The largest ever DNA survey of Indian heritage has revealed that the population of India was founded on just two ancient groups that are as genetically distinct from each other as they are from other Asians.
The findings of the study, conducted by a group of top international geneticists, have strong implications for health and medicine, and reveal important new information on caste in India.
The study shows that most Indian populations are genetic admixtures of two ancient but genetically divergent groups, which each contributed around 40-60 per cent of the DNA to most present-day Indians, Nature magazine reported Wednesday.
One ancestral lineage - genetically similar to Middle Eastern, Central Asian and European populations - was higher in upper-caste individuals and speakers of Indo-European languages such as Hindi, the researchers found.
The other lineage was not close to any group outside the Indian subcontinent, and was most common in people indigenous to the Andaman islands, says the study conducted by a team led by David Reich of the Broad Institute in Cambridge, Massachusetts, and Lalji Singh of the Centre for Cellular and Molecular Biology in Hyderabad, India.
Nature said that although India makes up around one-sixth of the world's population, it has been “sorely under-represented” in genome-wide studies of human genetic variation.
The Indian Genome Variation database, launched in 2003 to fill the gap, has so far studied only 420 DNA-letter differences, called single nucleotide polymorphisms (SNPs), in 75 genes.
In sharp contrast, the study reported by Nature has probed more than 560,000 SNPs across the genomes of 132 Indian individuals from 25 diverse ethnic and tribal groups dotted all over India.
The researchers also found that Indian populations were much more highly subdivided than European populations. But whereas European ancestry is mostly carved up by geography, Indian segregation was driven largely by caste.
"There are populations that have lived in the same town and same village for thousands of years without exchanging genes," said Reich.
The authors of the study said the new genetic evidence refutes the claim that the Indian caste structure was a modern invention of British colonialism.
"This idea that caste is thousands of years old is a big deal," said Nicole Boivin, an Oxford University archaeologist.
"To say that endogamy (the practice of marrying within a caste, community or tribe) goes back so far, and that genetics shows it, is going to be controversial to many anthropologists."
The study also suggests that Indian populations, although currently huge in number, were founded by relatively small bands of individuals - a finding that has clinical implications.
"There will be a lot of recessive diseases in India that will be different in each population and that can be searched for and mapped genetically," Reich said.
"That will be important for health in India."