Denisovan DNA found in sediments of Baishiya Karst Cave on Tibetan Plateau

One year after the publication of research on the Xiahe mandible, the first Denisovan fossil found outside of Denisova Cave, the same research team has now reported their findings of Denisovan DNA from sediments of the Baishiya Karst Cave (BKC) on the Tibetan Plateau where the Xiahe mandible was found. 

Baishiya Karst Cave [Credit: HAN Yuanyuan]

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

Using cutting-edge paleogenetic technology, the researchers successfully extracted Denisovan mtDNA from Late Pleistocene sediment samples collected during the excavation of BKC. Their results show that this Denisovan group is closely related to the late Denisovans from Denisova Cave, indicating Denisovans occupied the Tibetan Plateau for a rather long time and had probably adapted to the high-altitude environment.

Denisovans were first discovered and identified in 2010 by a research team led by Prof. Svante Paabo. Almost a decade later, the Xiahe mandible was found on the Tibetan Plateau. As the first Denisovan fossil found outside of Denisova Cave, it confirmed that Denisovans had occupied the roof of the world in the late Middle Pleistocene and were widespread. Although the Xiahe mandible shed great new light on Denisovan studies, without DNA and secure stratigraphic and archaeological context, the information it revealed about Denisovans was still considerably restricted.

Collecting sediment DNA samples [Credit: HAN Yuanyuan]

In 2010, a research team from Lanzhou University led by Prof. CHEN Fahu, current director of ITP, began to work in BKC and the Ganjia basin where it is located. Since then, thousands of pieces of stone artifacts and animal bones have been found. Subsequent analysis indicated that the stone artifacts were mainly produced using simple core-flake technology. Among animal species represented, gazelles and foxes dominated in the upper layers, but rhinoceros, wild bos and hyena dominated in the lower layers. Some of the bones had been burnt or have cut-marks, indicating that humans occupied the cave for a rather long time.

To determine when people occupied the cave, researchers used radiocarbon dating of bone fragments recovered from the upper layers and optical dating of sediments collected from all layers in the excavated profile. They measured 14 bone fragments and about 30,000 individual grains of feldspar and quartz minerals from 12 sediment samples to construct a robust chronological framework for the site. Dating results suggest that the deepest excavated deposits contain stone artifacts buried 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, researchers used sedimentary DNA technology to analyze 35 sediment samples specially collected during the excavation for DNA analysis. They captured 242 mammalian and human mtDNA samples, thus enriching the record of DNA related to ancient hominins. Interestingly, they detected ancient human fragments that matched mtDNA associated with Denisovans in four different sediment layers deposited ~100 ka and ~60 ka.

Preparing sediment samples in IVPP cleanroom [Credit: WANG Xiao]

More interestingly, they found that the hominin mtDNA from 60 ka share the closest genetic relationship to Denisova 3 and 4 - i.e., specimens sampled from Denisova Cave in Altai, Russia. In contrast, mtDNA dating to ~100 ka shows a separation from the lineage leading to Denisova 3 and 4.

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

However, there are still many questions left. For example, what's the latest age of Denisovans in BKC? Due to the reworked nature of the top three layers, it is difficult to directly associate the mtDNA with their depositional ages, which are as late as 20-30 ka BP. Therefore, it is uncertain whether these late Denisovans had encountered modern humans or not. In addition, just based on mtDNA, we still don't know the exact relationship between the BKC Denisovans, those from Denisova Cave in Siberia and modern Tibetans. Future nuclear DNA from this site may provide a tool to further explore these questions.

The study was published in Science.

Source: Chinese Academy of Sciences [October 30, 2020]

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Tracking the Himalayan history from the evolution of hundreds of frogs, lizards and snakes

The Himalaya are among the youngest and highest mountains in the world, but the exact timing of their uplift and origins of their biodiversity are still in debate. Generally, there are two hypotheses about the uplift process of the Himalaya. The "Stepwise Hypothesis" states that the Himalaya rose slowly from 1000-2500 m during 56-23 million years ago (Ma), before an additional rapid uplift to 4000 m during 23-19 Ma, and a final rise to the current average elevations (~5000 m) at around 15 Ma. Alternatively, recent hydrological and thermal evidences support that this region was probably not elevated to current elevation till mid-Pliocene ("Late Orogeny Hypothesis").

The Himalaya and representative amphibians and reptiles
[Credit: Science China Press]

Time-based records of biological processes can be informative about montane histories and environmental changes. Various hypotheses about Himalayan origins can be tested using phylogenetic information and estimates of the timing of biological speciation events. To address the question about the timing of the Himalaya uplift, we carried out field work across the Himalaya to collect samples of amphibians and reptiles. The Himalayan region encompasses multiple countries and has many access challenges, so sampling across the entire region is difficult, which has inhibited integrative studies of the origin of the Himalayan biota.

Combining 14 time-calibrated phylogenies of Himalayan-associated amphibian and reptile families involving 85 genera and 1628 species, we estimated times of divergence among 183 species that occur in the Himalaya. We identified 230 biogeographic events related to the Himalayan species. The dynamics of in situ diversification and dispersal rates remained essentially parallel across the Cenozoic. Both the in situ diversification rate, as well as the dispersal rate into the Himalaya, fit the Stepwise Hypothesis for the origin of this mountain range. In contrast, our estimates of origination and peak diversification are not consistent with the late-uplift hypothesis.

Biotic assembly through time of herpetofauna in the Himalaya. (a): The rates of in situ diversification
 and dispersal of the Himalayan herpetofauna through time (smoothed across 5 Ma windows).
Dispersal indicates "dispersal into the Himalaya." MDivE = maximal number of observed
 in situ diversification events per Ma. MDisE = maximal number of observed dispersal events
per Ma. Ambiguous events are separately listed. (b): Dispersal events from adjacent regions
 into the Himalaya (smoothed across 5 Ma windows). MDisE = maximal number
of observed dispersal events per Ma [Credit: Science China Press]

The rapid Himalayan uplift and associated intensified South Asia Monsoon not only promoted a pulse of uplift-driven in situ diversification, but also affected the rates of biotic interchange. Biotic interchange was restricted by the lack of a moist environment that is required by many reptiles and amphibians. In contrast, an expanded tropical forest belt is thought to have persisted between the Himalaya and Southeast Asia since the middle Miocene, which likely accounts for the high dispersal rates between these two regions.

This work has important implications about the assembly process of Himalayan herpetofauna and its conservation. Our analyses show a deep-rooted origin of Himalayan herpetofauna originating in the Paleocene, but with rapid diversification in the Miocene.

The study is published in the National Science Review 2020.

Source: South China Press [October 26, 2020]

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