We thank the volunteers from throughout India who donated DNA; A. G. Reddy, A. Shah and R. Tamang for generating the Y chromosome and mtDNA data; J. Neubauer for sample preparation; and A. Tandon for data curation. We thank B. N. Sarkar and A. G. Roy for helping with group census size estimates, and D. Falush, J. Novembre, A. Ruiz-Linares and S. Watkins for comments on the manuscript. D.R., N.P. and A.L.P. were supported by NIH grant HG004168, and D.R. was supported by a Burroughs Wellcome Career Development Award in the Biomedical Sciences. K.T. and L.S. were supported by grants from the Council of Scientific and Industrial Research of the Government of India, and K.T. was supported by a UKIERI Major Award (RG-4772).

Author Contributions K.T. and L.S. collected the DNA samples, D.R., K.T. and L.S. collected the genetic data, N.P. developed the mathematical theory for f-statistics, and D.R., K.T., N.P. and A.L.P. analysed the data. D.R. wrote the manuscript and Supplementary Information with input from all authors.