Journal article

Shared and Unique Components of Human Population Structure and Genome-Wide Signals of Positive Selection in South Asia

Mait Metspalu, Irene Gallego Romero, Bayazit Yunusbayev, Gyaneshwer Chaubey, Chandana Basu Mallick, Georgi Hudjashov, Mari Nelis, Reedik Maegi, Ene Metspalu, Maido Remm, Ramasamy Pitchappan, Lalji Singh, Kumarasamy Thangaraj, Richard Villems, Toomas Kivisild

American Journal of Human Genetics | CELL PRESS | Published : 2011

Abstract

South Asia harbors one of the highest levels genetic diversity in Eurasia, which could be interpreted as a result of its long-term large effective population size and of admixture during its complex demographic history. In contrast to Pakistani populations, populations of Indian origin have been underrepresented in previous genomic scans of positive selection and population structure. Here we report data for more than 600,000 SNP markers genotyped in 142 samples from 30 ethnic groups in India. Combining our results with other available genome-wide data, we show that Indian populations are characterized by two major ancestry components, one of which is spread at comparable frequency and haplo..

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University of Melbourne Researchers

Grants

Awarded by Estonian Basic Research


Awarded by Tartu University


Awarded by Estonian Science Foundation


Awarded by Estonian Ministry of Education and Research


Awarded by European Commission


Funding Acknowledgements

We thank A. Migliano, S. Raj, and P. Underhill for discussion; J. Pickrell and J. Barna for help calculating iHS and XP-EHH scores; A. Aasa, I. Hilpus, T. Reisberg, V. Soo, and L. Anton for technical assistance. R.V., M.M., G.C. and C.B.M. thank the European Union European Regional Development Fund through the Centre of Excellence in Genomics to Estonian Biocentre, and University of Tartu. This research was supported by Estonian Basic Research grant SF0270177As08 to R.V. and SF0180026s09 to M.R. and R.M.; Tartu University grant (PBGMR06901) to T.K.; Estonian Science Foundation grants (7858) to EM. and (8973) to M.M.; Estonian Ministry of Education and Research (0180142s08) and European Commission grant 245536 (OPENGENE) to M.N.; European Commission grant (ECOGENE 205419) to MM., I.G.R., B.Y., G.H, R.M., and R.V.; and Council of Scientific and Industrial Research, Government of India to L.S. and K.T. Calculations were carried out in the High Performance Computing Center, University of Tartu and with University of Cambridge Bioinformatics and Computational Biology services.