Large-scale application of palaeoproteomics (Zooarchaeology by Mass Spectrometry; ZooMS) in two Palaeolithic faunal assemblages from China

The application of Zooarchaeology by Mass Spectrometry (ZooMS) on Pleistocene sites in Europe and northern Asia has resulted in the discovery of important new hominin fossils and has expanded the range of identified fauna. However, no systematic, large-scale application of ZooMS on Palaeolithic sites in East Asia has been attempted thus far. Here, we analyse 866 morphologically non-diagnostic bones from Jinsitai Cave in northeast China and Yumidong Cave in South China, from archaeological horizons dating to 150–10 ka BP. Bones from both sites revealed a high degree of collagen preservation and potentially time-related deamidation patterns, despite being located in very distinct environmental settings. At Jinsitai, we identified 31 camel bones, five of which were radiocarbon dated to 37–20 ka BP. All dated specimens correspond to colder periods of Marine Isotope Stages 3 and 2. We regard the presence of camels at Jinsitai as evidence of wild camels being a megafauna taxon targeted, most likely by early modern humans, during their expansion across northeast Asia. This large-scale application of ZooMS in China highlights the potential of the method for furthering our knowledge of the palaeoanthropological and zooarchaeological records of East Asia.

[1]  A. Derevianko,et al.  The Middle Paleolithic of Tsagaan Agui Cave in the Gobi Altai region of Mongolia and its Siberian and Central Asian links , 2023, Archaeological Research in Asia.

[2]  A. Bacon,et al.  Late Pleistocene large-bodied mammalian fauna from Mocun cave in south China: Palaeontological, chronological and biogeographical implications , 2022, Quaternary Science Reviews.

[3]  A. Derevianko,et al.  Shelter in an extreme environment: the Pleistocene occupation of Tsagaan Agui Cave in the Gobi Desert , 2022, Antiquity.

[4]  C. Warinner,et al.  A primer for ZooMS applications in archaeology , 2022, Proceedings of the National Academy of Sciences of the United States of America.

[5]  P. Voinchet,et al.  Applying a Bayesian approach for refining the chronostratigraphy of the Yumidong site in the Three Gorges region, central China , 2022, Quaternary Geochronology.

[6]  A. Derevianko,et al.  First Documented Camelus knoblochi Nehring (1901) and Fossil Camelus ferus Przewalski (1878) From Late Pleistocene Archaeological Contexts in Mongolia , 2022, Frontiers in Earth Science.

[7]  M. Shunkov,et al.  Examining collagen preservation through glutamine deamidation at Denisova Cave , 2021 .

[8]  M. Shunkov,et al.  Pleistocene sediment DNA reveals hominin and faunal turnovers at Denisova Cave , 2021, Nature.

[9]  K. Douka,et al.  Distinguishing African bovids using Zooarchaeology by Mass Spectrometry (ZooMS): New peptide markers and insights into Iron Age economies in Zambia , 2021, PloS one.

[10]  A. Rosen,et al.  Zaraa Uul: An archaeological record of Pleistocene-Holocene palaeoecology in the Gobi Desert , 2021, PloS one.

[11]  C. Warinner,et al.  Ancient DNA analysis , 2021, Nature Reviews Methods Primers.

[12]  C. Stringer,et al.  Origins of modern human ancestry , 2021, Nature.

[13]  H. Bocherens,et al.  The Mammuthus-Coelodonta Faunal Complex at its southeastern limit: A biogeochemical paleoecology investigation in Northeast Asia , 2020, Quaternary International.

[14]  Wang Naihui,et al.  Testing the efficacy and comparability of ZooMS protocols on archaeological bone. , 2020, Journal of proteomics.

[15]  Xingjun Hu,et al.  An assemblage of Stegodon orientalis fossils from the Yumidong Cave site in Wushan, Chongqing, with emphasis on the taphonomic analysis , 2020 .

[16]  A. Rodríguez-Hidalgo,et al.  Neanderthal faunal exploitation and settlement dynamics at the Abri du Maras, level 5 (south-eastern France) , 2020, Quaternary Science Reviews.

[17]  E. Scott,et al.  The IntCal20 Northern Hemisphere Radiocarbon Age Calibration Curve (0–55 cal kBP) , 2020, Radiocarbon.

[18]  F. Monna,et al.  Images of camels on a mammoth tusk from West Siberia , 2020 .

[19]  M. Soressi,et al.  Non-destructive ZooMS identification reveals strategic bone tool raw material selection by Neandertals , 2020, Scientific Reports.

[20]  P. Manning,et al.  Collagen deamidation in archaeological bone as an assessment for relative decay rates , 2019, Archaeometry.

[21]  R. Irizarry.  ggplot2 , 2019, Introduction to Data Science.

[22]  J. Hublin,et al.  Combining ZooMS and zooarchaeology to study Late Pleistocene hominin behaviour at Fumane (Italy) , 2019, Scientific Reports.

[23]  Qiaomei Fu,et al.  A late Middle Pleistocene Denisovan mandible from the Tibetan Plateau , 2019, Nature.

[24]  F. Welker.  Palaeoproteomics for human evolution studies , 2018, Quaternary Science Reviews.

[25]  Laura T. Buck,et al.  Homo sapiens in Arabia by 85,000 years ago , 2018, Nature Ecology & Evolution.

[26]  Yu. S. Lyakhnitsky.  Conservation of paleolithic cave art in the Capova cave , 2018 .

[27]  K. Douka,et al.  On the origin of modern humans: Asian perspectives , 2017, Science.

[28]  S. Pääbo,et al.  Direct dating of Neanderthal remains from the site of Vindija Cave and implications for the Middle to Upper Paleolithic transition , 2017, Proceedings of the National Academy of Sciences.

[29]  E. Boëda,et al.  Recent discovery of a unique Paleolithic industry from the Yumidong Cave site in the Three Gorges region of Yangtze River, southwest China , 2017 .

[30]  Sabine Gaudzinski-Windheuser,et al.  Middle Pleistocene protein sequences from the rhinoceros genus Stephanorhinus and the phylogeny of extant and extinct Middle/Late Pleistocene Rhinocerotidae , 2017, PeerJ.

[31]  Y. Coppens,et al.  Additional evidence for early modern human morphological diversity in Southeast Asia at Tam Pa Ling, Laos , 2017 .

[32]  J. Sealy,et al.  Earliest Evidence for the Ivory Trade in Southern Africa: Isotopic and ZooMS Analysis of Seventh–Tenth Century ad Ivory from KwaZulu-Natal , 2016 .

[33]  J. Thomas-Oates,et al.  The effects of demineralisation and sampling point variability on the measurement of glutamine deamidation in type I collagen extracted from bone , 2016 .

[34]  Michael Buckley,et al.  Identification of a new hominin bone from Denisova Cave, Siberia using collagen fingerprinting and mitochondrial DNA analysis , 2016, Scientific Reports.

[35]  Elena R. Schroeter,et al.  Glutamine deamidation: an indicator of antiquity, or preservational quality? , 2016, Rapid communications in mass spectrometry : RCM.

[36]  Roman Fischer,et al.  Animal origin of 13th-century uterine vellum revealed using noninvasive peptide fingerprinting , 2015, Proceedings of the National Academy of Sciences.

[37]  J. Hublin,et al.  Using ZooMS to identify fragmentary bone from the Late Middle/Early Upper Palaeolithic sequence of Les Cottés, France , 2015 .

[38]  H. Fischer,et al.  A stratigraphic framework for abrupt climatic changes during the Last Glacial period based on three synchronized Greenland ice-core records: refining and extending the INTIMATE event stratigraphy , 2014 .

[39]  W. Dong,et al.  Late Pleistocene mammalian fauna from Wulanmulan Paleolithic Site, Nei Mongol, China , 2014 .

[40]  M. Buckley,et al.  Mid-Pliocene warm-period deposits in the High Arctic yield insight into camel evolution , 2013, Nature Communications.

[41]  D. Makowiecki,et al.  Palaeolithic Big Game Hunting at HP766 in Wadi Umm Rahau, Northern Sudan , 2012 .

[42]  Marie Soressi,et al.  Site-specific deamidation of glutamine: a new marker of bone collagen deterioration. , 2012, Rapid communications in mass spectrometry : RCM.

[43]  N. V. van Doorn,et al.  Assessing the extent of bone degradation using glutamine deamidation in collagen. , 2012, Analytical chemistry.

[44]  S. Kansa,et al.  Collagen fingerprinting of archaeological bone and teeth remains from Domuztepe, South Eastern Turkey , 2011 .

[45]  M. Buckley,et al.  Mammoth and Mastodon collagen sequences; survival and utility , 2011 .

[46]  Xing Gao,et al.  Zooarchaeological perspectives on the Chinese Early and Late Paleolithic from the Ma’anshan site (Guizhou, South China) , 2010 .

[47]  Martin Strohalm,et al.  mMass 3: a cross-platform software environment for precise analysis of mass spectrometric data. , 2010, Analytical chemistry.

[48]  C. Ramsey,et al.  Current Pretreatment Methods for AMS Radiocarbon Dating at the Oxford Radiocarbon Accelerator Unit (Orau) , 2010, Radiocarbon.

[49]  Michael Buckley,et al.  Species identification by analysis of bone collagen using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry. , 2009, Rapid communications in mass spectrometry : RCM.

[50]  Hadley Wickham,et al.  ggplot2 - Elegant Graphics for Data Analysis (2nd Edition) , 2017 .

[51]  C. J. Norton,et al.  Hominin-carnivore interactions during the Chinese Early Paleolithic: taphonomic perspectives from Xujiayao. , 2008, Journal of human evolution.

[52]  V. Titov.  Habitat conditions for Camelus knoblochi and factors in its extinction , 2008 .

[53]  L. Niven.  From carcass to cave: large mammal exploitation during the Aurignacian at Vogelherd, Germany. , 2007, Journal of human evolution.

[54]  D. Curnoe,et al.  Characteristics of Pleistocene megafauna extinctions in Southeast Asia , 2007 .

[55]  Marie-Louise Siggaard-Andersen,et al.  The Greenland Ice Core Chronology 2005, 15-42 ka. Part 1: constructing the time scale , 2006 .

[56]  T. Pickering.  Reconsideration of criteria for differentiating faunal assemblages accumulated by hyenas and hominids , 2002 .

[57]  G. Baryshnikov,et al.  Hyenas and hunters: zooarchaeological investigations at Prolom II Cave, Crimea , 2000 .

[58]  M. Germonpré,et al.  Mammalian Remains from the Upper Palaeolithic Site of Kamenka, Buryatia (Siberia) , 1996 .

[59]  K. Cruz-Uribe.  Distinguishing Hyena from Hominid Bone Accumulations , 1991 .

[60]  H. Zimmermann,et al.  Sampling and Extraction of Ancient DNA from Sediments. , 2019, Methods in molecular biology.

[61]  J. Southon,et al.  The easternmost Middle Paleolithic (Mousterian) from Jinsitai Cave, North China. , 2018, Journal of human evolution.

[62]  A. Pakhunov,et al.  PRELIMINARY RESULTS OF STUDIES OF THE CAMEL FIGURE AT THE CHAMBER OF CHAOS AT SHULGAN-TASH (KAPOVA) CAVE , 2018 .

[63]  S. Pääbo,et al.  Supplementary information to : Palaeoproteomic evidence identifies archaic hominins associated with the Châtelperronian at the Grotte du Renne , 2016 .

[64]  M. Buckley,et al.  Species identification of archaeological marine mammals using collagen fingerprinting , 2014 .

[65]  Ulf Boger,et al.  New Insights Gained from the Faunal Material Recovered During the Latest Excavations at Vogelherd Cave , 2014 .

[66]  Tong Hao-we.  Late Pleistocene Bison priscus from Dabusu in Qian'an County,Jilin,China , 2013 .

[67]  Wang Xiao-kun.  A Preliminary Study on the Excavation of the Jinsitai Cave Site , 2010 .

[68]  C. Griggo,et al.  Mousterian fauna from Dederiyeh Cave and comparisons with Fauna from Umm El Tlel and Douara Cave , 2004 .

[69]  A. Gautier.  The Middle Paleolithic Archaeofaunas from Bir Tarfawi (Western Desert, Egypt) , 1993 .

[70]  Central Asiatic Expeditions,et al.  Pleistocene mammals from the limestone fissures of Szechwan, China. Bulletin of the AMNH ; v. 102, article 1 , 1953 .