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Fabrizi I, Flament S, Delhon C, Gourichon L, Vuillien M, Oueslati T, Auguste P, Rolando C, Bray F. Low-Invasive Sampling Method with Tape-Disc Sampling for the Taxonomic Identification of Archeological and Paleontological Bones by Proteomics. J Proteome Res 2024; 23:3404-3417. [PMID: 39042361 DOI: 10.1021/acs.jproteome.4c00083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
Collagen from paleontological bones is an important organic material for isotopic measurement, radiocarbon analysis, and paleoproteomic analysis to provide information on diet, dating, taxonomy, and phylogeny. Current paleoproteomic methods are destructive and require from a few milligrams to several tens of milligrams of bone for analysis. In many cultures, bones are raw materials for artifacts that are conserved in museums, which hampers damage to these precious objects during sampling. Here, we describe a low-invasive sampling method that identifies collagen, taxonomy, and post-translational modifications from Holocene and Upper Pleistocene bones dated to 130,000 and 150 BC using dermatological skin tape discs for sampling. The sampled bone micropowders were digested following our highly optimized enhanced filter-aided sample preparation protocol and then analyzed by MALDI FTICR MS and LC-MS/MS for identifying the genus taxa of the bones. We show that this low-invasive sampling does not deteriorate the bones and achieves results similar to those obtained by more destructive sampling. Moreover, this sampling method can be carried out at archeological sites or in museums.
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Affiliation(s)
- Isabelle Fabrizi
- Univ. Lille, CNRS UAR 3290─MSAP─Miniaturisation pour la Synthèse, l'Analyse et la Protéomique, Lille F-59000, France
| | - Stéphanie Flament
- Univ. Lille, CNRS UAR 3290─MSAP─Miniaturisation pour la Synthèse, l'Analyse et la Protéomique, Lille F-59000, France
| | - Claire Delhon
- Université Côte d'Azur, CNRS, CEPAM (UMR 7264), Nice F-06300, France
| | - Lionel Gourichon
- Université Côte d'Azur, CNRS, CEPAM (UMR 7264), Nice F-06300, France
| | - Manon Vuillien
- Université Côte d'Azur, CNRS, CEPAM (UMR 7264), Nice F-06300, France
| | - Tarek Oueslati
- Univ. Lille, CNRS UMR 8164─HALMA─Histoire, Archéologie et Littérature des Mondes Anciens, Lille F-59000, France
| | - Patrick Auguste
- Univ. Lille, CNRS UMR 8198─EEP─Evolution, Ecology and Paleontology, Lille F-59000, France
| | - Christian Rolando
- Univ. Lille, CNRS UAR 3290─MSAP─Miniaturisation pour la Synthèse, l'Analyse et la Protéomique, Lille F-59000, France
- Shrieking Sixties, Villeneuve d'Ascq F-59650, France
| | - Fabrice Bray
- Univ. Lille, CNRS UAR 3290─MSAP─Miniaturisation pour la Synthèse, l'Analyse et la Protéomique, Lille F-59000, France
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2
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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: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [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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3
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Winter RM, de Kock W, Mackie M, Ramsøe M, Desiderà E, Collins M, Guidetti P, Presslee S, Alegre MM, Oueslati T, Muniz AM, Michailidis D, van den Hurk Y, Taurozzi AJ, Çakirlar C. Grouping groupers in the Mediterranean: Ecological baselines revealed by ancient proteins. Ecol Evol 2023; 13:e10625. [PMID: 37877101 PMCID: PMC10591212 DOI: 10.1002/ece3.10625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 09/29/2023] [Accepted: 10/04/2023] [Indexed: 10/26/2023] Open
Abstract
Marine historical ecology provides a means to establish baselines to inform current fisheries management. Groupers (Epinephelidae) are key species for fisheries in the Mediterranean, which have been heavily overfished. Species abundance and distribution prior to the 20th century in the Mediterranean remains poorly known. To reconstruct the past biogeography of Mediterranean groupers, we investigated whether Zooarchaeology by Mass Spectrometry (ZooMS) can be used for identifying intra-genus grouper bones to species level. We discovered 22 novel, species-specific ZooMS biomarkers for groupers. Applying these biomarkers to Kinet Höyük, a Mediterranean archaeological site, demonstrated 4000 years of regional Epinephelus aeneus dominance and resiliency through millennia of fishing pressures, habitat degradation and climatic changes. Combining ZooMS identifications with catch size reconstructions revealed the Epinephelus aeneus capacity for growing 30 cm larger than hitherto documented, revising the maximum Total Length from 120 to 150 cm. Our results provide ecological baselines for a key Mediterranean fishery which could be leveraged to define and assess conservation targets.
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Affiliation(s)
- Rachel M. Winter
- Groningen Institute of ArchaeologyUniversity of GroningenGroningenThe Netherlands
| | - Willemien de Kock
- Groningen Institute of ArchaeologyUniversity of GroningenGroningenThe Netherlands
- Marine Evolution and Conservation, Groningen Institute for Evolutionary Life SciencesUniversity of GroningenGroningenThe Netherlands
| | - Meaghan Mackie
- Faculty of Health and Medical Science, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
- Faculty of Health and Medical Science, Novo Nordisk Foundation Center for Protein ResearchUniversity of CopenhagenCopenhagenDenmark
| | - Max Ramsøe
- Faculty of Health and Medical Science, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
| | - Elena Desiderà
- Department of Integrative Marine Ecology (EMI)Stazione Zoologica Anton Dohrn–National Institute of Marine Biology, Ecology and Biotechnology—Genoa Marine CentreGenoaItaly
| | - Matthew Collins
- Faculty of Health and Medical Science, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
- Department of ArchaeologyUniversity of CambridgeCambridgeUK
| | - Paolo Guidetti
- Department of Integrative Marine Ecology (EMI)Stazione Zoologica Anton Dohrn–National Institute of Marine Biology, Ecology and Biotechnology—Genoa Marine CentreGenoaItaly
| | | | | | - Tarek Oueslati
- Centre National de la Recherche ScientifiqueUniversity of LilleLilleFrance
| | | | - Dimitris Michailidis
- Malcolm H. Wiener Lab, American School of Classical Studies at AthensAthensGreece
| | - Youri van den Hurk
- Department of Archaeology and Cultural HistoryNorwegian University of Science and TechnologyTrondheimNorway
| | - Alberto J. Taurozzi
- Faculty of Health and Medical Science, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
| | - Canan Çakirlar
- Groningen Institute of ArchaeologyUniversity of GroningenGroningenThe Netherlands
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4
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Oras E, Tõrv M, Johanson K, Rannamäe E, Poska A, Lõugas L, Lucquin A, Lundy J, Brown S, Chen S, Varul L, Haferberga V, Legzdiņa D, Zariņa G, Cramp L, Heyd V, Reay M, Pospieszny Ł, Robson HK, Nordqvist K, Heron C, Craig OE, Kriiska A. Parallel worlds and mixed economies: multi-proxy analysis reveals complex subsistence systems at the dawn of early farming in the northeast Baltic. ROYAL SOCIETY OPEN SCIENCE 2023; 10:230880. [PMID: 37800159 PMCID: PMC10548101 DOI: 10.1098/rsos.230880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 09/08/2023] [Indexed: 10/07/2023]
Abstract
The transition from foraging to farming was a key turning point in ancient socio-economies. Yet, the complexities and regional variations of this transformation are still poorly understood. This multi-proxy study provides a new understanding of the introduction and spread of early farming, challenging the notions of hierarchical economies. The most extensive biological and biomolecular dietary overview, combining zooarchaeological, archaeobotanical, dietary stable isotope and pottery lipid residue analyses is presented, to unravel the nature and extent of early farming in the 3rd millennium cal BCE in the northeast Baltic. Farming was introduced by incoming Corded Ware cultural groups (CWC), but some dietary segregation existed within these communities, with some having more access to domesticates, others incorporating more wild resources into their diet. The CWC groups coexisted in parallel with local hunter-fisher-gatherers (HFG) without any indication of the adoption of domesticates. There was no transition from foraging to farming in the 3rd millennium cal BCE in the NE Baltic. Instead, we see a complex system of parallel worlds with local HFGs continuing forager lifeways, and incoming farmers practising mixed economies, with the continuation of these subsistence strategies for at least a millennium after the first encounter with domesticated animals.
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Affiliation(s)
- Ester Oras
- Institute of Chemistry, University of Tartu, Ravila 14 a, 50411 Tartu, Estonia
- Institute of History and Archaeology, University of Tartu, Jakobi 2, 51005 Tartu, Estonia
- Swedish Collegium for Advanced Study (SCAS), Linneanum, Thunbergsvägen 2, 75238 Uppsala, Sweden
| | - Mari Tõrv
- Institute of Chemistry, University of Tartu, Ravila 14 a, 50411 Tartu, Estonia
- Institute of History and Archaeology, University of Tartu, Jakobi 2, 51005 Tartu, Estonia
| | - Kristiina Johanson
- Institute of History and Archaeology, University of Tartu, Jakobi 2, 51005 Tartu, Estonia
| | - Eve Rannamäe
- Institute of History and Archaeology, University of Tartu, Jakobi 2, 51005 Tartu, Estonia
| | - Anneli Poska
- Department of Geology, Tallinn University of Technology, Ehitajate Tee 5, 19086 Tallinn, Estonia
| | - Lembi Lõugas
- Archaeological Research Collection, Tallinn University, Rüütli 10, 10130 Tallinn, Estonia
| | - Alexandre Lucquin
- BioArCh, Department of Archaeology, University of York, Environment Building, Wentworth Way, YO10 5DD York, UK
| | - Jasmine Lundy
- BioArCh, Department of Archaeology, University of York, Environment Building, Wentworth Way, YO10 5DD York, UK
| | - Samantha Brown
- Institute for Archaeological Sciences, Department of Geosciences, University of Tübingen, Rümelinstrasse 23, 72070 Tübingen, Germany
| | - Shidong Chen
- Institute of Chemistry, University of Tartu, Ravila 14 a, 50411 Tartu, Estonia
| | - Liivi Varul
- School of Humanities, Division of History, Tallinn University, Narva rd 25, 10120 Tallinn, Estonia
| | - Vanda Haferberga
- Institute of Latvian History, University of Latvia, Kalpaka blvd 4, LV-1050 Riga, Latvia
| | - Dardega Legzdiņa
- Institute of Latvian History, University of Latvia, Kalpaka blvd 4, LV-1050 Riga, Latvia
| | - Gunita Zariņa
- Institute of Latvian History, University of Latvia, Kalpaka blvd 4, LV-1050 Riga, Latvia
| | - Lucy Cramp
- Department of Anthropology and Archaeology, University of Bristol, 43 Woodland Road, BS8 1UU Bristol, UK
| | - Volker Heyd
- Department of Cultures, University of Helsinki, Unioninkatu 38, 00014 Helsinki, Finland
| | - Michaela Reay
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, BS8 1TS Bristol, UK
| | - Łukasz Pospieszny
- Department of Anthropology and Archaeology, University of Bristol, 43 Woodland Road, BS8 1UU Bristol, UK
- Institute of Archaeology, University of Gdańsk, ul. Bielańska 5, 80-851 Gdańsk, Poland
| | - Harry K. Robson
- BioArCh, Department of Archaeology, University of York, Environment Building, Wentworth Way, YO10 5DD York, UK
| | - Kerkko Nordqvist
- Helsinki Collegium for Advanced Studies, University of Helsinki, Fabianinkatu 24, 00014 Helsinki, Finland
| | - Carl Heron
- Department of Scientific Research, The British Museum, WC1B 3DG London, UK
| | - Oliver E. Craig
- BioArCh, Department of Archaeology, University of York, Environment Building, Wentworth Way, YO10 5DD York, UK
| | - Aivar Kriiska
- Institute of History and Archaeology, University of Tartu, Jakobi 2, 51005 Tartu, Estonia
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5
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Wilkin S, Hommel P, Ventresca Miller A, Boivin N, Pedergnana A, Shishlina N, Trifonov V. Curated cauldrons: Preserved proteins from early copper-alloy vessels illuminate feasting practices in the Caucasian steppe. iScience 2023; 26:107482. [PMID: 37744407 PMCID: PMC10517358 DOI: 10.1016/j.isci.2023.107482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 05/26/2023] [Accepted: 07/24/2023] [Indexed: 09/26/2023] Open
Abstract
Large metal and metal-alloy cauldrons first appear on the far western steppe and Caucasus region during the Maykop period (3700-2900 BCE); however, the types of foods or beverages cooked in and served from these vessels have remained mysterious. Here, we present proteomic analysis of nine residues from copper-alloy cauldrons from Maykop burial contexts where we identify muscle, blood, and milk proteins specific to domesticated, and possibly wild, ruminants. This study clearly demonstrates that the earliest, large-volume feasting vessels contained both primary and secondary animal products, likely prepared in the form of a stew.
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Affiliation(s)
- Shevan Wilkin
- Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland
- Max Planck Institute of Geoanthropology, Jena, Germany
- Australian Research Centre for Human Evolution (ARCHE), Griffith University, Brisbane, QLD, Australia
| | - Peter Hommel
- Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool, UK
| | - Alicia Ventresca Miller
- Department of Anthropology, University of Michigan, Ann Arbor, MI, USA
- Museum of Anthropological Archaeology, University of Michigan, Ann Arbor, MI, USA
| | - Nicole Boivin
- Max Planck Institute of Geoanthropology, Jena, Germany
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
- School of Social Science, University of Queensland, Brisbane, QLD, Australia
- Griffith Sciences, Griffith University, Brisbane, QLD, Australia
| | | | - Natalia Shishlina
- State Historical Museum, Moscow, Russia
- Peter the Great Museum of Anthropology and Ethnography (the Kunstkamera), St Petersburg, Russia
| | - Viktor Trifonov
- Institute for the History of Material Culture, St Petersburg, Russia
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6
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Dierickx K, Presslee S, Harvey VL. Rapid collagen peptide mass fingerprinting as a tool to authenticate Pleuronectiformes in the food industry. Food Control 2023. [DOI: 10.1016/j.foodcont.2023.109680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
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7
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Abstract
Paleoproteomics, the study of ancient proteins, is a rapidly growing field at the intersection of molecular biology, paleontology, archaeology, paleoecology, and history. Paleoproteomics research leverages the longevity and diversity of proteins to explore fundamental questions about the past. While its origins predate the characterization of DNA, it was only with the advent of soft ionization mass spectrometry that the study of ancient proteins became truly feasible. Technological gains over the past 20 years have allowed increasing opportunities to better understand preservation, degradation, and recovery of the rich bioarchive of ancient proteins found in the archaeological and paleontological records. Growing from a handful of studies in the 1990s on individual highly abundant ancient proteins, paleoproteomics today is an expanding field with diverse applications ranging from the taxonomic identification of highly fragmented bones and shells and the phylogenetic resolution of extinct species to the exploration of past cuisines from dental calculus and pottery food crusts and the characterization of past diseases. More broadly, these studies have opened new doors in understanding past human-animal interactions, the reconstruction of past environments and environmental changes, the expansion of the hominin fossil record through large scale screening of nondiagnostic bone fragments, and the phylogenetic resolution of the vertebrate fossil record. Even with these advances, much of the ancient proteomic record still remains unexplored. Here we provide an overview of the history of the field, a summary of the major methods and applications currently in use, and a critical evaluation of current challenges. We conclude by looking to the future, for which innovative solutions and emerging technology will play an important role in enabling us to access the still unexplored "dark" proteome, allowing for a fuller understanding of the role ancient proteins can play in the interpretation of the past.
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Affiliation(s)
- Christina Warinner
- Department
of Anthropology, Harvard University, Cambridge, Massachusetts 02138, United States
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Kristine Korzow Richter
- Department
of Anthropology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Matthew J. Collins
- Department
of Archaeology, Cambridge University, Cambridge CB2 3DZ, United Kingdom
- Section
for Evolutionary Genomics, Globe Institute,
University of Copenhagen, Copenhagen 1350, Denmark
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8
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Dierickx K, Presslee S, Hagan R, Oueslati T, Harland J, Hendy J, Orton D, Alexander M, Harvey VL. Peptide mass fingerprinting of preserved collagen in archaeological fish bones for the identification of flatfish in European waters. ROYAL SOCIETY OPEN SCIENCE 2022; 9:220149. [PMID: 35911190 PMCID: PMC9326269 DOI: 10.1098/rsos.220149] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 07/06/2022] [Indexed: 06/15/2023]
Abstract
Bones of Pleuronectiformes (flatfish) are often not identified to species due to the lack of diagnostic features on bones that allow adequate distinction between taxa. This hinders in-depth understanding of archaeological fish assemblages and particularly flatfish fisheries throughout history. This is especially true for the North Sea region, where several commercially significant species have been exploited for centuries, yet their archaeological remains continue to be understudied. In this research, eight peptide biomarkers for 18 different species of Pleuronectiformes from European waters are described using MALDI-TOF MS and liquid chromatography tandem mass spectrometry data obtained from modern reference specimens. Bone samples (n = 202) from three archaeological sites in the UK and France dating to the medieval period (ca seventh-sixteenth century CE) were analysed using zooarchaeology by mass spectrometry (ZooMS). Of the 201 that produced good quality spectra, 196 were identified as flatfish species, revealing a switch in targeted species through time and indicating that ZooMS offers a more reliable and informative approach for species identification than osteological methods alone. We recommend this approach for future studies of archaeological flatfish remains as the precise species uncovered from a site can tell much about the origin of the fish, where people fished and whether they traded between regions.
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Affiliation(s)
- Katrien Dierickx
- Department of Archaeology, University of York, Heslington YO10 5DD, York, UK
| | - Samantha Presslee
- Department of Archaeology, University of York, Heslington YO10 5DD, York, UK
| | - Richard Hagan
- Department of Archaeology, University of York, Heslington YO10 5DD, York, UK
| | - Tarek Oueslati
- Centre National de la Recherche Scientifique, University of Lille, Lille, France
| | - Jennifer Harland
- Department of Archaeology, University of York, Heslington YO10 5DD, York, UK
- Archaeology Institute, University of the Highlands and Islands, Kirkwall, UK
| | - Jessica Hendy
- Department of Archaeology, University of York, Heslington YO10 5DD, York, UK
| | - David Orton
- Department of Archaeology, University of York, Heslington YO10 5DD, York, UK
| | - Michelle Alexander
- Department of Archaeology, University of York, Heslington YO10 5DD, York, UK
| | - Virginia L. Harvey
- Department of Archaeology, University of York, Heslington YO10 5DD, York, UK
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9
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Abstract
Collagen peptide mass fingerprinting by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry, also known as zooarchaeology by mass spectrometry (ZooMS), is a rapidly growing analytical technique in the fields of archaeology, ecology, and cultural heritage. Minimally destructive and cost effective, ZooMS enables rapid taxonomic identification of large bone assemblages, cultural heritage objects, and other organic materials of animal origin. As its importance grows as both a research and a conservation tool, it is critical to ensure that its expanding body of users understands its fundamental principles, strengths, and limitations. Here, we outline the basic functionality of ZooMS and provide guidance on interpreting collagen spectra from archaeological bones. We further examine the growing potential of applying ZooMS to nonmammalian assemblages, discuss available options for minimally and nondestructive analyses, and explore the potential for peptide mass fingerprinting to be expanded to noncollagenous proteins. We describe the current limitations of the method regarding accessibility, and we propose solutions for the future. Finally, we review the explosive growth of ZooMS over the past decade and highlight the remarkably diverse applications for which the technique is suited.
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10
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Are We Betting on the Wrong Horse? Insignificant Archaeological Leather Fragments Provide the First Evidence for the Exploitation of Horsehide in Renaissance Denmark. HERITAGE 2022. [DOI: 10.3390/heritage5020053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
Large archaeological, organic materials can be difficult to preserve, conserve, and store in their entirety, which is why prioritisation is often necessary. Priority is generally given to recognisable objects rather than smaller fragments. Nevertheless, for archaeological leather, exactly such insignificant fragments can provide new information on the diversity of species exploited. In this pilot study, we use a Citizen Science approach for the first time to identify archaeological leather fragments using the protein-based method Zooarchaeology by Mass Spectrometry (ZooMS). By inviting the public to participate in archaeological research, the project’s first 52 samples, including both recognisable and unidentifiable objects, were analysed. We show that the participants not only generated good data, but also contributed to current knowledge by identifying two hitherto undescribed animal species for leather in medieval and Renaissance Copenhagen. The finding of deer suggests that Copenhagen citizens now and then had access to game through the nobility and the finding of horse suggests that the unclean status of horses was sometimes overlooked to exploit its hide. Our findings are promising for more identifications and the new knowledge the project will generate. The study calls into question how we prioritise and assign value to cultural heritage materials.
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11
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SPIN enables high throughput species identification of archaeological bone by proteomics. Nat Commun 2022; 13:2458. [PMID: 35513387 PMCID: PMC9072323 DOI: 10.1038/s41467-022-30097-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 04/18/2022] [Indexed: 12/29/2022] Open
Abstract
Species determination based on genetic evidence is an indispensable tool in archaeology, forensics, ecology, and food authentication. Most available analytical approaches involve compromises with regard to the number of detectable species, high cost due to low throughput, or a labor-intensive manual process. Here, we introduce "Species by Proteome INvestigation" (SPIN), a shotgun proteomics workflow for analyzing archaeological bone capable of querying over 150 mammalian species by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Rapid peptide chromatography and data-independent acquisition (DIA) with throughput of 200 samples per day reduce expensive MS time, whereas streamlined sample preparation and automated data interpretation save labor costs. We confirm the successful classification of known reference bones, including domestic species and great apes, beyond the taxonomic resolution of the conventional peptide mass fingerprinting (PMF)-based Zooarchaeology by Mass Spectrometry (ZooMS) method. In a blinded study of degraded Iron-Age material from Scandinavia, SPIN produces reproducible results between replicates, which are consistent with morphological analysis. Finally, we demonstrate the high throughput capabilities of the method in a high-degradation context by analyzing more than two hundred Middle and Upper Palaeolithic bones from Southern European sites with late Neanderthal occupation. While this initial study is focused on modern and archaeological mammalian bone, SPIN will be open and expandable to other biological tissues and taxa.
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12
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Abstract
Archaeological and paleontological records offer tremendous yet often untapped potential for examining long-term biodiversity trends and the impact of climate change and human activity on ecosystems. Yet, zooarchaeological and fossil remains suffer various limitations, including that they are often highly fragmented and morphologically unidentifiable, preventing them from being optimally leveraged for addressing fundamental research questions in archaeology, paleontology, and conservation paleobiology. Here, we explore the potential of palaeoproteomics—the study of ancient proteins—to serve as a critical tool for creating richer, more informative datasets about biodiversity change that can be leveraged to generate more realistic, constructive, and effective conservation and restoration strategies into the future.
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13
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Welker F. Editorial. J Proteomics 2021; 253:104460. [PMID: 34955453 DOI: 10.1016/j.jprot.2021.104460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Frido Welker
- GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.
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14
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Peters C, Richter KK, Manne T, Dortch J, Paterson A, Travouillon K, Louys J, Price GJ, Petraglia M, Crowther A, Boivin N. Species identification of Australian marsupials using collagen fingerprinting. ROYAL SOCIETY OPEN SCIENCE 2021; 8:211229. [PMID: 34729210 PMCID: PMC8548793 DOI: 10.1098/rsos.211229] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 09/30/2021] [Indexed: 06/13/2023]
Abstract
The study of faunal remains from archaeological sites is often complicated by the presence of large numbers of highly fragmented, morphologically unidentifiable bones. In Australia, this is the combined result of harsh preservation conditions and frequent scavenging by marsupial carnivores. The collagen fingerprinting method known as zooarchaeology by mass spectrometry (ZooMS) offers a means to address these challenges and improve identification rates of fragmented bones. Here, we present novel ZooMS peptide markers for 24 extant marsupial and monotreme species that allow for genus-level distinctions between these species. We demonstrate the utility of these new peptide markers by using them to taxonomically identify bone fragments from a nineteenth-century colonial-era pearlshell fishery at Bandicoot Bay, Barrow Island. The suite of peptide biomarkers presented in this study, which focus on a range of ecologically and culturally important species, have the potential to significantly amplify the zooarchaeological and paleontological record of Australia.
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Affiliation(s)
- Carli Peters
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
| | | | - Tiina Manne
- School of Social Science, The University of Queensland, Brisbane, Qld 4071, Australia
| | - Joe Dortch
- School of Social Sciences, University of Western Australia, Perth, WA 6009, Australia
| | - Alistair Paterson
- School of Social Sciences, University of Western Australia, Perth, WA 6009, Australia
| | - Kenny Travouillon
- Western Australian Museum, Collections and Research, 49 Kew Street, Welshpool, WA 6106, Australia
| | - Julien Louys
- Australian Research Centre for Human Evolution, Griffith University, Nathan, Qld 4111, Australia
| | - Gilbert J. Price
- School of Earth and Environmental Sciences, The University of Queensland, Brisbane, Qld 4072, Australia
| | - Michael Petraglia
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
- School of Social Science, The University of Queensland, Brisbane, Qld 4071, Australia
- Australian Research Centre for Human Evolution, Griffith University, Nathan, Qld 4111, Australia
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Alison Crowther
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
- School of Social Science, The University of Queensland, Brisbane, Qld 4071, Australia
| | - Nicole Boivin
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
- School of Social Science, The University of Queensland, Brisbane, Qld 4071, Australia
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
- Department of Anthropology and Archaeology, University of Calgary, Calgary, Canada
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15
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Harvey VL, Keating JN, Buckley M. Phylogenetic analyses of ray-finned fishes (Actinopterygii) using collagen type I protein sequences. ROYAL SOCIETY OPEN SCIENCE 2021; 8:201955. [PMID: 34430038 PMCID: PMC8355665 DOI: 10.1098/rsos.201955] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 07/20/2021] [Indexed: 05/12/2023]
Abstract
Ray-finned fishes (Actinopterygii) are the largest and most diverse group of vertebrates, comprising over half of all living vertebrate species. Phylogenetic relationships between ray-finned fishes have historically pivoted on the study of morphology, which has notoriously failed to resolve higher order relationships, such as within the percomorphs. More recently, comprehensive genomic analyses have provided further resolution of actinopterygian phylogeny, including higher order relationships. Such analyses are rightfully regarded as the 'gold standard' for phylogenetics. However, DNA retrieval requires modern or well-preserved tissue and is less likely to be preserved in archaeological or fossil specimens. By contrast, some proteins, such as collagen, are phylogenetically informative and can survive into deep time. Here, we test the utility of collagen type I amino acid sequences for phylogenetic estimation of ray-finned fishes. We estimate topology using Bayesian approaches and compare the congruence of our estimated trees with published genomic phylogenies. Furthermore, we apply a Bayesian molecular clock approach and compare estimated divergence dates with previously published genomic clock analyses. Our collagen-derived trees exhibit 77% of node positions as congruent with recent genomic-derived trees, with the majority of discrepancies occurring in higher order node positions, almost exclusively within the Percomorpha. Our molecular clock trees present divergence times that are fairly comparable with genomic-based phylogenetic analyses. We estimate the mean node age of Actinopteri at ∼293 million years (Ma), the base of Teleostei at ∼211 Ma and the radiation of percomorphs beginning at ∼141 Ma (∼350 Ma, ∼250-283 Ma and ∼120-133 Ma in genomic trees, respectively). Finally, we show that the average rate of collagen (I) sequence evolution is 0.9 amino acid substitutions for every million years of divergence, with the α3 (I) sequence evolving the fastest, followed by the α2 (I) chain. This is the quickest rate known for any vertebrate group. We demonstrate that phylogenetic analyses using collagen type I amino acid sequences generate tangible signals for actinopterygians that are highly congruent with recent genomic-level studies. However, there is limited congruence within percomorphs, perhaps due to clade-specific functional constraints acting upon collagen sequences. Our results provide important insights for future phylogenetic analyses incorporating extinct actinopterygian species via collagen (I) sequencing.
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Affiliation(s)
- Virginia L. Harvey
- Department of Earth and Environmental Sciences, School of Natural Sciences, University of Manchester, Manchester M13 9PL, UK
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - Joseph N. Keating
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Michael Buckley
- Department of Earth and Environmental Sciences, School of Natural Sciences, University of Manchester, Manchester M13 9PL, UK
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
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16
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Brown S, Wang N, Oertle A, Kozlikin MB, Shunkov MV, Derevianko AP, Comeskey D, Jope-Street B, Harvey VL, Chowdhury MP, Buckley M, Higham T, Douka K. Zooarchaeology through the lens of collagen fingerprinting at Denisova Cave. Sci Rep 2021; 11:15457. [PMID: 34326389 PMCID: PMC8322063 DOI: 10.1038/s41598-021-94731-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 07/15/2021] [Indexed: 11/09/2022] Open
Abstract
Denisova Cave, a Pleistocene site in the Altai Mountains of Russian Siberia, has yielded significant fossil and lithic evidence for the Pleistocene in Northern Asia. Abundant animal and human bones have been discovered at the site, however, these tend to be highly fragmented, necessitating new approaches to identifying important hominin and faunal fossils. Here we report the results for 8253 bone fragments using ZooMS. Through the integration of this new ZooMS-based data with the previously published macroscopically-identified fauna we aim to create a holistic picture of the zooarchaeological record of the site. We identify trends associated with climate variability throughout the Middle and Upper Pleistocene as well as patterns explaining the process of bone fragmentation. Where morphological analysis of bones from the site have identified a high proportion of carnivore bones (30.2%), we find that these account for only 7.6% of the ZooMS assemblage, with large mammals between 3 and 5 more abundant overall. Our analysis suggests a cyclical pattern in fragmentation of bones which sees initial fragmentation by hominins using percussive tools and secondary carnivore action, such as gnawing and digestion, likely furthering the initial human-induced fragmentation.
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Affiliation(s)
- Samantha Brown
- Institute for Scientific Archaeology, Eberhard Karls University of Tübingen, Tübingen, Germany. .,Max Planck Institute for the Science of Human History, Jena, Germany.
| | - Naihui Wang
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Annette Oertle
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Maxim B Kozlikin
- Institute of Archeology and Ethnography, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Michael V Shunkov
- Institute of Archeology and Ethnography, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Anatoly P Derevianko
- Institute of Archeology and Ethnography, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Daniel Comeskey
- Oxford Radiocarbon Accelerator Unit, RLAHA, University of Oxford, Oxford, OX1 3QY, UK
| | - Blair Jope-Street
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Virginia L Harvey
- Department of Earth and Environmental Sciences, School of Natural Sciences, The University of Manchester, Manchester, M13 9PL, UK.,Manchester Institute of Biotechnology, The University of Manchester, Manchester, M1 7DN, UK
| | - Manasij Pal Chowdhury
- Department of Earth and Environmental Sciences, School of Natural Sciences, The University of Manchester, Manchester, M13 9PL, UK.,Manchester Institute of Biotechnology, The University of Manchester, Manchester, M1 7DN, UK
| | - Michael Buckley
- Department of Earth and Environmental Sciences, School of Natural Sciences, The University of Manchester, Manchester, M13 9PL, UK.,Manchester Institute of Biotechnology, The University of Manchester, Manchester, M1 7DN, UK
| | - Thomas Higham
- Oxford Radiocarbon Accelerator Unit, RLAHA, University of Oxford, Oxford, OX1 3QY, UK.,Department of Evolutionary Anthropology, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Katerina Douka
- Max Planck Institute for the Science of Human History, Jena, Germany. .,Department of Evolutionary Anthropology, Faculty of Life Sciences, University of Vienna, Vienna, Austria.
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17
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Coutu AN, Taurozzi AJ, Mackie M, Jensen TZT, Collins MJ, Sealy J. Palaeoproteomics confirm earliest domesticated sheep in southern Africa ca. 2000 BP. Sci Rep 2021; 11:6631. [PMID: 33758223 PMCID: PMC7988125 DOI: 10.1038/s41598-021-85756-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 03/01/2021] [Indexed: 12/18/2022] Open
Abstract
We used palaeoproteomics and peptide mass fingerprinting to obtain secure species identifications of key specimens of early domesticated fauna from South Africa, dating to ca. 2000 BP. It can be difficult to distinguish fragmentary remains of early domesticates (sheep) from similar-sized local wild bovids (grey duiker, grey rhebok, springbok-southern Africa lacks wild sheep) based on morphology alone. Our analysis revealed a Zooarchaeology by Mass Spectrometry (ZooMS) marker (m/z 1532) present in wild bovids and we demonstrate through LC-MS/MS that it is capable of discriminating between wild bovids and caprine domesticates. We confirm that the Spoegrivier specimen dated to 2105 ± 65 BP is indeed a sheep. This is the earliest directly dated evidence of domesticated animals in southern Africa. As well as the traditional method of analysing bone fragments, we show the utility of minimally destructive sampling methods such as PVC eraser and polishing films for successful ZooMS identification. We also show that collagen extracted more than 25 years ago for the purpose of radiocarbon dating can yield successful ZooMS identification. Our study demonstrates the importance of developing appropriate regional frameworks of comparison for future research using ZooMS as a method of biomolecular species identification.
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Affiliation(s)
- Ashley N Coutu
- Pitt Rivers Museum, University of Oxford, Oxford, OX1 3PP, UK.,BioArCh, University of York, York, YO10 5DD, UK.,Department of Archaeology, University of Cape Town, Private Bag X3, Rondebosch, 7701, South Africa
| | - Alberto J Taurozzi
- Section for Evolutionary Genomics, GLOBE Institute, Faculty of Health and Medical Science, University of Copenhagen, Øster Farimagsgade 5, 1353, Copenhagen, Denmark.
| | - Meaghan Mackie
- Section for Evolutionary Genomics, GLOBE Institute, Faculty of Health and Medical Science, University of Copenhagen, Øster Farimagsgade 5, 1353, Copenhagen, Denmark.,Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3b, 2200, Copenhagen N, Denmark
| | - Theis Zetner Trolle Jensen
- Section for Evolutionary Genomics, GLOBE Institute, Faculty of Health and Medical Science, University of Copenhagen, Øster Farimagsgade 5, 1353, Copenhagen, Denmark
| | - Matthew J Collins
- Section for Evolutionary Genomics, GLOBE Institute, Faculty of Health and Medical Science, University of Copenhagen, Øster Farimagsgade 5, 1353, Copenhagen, Denmark.,McDonald Institute for Archaeological Research, University of Cambridge, West Tower, Downing St, Cambridge, CB2 3ER, UK
| | - Judith Sealy
- Department of Archaeology, University of Cape Town, Private Bag X3, Rondebosch, 7701, South Africa.
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18
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Brandt LØ, Mannering U. Taxonomic identification of Danish Viking Age shoes and skin objects by ZooMS (Zooarchaeology by mass spectrometry). J Proteomics 2020; 231:104038. [PMID: 33152502 DOI: 10.1016/j.jprot.2020.104038] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 09/14/2020] [Accepted: 10/29/2020] [Indexed: 11/30/2022]
Affiliation(s)
- Luise Ørsted Brandt
- The GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5, Bygning 7, 1330 København K, Denmark.
| | - Ulla Mannering
- Ancient Cultures of Denmark and the Mediterranean, National Museum of Denmark, Frederiksholms Kanal 12, DK1220 Copenhagen, Denmark.
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