doi:10.1038/nindia.2016.11 Published online 27 January 2016

Mainland Indians had four ancestors, not two

K. S. Jayaraman

A new study exploring the genetic history of present-day Indians, reconstructed using DNA information, has found they are descendants of four major ancestral populations in mainland India1.

Partha Majumder and co-workers at the National Institute of Biomedical Genomics (NIBG) in Kalyani, West Bengal, report that their finding contrasts with an earlier inference2 by an international team that present-day Indians are derived from only two ancestral stocks of people — one ancestral to all north Indians and, the other, ancestral to all south Indians. 

A researcher taking a sample from a tribal woman
The NIBG team has now discovered two more ancestries — Austro-Asiatic and Tibeto-Burman. In addition, the authors identified a fifth ancestral lineage that is dominant among the Jarawa and Onge tribals of Andaman and Nicobar Islands, also ancestral to the present-day Pacific Islanders.

"The study was done using judiciously selected populations who provide a more complete representation of Indians resident of diverse geo-cultural ecosystems of India, and also using about double the number of DNA variants per individual than the previous major study," Majumder told Nature India.

The researchers said they systematically explored DNA variation in about 400 unrelated Indians belonging to 20 ethnic groups including two Negrito tribal groups residing in the Andaman and Nicobar islands. The remaining 18 groups – both tribal and caste groups – are from mainland India. 

While studies have been conducted in the past by various groups, "this is the largest DNA variation study conducted in India, taking into account both the number of ethnic groups and the number of DNA variants (over 1 million) examined on each individual," Majumder said. 

While this study has also used publicly available data from the Human Genome Diversity Panel (HGDP) — a repository of genomic data representing hundreds of people worldwide — to derive ancestral inferences about Indians, "the entire study was conducted in India by researchers of a single Indian institution," he said adding that it has been able to provide robust evidence that four — not two — ancestral stocks contributed to the genetic diversity of present-day Indians.

These ancestral stocks are roughly identifiable with the four language families in India – Indo-European (north India), Dravidian (south India), Tibeto-Burman (north-east India) and Austro-Asiatic (fragmented in east and central India; spoken exclusively by the tribals). 

Although present-day Indians largely group themselves in relatively-isolated social groups, with negligible proportion of marriages taking place between individuals belonging to different social groups, this situation did not prevail in the past, says Majumder.

"Our analysis showed that gene exchange was widespread among the four ancestral groups of the present-day Indians, suggesting that difference in social position was not a major bar to marriage," he said. This practice of inter-marriage was rapidly replaced by strict endogamy marriage within upper-caste Indo-European speakers leading to the formation of endogamous groups — that is, groups whose members marry only within their groups but not outside.

"Our study, using DNA data, estimated that the transition in India from free intermarriage to endogamy took place about 70 generations or about 1600 years ago," Majumder said. The timing, he said, coincides with the period of the of the Gupta empire when a lot of social transformation took place — notably the enforcement of social strictures against marriage between castes — that resulted in a shift to endogamy, the authors said.

The researchers say the number of ancestral components in the populations of India may have been underestimated by previous researchers because of lack of inclusion of tribal populations and inadequate representation of the geocultural diversity of India in the set of sampled populations. "Our study has corrected this deficiency and has provided a more robust explanation of the genomic diversities and affinities among extant populations of the Indian subcontinent, elucidating in finer detail the peopling of the region."

Ramasamy Pitchappan, an expert in human genomics and director of research at Chettinad University in Tamil Nadu says the finding is not new. "Most of the observations reported in this work overlap with facts earlier publishedby us." 


1.  Basu, A. et al. Genomic reconstruction of the history of extant populations of India reveals five distinct ancestral components and a complex structure. Proc. Natl. Acad. Sci. (2016) doi: 10.1073/pnas.1513197113
2. Reich, D. et al. Reconstructing Indian population history. Nature 461, 489-494 (2009) doi: 10.1038/nature08365
3. Kumar, A. et al. Genome-wide signatures of male-mediated migration shaping the Indian gene pool. J. Human Genet. 60, 493-499 (2015) doi: 10.1038/jhg.2015.51