Thanks to DNA extracted from a large fossilized tooth dubbed “Denisova 8,” researchers have discovered that ancient cousins of modern humans — the Denisovans — may have co-existed and interbred with Neanderthals and Homo sapiens.
This sister group of Neanderthals was initially identified by a nuclear genome sequence taken from a finger phalanx bone found in Denisova Cave in Siberia — hence the origin of Denisovan’s name. The only other Denisovan specimen so far is a molar from the same area. These bones had been estimated at 50,000 years old.
This analysis means that the oldest known evidence for Denisovans now goes back an additional 60,000 years. Also, the results suggest that the Denisovans could have bred with other ancient hominins (relatives of modern humans), as yet undiscovered by science. According to scientific estimates, Neanderthals and Denisovans split on the human family tree about 400,000 years ago.
Nuclear DNA sequences and a morphological description were taken from this molar, as well as mitochondrial and nuclear DNA sequences from another molar in the cave. This means that there are now three known Denisovan individuals. The nuclear DNA sequence diversity among the Denisovans is higher than among Neandertals, but lower than among present-day humans. The mtDNA taken from one molar suggests that Denisovans endured that region’s harsh climate for several millennia.
The paper, “Nuclear and mitochondrial DNA sequences from two Denisovan individuals,” was published in the Proceedings of the National Academy of Sciences. In the paper, the researchers describe how DNA was extracted from 36 mg dentine from Denisova 8 in a cleanroom facility at the Max Planck Institute for Evolutionary Anthropology in Germany. DNA libraries from this specimen, as well as from a previously prepared extract of the other tooth (“Denisova 4”), were prepared. Random DNA fragments were sequenced from both teeth, and mapped to the human reference genome. Additionally, mtDNA fragments were isolated from the libraries and sequenced.
The researchers utilized three approaches to estimate present-day human DNA contamination in the two libraries. The three methods yielded different contamination estimates, but they all say that there is substantial nuclear DNA contamination in both libraries — particularly in Denisova 4, where it is likely to exceed 50 percent. Therefore, in order to reduce the influence of DNA contamination, the researchers “restricted the analyses of nuclear DNA to fragments that carry thymine residues at the first and/or last two positions at sites where the human reference sequence carries cytosine residues (but remove these C/T sites themselves in the analyses). Using these criteria, a total of 1.0 Mb of nuclear DNA sequences for Denisova 4 and 24.1 Mb for Denisova 8 could be analyzed.” Further information can be found in the 2013 PNAS article “Separating endogenous ancient DNA from modern day contamination in a Siberian Neandertal.”
“It feels a bit surreal,” said Susanna Sawyer of the Max Planck Institute for Evolutionary Anthropology, in a National Geographic interview. “Sometimes when I’m sitting in the cleanroom, I stop to think about how crazy it is that I am holding one of the only remains known to date from a new and mysterious hominid group.”
The research shows that the Denisovans had nearly as much genetic diversity as modern Europeans, despite the fact that the specimens were all found in the same cave. The researchers speculate that Neanderthals wound up inbreeding because glaciers during the ice age forced them to move to isolated areas of southern Europe … however, the Denisovans moved south throughout Asia and avoided the glaciers. Other evidence that the Denisovans — bits of Denisovan DNA can be found in Australian aborigines, New Guineans, and Polynesians.
It’s possible that modern-day humans could have inherited traits from the Denisovans — for example, how people in Tibet have adapted to live in high altitudes with little oxygen.
The DNA also suggests that Denisovans inbred with another Asian hominin species. It could have been a known species such as Homo erectus … or if could have been an as-yet unknown species. Fossils found in the future may help answer these questions, but so far the evidence suggests that our ancient relatives were more complex and adoptable than we may have thought.