Genetic diversity in India and the inference of Eurasian population expansion

Jinchuan Xing,Donna M Muzny,Aniko Sabo,Ya Hu,Richard A Gibbs,Fuli Yu,Michael J Bamshad,Lynn B Jorde,Chad D Huff,W Scott Watkins

doi:10.1186/gb-2010-11-11-r113

Abstract

BackgroundGenetic studies of populations from the Indian subcontinent are of great interest because of India's large population size, complex demographic history, and unique social structure. Despite recent large-scale efforts in discovering human genetic variation, India's vast reservoir of genetic diversity remains largely unexplored.ResultsTo analyze an unbiased sample of genetic diversity in India and to investigate human migration history in Eurasia, we resequenced one 100-kb ENCODE region in 92 samples collected from three castes and one tribal group from the state of Andhra Pradesh in south India. Analyses of the four Indian populations, along with eight HapMap populations (692 samples), showed that 30% of all SNPs in the south Indian populations are not seen in HapMap populations. Several Indian populations, such as the Yadava, Mala/Madiga, and Irula, have nucleotide diversity levels as high as those of HapMap African populations. Using unbiased allele-frequency spectra, we investigated the expansion of human populations into Eurasia. The divergence time estimates among the major population groups suggest that Eurasian populations in this study diverged from Africans during the same time frame (approximately 90 to 110 thousand years ago). The divergence among different Eurasian populations occurred more than 40,000 years after their divergence with Africans.ConclusionsOur results show that Indian populations harbor large amounts of genetic variation that have not been surveyed adequately by public SNP discovery efforts. Our data also support a delayed expansion hypothesis in which an ancestral Eurasian founding population remained isolated long after the out-of-Africa diaspora, before expanding throughout Eurasia.

Highlights

Genetic studies of populations from the Indian subcontinent are of great interest because of India’s large population size, complex demographic history, and unique social structure
Studies of maternal lineages by mitochondrial resequencing have shown that the two major mitochondrial lineages that emerged from Africa (haplogroups M and N, dating to approximately 60 thousand years ago) are both very diverse among Indian populations [6,7]
To determine the accuracy of the newly identified single nucleotide polymorphism (SNP), we carried out additional experiments using the Roche 454 sequencing platform to validate the Indian-specific SNPs in individuals with heterozygous genotypes

Summary

Introduction

Genetic studies of populations from the Indian subcontinent are of great interest because of India’s large population size, complex demographic history, and unique social structure. Additional studies of mitochondrial haplogroups show that an early migration may have populated the Indian subcontinent, leaving ‘relic’ populations in present-day India represented by some Austroasiatic-and Dravidianspeaking tribal populations [7,8,9,10]. These results highlight that the initial peopling of the Indian subcontinent likely occurred early in the history of anatomically modern humans. Recent studies of autosomal SNPs and STRs demonstrate a high degree of genetic differentiation among Indian ethnic and linguistic groups [12,13,14]

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Discussion

Conclusion