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DBT support helps identify single origin & expansion out of Africa

Rapid Fire

  • All Asian and Pacific populations share a single origin & expansion out of Africa
  • South & Southeast Asia harbor a small proportion of genetic fragments from a hitherto unknown extinct hominin ancestor
  • These populations also possess genetic fragments from other extinct hominins – the Neanderthal and the Denisovan.
  • Andamanese show closer genetic affinities with mainland Indians and other Asians than with Pacific populations
  • Jarawas & Onges have remained isolated and there was no evidence of any recent admixture
  • Natural selection has favoured the retention of short height among the Jarawas & Onges

All Asian and Pacific populations share a single origin and expansion out of Africa, a new study has found contradicting earlier suggestions of two or more independent waves of migration from Africa.

The team of scientists from the National Institute of Biomedical Genomics (NIBMG) analysed whole-genome sequences from 10 Andamanese individuals and compared them with sequences for 60 individuals from mainland Indian populations with different ethnic histories and with publicly available data from other global populations. The sample collection was carried out over more than 15 years with DBT support provided for conduct of various human genome diversity projects.

The study published in Nature Genetics on July 25, 2016, also found that populations from South and Southeast Asia harbor a small proportion of ancestry from an unknown extinct hominin, in addition to the Neanderthal and the Denisovan. The ancestry from the unknown hominin is absent from contemporary Europeans and East Asians.
The footprints of adaptive selection in the genomes of the Andamanese show that characteristic distinctive phenotypes of this population including very short stature, do not reflect an ancient African origin but instead result from strong natural selection on genes related to human body size.

It was so far believed that modern humans came out of Africa in multiple waves and that one of the first waves of the out-of-Africa migration came into India and following the coastal route populated the Andaman archipelago.
Some ethnic groups of the Andamans, such as the Jarawa and the Onge, look ‘African,’ with dark complexion, short stature and frizzly hair. They were therefore believed to be the ‘relic’ of the original out of Africa population. The language of these Andaman islanders remaining unclassified has bolstered this belief.

A recent study published in February 2016 in the Proceedings of the National Academy of Sciences, USA, by scientists of NIBMG (Analabha Basu, Neeta Sarkar-Roy and Partha Majumder) had shown that the ancestral genetic lineage characterizing the Jarawas and Onges is distinct from those characterizing ethnic groups of mainland India. This raised the question whether mainland India and the Andaman islands were populated by the same wave of out-of-Africa migration of modern humans.

With an aim to understand and identify the ancestral components in the genomes of the Andamanese, the scientists sequenced whole genomes of 60 individuals drawn from a carefully sampled set of diverse ethnic groups of mainland India and 10 Jarwas and Onges. For comparative purposes and for drawing more robust inferences, they also downloaded data available in the public domain from various sources (1000 Genomes study, Great Apes Genome Project, 69 Genomes project of Complete Genomics, and other) and carried out joint statistical analysis with their data.

They found that Andamanese show closer genetic affinities with mainland Indians and other Asians than with Pacific populations. The scientists also showed that the Jarawas and Onges have remained isolated and there was no evidence of any recent admixture. Also, this population was distinctive from the mainland Indian populations, as earlier found. However, this distinctiveness did not translate to their having been derived from a separate out-of-Africa migration wave. Although the Andamanese show closer genetic affinities with mainland Indians and other Asians than with Pacific populations, all Asian and Pacific populations were derived in a common wave of out-of-Africa migration of modern humans.

An analysis of the contribution of extinct hominin populations – Neanderthal and Denisovan – to the gene pools of extant populations supported a single origin for modern Asians, including the Andamanese.

Delving into the question ‘why are the Andamanese short?’ the scientists carried out extensive analysis of regions of the genome on which natural selection may have acted strongly. They identified 107 genes harbouring segments that evolved under the impact of positive, advantageous natural selection, of which 10% (11 or 107) were found involved in the determination of height concluding thereby that natural selection has favoured the retention of short height among the Jarawas and Onges.