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Fagernäs Z, Troché G, Olsen JV, Welker F. Digging deeper into ancient skeletal proteomes through consecutive digestion with multiple proteases. J Proteomics 2024; 298:105143. [PMID: 38423353 DOI: 10.1016/j.jprot.2024.105143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/23/2024] [Accepted: 02/26/2024] [Indexed: 03/02/2024]
Abstract
An increasing number of studies utilise the recovery of ancient skeletal proteomes for phylogenetic and evolutionary analysis. Although these studies manage to extract and analyse ancient peptides, the recovered proteomes are generally small in size and with low protein sequence coverage. We expand on previous observations which have shown that the parallel digestion and analysis of Pleistocene skeletal proteomes increases overall proteome size and protein sequence coverage. Furthermore, we demonstrate that the consecutive digestion of a skeletal proteome using two proteases, particularly the combination of Glu-C or chymotrypsin followed by trypsin digestion, enables the recovery of alternative proteome components not reachable through trypsin digestion alone. The proteomes preserved in Pleistocene skeletal specimens are larger than previously anticipated, but unlocking this protein sequence information requires adaptation of extraction and protein digestion protocols. The sequential utilisation of several proteases is, in this regard, a promising avenue for the study of highly degraded but unique hominin proteomes for phylogenetic purposes. SIGNIFICANCE: Palaeoproteomic analysis of archaeological materials, such as hominin skeletal elements, show great promise in studying past organisms and evolutionary relationships. However, as most proteomic methods are inherently destructive, it is essential to aim to recover as much information as possible from every sample. Currently, digestion with trypsin is the standard approach in most palaeoproteomic studies. We find that parallel or consecutive digestion with multiple proteases can improve proteome size and coverage for both Holocene and Pleistocene bone specimens. This allows for recovery of more proteomic data from a sample and maximises the chance of recovering phylogenetically relevant information.
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Affiliation(s)
- Zandra Fagernäs
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Gaudry Troché
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Jesper V Olsen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Frido Welker
- Globe Institute, University of Copenhagen, Copenhagen, Denmark.
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2
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Taurozzi AJ, Rüther PL, Patramanis I, Koenig C, Sinclair Paterson R, Madupe PP, Harking FS, Welker F, Mackie M, Ramos-Madrigal J, Olsen JV, Cappellini E. Deep-time phylogenetic inference by paleoproteomic analysis of dental enamel. Nat Protoc 2024:10.1038/s41596-024-00975-3. [PMID: 38671208 DOI: 10.1038/s41596-024-00975-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 01/12/2024] [Indexed: 04/28/2024]
Abstract
In temperate and subtropical regions, ancient proteins are reported to survive up to about 2 million years, far beyond the known limits of ancient DNA preservation in the same areas. Accordingly, their amino acid sequences currently represent the only source of genetic information available to pursue phylogenetic inference involving species that went extinct too long ago to be amenable for ancient DNA analysis. Here we present a complete workflow, including sample preparation, mass spectrometric data acquisition and computational analysis, to recover and interpret million-year-old dental enamel protein sequences. During sample preparation, the proteolytic digestion step, usually an integral part of conventional bottom-up proteomics, is omitted to increase the recovery of the randomly degraded peptides spontaneously generated by extensive diagenetic hydrolysis of ancient proteins over geological time. Similarly, we describe other solutions we have adopted to (1) authenticate the endogenous origin of the protein traces we identify, (2) detect and validate amino acid variation in the ancient protein sequences and (3) attempt phylogenetic inference. Sample preparation and data acquisition can be completed in 3-4 working days, while subsequent data analysis usually takes 2-5 days. The workflow described requires basic expertise in ancient biomolecules analysis, mass spectrometry-based proteomics and molecular phylogeny. Finally, we describe the limits of this approach and its potential for the reconstruction of evolutionary relationships in paleontology and paleoanthropology.
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Affiliation(s)
| | - Patrick L Rüther
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | | | - Claire Koenig
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | | | - Palesa P Madupe
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Florian Simon Harking
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Frido Welker
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Meaghan Mackie
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | | | - Jesper V Olsen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
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3
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Pederzani S, Britton K, Trost M, Fewlass H, Bourgon N, McCormack J, Jaouen K, Dietl H, Döhle HJ, Kirchner A, Lauer T, Le Corre M, McPherron SP, Meller H, Mylopotamitaki D, Orschiedt J, Rougier H, Ruebens K, Schüler T, Sinet-Mathiot V, Smith GM, Talamo S, Tütken T, Welker F, Zavala EI, Weiss M, Hublin JJ. Stable isotopes show Homo sapiens dispersed into cold steppes ~45,000 years ago at Ilsenhöhle in Ranis, Germany. Nat Ecol Evol 2024; 8:578-588. [PMID: 38297139 PMCID: PMC10927559 DOI: 10.1038/s41559-023-02318-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 12/19/2023] [Indexed: 02/02/2024]
Abstract
The spread of Homo sapiens into new habitats across Eurasia ~45,000 years ago and the concurrent disappearance of Neanderthals represents a critical evolutionary turnover in our species' history. 'Transitional' technocomplexes, such as the Lincombian-Ranisian-Jerzmanowician (LRJ), characterize the European record during this period but their makers and evolutionary significance have long remained unclear. New evidence from Ilsenhöhle in Ranis, Germany, now provides a secure connection of the LRJ to H. sapiens remains dated to ~45,000 years ago, making it one of the earliest forays of our species to central Europe. Using many stable isotope records of climate produced from 16 serially sampled equid teeth spanning ~12,500 years of LRJ and Upper Palaeolithic human occupation at Ranis, we review the ability of early humans to adapt to different climate and habitat conditions. Results show that cold climates prevailed across LRJ occupations, with a temperature decrease culminating in a pronounced cold excursion at ~45,000-43,000 cal BP. Directly dated H. sapiens remains confirm that humans used the site even during this very cold phase. Together with recent evidence from the Initial Upper Palaeolithic, this demonstrates that humans operated in severe cold conditions during many distinct early dispersals into Europe and suggests pronounced adaptability.
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Affiliation(s)
- Sarah Pederzani
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
- Archaeological Micromorphology and Biomarkers Laboratory (AMBI Lab), Instituto Universitario de Bio-Orgánica Antonio González, Universidad de La Laguna, San Cristóbal de La Laguna, Spain.
| | - Kate Britton
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Archaeology, University of Aberdeen, Aberdeen, UK
| | - Manuel Trost
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Helen Fewlass
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Ancient Genomics Lab, The Francis Crick Institute, London, UK
| | - Nicolas Bourgon
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- isoTROPIC Research Group, Max Planck Institute for Geoanthropology, Jena, Germany
| | - Jeremy McCormack
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Institute of Geosciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Klervia Jaouen
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Géosciences Environnement Toulouse, Observatoire Midi Pyrénées, UMR 5563, CNRS, Toulouse, France
| | - Holger Dietl
- State Office for Heritage Management and Archaeology Saxony-Anhalt-State Museum of Prehistory, Halle, Germany
| | - Hans-Jürgen Döhle
- State Office for Heritage Management and Archaeology Saxony-Anhalt-State Museum of Prehistory, Halle, Germany
| | - André Kirchner
- State Authority for Mining, Energy and Geology of Lower Saxony (LBEG), Hannover, Germany
| | - Tobias Lauer
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Terrestrial Sedimentology, Department of Geosciences, University of Tübingen, Tübingen, Germany
| | - Mael Le Corre
- Department of Archaeology, University of Aberdeen, Aberdeen, UK
- CNRS, UMR 7209 Archéozoologie et Archéobotanique-Sociétés, Pratiques et Environnements (MNHN-CNRS), Paris, France
| | - Shannon P McPherron
- Department of Human Origins, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Harald Meller
- State Office for Heritage Management and Archaeology Saxony-Anhalt-State Museum of Prehistory, Halle, Germany
| | - Dorothea Mylopotamitaki
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Chair of Paleoanthropology, CIRB (UMR 7241-U1050), Collège de France, Paris, France
| | - Jörg Orschiedt
- State Office for Heritage Management and Archaeology Saxony-Anhalt-State Museum of Prehistory, Halle, Germany
| | - Hélène Rougier
- Department of Anthropology, California State University Northridge, Northridge, CA, USA
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Karen Ruebens
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Chair of Paleoanthropology, CIRB (UMR 7241-U1050), Collège de France, Paris, France
| | - Tim Schüler
- Thuringian State Office for the Preservation of Historical Monuments and Archaeology, Weimar, Germany
| | - Virginie Sinet-Mathiot
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- University of Bordeaux, CNRS, Ministère de la Culture, PACEA, UMR 5199, Pessac, France
| | - Geoff M Smith
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- School of Anthropology and Conservation, University of Kent, Canterbury, UK
| | - Sahra Talamo
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Chemistry G. Ciamician, Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Thomas Tütken
- Applied and Analytical Palaeontology, Institute of Geosciences, Johannes Gutenberg University, Mainz, Germany
| | - Frido Welker
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Elena I Zavala
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
| | - Marcel Weiss
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Institut für Ur- und Frühgeschichte, Erlangen, Germany
| | - Jean-Jacques Hublin
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Chair of Paleoanthropology, CIRB (UMR 7241-U1050), Collège de France, Paris, France
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4
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Smith GM, Ruebens K, Zavala EI, Sinet-Mathiot V, Fewlass H, Pederzani S, Jaouen K, Mylopotamitaki D, Britton K, Rougier H, Stahlschmidt M, Meyer M, Meller H, Dietl H, Orschiedt J, Krause J, Schüler T, McPherron SP, Weiss M, Hublin JJ, Welker F. The ecology, subsistence and diet of ~45,000-year-old Homo sapiens at Ilsenhöhle in Ranis, Germany. Nat Ecol Evol 2024; 8:564-577. [PMID: 38297138 DOI: 10.1038/s41559-023-02303-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 12/07/2023] [Indexed: 02/02/2024]
Abstract
Recent excavations at Ranis (Germany) identified an early dispersal of Homo sapiens into the higher latitudes of Europe by 45,000 years ago. Here we integrate results from zooarchaeology, palaeoproteomics, sediment DNA and stable isotopes to characterize the ecology, subsistence and diet of these early H. sapiens. We assessed all bone remains (n = 1,754) from the 2016-2022 excavations through morphology (n = 1,218) or palaeoproteomics (zooarchaeology by mass spectrometry (n = 536) and species by proteome investigation (n = 212)). Dominant taxa include reindeer, cave bear, woolly rhinoceros and horse, indicating cold climatic conditions. Numerous carnivore modifications, alongside sparse cut-marked and burnt bones, illustrate a predominant use of the site by hibernating cave bears and denning hyaenas, coupled with a fluctuating human presence. Faunal diversity and high carnivore input were further supported by ancient mammalian DNA recovered from 26 sediment samples. Bulk collagen carbon and nitrogen stable isotope data from 52 animal and 10 human remains confirm a cold steppe/tundra setting and indicate a homogenous human diet based on large terrestrial mammals. This lower-density archaeological signature matches other Lincombian-Ranisian-Jerzmanowician sites and is best explained by expedient visits of short duration by small, mobile groups of pioneer H. sapiens.
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Affiliation(s)
- Geoff M Smith
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
- School of Anthropology and Conservation, University of Kent, Kent, UK.
| | - Karen Ruebens
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Chaire de Paléoanthropologie, CIRB (UMR 7241-U1050), Collège de France, Paris, France
| | - Elena Irene Zavala
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Virginie Sinet-Mathiot
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Univ. Bordeaux, CNRS, Ministère de la Culture, PACEA, UMR 5199, Pessac, France
| | - Helen Fewlass
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Ancient Genomics Lab, Francis Crick Institute, London, UK
| | - Sarah Pederzani
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Archaeological Micromorphology and Biomarker Lab, University of La Laguna, San Cristóbal de La Laguna, Spain
| | - Klervia Jaouen
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Géosciences Environnement Toulouse (GET), Observatoire Midi-Pyrénées (OMP), Toulouse, France
| | - Dorothea Mylopotamitaki
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Chaire de Paléoanthropologie, CIRB (UMR 7241-U1050), Collège de France, Paris, France
| | - Kate Britton
- Department of Archaeology, School of Geosciences, University of Aberdeen, Aberdeen, Scotland
| | - Hélène Rougier
- Department of Anthropology, California State University Northridge, Northridge, CA, USA
| | - Mareike Stahlschmidt
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria
| | - Matthias Meyer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Harald Meller
- State Office for Heritage Management and Archaeology Saxony-Anhalt-State Museum of Prehistory, Halle, Germany
| | - Holger Dietl
- State Office for Heritage Management and Archaeology Saxony-Anhalt-State Museum of Prehistory, Halle, Germany
| | - Jörg Orschiedt
- State Office for Heritage Management and Archaeology Saxony-Anhalt-State Museum of Prehistory, Halle, Germany
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Tim Schüler
- Thuringian State Office for the Preservation of Historical Monuments and Archaeology, Weimar, Germany
| | - Shannon P McPherron
- Department of Human Origins, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Marcel Weiss
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Institut für Ur- und Frühgeschichte, Erlangen, Germany
| | - Jean-Jacques Hublin
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Chaire de Paléoanthropologie, CIRB (UMR 7241-U1050), Collège de France, Paris, France
| | - Frido Welker
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
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5
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Bae CJ, Aiello LC, Hawks J, Kaifu Y, Lindal J, Martinón-Torres M, Ni X, Posth C, Radović P, Reed D, Schroeder L, Schwartz JH, Silcox MT, Welker F, Wu XJ, Zanolli C, Roksandic M. Moving away from "the Muddle in the Middle" toward solving the Chibanian puzzle. Evol Anthropol 2024; 33:e22011. [PMID: 37943093 DOI: 10.1002/evan.22011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 10/17/2023] [Indexed: 11/10/2023]
Affiliation(s)
- Christopher J Bae
- Department of Anthropology, University of Hawai'i at Manoa, Honolulu, Hawai, USA
| | - Leslie C Aiello
- Department of Anthropology, University College London, London, UK
- The Wenner-Gren Foundation for Anthropological Research Inc., New York, New York, USA
| | - John Hawks
- Department of Anthropology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Yousuke Kaifu
- The University Museum, The University of Tokyo, Tokyo, Japan
| | - Joshua Lindal
- Department of Anthropology, University of Winnipeg, Winnipeg, Manitoba, Canada
| | - María Martinón-Torres
- Department of Anthropology, University College London, London, UK
- CENIEH (National Research Center on Human Evolution), Burgos, Spain
| | - Xijun Ni
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
| | - Cosimo Posth
- Archaeo- and Palaeogenetics, Department of Geosciences and the Senckenberg Centre for Human Evolution and Palaeoenvironment, Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
| | - Predrag Radović
- Department of Archaeology, Faculty of Philosophy, University of Belgrade, Belgrade, Serbia
- National Museum Kraljevo, Kraljevo, Serbia
| | - Denne Reed
- Department of Anthropology, University of Texas at Austin, Austin, Texas, USA
| | - Lauren Schroeder
- Department of Anthropology, University of Toronto Mississauga, Mississauga, Ontario, Canada
- The Human Evolution Research Institute, University of Cape Town, Rondebosch, South Africa
| | - Jeffrey H Schwartz
- Departments of Anthropology and History and Philosophy of Science, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Mary T Silcox
- Department of Anthropology, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Frido Welker
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Xiu-Jie Wu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
| | - Clément Zanolli
- Univ. Bordeaux, CNRS, MCC, PACEA, UMR 5199, F-33600 Pessac, France
| | - Mirjana Roksandic
- Department of Anthropology, University of Winnipeg, Winnipeg, Manitoba, Canada
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6
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Mylopotamitaki D, Weiss M, Fewlass H, Zavala EI, Rougier H, Sümer AP, Hajdinjak M, Smith GM, Ruebens K, Sinet-Mathiot V, Pederzani S, Essel E, Harking FS, Xia H, Hansen J, Kirchner A, Lauer T, Stahlschmidt M, Hein M, Talamo S, Wacker L, Meller H, Dietl H, Orschiedt J, Olsen JV, Zeberg H, Prüfer K, Krause J, Meyer M, Welker F, McPherron SP, Schüler T, Hublin JJ. Homo sapiens reached the higher latitudes of Europe by 45,000 years ago. Nature 2024; 626:341-346. [PMID: 38297117 PMCID: PMC10849966 DOI: 10.1038/s41586-023-06923-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 11/30/2023] [Indexed: 02/02/2024]
Abstract
The Middle to Upper Palaeolithic transition in Europe is associated with the regional disappearance of Neanderthals and the spread of Homo sapiens. Late Neanderthals persisted in western Europe several millennia after the occurrence of H. sapiens in eastern Europe1. Local hybridization between the two groups occurred2, but not on all occasions3. Archaeological evidence also indicates the presence of several technocomplexes during this transition, complicating our understanding and the association of behavioural adaptations with specific hominin groups4. One such technocomplex for which the makers are unknown is the Lincombian-Ranisian-Jerzmanowician (LRJ), which has been described in northwestern and central Europe5-8. Here we present the morphological and proteomic taxonomic identification, mitochondrial DNA analysis and direct radiocarbon dating of human remains directly associated with an LRJ assemblage at the site Ilsenhöhle in Ranis (Germany). These human remains are among the earliest directly dated Upper Palaeolithic H. sapiens remains in Eurasia. We show that early H. sapiens associated with the LRJ were present in central and northwestern Europe long before the extinction of late Neanderthals in southwestern Europe. Our results strengthen the notion of a patchwork of distinct human populations and technocomplexes present in Europe during this transitional period.
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Affiliation(s)
- Dorothea Mylopotamitaki
- Chair of Paleoanthropology, CIRB (UMR 7241-U1050), Collège de France, Paris, France
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Marcel Weiss
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Institut für Ur- und Frühgeschichte, Erlangen, Germany.
| | - Helen Fewlass
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Ancient Genomics Lab, Francis Crick Institute, London, UK
| | - Elena Irene Zavala
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
| | - Hélène Rougier
- Department of Anthropology, California State University Northridge, Northridge, CA, USA
| | - Arev Pelin Sümer
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Mateja Hajdinjak
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Geoff M Smith
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- School of Anthropology and Conservation, University of Kent, Canterbury, UK
| | - Karen Ruebens
- Chair of Paleoanthropology, CIRB (UMR 7241-U1050), Collège de France, Paris, France
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Virginie Sinet-Mathiot
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Univ. Bordeaux, CNRS, Ministère de la Culture, PACEA, UMR 5199, Bordeaux, France
| | - Sarah Pederzani
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Archaeological Micromorphology and Biomarker Lab, University of La Laguna, San Cristóbal de La Laguna, Spain
| | - Elena Essel
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Florian S Harking
- Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Huan Xia
- College of Earth and Environmental Sciences, Lanzhou University, Lanzhou, China
| | - Jakob Hansen
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Departament de Prehistòria, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - André Kirchner
- Department of Soil Protection and Soil Survey, State Authority for Mining, Energy and Geology of Lower Saxony (LBEG), Hannover, Germany
| | - Tobias Lauer
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Terrestrial Sedimentology, Department of Geosciences, University of Tübingen, Tübingen, Germany
| | - Mareike Stahlschmidt
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Evolutionary Anthropology and Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria
| | - Michael Hein
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Institute of Ecology, Leuphana University, Lüneburg, Germany
- Historical Anthropospheres Working Group, Leipzig Lab, Leipzig University, Leipzig, Germany
| | - Sahra Talamo
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Chemistry G. Ciamician, Bologna University, Bologna, Italy
| | - Lukas Wacker
- Ion Beam Physics, ETH Zurich, Zurich, Switzerland
| | - Harald Meller
- Landesamt für Denkmalpflege und Archäologie Sachsen-Anhalt - Landesmuseum für Vorgeschichte, Halle, Germany
| | - Holger Dietl
- Landesamt für Denkmalpflege und Archäologie Sachsen-Anhalt - Landesmuseum für Vorgeschichte, Halle, Germany
| | - Jörg Orschiedt
- Landesamt für Denkmalpflege und Archäologie Sachsen-Anhalt - Landesmuseum für Vorgeschichte, Halle, Germany
| | - Jesper V Olsen
- Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Hugo Zeberg
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Kay Prüfer
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Johannes Krause
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Matthias Meyer
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Frido Welker
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Tim Schüler
- Thuringian State Office for the Preservation of Historical Monuments and Archaeology, Weimar, Germany
| | - Jean-Jacques Hublin
- Chair of Paleoanthropology, CIRB (UMR 7241-U1050), Collège de France, Paris, France.
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
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7
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Le Meillour L, Zazzo A, Zirah S, Tombret O, Barriel V, Arthur KW, Arthur JW, Cauliez J, Chaix L, Curtis MC, Gifford-Gonzalez D, Gunn I, Gutherz X, Hildebrand E, Khalidi L, Millet M, Mitchell P, Studer J, Vila E, Welker F, Pleurdeau D, Lesur J. The name of the game: palaeoproteomics and radiocarbon dates further refine the presence and dispersal of caprines in eastern and southern Africa. R Soc Open Sci 2023; 10:231002. [PMID: 38026023 PMCID: PMC10663795 DOI: 10.1098/rsos.231002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 11/03/2023] [Indexed: 12/01/2023]
Abstract
We report the first large-scale palaeoproteomics research on eastern and southern African zooarchaeological samples, thereby refining our understanding of early caprine (sheep and goat) pastoralism in Africa. Assessing caprine introductions is a complicated task because of their skeletal similarity to endemic wild bovid species and the sparse and fragmentary state of relevant archaeological remains. Palaeoproteomics has previously proved effective in clarifying species attributions in African zooarchaeological materials, but few comparative protein sequences of wild bovid species have been available. Using newly generated type I collagen sequences for wild species, as well as previously published sequences, we assess species attributions for elements originally identified as caprine or 'unidentifiable bovid' from 17 eastern and southern African sites that span seven millennia. We identified over 70% of the archaeological remains and the direct radiocarbon dating of domesticate specimens allows refinement of the chronology of caprine presence in both African regions. These results thus confirm earlier occurrences in eastern Africa and the systematic association of domesticated caprines with wild bovids at all archaeological sites. The combined biomolecular approach highlights repeatability and accuracy of the methods for conclusive contribution in species attribution of archaeological remains in dry African environments.
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Affiliation(s)
- Louise Le Meillour
- Unité Archéozoologie, Archéobotanique: Sociétés, Pratiques, Environnements (AASPE), Muséum national d'Histoire naturelle, CNRS, CP 56, 55 rue Buffon, 75005 Paris, France
- Unité Molécules de Communication et Adaptations des Micro-organismes (MCAM), Muséum national d'Histoire naturelle, CNRS, CP 54, 57 rue Cuvier, 75005 Paris, France
- Section for Molecular Ecology and Evolution, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5, 1353 København, Denmark
| | - Antoine Zazzo
- Unité Archéozoologie, Archéobotanique: Sociétés, Pratiques, Environnements (AASPE), Muséum national d'Histoire naturelle, CNRS, CP 56, 55 rue Buffon, 75005 Paris, France
| | - Séverine Zirah
- Unité Molécules de Communication et Adaptations des Micro-organismes (MCAM), Muséum national d'Histoire naturelle, CNRS, CP 54, 57 rue Cuvier, 75005 Paris, France
| | - Olivier Tombret
- Unité Archéozoologie, Archéobotanique: Sociétés, Pratiques, Environnements (AASPE), Muséum national d'Histoire naturelle, CNRS, CP 56, 55 rue Buffon, 75005 Paris, France
- Unité Histoire naturelle de l'Homme Préhistorique (HNHP), Muséum national d'Histoire naturelle, CNRS, UPVD, 1 rue René Panhard, 75013 Paris, France
| | - Véronique Barriel
- Centre de Recherche en Paléontologie – Paris (CR2P), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, CP 38, 8 rue Buffon, 75005 Paris, France
| | - Kathryn W. Arthur
- Department of Anthropology, University of South Florida St. Petersburg, 140 7th Avenue South, St. Petersburg, FL 33713, USA
| | - John W. Arthur
- Department of Anthropology, University of South Florida St. Petersburg, 140 7th Avenue South, St. Petersburg, FL 33713, USA
| | - Jessie Cauliez
- Unité Travaux et Recherches Archéologiques sur les Cultures, les Espaces et les Sociétés (TRACES), CNRS, Université Toulouse Jean Jaurès, 5 allées Antonio Machado, 31058 Toulouse, France
| | - Louis Chaix
- Département d'archéozoologie, Muséum d'histoire naturelle (MHNG), 1 route de Malagnou, 1208 Genève, Switzerland
| | - Matthew C. Curtis
- Anthropology Program, California State University Channel Islands, 1 University Drive, Camarillo, CA 93012, USA
| | - Diane Gifford-Gonzalez
- Department of Anthropology, University of California, Santa Cruz, Social Sciences 1 Faculty Svcs, 1156 High Street, Santa Cruz, CA 95064-1077, USA
| | - Imogen Gunn
- Museum of Archaeology and Anthropology, University of Cambridge, Downing Street, Cambridge CB2 3DZ, UK
| | - Xavier Gutherz
- Unité Archéologie des Sociétés Méditerranéennes (ASM), CNRS, Université Montpellier III, Ministère de la Culture, INRAP, Montpellier, France
| | | | - Lamya Khalidi
- Unité Cultures et Environnements. Préhistoire, Antiquité, Moyen Age (CEPAM), Université Côte d'Azur, CNRS, 24 avenue des Diables Bleus, 06300 Nice, France
| | - Marie Millet
- Département des Antiquités Égyptiennes, Musée du Louvre, Paris, France
| | - Peter Mitchell
- School of Archaeology, University of Oxford, Oxford, OX1 3TG, United Kingdom and Rock Art Research Institute, University of the Witwatersrand, PO Wits 2050, Johannesburg, South Africa
| | - Jacqueline Studer
- Département d'archéozoologie, Muséum d'histoire naturelle (MHNG), 1 route de Malagnou, 1208 Genève, Switzerland
| | - Emmanuelle Vila
- Unité Archéorient, Environnements et sociétés de l'Orient ancien, CNRS, Université de Lyon 2, Maison de l'Orient et de la Méditerranée, 7 rue Raulin, 69007 Lyon, France
| | - Frido Welker
- Section for Molecular Ecology and Evolution, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5, 1353 København, Denmark
| | - David Pleurdeau
- Unité Histoire naturelle de l'Homme Préhistorique (HNHP), Muséum national d'Histoire naturelle, CNRS, UPVD, 1 rue René Panhard, 75013 Paris, France
| | - Joséphine Lesur
- Unité Archéozoologie, Archéobotanique: Sociétés, Pratiques, Environnements (AASPE), Muséum national d'Histoire naturelle, CNRS, CP 56, 55 rue Buffon, 75005 Paris, France
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8
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Mylopotamitaki D, Harking FS, Taurozzi AJ, Fagernäs Z, Godinho RM, Smith GM, Weiss M, Schüler T, McPherron SP, Meller H, Cascalheira J, Bicho N, Olsen JV, Hublin JJ, Welker F. Comparing extraction method efficiency for high-throughput palaeoproteomic bone species identification. Sci Rep 2023; 13:18345. [PMID: 37884544 PMCID: PMC10603084 DOI: 10.1038/s41598-023-44885-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 10/13/2023] [Indexed: 10/28/2023] Open
Abstract
High-throughput proteomic analysis of archaeological skeletal remains provides information about past fauna community compositions and species dispersals in time and space. Archaeological skeletal remains are a finite resource, however, and therefore it becomes relevant to optimize methods of skeletal proteome extraction. Ancient proteins in bone specimens can be highly degraded and consequently, extraction methods for well-preserved or modern bone might be unsuitable for the processing of highly degraded skeletal proteomes. In this study, we compared six proteomic extraction methods on Late Pleistocene remains with variable levels of proteome preservation. We tested the accuracy of species identification, protein sequence coverage, deamidation, and the number of post-translational modifications per method. We find striking differences in obtained proteome complexity and sequence coverage, highlighting that simple acid-insoluble proteome extraction methods perform better in highly degraded contexts. For well-preserved specimens, the approach using EDTA demineralization and protease-mix proteolysis yielded a higher number of identified peptides. The protocols presented here allowed protein extraction from ancient bone with a minimum number of working steps and equipment and yielded protein extracts within three working days. We expect further development along this route to benefit large-scale screening applications of relevance to archaeological and human evolution research.
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Affiliation(s)
- Dorothea Mylopotamitaki
- Chaire de Paléoanthropologie, CIRB (UMR 7241-U1050), Collège de France, Paris, France.
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Florian S Harking
- Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | | | - Zandra Fagernäs
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Ricardo M Godinho
- Interdisciplinary Center for Archaeology and Evolution of Human Behaviour, University of Algarve, Faro, Portugal
| | - Geoff M Smith
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- School of Anthropology and Conservation, University of Kent, Kent, UK
| | - Marcel Weiss
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Institut für Ur- und Frühgeschichte, Friedrich-Alexander-Universität, Erlangen, Germany
| | - Tim Schüler
- Thuringian State Office for the Preservation of Historical Monuments and Archaeology, Weimar, Germany
| | - Shannon P McPherron
- Department of Human Origins, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Harald Meller
- State Office for Heritage Management and Archaeology, Saxony-Anhalt-State Museum of Prehistory, Halle (Saale), Germany
| | - João Cascalheira
- Interdisciplinary Center for Archaeology and Evolution of Human Behaviour, University of Algarve, Faro, Portugal
| | - Nuno Bicho
- Interdisciplinary Center for Archaeology and Evolution of Human Behaviour, University of Algarve, Faro, Portugal
| | - Jesper V Olsen
- Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Jean-Jacques Hublin
- Chaire de Paléoanthropologie, CIRB (UMR 7241-U1050), Collège de France, Paris, France
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Frido Welker
- Globe Institute, University of Copenhagen, Copenhagen, Denmark.
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9
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Affiliation(s)
- Frido Welker
- GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.
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10
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Sinet-Mathiot V, Martisius NL, Schulz-Kornas E, van Casteren A, Tsanova TR, Sirakov N, Spasov R, Welker F, Smith GM, Hublin JJ. The effect of eraser sampling for proteomic analysis on Palaeolithic bone surface microtopography. Sci Rep 2021; 11:23611. [PMID: 34880290 PMCID: PMC8655045 DOI: 10.1038/s41598-021-02823-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 11/19/2021] [Indexed: 11/17/2022] Open
Abstract
Bone surface modifications are crucial for understanding human subsistence and dietary behaviour, and can inform about the techniques employed in the production and use of bone tools. Permission to destructively sample such unique artefacts is not always granted. The recent development of non-destructive proteomic extraction techniques has provided some alternatives for the analysis of rare and culturally significant artefacts, including bone tools and personal ornaments. The Eraser Extraction Method (EEM), first developed for ZooMS analysis of parchment, has recently been applied to bone and ivory specimens. To test the potential impact of the EEM on ancient bone surfaces, we analyse six anthropogenically modified Palaeolithic bone specimens from Bacho Kiro Cave (Bulgaria) through a controlled sampling experiment using qualitative and 3D quantitative microscopy. Although the overall bone topography is generally preserved, our findings demonstrate a slight flattening of the microtopography alongside the formation of micro-striations associated with the use of the eraser for all bone specimens. Such modifications are similar to ancient use-wear traces. We therefore consider the EEM a destructive sampling approach for Palaeolithic bone surfaces. Together with low ZooMS success rates in some of the reported studies, the EEM might not be a suitable approach to taxonomically identify Pleistocene bone specimens.
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Affiliation(s)
- Virginie Sinet-Mathiot
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Naomi L. Martisius
- grid.419518.00000 0001 2159 1813Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany ,grid.267360.60000 0001 2160 264XDepartment of Anthropology, The University of Tulsa, Tulsa, OK USA
| | - Ellen Schulz-Kornas
- grid.419518.00000 0001 2159 1813Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany ,grid.9647.c0000 0004 7669 9786Department of Cariology, Endodontology and Periodontology, University of Leipzig, Leipzig, Germany
| | - Adam van Casteren
- grid.419518.00000 0001 2159 1813Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Tsenka R. Tsanova
- grid.419518.00000 0001 2159 1813Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Nikolay Sirakov
- grid.410344.60000 0001 2097 3094National Institute of Archaeology with Museum, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Rosen Spasov
- grid.5507.70000 0001 0740 5199Archaeology Department, New Bulgarian University, Sofia, Bulgaria
| | - Frido Welker
- grid.5254.60000 0001 0674 042XSection for Evolutionary Genomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Geoff M. Smith
- grid.419518.00000 0001 2159 1813Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Jean-Jacques Hublin
- grid.419518.00000 0001 2159 1813Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany ,grid.410533.00000 0001 2179 2236Collège de France, Paris, France
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11
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Talamo S, Urbanowski M, Picin A, Nowaczewska W, Vazzana A, Binkowski M, Cercatillo S, Diakowski M, Fewlass H, Marciszak A, Paleček D, Richards MP, Ryder CM, Sinet-Mathiot V, Smith GM, Socha P, Sponheimer M, Stefaniak K, Welker F, Winter H, Wiśniewski A, Żarski M, Benazzi S, Nadachowski A, Hublin JJ. A 41,500 year-old decorated ivory pendant from Stajnia Cave (Poland). Sci Rep 2021; 11:22078. [PMID: 34837003 PMCID: PMC8626500 DOI: 10.1038/s41598-021-01221-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 10/22/2021] [Indexed: 01/03/2023] Open
Abstract
Evidence of mobiliary art and body augmentation are associated with the cultural innovations introduced by Homo sapiens at the beginning of the Upper Paleolithic. Here, we report the discovery of the oldest known human-modified punctate ornament, a decorated ivory pendant from the Paleolithic layers at Stajnia Cave in Poland. We describe the features of this unique piece, as well as the stratigraphic context and the details of its chronometric dating. The Stajnia Cave plate is a personal 'jewellery' object that was created 41,500 calendar years ago (directly radiocarbon dated). It is the oldest known of its kind in Eurasia and it establishes a new starting date for a tradition directly connected to the spread of modern Homo sapiens in Europe.
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Affiliation(s)
- Sahra Talamo
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany. .,Department of Chemistry G. Ciamician, University of Bologna, Via Selmi 2, 40126, Bologna, Italy.
| | | | - Andrea Picin
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
| | - Wioletta Nowaczewska
- Department of Human Biology, University of Wrocław, ul. Przybyszewskiego 63, 51-148, Wrocław, Poland
| | - Antonino Vazzana
- Department of Cultural Heritage, University of Bologna, Via degli Ariani 1, 48121, Ravenna, Italy
| | - Marcin Binkowski
- X-Ray Microtomography Lab, Department of Biomedical Computer Systems, Institute of Computer Science, Faculty of Computer and Materials Science, University of Silesia, Będzińska 39, 41-200, Sosnowiec, Poland
| | - Silvia Cercatillo
- Department of Chemistry G. Ciamician, University of Bologna, Via Selmi 2, 40126, Bologna, Italy
| | - Marcin Diakowski
- Department of Stone Age Archaeology, Institute of Archeology, University of Wrocław, Szewska 48, 50-139, Wrocław, Poland
| | - Helen Fewlass
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
| | - Adrian Marciszak
- Department of Paleozoology, University of Wrocław, Sienkiewicza 21, 50-335, Wrocław, Poland
| | - Dragana Paleček
- Department of Chemistry G. Ciamician, University of Bologna, Via Selmi 2, 40126, Bologna, Italy
| | - Michael P Richards
- Department of Archaeology, Simon Fraser University, Burnaby, BC, V5A, 1S6, Canada
| | - Christina M Ryder
- Department of Anthropology, University of Colorado Boulder, Boulder, CO, 80309, USA
| | - Virginie Sinet-Mathiot
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
| | - Geoff M Smith
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
| | - Paweł Socha
- Department of Paleozoology, University of Wrocław, Sienkiewicza 21, 50-335, Wrocław, Poland
| | - Matt Sponheimer
- Department of Anthropology, University of Colorado Boulder, Boulder, CO, 80309, USA.,Centre for the Exploration of the Deep Human Journey, University of the Witwatersrand, Johannesburg, Gauteng, South Africa
| | - Krzysztof Stefaniak
- Department of Paleozoology, University of Wrocław, Sienkiewicza 21, 50-335, Wrocław, Poland
| | - Frido Welker
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany.,Evolutionary Genomics Section, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Hanna Winter
- Polish Geological Institute-National Research Institute, Rakowiecka 4, 00-975, Warsaw, Poland
| | - Andrzej Wiśniewski
- Department of Stone Age Archaeology, Institute of Archeology, University of Wrocław, Szewska 48, 50-139, Wrocław, Poland
| | - Marcin Żarski
- Polish Geological Institute-National Research Institute, Rakowiecka 4, 00-975, Warsaw, Poland
| | - Stefano Benazzi
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany.,Department of Cultural Heritage, University of Bologna, Via degli Ariani 1, 48121, Ravenna, Italy
| | - Adam Nadachowski
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Sławkowska 17, 016, Kraków, Poland
| | - Jean-Jacques Hublin
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany.,Collège de France, 11 Place Marcellin Berthelot, 75005, Paris, France
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12
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Bacon AM, Bourgon N, Welker F, Cappellini E, Fiorillo D, Tombret O, Thi Mai Huong N, Anh Tuan N, Sayavonkhamdy T, Souksavatdy V, Sichanthongtip P, Antoine PO, Duringer P, Ponche JL, Westaway K, Joannes-Boyau R, Boesch Q, Suzzoni E, Frangeul S, Patole-Edoumba E, Zachwieja A, Shackelford L, Demeter F, Hublin JJ, Dufour É. A multi-proxy approach to exploring Homo sapiens' arrival, environments and adaptations in Southeast Asia. Sci Rep 2021; 11:21080. [PMID: 34702921 PMCID: PMC8548499 DOI: 10.1038/s41598-021-99931-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 10/05/2021] [Indexed: 01/29/2023] Open
Abstract
The capability of Pleistocene hominins to successfully adapt to different types of tropical forested environments has long been debated. In order to investigate environmental changes in Southeast Asia during a critical period for the turnover of hominin species, we analysed palaeoenvironmental proxies from five late Middle to Late Pleistocene faunas. Human teeth discoveries have been reported at Duoi U'Oi, Vietnam (70-60 ka) and Nam Lot, Laos (86-72 ka). However, the use of palaeoproteomics allowed us to discard the latter, and, to date, no human remains older than ~ 70 ka are documented in the area. Our findings indicate that tropical rainforests were highly sensitive to climatic changes over that period, with significant fluctuations of the canopy forests. Locally, large-bodied faunas were resilient to these fluctuations until the cooling period of the Marine Isotope Stage 4 (MIS 4; 74-59 ka) that transformed the overall biotope. Then, under strong selective pressures, populations with new phenotypic characteristics emerged while some other species disappeared. We argue that this climate-driven shift offered new foraging opportunities for hominins in a novel rainforest environment and was most likely a key factor in the settlement and dispersal of our species during MIS 4 in SE Asia.
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Affiliation(s)
- Anne-Marie Bacon
- grid.508487.60000 0004 7885 7602UMR 8045 BABEL, CNRS, Université de Paris, Faculté de Chirurgie dentaire, 1 rue Maurice Arnoux, 92120 Montrouge, France
| | - Nicolas Bourgon
- grid.419518.00000 0001 2159 1813Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany ,grid.5802.f0000 0001 1941 7111Applied and Analytical Palaeontology, Institute of Geosciences, Johannes Gutenberg University, Mainz, Germany
| | - Frido Welker
- grid.5254.60000 0001 0674 042XSection for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Enrico Cappellini
- grid.5254.60000 0001 0674 042XSection for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Denis Fiorillo
- UMR 7209 Archéozoologie, Archéobotanique: Sociétés, Pratiques, Environnements, Muséum National d’Histoire Naturelle, CNRS, Paris, France
| | - Olivier Tombret
- UMR 7209 Archéozoologie, Archéobotanique: Sociétés, Pratiques, Environnements, Muséum National d’Histoire Naturelle, CNRS, Paris, France
| | - Nguyen Thi Mai Huong
- Anthropological and Palaeoenvironmental Department, Institute of Archaeology, Hoan Kiem District, Ha Noi, Vietnam
| | - Nguyen Anh Tuan
- Anthropological and Palaeoenvironmental Department, Institute of Archaeology, Hoan Kiem District, Ha Noi, Vietnam
| | - Thongsa Sayavonkhamdy
- Department of Heritage, Ministry of Information, Culture and Tourism, Vientiane, Laos
| | - Viengkeo Souksavatdy
- Department of Heritage, Ministry of Information, Culture and Tourism, Vientiane, Laos
| | | | - Pierre-Olivier Antoine
- grid.121334.60000 0001 2097 0141Institut des Sciences de l’Évolution de Montpellier, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Philippe Duringer
- grid.11843.3f0000 0001 2157 9291Ecole et Observatoire des Sciences de la Terre (EOST Géologie), Institut de Physique du Globe de Strasbourg (IPGS) (CNRS/UMR 7516), Institut de Géologie, Université de Strasbourg, Strasbourg, France
| | - Jean-Luc Ponche
- grid.463965.b0000 0004 0452 6077UMR 7362 Laboratoire Image Ville et Environnement, Institut de Géologie, Strasbourg, France
| | - Kira Westaway
- grid.1004.50000 0001 2158 5405Department of Earth and Environmental Sciences, Traps’ MQ Luminescence Dating Facility, Macquarie University, Sydney, Australia
| | - Renaud Joannes-Boyau
- grid.1031.30000000121532610Geoarchaeology & Archaeometry Research Group, Southern Cross University, Lismore, Australia ,grid.458456.e0000 0000 9404 3263Institute of Vertebrate Paleontology and Paleoanthropology (IVPP) of the Chinese Academy of Sciences, Beijing, China
| | - Quentin Boesch
- grid.11843.3f0000 0001 2157 9291Ecole et Observatoire des Sciences de la Terre (EOST Géologie), Institut de Physique du Globe de Strasbourg (IPGS) (CNRS/UMR 7516), Institut de Géologie, Université de Strasbourg, Strasbourg, France
| | - Eric Suzzoni
- Spitteurs Pan, Technical Cave Supervision and Exploration, La Chapelle-en-Vercors, France
| | - Sébastien Frangeul
- Spitteurs Pan, Technical Cave Supervision and Exploration, La Chapelle-en-Vercors, France
| | - Elise Patole-Edoumba
- grid.410350.30000 0001 2174 9334Muséum d’Histoire Naturelle, La Rochelle, France
| | - Alexandra Zachwieja
- grid.17635.360000000419368657Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN USA
| | - Laura Shackelford
- grid.35403.310000 0004 1936 9991Department of Anthropology, University of Illinois at Urbana-Champaign, Urbana, IL USA
| | - Fabrice Demeter
- grid.452548.a0000 0000 9817 5300Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, Copenhagen, Denmark ,UMR 7206 Eco-Anthropologie, Muséum National d’Histoire Naturelle, CNRS, Paris, France
| | - Jean-Jacques Hublin
- grid.419518.00000 0001 2159 1813Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany ,grid.410533.00000 0001 2179 2236Collège de France, Chaire de Paléoanthropologie, Paris, France
| | - Élise Dufour
- UMR 7209 Archéozoologie, Archéobotanique: Sociétés, Pratiques, Environnements, Muséum National d’Histoire Naturelle, CNRS, Paris, France
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13
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Hajdinjak M, Mafessoni F, Skov L, Vernot B, Hübner A, Fu Q, Essel E, Nagel S, Nickel B, Richter J, Moldovan OT, Constantin S, Endarova E, Zahariev N, Spasov R, Welker F, Smith GM, Sinet-Mathiot V, Paskulin L, Fewlass H, Talamo S, Rezek Z, Sirakova S, Sirakov N, McPherron SP, Tsanova T, Hublin JJ, Peter BM, Meyer M, Skoglund P, Kelso J, Pääbo S. Initial Upper Palaeolithic humans in Europe had recent Neanderthal ancestry. Nature 2021; 592:253-257. [PMID: 33828320 PMCID: PMC8026394 DOI: 10.1038/s41586-021-03335-3] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 02/05/2021] [Indexed: 02/01/2023]
Abstract
Modern humans appeared in Europe by at least 45,000 years ago1-5, but the extent of their interactions with Neanderthals, who disappeared by about 40,000 years ago6, and their relationship to the broader expansion of modern humans outside Africa are poorly understood. Here we present genome-wide data from three individuals dated to between 45,930 and 42,580 years ago from Bacho Kiro Cave, Bulgaria1,2. They are the earliest Late Pleistocene modern humans known to have been recovered in Europe so far, and were found in association with an Initial Upper Palaeolithic artefact assemblage. Unlike two previously studied individuals of similar ages from Romania7 and Siberia8 who did not contribute detectably to later populations, these individuals are more closely related to present-day and ancient populations in East Asia and the Americas than to later west Eurasian populations. This indicates that they belonged to a modern human migration into Europe that was not previously known from the genetic record, and provides evidence that there was at least some continuity between the earliest modern humans in Europe and later people in Eurasia. Moreover, we find that all three individuals had Neanderthal ancestors a few generations back in their family history, confirming that the first European modern humans mixed with Neanderthals and suggesting that such mixing could have been common.
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Affiliation(s)
- Mateja Hajdinjak
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
- Francis Crick Institute, London, UK.
| | - Fabrizio Mafessoni
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Laurits Skov
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Benjamin Vernot
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Alexander Hübner
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, IVPP, Center for Excellence in Life and Paleoenvironment, Beijing, China
| | - Elena Essel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Sarah Nagel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Birgit Nickel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Julia Richter
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Oana Teodora Moldovan
- Emil Racovita Institute of Speleology, Cluj Department, Cluj-Napoca, Romania
- Romanian Institute of Science and Technology, Cluj-Napoca, Romania
| | - Silviu Constantin
- Department of Geospeleology and Paleontology, Emil Racovita Institute of Speleology, Bucharest, Romania
- Centro Nacional de Investigación sobre la Evolución Humana, CENIEH, Burgos, Spain
| | | | - Nikolay Zahariev
- Archaeology Department, New Bulgarian University, Sofia, Bulgaria
| | - Rosen Spasov
- Archaeology Department, New Bulgarian University, Sofia, Bulgaria
| | - Frido Welker
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Geoff M Smith
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Virginie Sinet-Mathiot
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Helen Fewlass
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Sahra Talamo
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Chemistry 'G. Ciamician', University of Bologna, Bologna, Italy
| | - Zeljko Rezek
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- University of Pennsylvania Museum of Archaeology and Anthropology, University of Pennsylvania, Philadelphia, PA, USA
| | - Svoboda Sirakova
- National Institute of Archaeology with Museum, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Nikolay Sirakov
- National Institute of Archaeology with Museum, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Shannon P McPherron
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Tsenka Tsanova
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Jean-Jacques Hublin
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Chaire de Paléoanthropologie, Collège de France, Paris, France
| | - Benjamin M Peter
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Matthias Meyer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Janet Kelso
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Svante Pääbo
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
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14
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Lanigan LT, Mackie M, Feine S, Hublin JJ, Schmitz RW, Wilcke A, Collins MJ, Cappellini E, Olsen JV, Taurozzi AJ, Welker F. Multi-protease analysis of Pleistocene bone proteomes. J Proteomics 2020; 228:103889. [DOI: 10.1016/j.jprot.2020.103889] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/08/2020] [Accepted: 06/25/2020] [Indexed: 12/11/2022]
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15
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Welker F, Ramos-Madrigal J, Gutenbrunner P, Mackie M, Tiwary S, Jersie-Christensen RR, Chiva C, Dickinson MR, Kuhlwilm M, de Manuel M, Gelabert P, Martinón-Torres M, Margvelashvili A, Arsuaga JL, Carbonell E, Marques-Bonet T, Penkman K, Sabidó E, Cox J, Olsen JV, Lordkipanidze D, Racimo F, Lalueza-Fox C, de Castro JMB, Willerslev E, Cappellini E. Author Correction: The dental proteome of Homo antecessor. Nature 2020; 584:E19. [PMID: 32724207 DOI: 10.1038/s41586-020-2580-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Frido Welker
- Evolutionary Genomics Section, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
| | - Jazmín Ramos-Madrigal
- Evolutionary Genomics Section, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Petra Gutenbrunner
- Computational Systems Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Meaghan Mackie
- Evolutionary Genomics Section, Globe Institute, University of Copenhagen, Copenhagen, Denmark.,The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Shivani Tiwary
- Computational Systems Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
| | | | - Cristina Chiva
- Center for Genomic Regulation (CNAG-CRG), Barcelona Institute of Science and Technology, Barcelona, Spain.,Proteomics Unit, University Pompeu Fabra, Barcelona, Spain
| | | | - Martin Kuhlwilm
- Institute of Evolutionary Biology (UPF-CSIC), University Pompeu Fabra, Barcelona, Spain
| | - Marc de Manuel
- Institute of Evolutionary Biology (UPF-CSIC), University Pompeu Fabra, Barcelona, Spain
| | - Pere Gelabert
- Institute of Evolutionary Biology (UPF-CSIC), University Pompeu Fabra, Barcelona, Spain
| | - María Martinón-Torres
- Centro Nacional de Investigación sobre la Evolución Humana (CENIEH), Burgos, Spain.,Anthropology Department, University College London, London, UK
| | | | - Juan Luis Arsuaga
- Centro Mixto UCM-ISCIII de Evolución y Comportamiento Humanos, Madrid, Spain.,Departamento de Paleontología, Facultad de Ciencias Geológicas, Universidad Complutense de Madrid, Madrid, Spain
| | - Eudald Carbonell
- Departamento d'Història i Història de l'Art, Universidad Rovira i Virgili, Tarragona, Spain.,Institut Català de Paleoecologia Humana i Evolució Social (IPHES), Tarragona, Spain
| | - Tomas Marques-Bonet
- Center for Genomic Regulation (CNAG-CRG), Barcelona Institute of Science and Technology, Barcelona, Spain.,Institute of Evolutionary Biology (UPF-CSIC), University Pompeu Fabra, Barcelona, Spain.,Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain.,Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
| | | | - Eduard Sabidó
- Center for Genomic Regulation (CNAG-CRG), Barcelona Institute of Science and Technology, Barcelona, Spain.,Proteomics Unit, University Pompeu Fabra, Barcelona, Spain
| | - Jürgen Cox
- Computational Systems Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Jesper V Olsen
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - David Lordkipanidze
- Georgian National Museum, Tbilisi, Georgia.,Tbilisi State University, Tbilisi, Georgia
| | - Fernando Racimo
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Carles Lalueza-Fox
- Institute of Evolutionary Biology (UPF-CSIC), University Pompeu Fabra, Barcelona, Spain
| | - José María Bermúdez de Castro
- Centro Nacional de Investigación sobre la Evolución Humana (CENIEH), Burgos, Spain. .,Anthropology Department, University College London, London, UK.
| | - Eske Willerslev
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark. .,Department of Zoology, University of Cambridge, Cambridge, UK. .,Wellcome Sanger Institute, Hinxton, UK. .,Danish Institute for Advanced Study, University of Southern Denmark, Odense, Denmark.
| | - Enrico Cappellini
- Evolutionary Genomics Section, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
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16
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Martisius NL, Welker F, Dogandžić T, Grote MN, Rendu W, Sinet-Mathiot V, Wilcke A, McPherron SJP, Soressi M, Steele TE. Non-destructive ZooMS identification reveals strategic bone tool raw material selection by Neandertals. Sci Rep 2020; 10:7746. [PMID: 32385291 PMCID: PMC7210944 DOI: 10.1038/s41598-020-64358-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 04/14/2020] [Indexed: 02/02/2023] Open
Abstract
Five nearly identical fragments of specialized bone tools, interpreted as lissoirs (French for “smoothers”), have been found at two Middle Paleolithic sites in southwest France. The finds span three separate archaeological deposits, suggesting continuity in the behavior of late Neandertals. Using standard morphological assessments, we determined that the lissoirs were produced on ribs of medium-sized ungulates. However, since these bones are highly fragmented and anthropogenically modified, species determinations were challenging. Also, conservative curation policy recommends minimizing destructive sampling of rare, fragile, or small artifacts for molecular identification methods. To better understand raw material selection for these five lissoirs, we reassess their taxonomy using a non-destructive ZooMS methodology based on triboelectric capture of collagen. We sampled four storage containers and obtained identifiable MALDI-TOF MS collagen fingerprints, all indicative of the same taxonomic clade, which includes aurochs and bison (Bos sp. and Bison sp.). The fifth specimen, which was stored in a plastic bag, provided no useful MALDI-TOF MS spectra. We show that the choice of large bovid ribs in an archaeological layer dominated by reindeer (Rangifer tarandus) demonstrates strategic selection by these Neandertals. Furthermore, our results highlight the value of a promising technique for the non-destructive analysis of bone artifacts.
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Affiliation(s)
- Naomi L Martisius
- Department of Anthropology, University of California, Davis, Davis, CA, 95616-8522, USA.
| | - Frido Welker
- Evolutionary Genomics Section, Globe Institute, University of Copenhagen, Øster Farimagsgade 5, 1353, Copenhagen, Denmark.,Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103, Leipzig, Germany
| | - Tamara Dogandžić
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103, Leipzig, Germany.,Department of Anthropology, University of Pennsylvania, 3260 South Street, Philadelphia, PA, 19104-6398, USA
| | - Mark N Grote
- Department of Anthropology, University of California, Davis, Davis, CA, 95616-8522, USA
| | - William Rendu
- Centre National de la Recherche Scientifique, MCC, Préhistoire à l'Actuel, Cultures, Environnement, Anthropologie, UMR5199, Université de Bordeaux, FR-33615, Pessac, France
| | - Virginie Sinet-Mathiot
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103, Leipzig, Germany
| | - Arndt Wilcke
- Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, D-04013, Leipzig, Germany
| | - Shannon J P McPherron
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103, Leipzig, Germany
| | - Marie Soressi
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103, Leipzig, Germany.,Faculty of Archaeology, Leiden University, 2300 RA, Leiden, The Netherlands
| | - Teresa E Steele
- Department of Anthropology, University of California, Davis, Davis, CA, 95616-8522, USA.,Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103, Leipzig, Germany
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17
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Swift JA, Bunce M, Dortch J, Douglass K, Faith JT, Fellows Yates JA, Field J, Haberle SG, Jacob E, Johnson CN, Lindsey E, Lorenzen ED, Louys J, Miller G, Mychajliw AM, Slon V, Villavicencio NA, Waters MR, Welker F, Wood R, Petraglia M, Boivin N, Roberts P. Micro Methods for Megafauna: Novel Approaches to Late Quaternary Extinctions and Their Contributions to Faunal Conservation in the Anthropocene. Bioscience 2019; 69:877-887. [PMID: 31719710 PMCID: PMC6829010 DOI: 10.1093/biosci/biz105] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Drivers of Late Quaternary megafaunal extinctions are relevant to modern conservation policy in a world of growing human population density, climate change, and faunal decline. Traditional debates tend toward global solutions, blaming either dramatic climate change or dispersals of Homo sapiens to new regions. Inherent limitations to archaeological and paleontological data sets often require reliance on scant, poorly resolved lines of evidence. However, recent developments in scientific technologies allow for more local, context-specific approaches. In the present article, we highlight how developments in five such methodologies (radiocarbon approaches, stable isotope analysis, ancient DNA, ancient proteomics, microscopy) have helped drive detailed analysis of specific megafaunal species, their particular ecological settings, and responses to new competitors or predators, climate change, and other external phenomena. The detailed case studies of faunal community composition, extinction chronologies, and demographic trends enabled by these methods examine megafaunal extinctions at scales appropriate for practical understanding of threats against particular species in their habitats today.
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Affiliation(s)
- Jillian A Swift
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
- Anthropology Department of Bernice Pauahi Bishop Museum, Honolulu, Hawai’i
| | - Michael Bunce
- Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Joe Dortch
- Centre for Rock Art Research and Management, University of Western Australia, Perth, Australia
| | - Kristina Douglass
- Department of Anthropology and with the Institutes for Energy and the Environment, The Pennsylvania State University, State College, Pennsylvania
| | - J Tyler Faith
- Natural History Museum of Utah and with the Department of Anthropology, University of Utah, Salt Lake City, Utah
| | - James A Fellows Yates
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Judith Field
- School of Biological, Earth, and Environmental Science, University of New South Wales, Sydney, Australia
| | - Simon G Haberle
- College of Asia and the Pacific and the School of Culture, History, and Language, Australian National University, Canberra, Australia
- Australian Research Council Centre of Excellence, Australian Biodiversity and Heritage, Wollongong, New South Wales, Australia
| | - Eileen Jacob
- Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, England
| | - Chris N Johnson
- Australian Research Council Centre of Excellence, Australian Biodiversity and Heritage, Wollongong, New South Wales, Australia
- School of Natural Sciences, University of Tasmania, Hobart, Australia
| | - Emily Lindsey
- La Brea Tar Pits and Museum, part of the Natural History Museum, Los Angeles County, Los Angeles, California
| | - Eline D Lorenzen
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Julien Louys
- Australian Research Center for Human Evolution, Environmental Futures Research Institute, Griffith University, Brisbane, Queensland, Australia
| | - Gifford Miller
- INSTAAR and Department of Geological Sciences, University of Colorado, Boulder
| | - Alexis M Mychajliw
- La Brea Tar Pits and Museum, part of the Natural History Museum, Los Angeles County, Los Angeles, California
| | - Viviane Slon
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Natalia A Villavicencio
- Departamento de Ecología, in the Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Instituto de Ecología and Biodiversidad, Santiago, Chile
| | - Michael R Waters
- Center for the Study of the First Americans, the Department of Anthropology, Texas A&M University, College Station, Texas
| | - Frido Welker
- Evolutionary Genomics Section of the GLOBE Institute, University of Copenhagen, Copenhagen, Denmark, and with the Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Rachel Wood
- Research School of Earth Sciences, Australian National University, Canberra, Australia
| | - Michael Petraglia
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Nicole Boivin
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Patrick Roberts
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
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18
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Cappellini E, Welker F, Pandolfi L, Ramos-Madrigal J, Samodova D, Rüther PL, Fotakis AK, Lyon D, Moreno-Mayar JV, Bukhsianidze M, Rakownikow Jersie-Christensen R, Mackie M, Ginolhac A, Ferring R, Tappen M, Palkopoulou E, Dickinson MR, Stafford TW, Chan YL, Götherström A, Nathan SKSS, Heintzman PD, Kapp JD, Kirillova I, Moodley Y, Agusti J, Kahlke RD, Kiladze G, Martínez-Navarro B, Liu S, Sandoval Velasco M, Sinding MHS, Kelstrup CD, Allentoft ME, Orlando L, Penkman K, Shapiro B, Rook L, Dalén L, Gilbert MTP, Olsen JV, Lordkipanidze D, Willerslev E. Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny. Nature 2019; 574:103-107. [PMID: 31511700 PMCID: PMC6894936 DOI: 10.1038/s41586-019-1555-y] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 08/12/2019] [Indexed: 11/10/2022]
Abstract
Ancient DNA (aDNA) sequencing has enabled reconstruction of speciation, migration, and admixture events for extinct taxa1. Outside the permafrost, however, irreversible aDNA post-mortem degradation2 has so far limited aDNA recovery to the past ~0.5 million years (Ma)3. Contrarily, tandem mass spectrometry (MS) allowed sequencing ~1.5 million year (Ma) old collagen type I (COL1)4 and suggested the presence of protein residues in Cretaceous fossil remains5, although with limited phylogenetic use6. In the absence of molecular evidence, the speciation of several Early and Middle Pleistocene extinct species remain contentious. In this study, we address the phylogenetic relationships of the Eurasian Pleistocene Rhinocerotidae7–9 using a ~1.77 Ma old dental enamel proteome of a Stephanorhinus specimen from the Dmanisi archaeological site in Georgia (South Caucasus)10. Molecular phylogenetic analyses place the Dmanisi Stephanorhinus as a sister group to the woolly (Coelodonta antiquitatis) and Merck’s rhinoceros (S. kirchbergensis) clade. We show that Coelodonta evolved from an early Stephanorhinus lineage and that the latter includes at least two distinct evolutionary lines. As such, the genus Stephanorhinus is currently paraphyletic and its systematic revision is therefore needed. We demonstrate that Early Pleistocene dental enamel proteome sequencing overcomes the limits of ancient collagen- and aDNA-based phylogenetic inference. It also provides additional information about the sex and taxonomic assignment of the specimens analysed. Dental enamel, the hardest tissue in vertebrates11, is highly abundant in the fossil record. Our findings reveal that palaeoproteomic investigation of this material can push biomolecular investigation further back into the Early Pleistocene.
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Affiliation(s)
- Enrico Cappellini
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark. .,Evolutionary Genomics Section, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
| | - Frido Welker
- Evolutionary Genomics Section, Globe Institute, University of Copenhagen, Copenhagen, Denmark.,Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Luca Pandolfi
- Dipartimento di Scienze della Terra, Università degli Studi di Firenze, Florence, Italy
| | - Jazmín Ramos-Madrigal
- Evolutionary Genomics Section, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Diana Samodova
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Patrick L Rüther
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Anna K Fotakis
- Evolutionary Genomics Section, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - David Lyon
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - J Víctor Moreno-Mayar
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Meaghan Mackie
- Evolutionary Genomics Section, Globe Institute, University of Copenhagen, Copenhagen, Denmark.,Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Aurélien Ginolhac
- Life Sciences Research Unit, University of Luxembourg, Belvaux, Luxembourg
| | - Reid Ferring
- Department of Geography and Environment, University of North Texas, Denton, TX, USA
| | - Martha Tappen
- Department of Anthropology, University of Minnesota, Minneapolis, MN, USA
| | | | | | | | - Yvonne L Chan
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Anders Götherström
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | | | - Peter D Heintzman
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA.,Tromsø University Museum, The Arctic University of Norway (UiT), Tromsø, Norway
| | - Joshua D Kapp
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Irina Kirillova
- Ice Age Museum, National Alliance of Shidlovskiy 'Ice Age', Moscow, Russia
| | - Yoshan Moodley
- Department of Zoology, University of Venda, Thohoyandou, South Africa
| | - Jordi Agusti
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.,Institut Català de Paleoecologia Humana i Evolució Social, Universitat Rovira i Virgili, Tarragona, Spain
| | | | - Gocha Kiladze
- Geology Department, Tbilisi State University, Tbilisi, Georgia
| | - Bienvenido Martínez-Navarro
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.,Institut Català de Paleoecologia Humana i Evolució Social, Universitat Rovira i Virgili, Tarragona, Spain.,Departament d'Història i Geografia, Universitat Rovira i Virgili, Tarragona, Spain
| | - Shanlin Liu
- Evolutionary Genomics Section, Globe Institute, University of Copenhagen, Copenhagen, Denmark.,BGI Shenzhen, Shenzen, China
| | | | - Mikkel-Holger S Sinding
- Evolutionary Genomics Section, Globe Institute, University of Copenhagen, Copenhagen, Denmark.,Greenland Institute of Natural Resources, Nuuk, Greenland
| | - Christian D Kelstrup
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Morten E Allentoft
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Ludovic Orlando
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.,Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, Université Paul Sabatier, Toulouse, France
| | | | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA.,Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Lorenzo Rook
- Dipartimento di Scienze della Terra, Università degli Studi di Firenze, Florence, Italy
| | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - M Thomas P Gilbert
- Evolutionary Genomics Section, Globe Institute, University of Copenhagen, Copenhagen, Denmark.,University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Jesper V Olsen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.
| | | | - Eske Willerslev
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark. .,Department of Zoology, University of Cambridge, Cambridge, UK. .,Wellcome Trust Sanger Institute, Hinxton, UK. .,Danish Institute for Advanced Study, University of Southern Denmark, Odense, Denmark.
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19
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Sinet-Mathiot V, Smith GM, Romandini M, Wilcke A, Peresani M, Hublin JJ, Welker F. Combining ZooMS and zooarchaeology to study Late Pleistocene hominin behaviour at Fumane (Italy). Sci Rep 2019; 9:12350. [PMID: 31451791 PMCID: PMC6710433 DOI: 10.1038/s41598-019-48706-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 07/25/2019] [Indexed: 12/14/2022] Open
Abstract
Collagen type I fingerprinting (ZooMS) has recently been used to provide either palaeoenvironmental data or to identify additional hominin specimens in Pleistocene contexts, where faunal assemblages are normally highly fragmented. However, its potential to elucidate hominin subsistence behaviour has been unexplored. Here, ZooMS and zooarchaeology have been employed in a complementary approach to investigate bone assemblages from Final Mousterian and Uluzzian contexts at Fumane cave (Italy). Both approaches produced analogous species composition, but differ significantly in species abundance, particularly highlighted by a six fold-increase in the quantity of Bos/Bison remains in the molecularly identified component. Traditional zooarchaeological methods would therefore underestimate the proportion of Bos/Bison in these levels to a considerable extent. We suggest that this difference is potentially due to percussion-based carcass fragmentation of large Bos/Bison bone diaphyses. Finally, our data demonstrates high variability in species assignment to body size classes based on bone cortical thickness and fragment size. Thus, combining biomolecular and traditional zooarchaeological methods allows us to refine our understanding of bone assemblage composition associated with hominin occupation at Fumane.
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Affiliation(s)
- Virginie Sinet-Mathiot
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Geoff M Smith
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Matteo Romandini
- University of Bologna, Department of Cultural Heritage, Ravenna, Italy.,University of Ferrara, Department of Humanities, Section of Prehistory and Anthropology, Ferrara, Italy
| | - Arndt Wilcke
- Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Marco Peresani
- University of Ferrara, Department of Humanities, Section of Prehistory and Anthropology, Ferrara, Italy.
| | - Jean-Jacques Hublin
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Frido Welker
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. .,Section for Evolutionary Genomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark.
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Cappellini E, Prohaska A, Racimo F, Welker F, Pedersen MW, Allentoft ME, de Barros Damgaard P, Gutenbrunner P, Dunne J, Hammann S, Roffet-Salque M, Ilardo M, Moreno-Mayar JV, Wang Y, Sikora M, Vinner L, Cox J, Evershed RP, Willerslev E. Ancient Biomolecules and Evolutionary Inference. Annu Rev Biochem 2018; 87:1029-1060. [PMID: 29709200 DOI: 10.1146/annurev-biochem-062917-012002] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Over the past three decades, studies of ancient biomolecules-particularly ancient DNA, proteins, and lipids-have revolutionized our understanding of evolutionary history. Though initially fraught with many challenges, today the field stands on firm foundations. Researchers now successfully retrieve nucleotide and amino acid sequences, as well as lipid signatures, from progressively older samples, originating from geographic areas and depositional environments that, until recently, were regarded as hostile to long-term preservation of biomolecules. Sampling frequencies and the spatial and temporal scope of studies have also increased markedly, and with them the size and quality of the data sets generated. This progress has been made possible by continuous technical innovations in analytical methods, enhanced criteria for the selection of ancient samples, integrated experimental methods, and advanced computational approaches. Here, we discuss the history and current state of ancient biomolecule research, its applications to evolutionary inference, and future directions for this young and exciting field.
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Affiliation(s)
- Enrico Cappellini
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; ,
| | - Ana Prohaska
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, United Kingdom
| | - Fernando Racimo
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; ,
| | - Frido Welker
- Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark.,Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | | | - Morten E Allentoft
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; ,
| | - Peter de Barros Damgaard
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; ,
| | - Petra Gutenbrunner
- Computational Systems Biochemistry, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Julie Dunne
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom;
| | - Simon Hammann
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom; .,Department of Anthropology and Archaeology, University of Bristol, Bristol BS8 1UU, United Kingdom
| | - Mélanie Roffet-Salque
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom;
| | - Melissa Ilardo
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; ,
| | - J Víctor Moreno-Mayar
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; ,
| | - Yucheng Wang
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; ,
| | - Martin Sikora
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; ,
| | - Lasse Vinner
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; ,
| | - Jürgen Cox
- Computational Systems Biochemistry, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Richard P Evershed
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom;
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; , .,Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, United Kingdom.,Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
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Hendy J, Welker F, Demarchi B, Speller C, Warinner C, Collins MJ. A guide to ancient protein studies. Nat Ecol Evol 2018; 2:791-799. [PMID: 29581591 DOI: 10.1038/s41559-018-0510-x] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 02/19/2018] [Indexed: 12/24/2022]
Abstract
Palaeoproteomics is an emerging neologism used to describe the application of mass spectrometry-based approaches to the study of ancient proteomes. As with palaeogenomics (the study of ancient DNA), it intersects evolutionary biology, archaeology and anthropology, with applications ranging from the phylogenetic reconstruction of extinct species to the investigation of past human diets and ancient diseases. However, there is no explicit consensus at present regarding standards for data reporting, data validation measures or the use of suitable contamination controls in ancient protein studies. Additionally, in contrast to the ancient DNA community, no consolidated guidelines have been proposed by which researchers, reviewers and editors can evaluate palaeoproteomics data, in part due to the novelty of the field. Here we present a series of precautions and standards for ancient protein research that can be implemented at each stage of analysis, from sample selection to data interpretation. These guidelines are not intended to impose a narrow or rigid list of authentication criteria, but rather to support good practices in the field and to ensure the generation of robust, reproducible results. As the field grows and methodologies change, so too will best practices. It is therefore essential that researchers continue to provide necessary details on how data were generated and authenticated so that the results can be independently and effectively evaluated. We hope that these proposed standards of practice will help to provide a firm foundation for the establishment of palaeoproteomics as a viable and powerful tool for archaeologists, anthropologists and evolutionary biologists.
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Affiliation(s)
- Jessica Hendy
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany.
| | - Frido Welker
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. .,Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
| | - Beatrice Demarchi
- Department of Life Science and Systems Biology, University of Turin, Turin, Italy.,BioArCh, Department of Archaeology, University of York, York, UK
| | - Camilla Speller
- BioArCh, Department of Archaeology, University of York, York, UK
| | - Christina Warinner
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.,Department of Anthropology, University of Oklahoma, Norman, OK, USA.,Institute for Evolutionary Medicine, University of Zürich, Zürich, Switzerland
| | - Matthew J Collins
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,BioArCh, Department of Archaeology, University of York, York, UK
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Welker F. Elucidation of cross-species proteomic effects in human and hominin bone proteome identification through a bioinformatics experiment. BMC Evol Biol 2018; 18:23. [PMID: 29463217 PMCID: PMC5819086 DOI: 10.1186/s12862-018-1141-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 02/15/2018] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND The study of ancient protein sequences is increasingly focused on the analysis of older samples, including those of ancient hominins. The analysis of such ancient proteomes thereby potentially suffers from "cross-species proteomic effects": the loss of peptide and protein identifications at increased evolutionary distances due to a larger number of protein sequence differences between the database sequence and the analyzed organism. Error-tolerant proteomic search algorithms should theoretically overcome this problem at both the peptide and protein level; however, this has not been demonstrated. If error-tolerant searches do not overcome the cross-species proteomic issue then there might be inherent biases in the identified proteomes. Here, a bioinformatics experiment is performed to test this using a set of modern human bone proteomes and three independent searches against sequence databases at increasing evolutionary distances: the human (0 Ma), chimpanzee (6-8 Ma) and orangutan (16-17 Ma) reference proteomes, respectively. RESULTS Incorrectly suggested amino acid substitutions are absent when employing adequate filtering criteria for mutable Peptide Spectrum Matches (PSMs), but roughly half of the mutable PSMs were not recovered. As a result, peptide and protein identification rates are higher in error-tolerant mode compared to non-error-tolerant searches but did not recover protein identifications completely. Data indicates that peptide length and the number of mutations between the target and database sequences are the main factors influencing mutable PSM identification. CONCLUSIONS The error-tolerant results suggest that the cross-species proteomics problem is not overcome at increasing evolutionary distances, even at the protein level. Peptide and protein loss has the potential to significantly impact divergence dating and proteome comparisons when using ancient samples as there is a bias towards the identification of conserved sequences and proteins. Effects are minimized between moderately divergent proteomes, as indicated by almost complete recovery of informative positions in the search against the chimpanzee proteome (≈90%, 6-8 Ma). This provides a bioinformatic background to future phylogenetic and proteomic analysis of ancient hominin proteomes, including the future description of novel hominin amino acid sequences, but also has negative implications for the study of fast-evolving proteins in hominins, non-hominin animals, and ancient bacterial proteins in evolutionary contexts.
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Affiliation(s)
- F Welker
- Department of Human Evolution, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany.
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
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Welker F, Smith GM, Hutson JM, Kindler L, Garcia-Moreno A, Villaluenga A, Turner E, Gaudzinski-Windheuser S. Middle Pleistocene protein sequences from the rhinoceros genus Stephanorhinus and the phylogeny of extant and extinct Middle/Late Pleistocene Rhinocerotidae. PeerJ 2017; 5:e3033. [PMID: 28316883 PMCID: PMC5354071 DOI: 10.7717/peerj.3033] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 01/26/2017] [Indexed: 11/20/2022] Open
Abstract
Background Ancient protein sequences are increasingly used to elucidate the phylogenetic relationships between extinct and extant mammalian taxa. Here, we apply these recent developments to Middle Pleistocene bone specimens of the rhinoceros genus Stephanorhinus. No biomolecular sequence data is currently available for this genus, leaving phylogenetic hypotheses on its evolutionary relationships to extant and extinct rhinoceroses untested. Furthermore, recent phylogenies based on Rhinocerotidae (partial or complete) mitochondrial DNA sequences differ in the placement of the Sumatran rhinoceros (Dicerorhinus sumatrensis). Therefore, studies utilising ancient protein sequences from Middle Pleistocene contexts have the potential to provide further insights into the phylogenetic relationships between extant and extinct species, including Stephanorhinus and Dicerorhinus. Methods ZooMS screening (zooarchaeology by mass spectrometry) was performed on several Late and Middle Pleistocene specimens from the genus Stephanorhinus, subsequently followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) to obtain ancient protein sequences from a Middle Pleistocene Stephanorhinus specimen. We performed parallel analysis on a Late Pleistocene woolly rhinoceros specimen and extant species of rhinoceroses, resulting in the availability of protein sequence data for five extant species and two extinct genera. Phylogenetic analysis additionally included all extant Perissodactyla genera (Equus, Tapirus), and was conducted using Bayesian (MrBayes) and maximum-likelihood (RAxML) methods. Results Various ancient proteins were identified in both the Middle and Late Pleistocene rhinoceros samples. Protein degradation and proteome complexity are consistent with an endogenous origin of the identified proteins. Phylogenetic analysis of informative proteins resolved the Perissodactyla phylogeny in agreement with previous studies in regards to the placement of the families Equidae, Tapiridae, and Rhinocerotidae. Stephanorhinus is shown to be most closely related to the genera Coelodonta and Dicerorhinus. The protein sequence data further places the Sumatran rhino in a clade together with the genus Rhinoceros, opposed to forming a clade with the black and white rhinoceros species. Discussion The first biomolecular dataset available for Stephanorhinus places this genus together with the extinct genus Coelodonta and the extant genus Dicerorhinus. This is in agreement with morphological studies, although we are unable to resolve the order of divergence between these genera based on the protein sequences available. Our data supports the placement of the genus Dicerorhinus in a clade together with extant Rhinoceros species. Finally, the availability of protein sequence data for both extinct European rhinoceros genera allows future investigations into their geographic distribution and extinction chronologies.
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Affiliation(s)
- Frido Welker
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany; BioArCh, Department of Archaeology, University of York, York, UK
| | - Geoff M Smith
- MONREPOS Archaeological Research Centre and Museum for Human Behavioural Evolution, RGZM, Neuwied, Germany; Department of Anthropology, University of California Davis, Davis, CA, USA
| | - Jarod M Hutson
- MONREPOS Archaeological Research Centre and Museum for Human Behavioural Evolution, RGZM, Neuwied, Germany; Current affiliation: Department of Paleobiology, Smithsonian Institution, Washington, D.C., USA
| | - Lutz Kindler
- MONREPOS Archaeological Research Centre and Museum for Human Behavioural Evolution, RGZM, Neuwied, Germany; Department of Pre- and Protohistoric Archaeology, Institute of Ancient Studies, Johannes-Gutenberg Universität Mainz, Mainz, Germany
| | - Alejandro Garcia-Moreno
- MONREPOS Archaeological Research Centre and Museum for Human Behavioural Evolution, RGZM , Neuwied , Germany
| | - Aritza Villaluenga
- MONREPOS Archaeological Research Centre and Museum for Human Behavioural Evolution, RGZM , Neuwied , Germany
| | - Elaine Turner
- MONREPOS Archaeological Research Centre and Museum for Human Behavioural Evolution, RGZM , Neuwied , Germany
| | - Sabine Gaudzinski-Windheuser
- MONREPOS Archaeological Research Centre and Museum for Human Behavioural Evolution, RGZM, Neuwied, Germany; Department of Pre- and Protohistoric Archaeology, Institute of Ancient Studies, Johannes-Gutenberg Universität Mainz, Mainz, Germany
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Abstract
Diagnostic ultrasound permits the clinician to image the beating heart, quantitate cardiac dimensions, identify specific congenital and acquired cardiac lesions, and estimate the degree of cardiac compensation and muscle failure that accompanies a specific lesion. The M-mode (motion) echocardiogram and two-dimensional echocardiogram are complementary studies that have proved useful for identification of cardiac septal defects, endocarditis, pericardial effusion, intracardiac shunting, cardiomegaly, and heart muscle failure. Appreciation of the technique and basic knowledge of the types of information that can be obtained from echocardiography are necessary to appropriately refer horses for these studies.
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