Denisova Cave Used by Denisovans for many thousands of Years

Australia: The Land Where Time Began

DNA sequencing of genetic material extracted from a finger of a young girl that had been found in Denisova Cave in the Altai Mountains of Siberia resulted in the discovery of a new type of hominin, Denisovans. A small number of Denisovan molars were found in the cave and together with new dates for the material show that the cave was being occupied by the Denisovans over a very long period. It is suggested by the data that the girl lived about 50,000 BP and 2 other Denisovan individuals died in the cave at least 110,000 years ago and possibly as long ago as 170,000 BP. The new dates have helped to improve the murky view of Denisovans, who left very little evidence of their presence, and provide more convincing evidence of their multiple occupations of the cave over a very long period, according to Fred Spooner, a paleoanthropologist.

Layer 11, a thick sandstone band, is where most of the key fossils in the cave have been found. The first attempt to date the animal bones and artefacts from the sandstone layer varied widely between 30,000 and 50,000 BP. When 20 samples of artefacts and animal bones that had cut marks indicating they had been butchered by the occupants of the cave gave ages on a second dating of likely older than 48,000-50,000 BP. The sediments at the base of the sandstone layer, where the finger bone was discovered, gave dates at the very limit of radiocarbon dating, so are probably older.

The dates that had been obtained were from bones with cut marks, and ornaments, and the dates were consistent across 3 caves, as well as fitting with genetic evidence.

Nuclear DNA sequencing was carried out on 3 molars recovered from layer 11 and the molar of a child recovered from a deeper layer, 22. Thermoluminescence, a dating method that is considered to be experimental in the case of cave dating, gave a date of 170,000 BP for layer 22.

A significant amount of nuclear DNA from 3 teeth that was analysed proved to be from Denisovans, and a 4^th was Neanderthal. When key sites on the tooth DNA were compared with corresponding sites in the high quality genomes from the Denisovan girl, Neanderthal and modern humans, it was revealed that the Denisovan inhabitants of the cave were not closely related. The Denisovans displayed more genetic variation among them than the entire DNA that has been sequenced from all the Neanderthals tested to date, though Neanderthals are known to be genetically similar.

The entire mtDNA genomes of the Denisovans were sequenced to determine when the Denisovans were in the cave and they were placed on a family tree. The number of mtDNA differences between individuals was counted and the mutation rate of modern humans was used to estimate the length of time it would require for these mutations to appear. By this method it was concluded that the girl was in the cave about 65,000 after the oldest Denisovan, who was there at least 110,000 years ago, though possibly earlier.

Pääbo’s team has sequenced the DNA from a Neanderthal toe bone and a molar recovered from the cave. Also, modern humans were apparently in the cave, which was large and light-filled, as indicated by more recent artefacts. It appears from the interdigitisation of the Denisovans and the Neanderthals both groups were in and out of the cave.

A new technique, ZooMS, was used to scan 2,315 bones from the cave searching for proteins that were uniquely of human origin, which found a fragment of a human toe bone.

Ancient DNA reveals tryst between extinct human species ²

The woman had a Neanderthal mother and a Denisovan father. She may have been a teenager when she died more than 50,000 BP. There was enough ancient DNA in the 2 cm fragment of her finger bone to reveal her unexpected ancestry: She was the direct offspring of 2 different species of ancient humans. The report of the genome of the woman that was published in Nature indicates that her mother was Neanderthal and her father was Denisovan. It is the most direct evidence so far found that various ancient humans mated with each other and had offspring.

Researchers had already concluded, based on other ancient genomes, which Denisovans, Neanderthals, and modern humans interbred in Europe and Asia in the ice age. Many people of the present carry genes from both archaic human species. It has been shown by other fossils that were fund in the Siberian cave that all 3 species lived there at different times. According to Johannes Krause, an ancient DNA researcher at the Max Plank Institute, this find is sensational, because they now have the genome of the love child between 2 different hominin groups, and found in a place where members of both groups have been found. According to Viviane Slon, the palaeontologist who carried out the analysis, on seeing the results her first reaction was disbelief. She repeated the analysis several times before she and her group were convinced. That the direct offspring between 2 ancient humans was present among the first few fossil genomes that were recovered from the cave suggests, according to Svante Pääbo, that when these groups met, they actually mixed quite freely with each other.

The characteristics of the fragments of bone suggest it came from someone who was at least 13 years old. Slon et al. found that the person the bone came from was female, and that her genome matched that of Neanderthal and Denisovan in roughly equal amounts. Also, the proportion of genes in which her chromosome pairs contained different variants, heterozygous alleles, was close to 50% for all chromosomes, which suggests the maternal and paternal chromosomes came from different groups. And her mitochondrial DNA, which is inherited from the mother, was uniformly Neanderthal, so it was concluded by the researchers that she was a first generation hybrid of a Denisovan man and a Neanderthal woman.

Further study of the genome found that her father also had some Neanderthal ancestry, possibly from several hundred generations back. And the woman’s Neanderthal genes are closer to those of a Neanderthal found in Croatia than those from the Siberian cave. It is suggested by this that distinct groups of Neanderthals migrated back and forth between western Europe and Siberia a number of times.

It appears they freely spread their genes to outsiders along the way. According to Krause that highlights the question of why the Denisovans and Neanderthals nevertheless remained groups that were genetically distinct. He posed the question that if they came together from time to time why didn’t they come together as a single population. The researchers suggested that a role was probably played by geographic barriers, though to understand the true legacy of these prehistoric couplings more fossils with ancient DNA are required.

Sources & Further reading

1. Gibbons, A. (2015). "Cave was lasting home to Denisovans." Science 349(6254): 1270-1271.

2. Vogel, G., 2018, Science, Ancient DNA reveals tryst between extinct human species VOL 361 ISSUE 6404