Genomic reconstruction of the history of extant populations of India reveals five distinct ancestral components and a complex structure

India, harboring more than one-sixth of the world population, has been underrepresented in genome-wide studies of variation. Our analysis reveals that there are four dominant ancestries in mainland populations of India, contrary to two ancestries inferred earlier. We also show that (i) there is a distinctive ancestry of the Andaman and Nicobar Islands populations that is likely ancestral also to Oceanic populations, and (ii) the extant mainland populations admixed widely irrespective of ancestry, which was rapidly replaced by endogamy, particularly among Indo-European-speaking upper castes, about 70 generations ago. This coincides with the historical period of formulation and adoption of some relevant sociocultural norms.