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Study Highlights Admixture between Ancestral Indian Populations Prior to Caste System

NEW YORK (GenomeWeb News) – India's two main ancestral populations appear to have mixed extensively with one another within the past few thousand years, a new study suggests, pointing to a period that preceded the relative genetic isolation associated with the country's caste system.

As they reported online yesterday in the American Journal of Human Genetics, researchers from the US and India genotyped individuals from more than 70 groups in and around India as part of their effort to more clearly define the country's population history. Findings from the analysis suggest the genetically distinct Ancestral North Indians and Ancestral South Indians admixed between around 1,900 and 4,200 years ago, leaving traces of their ancestry in virtually all of the country's present-day populations.

"The most remarkable aspect of the [Ancestral North Indian-Ancestral South Indian] mixture is how pervasive it was: it affected not just traditionally upper-caste groups, but also traditionally lower-caste and isolated tribal groups, all of whom are united in their history of mixture in the past few thousand years," the study's co-first author Priya Moorjani, a graduate student in co-senior author David Reich's Harvard Medical School lab, said in a statement.

Although those interactions left their mark on populations across India, Moorjani and her colleagues noted, they were followed by a period of increasing isolation between populations that coincided with a rise in endogamy, characterized by marriages almost exclusively within a specified population or cultural group.

"The fact that every population in India evolved from randomly mixed populations suggests that social classifications like the caste system are not likely to have existed in the same way before the mixture," co-senior author Lalji Singh said in a statement. "Thus, the present-day structure of the caste system came into being only relatively recently in Indian history."

Singh, who was a researcher with the CSIR-Centre for Cellular and Molecular Biology in Hyderabad, India when the research was performed, is now based at Banaras Hindu University.

In a study published in Nature in 2009, Singh, Reich, and colleagues used genetic data from more than two-dozen populations in India to show that most groups in India share genetic features that can be traced back to ancestral populations nicknamed the Ancestral North Indians, or ANI, and the Ancestral South Indians (ASI).

Whereas the ANI ancestral group has genetic ties to Middle Eastern, Caucasian, European, and Central Asian populations, they reported at that time, the ASI group appears to be only distantly related to populations from outside of India.

For their latest analysis, researchers turned to genetics to try to get a clearer picture of when and where interactions between the ANI and ASI groups may have occurred. Using Affymetrix and Illumina arrays, they genotyped 571 individuals representing 71 groups in mainland India and the Andaman and Nicobar Islands and two groups from Pakistan.

After tossing out data from related individuals, suspicious samples, and so on, the team sorted through the SNP data to estimate the proportion of ANI and ASI sequences in each individual's genome, using additional information from the Human Genome Diversity Project and HapMap project to help in the analysis.

With data from Indian populations that clustered along an ancestry spectrum characterized by varying proportions of ANI and ASI ancestry, the investigators went on to retrace historical ANI-ASI admixture events and estimate their timing.

In particular, their data suggest admixture between the groups began roughly 4,200 years ago and was widespread for many years afterwards.

Genetic features found in India's present-day populations suggest that that admixture persisted somewhat longer in northern India than in southern parts of the country, though it ultimately tapered off around 1,900 years ago, the team determined.

Findings from the analysis suggest that some of the most recent examples of admixture involved northern and Indo-European populations and groups once classified as middle- or upper-caste, with genetic features in these groups pointing to the possibility of multiple mixing stages with ancestors from slightly different ANI groups.

Even so, populations across the country appear to have become more and more differentiated from one another with the establishment of India's caste system and the subsequent onset of endogamy — a decline in inter-mixing that has contributed to some of the features found in Indian populations today, such as population-specific differences in susceptibility to some diseases.

"This genetic data tells us a three-part cultural and historical story," Harvard's Reich said in a statement.

"Prior to about 4,000 years ago there was no mixture. After that, widespread mixture affected almost every group in India, even the most isolated tribal groups. And finally, endogamy set in and froze everything in place," he said.