1. Michael Bamshad1,10,12,
2. Toomas Kivisild2,
3. W. Scott Watkins3,
4. Mary E. Dixon3,
5. Chris E. Ricker3,
6. Baskara B. Rao4,
7. J. Mastan Naidu4,
8. B.V. Ravi Prasad4,5,
9. P. Govinda Reddy6,
10. Arani Rasanayagam7,
11. Surinder S. Papiha8,
12. Richard Villems2,
13. Alan J. Redd7,
14. Michael F. Hammer7,
15. Son V. Nguyen9,
16. Marion L. Carroll9,
17. Mark A. Batzer9,11, and
18. Lynn B. Jorde3

1. ¹Department of Pediatrics, University of Utah, Salt Lake City, Utah 84112, USA;²Institute of Molecular and Cell Biology, Tartu University and Estonian Biocentre, Tartu 51010, Estonia;³Department of Human Genetics, University of Utah, Salt Lake City, Utah 84112, USA;⁴Department of Anthropology, Andhra University, Visakhapatnam, Andhra Pradesh, India;⁵Anthropological Survey of India, Calcutta, India;⁶Department of Anthropology, University of Madras, Madras, Tamil Nadu, India;⁷Laboratory of Molecular Systematics and Evolution, University of Arizona, Tucson, Arizona 85721, USA;⁸Department of Human Genetics, University of Newcastle-upon-Tyne, UK;⁹Department of Pathology, Biometry and Genetics, Biochemistry and Molecular Biology, Stanley S. Scott Cancer Center, Louisiana State University Health Science Center, New Orleans, Louisiana 70112, USA

Abstract

The origins and affinities of the ∼1 billion people living on the subcontinent of India have long been contested. This is owing, in part, to the many different waves of immigrants that have influenced the genetic structure of India. In the most recent of these waves, Indo-European-speaking people from West Eurasia entered India from the Northwest and diffused throughout the subcontinent. They purportedly admixed with or displaced indigenous Dravidic-speaking populations. Subsequently they may have established the Hindu caste system and placed themselves primarily in castes of higher rank. To explore the impact of West Eurasians on contemporary Indian caste populations, we compared mtDNA (400 bp of hypervariable region 1 and 14 restriction site polymorphisms) and Y-chromosome (20 biallelic polymorphisms and 5 short tandem repeats) variation in ∼265 males from eight castes of different rank to ∼750 Africans, Asians, Europeans, and other Indians. For maternally inherited mtDNA, each caste is most similar to Asians. However, 20%–30% of Indian mtDNA haplotypes belong to West Eurasian haplogroups, and the frequency of these haplotypes is proportional to caste rank, the highest frequency of West Eurasian haplotypes being found in the upper castes. In contrast, for paternally inherited Y-chromosome variation each caste is more similar to Europeans than to Asians. Moreover, the affinity to Europeans is proportionate to caste rank, the upper castes being most similar to Europeans, particularly East Europeans. These findings are consistent with greater West Eurasian male admixture with castes of higher rank. Nevertheless, the mitochondrial genome and the Y chromosome each represents only a single haploid locus and is more susceptible to large stochastic variation, bottlenecks, and selective sweeps. Thus, to increase the power of our analysis, we assayed 40 independent, biparentally inherited autosomal loci (1 LINE-1 and 39Aluelements) in all of the caste and continental populations (∼600 individuals). Analysis of these data demonstrated that the upper castes have a higher affinity to Europeans than to Asians, and the upper castes are significantly more similar to Europeans than are the lower castes. Collectively, all five datasets show a trend toward upper castes being more similar to Europeans, whereas lower castes are more similar to Asians. We conclude that Indian castes are most likely to be of proto-Asian origin with West Eurasian admixture resulting in rank-related and sex-specific differences in the genetic affinities of castes to Asians and Europeans.

Footnotes

• Present addresses:¹⁰Eccles Institute of Human Genetics, 15 North 2030 East, Room 2100, University of Utah, Salt Lake City, UT 84112-5330, USA.¹¹Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, 508 Life Sciences Building, Baton Rouge, LA 70803, USA.

• ↵12 Corresponding author.

• E-MAILmike{at}genetics.utah.edu; FAX (801) 585-9148.

• Article published on-line before print:Genome Res., 10.1101/gr.173301.

• Article and publication are at www.genome.org/cgi/doi/10.1101/gr.173301.

• • Received November 29, 2000.
  • Accepted March 22, 2001.
• Cold Spring Harbor Laboratory Press

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