Ancient DNA reveals new branches of the Denisovan family tree


A representation of the double helical structure of DNA. Its four coding units (A, T, C, G) are color-coded in pink, orange, purple and yellow. Credit: NHGRI

It is widely accepted that anatomically modern humans crossed with their close relatives, the Neandertals and the Denisovans, when they dispersed out of Africa. But a study that examines the DNA fragments transmitted from these ancient hominids to modern people living on the island of Southeast Asia and New Guinea now suggests that the descent of the Papuans includes not only one but two distinct Denisovan lineages, which had separated from each other for hundreds of thousands of years. In fact, the researchers suggest that one of those Denisovan lineages is so different from the other that they should really be considered as a completely new species of archaic hominin.

The findings, based on a new collection of genomic data made possible by coauthors of the study of the Eijkman Institute of Molecular Biology in Jakarta, Indonesia, appear on April 11 in the journal. Cell. Taken together with the previous work, which has indicated a third lineage of Denisovan in the genomes of modern Siberians, Native Americans and East Asians, the evidence "suggests that modern humans crossed paths with multiple Denisovan populations, which were isolated geographically to each other in the deepest "evolutionary time", the researchers write.

The new findings show that modern humans leaving Africa for the first time were entering a new world that looked completely different from what we see today. "We used to think we were just us, modern humans and Neanderthals," says lead author Murray Cox of Mbadey University in New Zealand. "Now we know that there was a great diversity of human groups all over the planet, our ancestors were in contact with them all the time."

The new evidence also unexpectedly shows an extra mix between the 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 on the Asian continent and far to the north," says Cox. "Our work, on the other hand, shows that the center of archaic diversity was not in Europe or in the frozen north, but in tropical Asia."

It had already become clear that the island of Southeast Asia and New Guinea was a special place, where individuals had more archaic hominid DNA than anywhere else on Earth. The region was also recognized as a key to the early evolution of Homo sapiens outside of Africa. But there were gaps in the story.

To help fill those gaps, the Cox team excavated archaic haplotypes of 161 new genomes that span 14 island groups on the island of Southeast Asia and New Guinea. Their badyzes discovered large stretches of DNA that did not match a single introgression of Denisovans genes in humans in the region. Instead, they report, modern Papuans carry hundreds of genetic variants of two deeply divergent Denisovan lineages. In fact, they estimate that these two groups of Denisovans had been separated from each other for 350,000 years.

The new findings highlight how "incredibly little studied" this part of the world has been, the researchers say. To put it in context, many of the study participants live in Indonesia, a country the size of Europe which is the fourth largest country according to the size of its population. And yet, aside from a pair of genomes reported in a global study of genomic diversity in 2016, the new article reports on the first sequences of the Indonesian genome. There has also been a strong bias in studies of archaic hominids in Europe and northern Eurasia because DNA collected from ancient bones survives better in the northern cold.

The researchers claim that this lack of global representation in the ancient and modern genome data is evident. "However, we do not believe that people have really understood the bias that this implies for scientific interpretations, such as, for example, the geographical distribution of archaic hominid populations," says Cox.

As fascinating as these new findings are, the researchers say their main goal is to use these new genomic data to help improve health care for people on the island of Southeast Asia. They say that this first genome study in the region now offers the reference information needed to start that work.

Evidence found of Denisovans crossing with humans in Southeast Asia more recently than previously thought

More information:
Cell, Jacobs et al.: "Multiple Ancestry of Denisovan Deeply Divergent in Papuans", DOI: 10.1016 / j.cell.2019.02. 035

Journal information:

Ancient DNA reveals new branches of the Denisovan family tree (2019, April 11)
retrieved on April 13, 2019

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