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Moubtahij Z, McCormack J, Bourgon N, Trost M, Sinet-Mathiot V, Fuller BT, Smith GM, Temming H, Steinbrenner S, Hublin JJ, Bouzouggar A, Turner E, Jaouen K. Isotopic evidence of high reliance on plant food among Later Stone Age hunter-gatherers at Taforalt, Morocco. Nat Ecol Evol 2024; 8:1035-1045. [PMID: 38684738 DOI: 10.1038/s41559-024-02382-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 03/01/2024] [Indexed: 05/02/2024]
Abstract
The transition from hunting-gathering to agriculture stands as one of the most important dietary revolutions in human history. Yet, due to a scarcity of well-preserved human remains from Pleistocene sites, little is known about the dietary practices of pre-agricultural human groups. Here we present the isotopic evidence of pronounced plant reliance among Late Stone Age hunter-gatherers from North Africa (15,000-13,000 cal BP), predating the advent of agriculture by several millennia. Employing a comprehensive multi-isotopic approach, we conducted zinc (δ66Zn) and strontium (87Sr/86Sr) analysis on dental enamel, bulk carbon (δ13C) and nitrogen (δ15N) and sulfur (δ34S) isotope analysis on dentin and bone collagen, and single amino acid analysis on human and faunal remains from Taforalt (Morocco). Our results unequivocally demonstrate a substantial plant-based component in the diets of these hunter-gatherers. This distinct dietary pattern challenges the prevailing notion of high reliance on animal proteins among pre-agricultural human groups. It also raises intriguing questions surrounding the absence of agricultural development in North Africa during the early Holocene. This study underscores the importance of investigating dietary practices during the transition to agriculture and provides insights into the complexities of human subsistence strategies across different regions.
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Affiliation(s)
- Zineb Moubtahij
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
- Géosciences Environnement Toulouse, UMR 5563, CNRS, Observatoire Midi Pyrénées, Toulouse, France.
| | - Jeremy McCormack
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Goethe University Frankfurt, Institute of Geosciences, Frankfurt am Main, Germany
| | - Nicolas Bourgon
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- IsoTROPIC Research Group, Max Planck Institute for Geoanthropology, Jena, Germany
| | - Manuel Trost
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Virginie Sinet-Mathiot
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- PACEA, UMR 5199, CNRS, Université de Bordeaux, Ministère de la Culture, Pessac, France
- CBMN, UMR 5248 and Bordeaux Proteome Platform, Bordeaux INP, CNRS, Université de Bordeaux, Bordeaux, France
| | - Benjamin T Fuller
- Géosciences Environnement Toulouse, UMR 5563, CNRS, Observatoire Midi Pyrénées, Toulouse, France
| | - Geoff M Smith
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- School of Anthropology and Conservation, University of Kent, Canterbury, UK
| | - Heiko Temming
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Sven Steinbrenner
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Jean-Jacques Hublin
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Chaire de Paléoanthropologie, CIRB (UMR 7241-U1050), Collège de France, Paris, France
| | - Abdeljalil Bouzouggar
- Institut National des Sciences de l'Archéologie et du Patrimoine, Origin and Evolution of Homo Sapiens Cultures, Rabat, Morocco
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Elaine Turner
- Monrepos Archaeological Research Centre and Museum for Human Behavioural Evolution, LEIZA, Neuwied, Germany
| | - Klervia Jaouen
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Géosciences Environnement Toulouse, UMR 5563, CNRS, Observatoire Midi Pyrénées, Toulouse, France
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2
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Végh EI, Douka K. SpecieScan: semi-automated taxonomic identification of bone collagen peptides from MALDI-ToF-MS. Bioinformatics 2024; 40:btae054. [PMID: 38337062 PMCID: PMC10918634 DOI: 10.1093/bioinformatics/btae054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 01/08/2024] [Accepted: 02/07/2024] [Indexed: 02/12/2024] Open
Abstract
MOTIVATION Zooarchaeology by Mass Spectrometry (ZooMS) is a palaeoproteomics method for the taxonomic determination of collagen, which traditionally involves challenging manual spectra analysis with limitations in quantitative results. As the ZooMS reference database expands, a faster and reproducible identification tool is necessary. Here we present SpecieScan, an open-access algorithm for automating taxa identification from raw MALDI-ToF mass spectrometry (MS) data. RESULTS SpecieScan was developed using R (pre-processing) and Python (automation). The algorithm's output includes identified peptide markers, closest matching taxonomic group (taxon, family, order), correlation scores with the reference databases, and contaminant peaks present in the spectra. Testing on original MS data from bones discovered at Palaeothic archaeological sites, including Denisova Cave in Russia, as well as using publicly-available, externally produced data, we achieved >90% accuracy at the genus-level and ∼92% accuracy at the family-level for mammalian bone collagen previously analysed manually. AVAILABILITY AND IMPLEMENTATION The SpecieScan algorithm, along with the raw data used in testing, results, reference database, and common contaminants lists are freely available on Github (https://github.com/mesve/SpecieScan).
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Affiliation(s)
- Emese I Végh
- Department of Evolutionary Anthropology, University of Vienna, University Biology Building, A-1030 Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria
- Archaeology, Environmental Changes, and Geochemistry, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Katerina Douka
- Department of Evolutionary Anthropology, University of Vienna, University Biology Building, A-1030 Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria
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3
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Taniguchi K, Miyaguchi H. COL1A2 Barcoding: Bone Species Identification via Shotgun Proteomics. J Proteome Res 2024; 23:377-385. [PMID: 38091499 DOI: 10.1021/acs.jproteome.3c00615] [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: 01/06/2024]
Abstract
Species identification of fragmentary bones remains a challenging task in archeology and forensics. A species identification method for such fragmentary bones that has recently attracted interest is the use of bone collagen proteins. Here, we describe a method similar to DNA barcoding that reads collagen protein sequences in bone and automatically determines the species by performing sequence database searches. The method is almost identical to conventional shotgun proteomics analysis of bone samples, except that the database used by the SEQUEST search engine consisted only of entries for collagen type 1 alpha 2 (COL1A2) proteins from various vertebrates. Accordingly, the COL1A2 peptides that differ in sequence among species act as species marker peptides. In SEQUEST-based shotgun proteomics, the protein entries that contain more marker peptide sequences are assigned higher scores; therefore, the highest-scoring protein entry will be the COL1A2 entry for the species from which the analyzed bone was derived. We tested our method using bone samples from 30 vertebrate species and found that all species were correctly identified. In conclusion, COL1A2 can be used as a bone protein barcode and can be read through shotgun proteomics, allowing for automatic bone species identification. Data are available via ProteomeXchange with the identifier PXD045402.
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Affiliation(s)
- Kei Taniguchi
- National Research Institute of Police Science, 6-3-1, Kashiwanoha, Kashiwa 277-0882, Chiba, Japan
| | - Hajime Miyaguchi
- National Research Institute of Police Science, 6-3-1, Kashiwanoha, Kashiwa 277-0882, Chiba, Japan
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4
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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. ROYAL SOCIETY OPEN SCIENCE 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] [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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Wang N, Xu Y, Tang Z, He C, Hu X, Cui Y, Douka K. Large-scale application of palaeoproteomics (Zooarchaeology by Mass Spectrometry; ZooMS) in two Palaeolithic faunal assemblages from China. Proc Biol Sci 2023; 290:20231129. [PMID: 37876197 PMCID: PMC10598447 DOI: 10.1098/rspb.2023.1129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 09/22/2023] [Indexed: 10/26/2023] Open
Abstract
The application of Zooarchaeology by Mass Spectrometry (ZooMS) on Pleistocene sites in Europe and northern Asia has resulted in the discovery of important new hominin fossils and has expanded the range of identified fauna. However, no systematic, large-scale application of ZooMS on Palaeolithic sites in East Asia has been attempted thus far. Here, we analyse 866 morphologically non-diagnostic bones from Jinsitai Cave in northeast China and Yumidong Cave in South China, from archaeological horizons dating to 150-10 ka BP. Bones from both sites revealed a high degree of collagen preservation and potentially time-related deamidation patterns, despite being located in very distinct environmental settings. At Jinsitai, we identified 31 camel bones, five of which were radiocarbon dated to 37-20 ka BP. All dated specimens correspond to colder periods of Marine Isotope Stages 3 and 2. We regard the presence of camels at Jinsitai as evidence of wild camels being a megafauna taxon targeted, most likely by early modern humans, during their expansion across northeast Asia. This large-scale application of ZooMS in China highlights the potential of the method for furthering our knowledge of the palaeoanthropological and zooarchaeological records of East Asia.
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Affiliation(s)
- Naihui Wang
- School of Life Sciences, Jilin University, 130012 Changchun, People's Republic of China
- Max Planck Institute of Geoanthropology, 07745, Jena, Germany
- Department of Early Prehistory and Quaternary Ecology, University of Tübingen, Schloss Hohentübingen, 72070 Tübingen, Germany
| | - Yang Xu
- School of Life Sciences, Jilin University, 130012 Changchun, People's Republic of China
| | - Zhuowei Tang
- School of Archaeology, Jilin University, 130012 Changchun, People's Republic of China
| | - Cunding He
- China-Central Asia ‘the Belt and Road’ Joint Laboratory on Human and Environment Research, 710127 Xi'an, People's Republic of China
- School of Cultural Heritage, Northwest University, 710127 Xi'an, People's Republic of China
| | - Xin Hu
- Chongqing China Three Gorges Museum, 400013 Chongqing, People's Republic of China
| | - Yinqiu Cui
- School of Life Sciences, Jilin University, 130012 Changchun, People's Republic of China
| | - Katerina Douka
- Max Planck Institute of Geoanthropology, 07745, Jena, Germany
- Department of Evolutionary Anthropology, Faculty of Life Sciences, University of Vienna, 1030 Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, 1030 Vienna, Austria
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6
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Jeanjean M, McGrath K, Valenzuela-Lamas S, Nieto-Espinet A, Schafberg R, Parés-Casanova PM, Jiménez-Manchón S, Guintard C, Tekkouk F, Ridouh R, Mureau C, Evin A. ZooMS confirms geometric morphometrics species identification of ancient sheep and goat. ROYAL SOCIETY OPEN SCIENCE 2023; 10:230672. [PMID: 37771960 PMCID: PMC10523075 DOI: 10.1098/rsos.230672] [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: 05/17/2023] [Accepted: 08/25/2023] [Indexed: 09/30/2023]
Abstract
Geometric morphometrics can effectively distinguish isolated third lower molars of present-day sheep and goat, but its applicability to archaeological specimens has yet to be established. Using a modern reference collection of 743 sheep and goats and a two-dimensional landmark-based geometric morphometric (GMM) protocol, this study aimed to morphometrically identify 109 archaeological specimens, used as case studies, dating from the Late Neolithic to the modern period/era. These morphometric identifications were then compared to molecular identifications via collagen peptide mass fingerprinting, known as Zooarcheology by Mass Spectrometry (ZooMS). ZooMS confirmed the morphometric identifications for 104 specimens, with the five misidentified specimens all morphometrically identified as goat. Modern sheep and goats have larger teeth and distinct shapes compared to their archaeological counterparts, suggesting strong differences between archaeological and modern specimens potentially linked with recent breed improvement or geographical origin of the specimens. In addition, for both species, some of the archaeological dental morphologies do not match with any of our modern references. This study validates the applicability of geometric morphometrics for identifying isolated archaeological sheep and goat teeth. It represents a stepping stone for future, non-destructive, bioarchaeological studies of the two species.
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Affiliation(s)
- Marine Jeanjean
- Institute of Evolutionary Science-Montpellier (ISEM), University of Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Krista McGrath
- Department of Prehistory & Institute of Environmental Science and Technology (ICTA), Universitat Autònoma de Barcelona, 08193, Barcelona, Spain
| | - Silvia Valenzuela-Lamas
- Archaeology of Social Dynamics (ASD), Institució Milà i Fontanals de Recerca en Humanitats, Consejo Superior de Investigaciones Científicas (IMF-CSIC), C/ Egipcíaques 15, 08001 Barcelona, Spain
| | - Ariadna Nieto-Espinet
- Grup d'Investigació Prehistòrica (GIP), Departament d'Història, Universidad de Lleida, 25005 Lleida, Spain
| | - Renate Schafberg
- Central Natural Science Collections, Martin Luther University Halle-Wittenberg, Domplatz 4, 06108 Halle (Saale), Germany
| | | | - Sergio Jiménez-Manchón
- Archaeology of Social Dynamics (ASD), Institució Milà i Fontanals de Recerca en Humanitats, Consejo Superior de Investigaciones Científicas (IMF-CSIC), C/ Egipcíaques 15, 08001 Barcelona, Spain
| | - Claude Guintard
- Laboratoire d'Anatomie comparée, Ecole Nationale Vétérinaire, de l'Agroalimentaire et de l'Alimentation, Nantes Atlantique – ONIRIS, Nantes Cedex 03, France
- GEROM, UPRES EA 4658, LABCOM ANR NEXTBONE, Faculté de santé de l'Université d'Angers, Angers, France
| | - Faiza Tekkouk
- Institut des Sciences Vétérinaires, Laboratoire « Gestion de la santé et productions animales », Université des frères Mentouri, El Khroub, Algérie
| | - Rania Ridouh
- Institut des Sciences Vétérinaires, Laboratoire « Gestion de la santé et productions animales », Université des frères Mentouri, El Khroub, Algérie
| | - Cyprien Mureau
- Institute of Evolutionary Science-Montpellier (ISEM), University of Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Allowen Evin
- Institute of Evolutionary Science-Montpellier (ISEM), University of Montpellier, CNRS, EPHE, IRD, Montpellier, France
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7
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de Kock W, Mackie M, Ramsøe M, Allentoft ME, Broderick AC, Haywood JC, Godley BJ, Snape RTE, Bradshaw PJ, Genz H, von Tersch M, Dee MW, Palsbøll PJ, Alexander M, Taurozzi AJ, Çakırlar C. Threatened North African seagrass meadows have supported green turtle populations for millennia. Proc Natl Acad Sci U S A 2023; 120:e2220747120. [PMID: 37459551 PMCID: PMC10372671 DOI: 10.1073/pnas.2220747120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 05/25/2023] [Indexed: 07/20/2023] Open
Abstract
"Protect and restore ecosystems and biodiversity" is the second official aim of the current UN Ocean Decade (2021 to 2030) calling for the identification and protection of critical marine habitats. However, data to inform policy are often lacking altogether or confined to recent times, preventing the establishment of long-term baselines. The unique insights gained from combining bioarchaeology (palaeoproteomics, stable isotope analysis) with contemporary data (from satellite tracking) identified habitats which sea turtles have been using in the Eastern Mediterranean over five millennia. Specifically, our analysis of archaeological green turtle (Chelonia mydas) bones revealed that they likely foraged on the same North African seagrass meadows as their modern-day counterparts. Here, millennia-long foraging habitat fidelity has been directly demonstrated, highlighting the significance (and long-term dividends) of protecting these critical coastal habitats that are especially vulnerable to global warming. We highlight the potential for historical ecology to inform policy in safeguarding critical marine habitats.
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Affiliation(s)
- Willemien de Kock
- Groningen Institute of Archaeology, Faculty of Arts, University of Groningen, 9712ERGroningen, Netherlands
- Marine Evolution and Conservation Group, Groningen Institute for Evolutionary Life Sciences, Faculty of Science and Engineering, University of Groningen, 9747AGGroningen, Netherlands
| | - Meaghan Mackie
- The Globe Institute, Faculty of Health and Medical Science, University of Copenhagen, 1353Copenhagen K, Denmark
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Science, University of Copenhagen, 2200Copenhagen K, Denmark
| | - Max Ramsøe
- The Globe Institute, Faculty of Health and Medical Science, University of Copenhagen, 1353Copenhagen K, Denmark
| | - Morten E. Allentoft
- Trace and Environmental DNA Lab, School of Molecular and Life Sciences, Curtin University, Perth, Western Australia6102, Australia
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, 1353Copenhagen K, Denmark
| | - Annette C. Broderick
- Centre for Ecology and Conservation, College of Life and Environmental Sciences, University of Exeter, Penryn Campus, PenrynTR10 9FE, United Kingdom
| | - Julia C. Haywood
- Centre for Ecology and Conservation, College of Life and Environmental Sciences, University of Exeter, Penryn Campus, PenrynTR10 9FE, United Kingdom
| | - Brendan J. Godley
- Centre for Ecology and Conservation, College of Life and Environmental Sciences, University of Exeter, Penryn Campus, PenrynTR10 9FE, United Kingdom
| | - Robin T. E. Snape
- Centre for Ecology and Conservation, College of Life and Environmental Sciences, University of Exeter, Penryn Campus, PenrynTR10 9FE, United Kingdom
- Society for the Protection of Turtles, Nicosia99150, North Cyprus
| | - Phil J. Bradshaw
- Centre for Ecology and Conservation, College of Life and Environmental Sciences, University of Exeter, Penryn Campus, PenrynTR10 9FE, United Kingdom
| | - Hermann Genz
- Department of History and Archaeology, American University of Beirut, Beirut1107 2020, Lebanon
| | - Matthew von Tersch
- BioArCh, Department of Archaeology, University of York, YorkYO10 5NG, United Kingdom
| | - Michael W. Dee
- Centre for Isotope Research, Faculty of Science and Engineering, University of Groningen, 9747AGGroningen, Netherlands
| | - Per J. Palsbøll
- Marine Evolution and Conservation Group, Groningen Institute for Evolutionary Life Sciences, Faculty of Science and Engineering, University of Groningen, 9747AGGroningen, Netherlands
- Center for Coastal Studies, Provincetown, MA02657
| | - Michelle Alexander
- BioArCh, Department of Archaeology, University of York, YorkYO10 5NG, United Kingdom
| | - Alberto J. Taurozzi
- The Globe Institute, Faculty of Health and Medical Science, University of Copenhagen, 1353Copenhagen K, Denmark
| | - Canan Çakırlar
- Groningen Institute of Archaeology, Faculty of Arts, University of Groningen, 9712ERGroningen, Netherlands
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8
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Bray F, Fabrizi I, Flament S, Locht JL, Antoine P, Auguste P, Rolando C. Robust High-Throughput Proteomics Identification and Deamidation Quantitation of Extinct Species up to Pleistocene with Ultrahigh-Resolution MALDI-FTICR Mass Spectrometry. Anal Chem 2023; 95:7422-7432. [PMID: 37130053 DOI: 10.1021/acs.analchem.2c03301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Peptide mass fingerprinting (PMF) using MALDI-TOF mass spectrometry allows the identification of bone species based on their type I collagen sequence. In the archaeological or paleontological field, PMF is known as zooarchaeology mass spectrometry (ZooMS) and is widely implemented to find markers for most species, including the extinct ones. In addition to the identification of bone species, ZooMS enables dating estimation by measuring the deamidation value of specific peptides. Herein, we report several enhancements to the classical ZooMS technique, which reduces to 10-fold the required bone sample amount (down to the milligram scale) and achieves robust deamidation value calculation in a high-throughput manner. These improvements rely on a 96-well plate samples preparation, a careful optimization of collagen extraction and digestion to avoid spurious post-translational modification production, and PMF at high resolution using matrix-assisted laser desorption ionization Fourier transform ion cyclotron resonance (MALDI-FTICR) analysis. This method was applied to the identification of a hundred bones of herbivores from the Middle Paleolithic site of Caours (Somme, France) well dated from the Eemian Last Interglacial climatic optimum. The method gave reliable species identification to bones already identified by their osteomorphology, as well as to more challenging samples consisting of small or burned bone fragments. Deamidation values of bones originating from the same geological layers have a low standard deviation. The method can be applied to archaeological bone remains and offers a robust capacity to identify traditionally unidentifiable bone fragments, thus increasing the number of identified specimens and providing invaluable information in specific contexts.
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Affiliation(s)
- Fabrice Bray
- Univ. Lille, CNRS, UAR 3290─MSAP - Miniaturisation pour La Synthèse, L'Analyse et La Protéomique, Lille F-59000, France
| | - 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
| | - Jean-Luc Locht
- Inrap Hauts-de-France, 32, avenue de l'Étoile-du-Sud, Glisy 80440, France
- Univ. Paris I & UPEC, CNRS, UMR 8591, Laboratoire de Géographie Physique, Environnements quaternaires et actuels, Thiais F-94230, France
| | - Pierre Antoine
- Univ. Paris I & UPEC, CNRS, UMR 8591, Laboratoire de Géographie Physique, Environnements quaternaires et actuels, Thiais F-94230, France
| | - Patrick Auguste
- Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paléo, 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, 1-3 Allée Lavoisier, Villeneuve-d'Ascq F-59650, France
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9
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Silvestrini S, Lugli F, Romandini M, Real C, Sommella E, Salviati E, Arrighi S, Bortolini E, Figus C, Higgins OA, Marciani G, Oxilia G, Delpiano D, Vazzana A, Piperno M, Crescenzi C, Campiglia P, Collina C, Peresani M, Spinapolice EE, Benazzi S. Integrating ZooMS and zooarchaeology: New data from the Uluzzian levels of Uluzzo C Rock Shelter, Roccia San Sebastiano cave and Riparo del Broion. PLoS One 2022; 17:e0275614. [PMID: 36227961 PMCID: PMC9560625 DOI: 10.1371/journal.pone.0275614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 09/20/2022] [Indexed: 11/19/2022] Open
Abstract
In this study we explore the potential of combining traditional zooarchaeological determination and proteomic identification of morphologically non-diagnostic bone fragments (ZooMS) collected from the Uluzzian levels of three Italian sites: Uluzzo C Rock Shelter, Roccia San Sebastiano cave, and Riparo del Broion. Moreover, we obtained glutamine deamidation ratios for all the contexts analysed during routine ZooMS screening of faunal samples, giving information on collagen preservation. We designed a selection protocol that maximizes the efficiency of the proteomics analyses by excluding particularly compromised fragments (e.g. from taphonomic processes), and that aims to identify new human fragments by favouring bones showing morphological traits more similar to Homo. ZooMS consistently provided taxonomic information in agreement with the faunal spectra outlined by traditional zooarchaeology. Our approach allows us to delineate and appreciate differences between the analysed contexts, particularly between the northern and southern sites, related to faunal, environmental, and climate composition, although no human remains were identified. We reconstructed the faunal assemblage of the different sites, giving voice to morphologically undiagnostic bone fragments. Thus, the combination of these analyses provides a more complete picture of the faunal assemblage and of the paleoenvironment during the Middle-Upper Palaeolithic transition in Italy.
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Affiliation(s)
- Sara Silvestrini
- Dipartimento di Beni Culturali, Università di Bologna, Ravenna, Italy
| | - Federico Lugli
- Dipartimento di Beni Culturali, Università di Bologna, Ravenna, Italy
| | - Matteo Romandini
- Dipartimento di Beni Culturali, Università di Bologna, Ravenna, Italy
| | - Cristina Real
- Dipartimento di Beni Culturali, Università di Bologna, Ravenna, Italy
- Departament de Prehistòria, Arqueologia i Història Antiga, Universitat de València, València, Spain
| | - Eduardo Sommella
- Dipartimento di Farmacia, Università di Salerno, Fisciano, Salerno, Italy
| | - Emanuela Salviati
- Dipartimento di Farmacia, Università di Salerno, Fisciano, Salerno, Italy
| | - Simona Arrighi
- Dipartimento di Beni Culturali, Università di Bologna, Ravenna, Italy
- Dipartimento di Scienze Fisiche, della Terra e dell’Ambiente, Unità di Ricerca di Preistoria e Antropologia, Università di Siena, Siena, Italy
| | - Eugenio Bortolini
- Dipartimento di Beni Culturali, Università di Bologna, Ravenna, Italy
| | - Carla Figus
- Dipartimento di Beni Culturali, Università di Bologna, Ravenna, Italy
| | | | - Giulia Marciani
- Dipartimento di Beni Culturali, Università di Bologna, Ravenna, Italy
- Dipartimento di Scienze Fisiche, della Terra e dell’Ambiente, Unità di Ricerca di Preistoria e Antropologia, Università di Siena, Siena, Italy
| | - Gregorio Oxilia
- Dipartimento di Beni Culturali, Università di Bologna, Ravenna, Italy
| | - Davide Delpiano
- Dipartimento di Studi Umanistici, Sezione di Scienze Preistoriche e Antropologiche, Università di Ferrara, Ferrara, Italy
| | - Antonino Vazzana
- Dipartimento di Beni Culturali, Università di Bologna, Ravenna, Italy
| | - Marcello Piperno
- Museo Civico Archeologico Biagio Greco, Mondragone, Caserta, Italy
| | - Carlo Crescenzi
- Dipartimento di Farmacia, Università di Salerno, Fisciano, Salerno, Italy
| | - Pietro Campiglia
- Dipartimento di Farmacia, Università di Salerno, Fisciano, Salerno, Italy
| | - Carmine Collina
- Museo Civico Archeologico Biagio Greco, Mondragone, Caserta, Italy
| | - Marco Peresani
- Dipartimento di Studi Umanistici, Sezione di Scienze Preistoriche e Antropologiche, Università di Ferrara, Ferrara, Italy
- Istituto di Geologia Ambientale e Geoingegneria, Consiglio Nazionale delle Ricerche, Milano, Italy
| | - Enza Elena Spinapolice
- Dipartimento di Scienze dell’Antichità, Università degli Studi di Roma “La Sapienza”, Roma, Italy
| | - Stefano Benazzi
- Dipartimento di Beni Culturali, Università di Bologna, Ravenna, Italy
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10
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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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11
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Bochaton C. Archaeological occurrences of terrestrial herpetofauna in the insular Caribbean: cultural and biological significance. ROYAL SOCIETY OPEN SCIENCE 2022; 9:220256. [PMID: 35845849 PMCID: PMC9277263 DOI: 10.1098/rsos.220256] [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: 03/01/2022] [Accepted: 06/23/2022] [Indexed: 06/15/2023]
Abstract
Although the importance of the archaeological record for addressing questions of biodiversity is gaining ground, its relevance for describing past faunal communities is still under-exploited, particularly for the most under-documented areas and species. Among the most poorly documented taxa are reptiles and amphibians, which are rarely studied in detail in the archaeological record, even in tropical areas where most of these species occur today. Here I evaluate the archaeological and paleontological significance of reptiles and amphibians from the Indigenous archaeological record of the insular Caribbean. Quantitative (bone counts) and qualitative (taxonomic identification) analyses allow researchers to discuss the role of herpetofauna in the subsistence strategies of Indigenous populations as well as their interest for assessing past insular biodiversity. This overview sheds light on both the poor representation of herpetofaunal taxa in Caribbean archaeological deposits and trends in the potential exploitation of reptiles and amphibians by Indigenous populations. In terms of paleoecology, the presented results reveal strong regional differences in the quality and density of data as well as the inadequacy of available archaeofaunal data for addressing questions of past biodiversity.
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Affiliation(s)
- Corentin Bochaton
- Max Planck Institute for the Science of Human History, Kahlaische Straße 10, D-07745 Jena, Germany
- PACEA – UMR CNRS 5199, Université de Bordeaux, 33 615 Pessac Cedex, France
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12
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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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13
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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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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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Culley C, Janzen A, Brown S, Prendergast ME, Wolfhagen J, Abderemane B, Ali AK, Haji O, Horton MC, Shipton C, Swift J, Tabibou TA, Wright HT, Boivin N, Crowther A. Collagen fingerprinting traces the introduction of caprines to island Eastern Africa. ROYAL SOCIETY OPEN SCIENCE 2021; 8:202341. [PMID: 34350011 PMCID: PMC8316820 DOI: 10.1098/rsos.202341] [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: 12/24/2020] [Accepted: 06/07/2021] [Indexed: 06/13/2023]
Abstract
The human colonization of eastern Africa's near- and offshore islands was accompanied by the translocation of several domestic, wild and commensal fauna, many of which had long-term impacts on local environments. To better understand the timing and nature of the introduction of domesticated caprines (sheep and goat) to these islands, this study applied collagen peptide fingerprinting (Zooarchaeology by Mass Spectrometry or ZooMS) to archaeological remains from eight Iron Age sites, dating between ca 300 and 1000 CE, in the Zanzibar, Mafia and Comoros archipelagos. Where previous zooarchaeological analyses had identified caprine remains at four of these sites, this study identified goat at seven sites and sheep at three, demonstrating that caprines were more widespread than previously known. The ZooMS results support an introduction of goats to island eastern Africa from at least the seventh century CE, while sheep in our sample arrived one-two centuries later. Goats may have been preferred because, as browsers, they were better adapted to the islands' environments. The results allow for a more accurate understanding of early caprine husbandry in the study region and provide a critical archaeological baseline for examining the potential long-term impacts of translocated fauna on island ecologies.
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Affiliation(s)
- Courtney Culley
- School of Social Science, The University of Queensland, St Lucia, Queensland, Australia
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Anneke Janzen
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
- Department of Anthropology, The University of Tennessee, Knoxville, USA
| | - Samantha Brown
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
- Institute for Scientific Archaeology, University of Tübingen, Tübingen, Germany
| | | | - Jesse Wolfhagen
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Bourhane Abderemane
- Centre National de Documentation et de Recherche Scientifique, Mutsamudu, Anjouan, Comoros
| | | | - Othman Haji
- Department of Museums and Antiquities, Zanzibar, Tanzania
| | - Mark C. Horton
- Cultural Heritage Institute, Royal Agricultural University, Cirencester, England
| | - Ceri Shipton
- Institute of Archaeology, Gordon Square, University College London, London, UK
- Centre of Excellence for Australian Biodiversity and Heritage, College of Asia and the Pacific, Australian National University, Canberra, Australia
| | - Jillian Swift
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
- Department of Anthropology, Bernice Pauahi Bishop Museum, Honolulu, HI, USA
| | - Tabibou A. Tabibou
- Centre National de Documentation et de Recherche Scientifique, Moroni, Grand Comore, Comoros
| | - Henry T. Wright
- Museum of Anthropological Archaeology, University of Michigan, Ann Arbor, Michigan, USA
| | - Nicole Boivin
- School of Social Science, The University of Queensland, St Lucia, Queensland, Australia
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
- Department of Anthropology and Archaeology, University of Calgary, Calgary, Canada
| | - Alison Crowther
- School of Social Science, The University of Queensland, St Lucia, Queensland, Australia
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
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