Denisovan DNA found in sediments of Baishiya Karst Cave

A year after the publication of studies on the Xiahe mandible, the first Denisovan fossil found outside the Denisova Cave, the same research team has now obtained the results of the Denisovan DNA from sediments of the Baishiya Karst Cave (BKC) in Tibetan Plateau reported Xiahe’s lower jaw was found. The study was published in science on October 29th.

The research team was led by Prof. CHEN Fahu from the Institute for Tibetan Plateau Research (ITP) of the Chinese Academy of Sciences (CAS), Prof. ZHANG Dongju from the University of Lanzhou, Prof. FU Qiaomei from the Institute of Paleontology and Paleoanthropology of Vertebrates (IVPP) from CAS, Prof. Svante Pääbo from the Max Planck Institute for Evolutionary Anthropology and Prof. LI Bo from the University of Wollongong.

Using state-of-the-art paleogenetic technology, the researchers successfully extracted Denisovan mtDNA from late Pleistocene sediment samples collected during the BKC excavation. Their results show that this Denisovan group is closely related to the deceased Denisovans from the Denisova Cave, which indicates that Denisovans occupied the Tibetan plateau for a period of time and probably adapted to the high altitude environment.

Denisovans were first discovered and identified in 2010 by a research team led by Prof. Svante Pääbo. Almost a decade later, the Xiahe lower jaw was found on the Tibetan plateau. The first Denisovan fossil to be found outside the Denisova Cave, it confirmed that Denisovans occupied the roof of the world and were widespread in the late Middle Pleistocene. Although the Xiahe mandible re-illuminated Denisovan’s DNA with no DNA and no secure stratigraphic and archaeological context, the information it contained about Denisovans was still significantly limited.

In 2010, a research team from Lanzhou University, led by Prof. CHEN Fahu, the current director of the ITP, began working at the BKC and the Ganjia Basin where it is located. Since then, thousands of stone artifacts and animal bones have been found. The subsequent analysis revealed that the stone artifacts were mainly created using the simple core flake technology. Among the animal species represented, gazelles and foxes dominated in the upper layers, while rhinos, wild bos and hyenas dominated in the lower layers. Some of the bones were burned or cut, indicating that humans occupied the cave for a period of time.

To determine when humans occupied the cave, researchers used radiocarbon dating of bone fragments recovered from the upper layers and optical dating of sediments collected from all layers of the excavated profile. They measured 14 bone fragments and approximately 30,000 individual grains of feldspar and quartz minerals from 12 sediment samples to provide a robust chronological framework for the location. The dating results suggest that the deepest deposits excavated contain stone artifacts buried for over ~ 190 ka (thousand years). Sediments and stone artifacts accumulated over time until at least ~ 45 ka or even later.

To determine who occupied the cave, the researchers used sediment DNA technology to analyze 35 sediment samples taken specifically for DNA analysis during the excavation. They took 242 mammalian and human mtDNA samples, enriching the record of DNA related to ancient hominins. Interestingly, they discovered ancient human fragments that matched the Denisovan’s associated mtDNA in four different sediment layers that deposited ~ 100 ka and ~ 60 ka.

Interestingly, they found that the 60 ka hominin mtDNA has the closest genetic relationship with Denisova 3 and 4 – that is, samples taken from the Denisova Cave in Altai, Russia. In contrast, mtDNA dating ~ 100 ka shows separation from the line leading to Denisova 3 and 4.

Using sediment DNA from BKC, the researchers found the first genetic evidence that Denisovans lived outside the Denisova Cave. This new study supports the idea that Denisovans had a wide geographic distribution that was not limited to Siberia, and that they may have adapted to life at high altitudes and contributed to such adaptation to modern humans on the Tibetan plateau.

However, many questions still remain open. For example, what is the newest age of the Denisovans in BKC? Due to the revised nature of the top three layers, it is difficult to directly associate the mtDNA with its deposition age, which is only 20 to 30 ka BP. Hence, it is uncertain whether or not these late Denisovans met modern humans. Furthermore, based on mtDNA, we still do not know the exact relationship between the BKC Denisovans, those from the Denisova Cave in Siberia, and modern Tibetans. Future nuclear DNA from this site could be a tool to investigate these questions further.

Reference: Zhang D., Xia H., Chen F. et al. Denisovan DNA in late Pleistocene sediments from the Baishiya karst cave on the Tibetan plateau. science. 2020; 370 (6516): 584. doi: 10.1126 / science.abb6320.

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