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Researchers Find Genetic Clues to India's Population History

NEW YORK (GenomeWeb News) – Populations found in India today are largely descended from two distinct ancestral groups, according to paper appearing online this afternoon in Nature.

Researchers from Harvard University, the Broad Institute, and the Centre for Cellular and Molecular Biology in Hyderabad, India, assessed more than half a million SNPs in the genomes of 132 individuals from dozens of Indian populations. Their results indicate that the populations present in India today are anciently mixed — but highly diverged — groups descended from so-called Ancestral North and Ancestral South Indians.

The study began as a project aimed at understanding the history of indigenous people on the Andaman Islands in the Indian Ocean, co-lead author David Reich, a geneticist affiliated with Harvard Medical School and the Broad Institute, told GenomeWeb Daily News.

The team subsequently expanded their sampling and testing in India in an effort to understand population genetics across the country — which they say has been under-represented in past genetic studies.

Researchers collected blood samples from 132 individuals and genotyped the DNA at 560,123 SNPs using Affymetrix 6.0 arrays. The team also included data from the International HapMap project and the Human Genome Diversity Panel in some of their analyses.

Among those sampled were individuals from 15 Indian states and six language groups, including two found on the Andaman Islands. The researchers also included individuals from several tribal groups as well as individuals from two states — Uttar Pradesh and Andhra Pradesh — who belong to groups that were once classified as "upper" and "lower" castes.

Based on the genetic patterns they found, the researchers concluded that a relatively small group of ancestors founded most Indian groups, which then remained largely isolated with limited gene flow for long periods of time.

The team also identified two main ancestral groups in India: an "Ancestral North Indian," or ANI group, which is distantly related to those in the Middle East, Central Asia, and Europe, and an "Ancestral South Indian," or ASI group, not related to groups outside India.

While indigenous populations with ASI but not ANI ancestry still exist on the Andaman Islands, the team explained, modern day populations on mainland India represent a mix of the two groups.

The team estimated that the mainland populations they tested had between 39 percent and 71 percent ANI ancestry. And ANI ancestry tended to be higher in the traditionally upper-caste groups and groups who spoke Indo-European languages.

Still, the researchers noted, their results show that genetics patterns in Indian populations have been shaped by a long history of genetic isolation between different groups that predates the caste system in place in India during colonialism.

"It is impossible to distinguish castes from tribes using the data," co-lead author Kumarasamy Thangaraj, a researcher with the Centre for Cellular and Molecular Biology in Hyderabad, India, said in a statement. "The genetics proves that they are not systematically different. This supports the view that castes grew directly out of tribal-like organizations during the formation of Indian society."

Reich noted that the genetic variation in Indian populations may have been masked in previous studies due to the presence of the European-related ANI ancestry. The findings also highlight the importance of doing genetic studies in India rather than relying on gene-disease associations detected in European populations, the team explained.

For instance, the researchers noted, past studies suggest a 25 base pair deletion in the MYBTC3 gene, which apparently increases the risk of heart failure by about seven times, is rare in most parts of the world but is present in some four percent of Indians. Interesting, the deletion also appears to be more common among individuals with high ASI ancestry, Reich said.

In addition, the results offer hints about the types of genetic disease that may dominate in India, the researchers emphasized, suggesting recessive diseases are likely quite common. While anecdotal evidence suggests that may be the case, Reich said, this hasn't really been looked at systematically.

"By showing that a large proportion of Indian groups descend from strong founder effects, these results highlight the importance of identifying recessive diseases in these groups and mapping causal genes," the authors concluded.

The team plans to assess more Indian populations in the future. Reich also hopes to see Indian populations included in future phases of the 1000 Genomes Project. "It seems really important, to me, that southern Indian groups be sampled," he said, noting that the 25 groups evaluated in the current study represent just a fraction of the populations found in India.