Genetic variation in South Asia: assessing the influences of geography, language and ethnicity for understanding history and disease risk

South Asia is home to more than 1.5 billion humans representing many diverse ethnicities, linguistic and religious groups and representing almost one-quarter of humanity. Modern humans arrived here soon after their departure from Africa ∼50 000-70 000 years before present (YBP) and several subsequent human migrations and invasions, as well as the unique social structure of the region, have helped shape the pattern of genetic diversity currently observed in these populations. Over the last few decades population geneticists and molecular anthropologists have analyzed DNA variation in indigenous populations from this region in order to catalog their genetic relationships and histories. The emphasis is gradually shifting from the study of population origins to high resolution surveys of DNA variation to address issues of population stratification and genetic susceptibility or resistance to diseases in genome-wide association surveys. We present a historical overview of the genetic studies carried out on populations from this region in order to understand the influence of geographic, linguistic and religious factors on population diversity in this region, and discuss future prospects in light of developments in high throughput genotyping and next generation sequencing technologies.