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Ancient DNA reveals new branches of the Denisovan family tree

Ancient DNA reveals new branches of the Denisovan family tree
© © Rozenn LE GUYADER / GQE - Le Moulon / CNRS Photothèque
It is now widely accepted that anatomically modern humans interbred with their close relatives, the Neanderthals and the Denisovans, as they dispersed out of Africa. An international research team including the Laboratory Evolution and Biological Diversity (EDB - CNRS / University of Toulouse III Paul Sabatier / IRD) brings surprising results on this little known chapter of the history of our species.

This study published in the journal Cell on April 11, 2019, used fragments of DNA from human populations currently living in the islands of Southeast Asia and New Guinea. It highlights a gene flow among these ancient hominins, and specifies that the ancestors of the Papuans have in their genome traces of two distinct Denisovan lineages, which had been separated from each other for hundreds of thousands of years. The researchers also suggest that one of those Denisovan lineages is so different from the other that it really should be considered an entirely new archaic hominin species.

Taken together with previous work —which identified a third Denisovan lineage in the genomes of modern Siberians, Native Americans, and East Asians - the evidence— all “suggest that modern humans interbred with multiple Denisova populations, which were geographically isolated from each other for extended periods of time to be genetically differentiated" said the researchers.

These new findings show that modern humans making their way out of Africa for the first time entered a new world that looked entirely different from the one we see today. "We used to think it was just us —modern humans— and Neanderthals" commented author Murray P Cox of Massey University in New Zealand. "We now know that there was a huge diversity of human-like groups found all over the planet. Our ancestors came into contact with each other all the time".

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Schéma synthétique de la rencontre et du mélange entre les groupes de Denisova et les Hommes modernes © Georgi Hudjashov

The new evidence also unexpectedly shows extra mixing between Papuans and one of the two Denisovan groups, suggesting that this group actually lived in New Guinea or its adjacent islands. "People used to think that Denisovans lived very far north on the Asian mainland," says François-Xavier Ricaut, researcher at the Evolution and Biological Diversity Laboratory member of TULIP. "Our work instead shows that the center of the diversity of these archaic hominids was not Europe or the Far North, but tropical Asia."

It was already clear that the Southeast Asia Islands and New Guinea were a special place, as individuals there carry more archaic hominin DNA than anywhere else on Earth. The region also was recognised as key to understanding the evolution of Homo sapiens outside Africa and new chapters of our history are now opening.

The international team excavated archaic haplotypes from 161 human genomes from 14 island groups in Southeast Asia Islands and New Guinea. Their analyzes uncovered large fragments of DNA whose presence cannot be explained by a single introgression event from Denisova into modern humans in the region. Instead, the current Papuan populations carry hundreds of gene variants from two deeply divergent Denisovan lineages, which had been separated from one another for at least 350,000 years.

Beyond the importance and innovation of this study, researchers point to the lack of research investment in this part of the world so far. To put it in context, many of the study’s participants live in Indonesia, a country the size of Europe with the fourth largest population in the world.

In fact, apart from a few genomes reported in a study on global diversity published in 20161 in Nature, this new article brings the first representative diversity of Indonesian genomes. In addition, there also has been a strong sampling bias in studies of archaic hominins towards Europe and northern Eurasia because DNA in ancient bones survives best in the cold north. This lack of global representation in both ancient and modern genome data is well noted, the researchers say. "However, we think that we have not yet realized just how much of a bias this introduces on scientific interpretations —such as, here, the geographical distribution of archaic hominin populations," report MP Cox and FX Ricaut.

See also

Multiple deeply divergent Denisovan ancestries in Papuans. Jacobs G, G Hudjashov, L Saag, P Kusuma, CC Darusallam, DJ Lawson, M Mondal, L Pagani, Ricaut F.-X., M Stoneking, M Metspalu, H Sudoyo, JS Lansing, MP Cox. 2019.  Cell, 11 avril 2019.