doi:10.1038/nindia.2017.12 Published online 30 January 2017

Gene detectives trace human evolution in India, find third gene trail

Anirban Ghosh

There was a third unknown hominid element – like the Neanderthals or Denisovans – who left some of their genes among ancestors of present day Indians, besides known contributions from the other two established ancestral hominid groups that lived in Europe and Central Asia, new research suggests1.

A group of international geneticists suggests that this third hominid group most likely inhabited the Indian neighbourhood before going extinct around 50,000 years ago. Genetic evidence points to this unknown hominid group being spread across the oceanic islands from Andaman and Nicobar to Australasia.

Scientists from National Institute of Bio Medical Genomics (NIBMG), Kalyani, West Bengal, India along with collaborators from Spain, UK, Netherlands and China found this novel third gene trail while analysing human genome samples from the Indian subcontinent. They attempted to trace back the history of the region through 1000 whole genome samples, including mitochondrial DNA, using high throughput techniques and advanced statistical methods. They found small fractions of gene sequences that did not match with modern human genome samples or with the existing traces of the other two hominid groups.

Some tribes in the Andaman and Nicobar islands carry 2-3% genes from the unknown hominid source.
© S. Priyadarshini
The Onge and Jarawa tribes inhabiting the Andaman and Nicobar islands carried a high of 2-3% genes from the unknown hominid source1. The scientists identified specific DNA regions and detected around 15 Mb of such unknown gene sequences from individual islanders. They also predicted a higher admixture rate in Australian aborigines, a conjecture that found support by a group of Australian scientists at the annual meeting American Society of Human Genetics in October 2016.

Majumder and his team had earlier analysed the Indian population to detect five distinct ethnicities, contrary to reports that identified two major ethnic groups2. “With more representative population sampling, dissecting the genome and rigorous statistical analysis, we identified two more ancestral lineages in Indian population as Ancestral Austro-Asian (AAA) and Ancestral Tibeto-Burman (ATB),” Majumder told Nature India. The study also found that the ancestry of population in the Andaman archipelago is distant from mainland Indians and closer to oceanic islanders of the region.

This led the gene detectives to the third hominid group, possibly inhabiting South-east Asia and Australia around 60,000 years ago and later, and predicted to have emerged from the African hominid stock over 300,000 years ago. The scientists suggest the probability of this group mixing with human stocks around 50,000 – 60,000 years back and ultimately replacing it. In true sense those earlier hominid inhabitants were not separate species, but sub-species of the modern ancestral stock that came out of Africa around 80,000 years ago to evolve as Homo sapiens sapiens of today.

The NIBMG scientists traced more or less similar amount of Neanderthal genes in Onges and Jarawas as in the mainlanders. This suggests that the admixture with Neanderthals occurred early in the primitive stock of migrating ancestral human populations.

Interestingly, the third gene trail also highlights the reason behind ethnic diversity in India. It urges a rethink on the route of dispersal of humans and the process of colonization in south-east Asian lands and Australia where India might have played an important transit point.

The study strengthens the ‘southern exit route’ of the ‘Out of Africa’ (OOA) theory which says that part of a hominid population from east Africa dispersed into different parts of Europe and Asia over 80,000 years back. Many went north to northern Eurasia, then migrated to central Asia (northern exit route) and may have gradually trickled back to southern Asia later. They encountered Neanderthals and Denisovans on this path. Another group took a southward route to enter Asia through Asia Minor, Arabian deserts and Hindu Kush mountains to the plains of India. They started their journey to south-eastern oceanic islands including the Australian land mass (southern exit route). In this path, Andaman and Nicobar islands was a transit point. The 2-3% mixing of unknown hominid genes in the Andaman islanders indicates the possibility of modern human invasion into an inhabited territory around 60,000 years ago.

“There might have been waves of human invaders through the southern route and Onges or Jarawas are probably the remnants of the earliest wave who had to face the older hominid group,” Majumder says. For thousands of years they remained isolated in the remote islands thus preserving the genetic relics. Also they show around 2% drop of African alleles, but their apparent physical similarities with Africans could be due to local adaptation and act of natural selection.

Majumder says the team’s dream would come true if some day hominid fossils excavated in south-east Asia or Australia show matched sequences in their ancient DNA with unknown sequences presently found in the inhabitants of Andaman and Nicobar islands.


1. Mondal, M. et al. Genomic Analysis of Andamanese provides insights into ancient human migration into Asia and adaptation. Nat. Genet. 48, 1066-1070 (2016) 

2. 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. USA. 113, 1594-99 (2016)