The discovery and journey of this fossil, into hands of scientists is an interesting one and well worth exploration. One of the team that identified it as Denisovan relates the story, which was passed on to him by local archaeologists.
Jean-Jacques Hublin (1), states “In 1980, an anonymous monk recovered the specimen while visiting the Baishiya Karst Cave, near Xiahe, to pray and meditate. Local people used to grind the “holy bones” collected in this cave to use them as medicine; this one, maybe more precious because it was clearly human, escaped destruction. Instead, it was offered to the Sixth Gung-Thang Living Buddha, who later passed it on to scientists at Lanzhou University. It was only in 2010 that a team from that university, led by paleoclimatologist and Quaternary geologist Fahu Chen, could start to investigate the Baishiya Karst Cave and its surroundings.”
Baishiya Cave, Tibet – one of the highest altitude hominin sites in the world at approximately 3280m a.s.l. the flags are Budhist prayer flags, indicating that the cave is a site of pilgrimage. Monks were previously known to retreat here for prayer and meditation. Photo credit: ref. 1.
The above account sounds fairly simple, however, the story from a Chinese source (2) is rather more complex: “A lama who was a hermit in the Baishiya Cave discovered it. This strange bone caught his attention - it was like a human bone, but not quite the same. Later, the lama took the fossil out of the cave and presented it to Dan Beiwangxu, the sixth living Buddah of Xiahe. The knowledgeable living Buddha recognized that this was a human fossil, and he wanted to find someone to study it.
The Sixth Gong Tangcang Rinpoche knew a couple. The husband was a professor in the Department of Chemistry at Lanzhou University, and the wife was a translator at the Institute of Environment and Engineering in Cold and Arid Regions of the Chinese Academy of Sciences. The couple saw the mandible and realized it was an important hominin fossil.
After the couple's matchmaking, the living Buddha Gongtangcang handed over this precious mandible fossil to Dong Guangrong. At that time, Dong Guangrong, a researcher at the Chinese Academy of Sciences who had long been engaged in Quaternary geological research in sandy areas, was doing research on desert evolution at the Salawusu site. Later, Dong Guangrong contacted Professor Chen Fahu, who was teaching in the Department of Geography of Lanzhou University at the time, and the two planned to study this fossil together. However, their respective research fields are not ancient humans, and the research tasks in their own fields are already quite heavy, and the research on Xiahe Man fossils has to be delayed again and again.
In 2004, Zhang Dongju entered Lanzhou University to study for a Ph.D. She joined Professor Chen Fahu's research team, mainly studying the activities of Paleolithic humans on the Loess Plateau. She has always had a strong interest in the fossils of Xiahe Man, but because her doctoral research project has not been completed, she has not been able to spend a lot of time on research.
After being put on hold for nearly 30 years, it was not until 2010 that the systematic study of the fossils of Xiahe Man was started. At this time, Zhang Dongju also graduated from the Ph.D. and stayed at the school, and she changed her future research direction from the Loess Plateau to the Qinghai-Tibet Plateau. The Xiahe Man fossil research, which has been discussed for decades, is finally on the agenda.”
The whereabouts of the cave that the fossil had been found in, however, were unknown. After many twists and turns, it took Zhang Dongju and colleagues, nearly six years to finally find the Baishiya Karst Cave in Xiahe County based on the descriptions and other information provided by the lamas at that time, and determined that this is the place where the Xiahe mandible fossil was unearthed. Needless to say, Fahu Chen became the paper’s lead author, while Zhang Dongju doesn’t even get a mention.
Zhang Dongju, (middle right) excavating at Baishiya Cave in 2018, ref 1.
Once the origin of the fossil had been determined, Zhang Dongju contacted Jean-Jacques Hublin of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, for his opininion on the fossil. She also sent photographs. As Hublin (1) says: “At the sight of the pictures on my screen, my heart jumped. The fossil was quite complete and clearly nonmodern.” By the end of September, less than 8 weeks later he was in Lanzhou, China, examining the mandible.
The Xiahe mandible from Baishiya Cave, China. Photo credit: ref 3. Original caption reads: Figure 1. The Xiahe mandible. Anterior (a), occlusal (b), lateral (c), and internal (d) views of the reconstructed specimen. The preservation of the symphyseal region of the mandible allows for a virtual reconstruction of the two sides of the mandible. Mirrored parts are in gray. The symphyseal section and the infradentale-gnathion angle are displayed on d.
On examination, of the fossil mandible, Hublin realised three exciting facts. Firstly the preservation was extremely good and thus ancient DNA extraction might be possible, secondly some of the matrix that the fossil must have, originally, been interred in was present on the base of the fossil and thus dating too might prove successful and finally, the specimen exhibited no chin – thus it definitely wasn’t a modern human, but something far more ancient, resembling a Neanderthal.
And so the European/Chinese collaboration set to work. Three year later, on the 1st of May 2019, the paper (3), was published in Nature.
The findings were:
- No evidence for the preservation of ancient DNA in the Xiahe mandible
- The mandible belonged to Denisovan, identified by ancient protein analysis, with the Xiahe specimen closest to Denisova 3. However the identification was tenuous and based on a single amino acid position
- The fossil jawbone was 160 thousand years old through U-series dating of an adhering carbonate matrix
- Finally, according to the authors “Among the pene-contemporaneous East Asian specimens, Xiahe is similar in several aspects to the Penghu 1 mandible24. The metrics of the two fossils that can be compared are very similar (SI Tab. 2) and their dental similarities are striking. Like Xiahe, Penghu 1 displays anagenesis of the M3. Although Penghu’s M2 is smaller than that of Xiahe, in both individuals the M2 crown is wider mesio-distally than bucco-lingualy. Xiahe’s and Penghu’s M2 roots are remarkable. In addition to mesial and distal plate-like roots there is a prominent accessory lingual root that branches off the mesial root below the cervix. This feature is of particular interest as three-rooted mandibular molars are very rare in non-Asian H. sapiens but appear much more frequently in recent Asian populations (see SI). Finally, in both specimens, the P3 displays Tomes’ root, a feature occasionally observed in other fossil hominins. Among other non-sapiens Chinese specimens, similarities with the Xujiayao material should also be underlined. For example, at the EDJ, the M2 displays a moderately complex occlusal basin, low dentine horns and a weakly expressed protostylid. These observations reinforce the idea that Denisovans are already represented in the described fossil record of China, particularly in fossils like Penghu 1 and Xujiayao.”
The paper also presents the phylogenetic position of the Xiahe proteome within great apes (Hominidae):
Photo credit, ref 3 Figure 2.
So, while the paper, and indeed its title claim the fossil to be, definitively a Denisovan, this is not an open-and-shut case.
While the paper itself presents a far from conclusive case that the mandible from Baishiya Cave, was indeed a Denisovan, further work at the cave, (4), would soon lead to a definitive species identification.
In 2018 and 2019, Zhang Dongju led excavations of tests pits at Baishiya cave. The motivation behind these excavations was to find out whether the cave had extant sediments coeval with partial mandible described and dated in the Chen et al. (3), paper as approximately 160,000 years old.
The excavation team, were extremely pleased with the results finding intact sediments, copious stone tools and a large bone assemblage.
Numerous soil samples were taken from ten excavated layers, for the purposes of OSL dating and more importantly the extraction of ancient DNA.
Stratigraphy and Bayesian modelling of OSL and Radiocarbon ages for Baishiya Cave excavation area T2. Original caption reads: “Fig. 2. Stratigraphy and dating results of T2. (A) Composite schematic stratigraphy of excavation area T2. The alternating colors are for illustration purposes only. The positions of sedimentary DNA samples from which Denisovan and animal DNA were found are shown as red stars and green stars, respectively. (B) Bayesian modelling results for all radiocarbon and optical ages. Red probability distributions represent the unmodelled ages (likelihoods) and green distributions represent the modelled ages (posterior probabilities). The narrow and wide bars beneath each distribution represent the 68.2% and 95.4% probability ranges of the modelled ages. Start and end ages have been modelled for each layer and phase, with age ranges (95.4% confidence interval, random-only errors) given in parentheses.” Photo credit ref 4.
The analysis of the ages of the sediment samples showed that they were in chronological order and were deeper, and older, than the original, fossil mandible discovered at the cave in 1980.
The eDNA extracted from the sediment samples were, everything and more than the archaeologists had hoped for. Sediment samples from layers except 1 and 5 had 50μl of DNA extracted. For extracts from a subset of the sediment samples, several libraries were generated based on positive ancient hominin results obtained in the first screening. The authors found that libraries from Layers 2, 3, 4, and 7 have between 15.6% and 50% C->T 29 terminal substitutions indicating the presence of ancient hominin DNA. They then determined which, hominin groups may have contributed mtDNA to these samples, they examined sequences for substitutions found to be unique to modern humans, Neanderthals, Denisovans, and a ~430,000-year-old hominin individual from Sima de los Huesos.
Twenty four of the libraries showed ancient DNA had been captured in various proportions. From the 24 libraries, between 31% (368/1186) and 95% (601/635) of the mtDNA fragments that covered informative positions matched the Denisovan state, while 0–14% (1/7) matched the Neanderthal state, 0–3.7% (5/135) the Sima state, and 0–67% (338/508) the modern human state.
By restricting the analysis to DNA fragments for sound technical reasons and merging deaminated hominin mtDNA fragments from libraries for each layer, they arrived at an average mtDNA coverage (for the Denisovan genome) for Layers 2, 3, 4, and 7 of 0.37-fold, 1.5-fold, 40-fold, and 1.3-fold, respectively.
The authors also tested whether the mtDNA was from multiple individuals and found: “DNA recovered from sediments may be derived from multiple different individuals, and this is the case at least in Layer 4..”
Lastly they tested which Denisovan genomes the recovered mtDNA sequenced best matched. These showed that on most analyses that all sequences formed a clade with Denisova 3 and 4.
Reference 4, Fig 4.
Original caption reads: MtDNA phylogenetic trees for sediment samples from
Layers 4 and 2 (A), Layers 4 and 3 (B) or Layers 4 and 7 (C) of the Baishiya
Karst Cave as well as mtDNA from four Denisovans from Denisova Cave and a
~430,000- year-old hominin from Sima de los Huesos in Spain.
It is notable that the mtDNA sequences from layer 7 fall closer to the Denisova 2 and 8 mtDNA sequences from Denisova cave. This is not surprising as the depositional age for Layer 7 (108–97 ka) is older than those 4 for Denisova 3 and 4, but younger than the ages for Denisova 2 (194–122ka) and Denisova 8 (136–105 ka).
The authors conclude: “..the stratigraphic, chronological and sedimentary DNA results presented show that Denisovans occupied BKC at ~100 and ~60 ka ago. This confirms that Denisovans were widely distributed in Asia during the late Pleistocene. Together with the older Xiahe mandible, it suggests that they had presumably adapted to the high-altitude environments on the Tibetan Plateau over a long, period, of time. It is tempting to speculate that the genetic adaptations to high altitudes seen in modern Tibetans and perhaps associated with a haplotype introgressed from Denisovans may have evolved during the extended occupation of this high-altitude environment by Denisovans.”
This second paper, thus provides conclusive proof that:
The Xiahe mandible is that of a Denisovan
Denisovans occupied Baishiya Cave for at least 40,000 years, and possibly, as long as 70,000 years if the tenuous mtDNA results from Layer 2, dated to 30Ka BP are confirmed.
The paper does not address the ‘elephant in the room’, however. This is the fact that, mtDNA sequences from Neanderthals and the individual from the ~430,000- year-old hominin from Sima de los Huesos were also detected.
These mtDNA, sequences are highly problematic for the Chinese as they are at odds with their multiregional model of human evolution and is at odds with the more widely accepted "Out of Africa" theory. It is therefore not surprising that they are not analysed, in more detail, in the paper as they call into question, the Chinese version of the timing and dispersal routes of ancient hominins. Furthermore, they subsequently, call into question, the identity of such specimens as that of the almost complete cranium from Harbin (5).
Perhaps when we look into the face of this specimen we are seeing what Denisovans truly looked like?
The Harbin cranium from ref 5. See also my post on the original announcement of the fossil’s discovery in China Daily (see here).
References
(1). Hublin, J-J. (2019). How We Found an Elusive Hominin in China. At: https://www.sapiens.org/biology/xiahe-jaw-denisovan/ accessed 26/07/2022
(2). Wu, B. (2019). This bone comes from a mysterious hominin, proving that 160,000 years ago, ancient humans had arrived on the Qinghai-Tibet Plateau. Sohu News, at: http://www.sohu.com/a/311511521_161795 accessed 26/07/2022.
(3). Chen, F., Welker, F., Shen, C.C., Bailey, S.E., Bergmann, I., Davis, S., Xia, H., Wang, H., Fischer, R., Freidline, S.E. and Yu, T.L., (2019). A late middle Pleistocene Denisovan mandible from the Tibetan Plateau. nature, 569(7756), pp.409-412.
(4). Zhang, D., Xia, H., Chen, F., Li, B., Slon, V., Cheng, T., Yang, R., Jacobs, Z., Dai, Q., Massilani, D. and Shen, X., 2020. Denisovan DNA in late Pleistocene sediments from Baishiya Karst Cave on the Tibetan plateau. Science, 370(6516), pp.584-587.
(5). Ni, X., Ji, Q., Wu, W., Shao, Q., Ji, Y., Zhang, C., Liang, L., Ge, J., Guo, Z., Li, J. and Li, Q., 2021. Massive cranium from Harbin in northeastern China establishes a new Middle Pleistocene human lineage. The Innovation, 2(3), p.100130.
