83.6% of the samples. They include HGs R1a1-M17 (24.4%), L*-M20 (13.1%), J2- M172 (11.9%), R2-M124 (7.4%), R1b-P25 (7.4%), GM201 (6.3%), C3-M217 (6.8%), H-M69* (6.3%), and L1-M76 (5.1%). In the East Asian samples studied, the following seven HGs exceed 5% frequency and account for 75.4% of the total: O3e-M134 (15.4%), C3-M217 (13.1%), N3-TAT (12.0%), O2a-M95 (10.9%), O3- M122(xO3e) (11%), N-M231(xN3) (6.3%), and R1b2- M73 (6.3%).

The widespread geographic distribution of HG R1a1-M17 across Eurasia and the current absence of informative subdivisions defined by binary markers leave uncertain the geographic origin of HG R1a1-M17. However, the contour map of R1a1-M17 variance shows the highest variance in the northwestern region of India

Range expansions of Ice Age hunter-gatherers into peninsular India from other source regions, not necessarily far from the mountains extending from Baluchistan to Hindu Kush, on both sides of which the R1a frequency is currently the highest— could have also contributed significantly to the observed distributions, both in India and in Central Asia (Kennedy 2000). In other words, there is no evidence whatsoever to conclude that Central Asia has been necessarily the recent donor and not the receptor of the R1a lineages.