A late Middle Pleistocene Denisovan mandible from the Tibetan Plateau

Abstract

Denisovans are members of a hominin group who are currently only known directly from fragmentary fossils, the genomes of which have been studied from a single site, Denisova Cave1,2,3 in Siberia. They are also known indirectly from their genetic legacy through gene flow into several low-altitude East Asian populations4,5 and high-altitude modern Tibetans6. The lack of morphologically informative Denisovan fossils hinders our ability to connect geographically and temporally dispersed fossil hominins from Asia and to understand in a coherent manner their relation to recent Asian populations. This includes understanding the genetic adaptation of humans to the high-altitude Tibetan Plateau7,8, which was inherited from the Denisovans. Here we report a Denisovan mandible, identified by ancient protein analysis9,10, found on the Tibetan Plateau in Baishiya Karst Cave, Xiahe, Gansu, China. We determine the mandible to be at least 160 thousand years old through U-series dating of an adhering carbonate matrix. The Xiahe specimen provides direct evidence of the Denisovans outside the Altai Mountains and its analysis unique insights into Denisovan mandibular and dental morphology. Our results indicate that archaic hominins occupied the Tibetan Plateau in the Middle Pleistocene epoch and successfully adapted to high-altitude hypoxic environments long before the regional arrival of modern Homo sapiens.

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Fig. 1: The Xiahe mandible.
Fig. 2: Phylogenetic position of the Xiahe proteome within Hominidae.
Fig. 3: The palaeoclimate background to human presence on the Tibetan Plateau.

Data availability

All the proteomic mass spectrometry data have been deposited in the ProteomeXchange Consortium repository (http://www.proteomexchange.org/) with the identifier PXD011377. Protein consensus sequences for the Xiahe hominin used for phylogenetic analysis are available in Supplementary Information 2. A surface scan model of the Xiahe mandible is publicly available at: https://www.eva.mpg.de/evolution/downloads/registration-form-xiahe.html.

Code availability

All R code used to generate protein deamidation and peptide cleavage patterns are available upon request from F.W. (frido.welker@palaeo.eu).

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Acknowledgements

We thank the sixth Gung-Thang Living Buddha, the anonymous monk, L. L. Wang and her husband for providing us the opportunity to study the fossil; D. Madsen, J. Brantingham, D. Rhode, C. Perreault, J. S. Yang, T. Cheng, X. K. Shen, J. T. Yao, Z. X. Yang, J. Chen, X. Z. Huang, M. H. Qiu and C.-R. Huang for their assistance with the fieldwork and in the laboratory; members of the local government of Xiahe County and Ganjia town for help, the monks in the Baishiya temple and people from Bajiao Ancient City for their support of the fieldwork; O. Jöris, G. Smith, P. Ungar and R. Grün for discussions and comments; many curators and colleagues who, over the years, gave us access to recent and fossil hominin specimens for computed tomography scanning, photogrammetry or analysis; E. Trinkaus for providing comparative data; H. Temming, S. Tuepke, C. Molenaar and Diondo for their technical assistance; S. Pääbo, V. Slon and A. Ayinuer-Petri for ancient DNA analytical support. We received support from the Strategic Priority Research Program of Chinese Academy of Sciences, Pan-Third Pole Environment Study for a Green Silk Road (Pan-TPE) (XDA20040000) and National Natural Science Foundation of China (41620104007). D.J.Z. received support from National Natural Science Foundation of China (41771225). Fieldwork in 2018 was supported by the Second Tibetan Plateau Scientific Expedition (Project no. 4). U–Th dating was supported by the Science Vanguard Research Program of the Ministry of Science and Technology (107-2119-M-002-051) and the Higher Education Sprout Project of the Ministry of Education, Taiwan (107L901001). J.-J.H. and F.W. thank the Max Planck Society for providing financial support.

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Nature thanks Aida Gómez-Robles, Antonio Rosas and the other anonymous reviewer(s) for their contribution to the peer review of this work.

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Contributions

F.H.C., J.-J.H. and D.J.Z. designed the study. D.J.Z., G.R.D., G.H.D., H.W., J.W. and H.X. collected field data. D.J.Z., H.X. and J.W. carried out sampling and subsampling process. C.-C.S. and T.-L.Y. conducted U–Th dating of the crust carbonates. Q.M.F. performed the ancient DNA extractions. Mandibular metrical and non-metrical data were compiled and analysed by J.-J.H. and I.B. Geometric morphometric analyses of the mandible were performed by S.E.F., S.S., I.B., D.J.Z. and J.-J.H. Dental metrical and non-metrical data were compiled and analysed by S.E.B. and M.M.S. H.X., F.W., R.F. and S.D. performed proteomic analysis. F.H.C., F.W., J.-J.H., D.J.Z. and C.-C.S. wrote the paper with contributions of all authors.

Corresponding authors

Correspondence to Fahu Chen or Dongju Zhang or Jean-Jacques Hublin.

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Extended data figures and tables

Extended Data Fig. 1 Location of Baishiya Karst Cave.

a, Location of Baishiya Karst Cave, archaic Homo sites, and selected Middle and Upper Palaeolithic sites in East and Central Asia. Numbers denoting the archaeological sites are: (1) Mezmaiskaya Cave; (2) Teshik-Tash Cave; (3) Okladnikov Cave; (4) Denisova Cave; (5) Kara-Bom; (6) Tongtian Cave; (7) Nyadem; (8) Quesang; (9) Chikhen Agui; (10) Shuidonggou; (11) Guanyin Cave, (12) Zhiren Cave; (13) Fuyan Cave; (14) Lingjing; (15) Xujiayao; (16) Tianyuan Cave; (17) Zhoukoudian Upper Cave; (18) Jinniushan. Denisovan ancestry is also detectable in other East and South Asian populations at low frequencies. b, Ganjia Basin with the Baishiya Karst Cave (red star) and two Palaeolithic sites (NML01, Nimalong01; WET01, Waerta01; blue triangles). Base maps generated by ArcGIS 10.3 using data provided by https://earthexplorer.usgs.gov/.

Extended Data Fig. 2 The Xiahe mandible with adhering carbonate crust.

af, Lateral (a), buccal (b), occlusal (c), inferior (d), anterior (e) and posterior (f) views. Sampling locations for ancient proteins and ancient DNA can be seen on the M2 and ascending ramus, and sampling location for U–Th dating on the inferior surface.

Extended Data Fig. 3 Surface model of the Xiahe mandible after digital removal of the adhering carbonate crust.

af, Lateral (a), buccal (b), occlusal (c), inferior (d), anterior (e) and posterior (f) views.

Extended Data Fig. 4 Preservation of the Xiahe dentine proteome.

a, Deamidation of five Xiahe proteins also identified in several proteomes from Middle and Late Pleistocene fossils. b, Glutamine deamidation of peptide P1105 observed in the zooarchaeology by mass spectrometry (ZooMS) analysis of the Xiahe dentine sample compared to reference data. n = number of specimens included. c, Correlation between deamidation observed in LC–MS/MS experiments for ammonium bicarbonate (AmBic) and acid-demineralization (Acid) extracts (R2 = 0.99). d, Length distribution of non-tryptic peptides in a Late Pleistocene Neanderthal and the Xiahe dentine proteome. AA, amino acids. Violins stretch from the minimum to the maximum value; box plots indicate the median (middle line), 25% and 75% (boxes) and stretch to 1.5× the interquartile range (whiskers). n = number of unique spectra included. Deamidation is based on quantitative MALDI–TOF-MS analysis (b) or semiquantitative LC–MS/MS spectral counting methods (a, c). ‘0%’ indicates an absence of deamidation and ‘100%’ indicates complete deamidation of asparagine and glutamine. a, d, Combined data for all six LC–MS/MS runs conducted on the Xiahe protein extracts. c, Combined data from the three replicates per extraction method. Samples are colour-coded according to geological age. Data were obtained from previous studies21,54,55,66.

Extended Data Fig. 5 Normalized frequencies of peptide cleavage patterns of selected proteins.

Spectral counts are based on the total number of ammonium bicarbonate and acid-demineralization PSMs (six runs) and include both N and C termini of each aligned PSM. Red colours indicate more PSMs than expected and green colours fewer PSMs than expected, compared to a random cleavage model for each protein separately. Note differences in colour scale. The title of each plot refers to the UniProt accession code for the relevant protein.

Extended Data Fig. 6 Geometric morphometrics of the mandible.

bgPCA of mandibular shape. Although some overlap exists, all groups show a distinct mandibular shape. Xiahe plots at the edge of the H. erectus distribution and within the range of Middle Pleistocene Homo. Surface models illustrate mandibular shape changes along bgPC1 (lateral view) and bgPC2 (lateral and superior view). Recent H. sapiens are shown in cyan, Upper Palaeolithic and Holocene H. sapiens in light blue, early H. sapiens in dark blue, Neanderthals in pink, H. erectus in green and other Middle Pleistocene fossil hominins in orange. SH, Sima de los Huesos. n = number of unique individuals contained in each hull. Further specimen names can be found in Supplementary Table 6.

Extended Data Fig. 7 Geometric morphometrics of the dental arcade.

a, bgPCA in form space. b, bgPCA in shape space. The wireframes illustrate form changes along bgPC1 and bgPC2. Colours are as in Extended Data Fig. 6. The wireframes show the form and shape changes along bgPC1 and bgPC2, respectively. Estimated wireframes used in the bgPCA are indicated by ‘est’. SH, Sima de los Huesos; D, Dmanisi. Further specimen names can be found in Supplementary Table 6. n = number of unique individuals contained in each hull.

Extended Data Fig. 8 Root morphology and EDJ shape.

a, The roots of the M1 are typical of lower molars with a mesial and distal plate-like root. There are mesial and distal plate-like roots on the M2; however, there is an additional accessory lingual root that splits off distally from the mesial root about 2/3 from the cervix. The P3 root is a Tomes’ form with a distinct lingual groove. b, A bgPCA of the EDJ ridge and cervix shape reveals a clear separation between early Homo and H. erectus on one side and Neanderthals and H. sapiens on the other side, with Middle Pleistocene hominins in between. Colours are as in Extended Data Fig. 6 for relevant groups. KRP, Krapina; LQ, La Quina. n = number of unique individuals contained in each hull. Note that the taxonomic status of Sangiran 5 is currently uncertain. Further specimen names can be found in Supplementary Table 6.

Extended Data Table 1 U–Th ages of the crust attached on Xiahe mandible
Extended Data Table 2 Endogenous protein coverage statistics

Supplementary information

Supplementary Information

This file contains Supplementary Information Sections 1-4, including an additional description of U-Th dating, comparative samples for morphological analysis, further notes on additional morphological results and reference data for palaeoproteomic phylogenetic analysis. It includes Supplementary Tables 1-5, Supplementary Figures 1-4 and additional references.

Reporting Summary

Supplementary Data

File in .fasta format containing consensus sequences derived from the Xiahe mandible proteomic analysis used for phylogenetic analysis.

Supplementary Table 6

This table contains specimen names and numbers used for the various morphological analysis conducted in comparison to the Xiahe mandible.

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Chen, F., Welker, F., Shen, C. et al. A late Middle Pleistocene Denisovan mandible from the Tibetan Plateau. Nature 569, 409–412 (2019). https://doi.org/10.1038/s41586-019-1139-x

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