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

Abstract

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.

Figure 1

Phylogenetic relationships and nomenclature of Y-chromosome binary HGs observed in India, Pakistan, and East Asia. The 69 informative binary markers that were haplotyped are indicated in plain font. The markers in italics are shown to provide phylogenetic context. The following polymorphisms were typed but not observed in Indian populations: M8, M25, M38, M39, M56, M67, M70, M88, M97, M147, M170, M204, M210, M217, M282, M297, and M319.

Figure 2

Revised phylogenetic relationships and nomenclature for Y-chromosome HG J2

Figure 3

Spatial frequency distribution of Eurasian HG J2a-M410–related lineages. Plus signs (+) indicate geographic locations of population samples listed in table 4.

Figure 4

Spatial frequency and mean microsatellite variance distributions of Y-chromosome HGs in present-day India and Pakistan

Figure 4

Spatial frequency and mean microsatellite variance distributions of Y-chromosome HGs in present-day India and Pakistan

Figure 5

Median-joining network of Y-microsatellite haplotypes with HG O2a-M95 HG among Austro-Asiatic and Dravidian (gray nodes) and Tibto-Burman (black nodes) populations.

Figure 6

Plot of R1a1-M17–derived chromosomes against values for the first two principal components for 10 microsatellite loci. Indian population codes are as described in table 1. The Central Asian data include 10 chromosomes described by Underhill et al. (2000). The Turkish data are from Cinnioğlu et al. (2004). The Greek data (R.K., unpublished data) include 19 chromosomes.