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1. Tracking the Near Eastern origins and European dispersal of the western house mouse

Author

Yannis Hamilakis, Fanis Mavridis, Melinda A. Zeder, François Raymond Valla, François Bonhomme, Régis Debruyne, Fereidoun Biglari, Greger Larson, Emma Jenkins, Cameron A. Petrie, Antoine Zazzo, Adrian Bălășescu, Alireza Sardari, Jean-Christophe Auffray, Roohollah Siahsarvi, Marjan Mashkour, Christiane Denys, Jean-Denis Vigne, Jamshid Darvish, Thomas Cucchi, Alan H. Simmons, Katerina Papayianni, Lloyd Weeks, Sophie Cersoy, Sepideh Maziar, Rémi Berthon, Laetitia Aznar-Cormano, David Orton, Jeremy B. Searle, Archéozoologie, archéobotanique : sociétés, pratiques et environnements (AASPE), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Wiener Laboratory, American School of Classical Studies at Athens, Centre de Recherche sur la Conservation (CRC ), Muséum national d'Histoire naturelle (MNHN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Centre de Recherche en Paléontologie - Paris (CR2P), Muséum national d'Histoire naturelle (MNHN)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Direction générale déléguée à la Recherche, à l’Expertise, à la Valorisation et à l’Enseignement-Formation (DGD.REVE), Muséum national d'Histoire naturelle (MNHN), Institute of Archaeology Vasile Parvan, Desert Research Institute (DRI), Archéologies et Sciences de l'Antiquité (ArScAn), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Brown University, Ephorate of Palaeoanthropology–Speleology, Hellenic Ministry of Culture and Sports (YPPO), Ferdowsi University of Mashhad, Center for Paleolithic Research, National Museum of Iran, Department of Archaeology and Anthropology, University of Cambridge, Cambridge, UK, School of Humanities, Arts and Social Sciences, University of New England, Armidale, New South Wales, Australia, Research Institute of Cultural Heritage and Tourism (RICHT), Iranian Center for Archaeological Research (ICAR), Tehran, Iran, Goethe-Universität Frankfurt am Main, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Departments of Archaeology [York] (BioArch), University of York [York, UK], Bournemouth University [Poole] (BU), Smithsonian Institution, National Museum of Natural History, Cornell University [New York], University of Oxford [Oxford], Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, ANR-11-IDEX-0004,SUPER,Sorbonne Universités à Paris pour l'Enseignement et la Recherche(2011), ANR-10-LABX-0003,BCDiv,Biological and Cultural Diversities : Origins, Evolution, Interactions, Future(2010), Petrie, Cameron [0000-0002-2926-7230], Apollo - University of Cambridge Repository, Université Panthéon-Sorbonne (UP1)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226, Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Institut national de recherches archéologiques préventives (Inrap)-Centre National de la Recherche Scientifique (CNRS), Ferdowsi University of Mashhad (FUM), University of Oxford, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), University of Cambridge [UK] (CAM), Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE)

Subjects
0301 basic medicine, 631/45, Molecular biology, [SDV]Life Sciences [q-bio], lcsh:Medicine, Introduced species, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 01 natural sciences, Biochemistry, House mouse, law.invention, [SHS]Humanities and Social Sciences, Mice, law, Radiocarbon dating, Europe, Eastern, lcsh:Science, 631/601, ComputingMilieux_MISCELLANEOUS, Multidisciplinary, Middle East, biology, Ecology, article, Mitochondria, Geography, Archaeology, [SDE]Environmental Sciences, 631/337, 010506 paleontology, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, DNA, Mitochondrial, 03 medical and health sciences, Human settlement, Asia, Western, Animals, Humans, Domestication, 0105 earth and related environmental sciences, lcsh:R, Radiometric Dating, Sequence Analysis, DNA, biology.organism_classification, Computational biology and bioinformatics, 030104 developmental biology, Cyprus, Biological dispersal, lcsh:Q, House mice, 631/114, 631/158, Introduced Species, Zoology
Abstract

The house mouse (Mus musculus) represents the extreme of globalization of invasive mammals. However, the timing and basis of its origin and early phases of dispersal remain poorly documented. To track its synanthropisation and subsequent invasive spread during the develoment of complex human societies, we analyzed 829 Mus specimens from 43 archaeological contexts in Southwestern Asia and Southeastern Europe, between 40,000 and 3,000 cal. BP, combining geometric morphometrics numerical taxonomy, ancient mitochondrial DNA and direct radiocarbon dating. We found that large late hunter-gatherer sedentary settlements in the Levant, c. 14,500 cal. BP, promoted the commensal behaviour of the house mouse, which probably led the commensal pathway to cat domestication. House mouse invasive spread was then fostered through the emergence of agriculture throughout the Near East 12,000 years ago. Stowaway transport of house mice to Cyprus can be inferred as early as 10,800 years ago. However, the house mouse invasion of Europe did not happen until the development of proto urbanism and exchange networks — 6,500 years ago in Eastern Europe and 4000 years ago in Southern Europe — which in turn may have driven the first human mediated dispersal of cats in Europe.

Published
2020
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2. A unique bacteriohopanetetrol stereoisomer of marine anammox

Author

Darci Rush, E. Alex Charlton, Philippe Schaeffer, Helen M. Talbot, Philippe Normand, D. Martin Jones, Rachel Schwartz-Narbonne, Jaap S. Sinninghe Damsté, Mike S. M. Jetten, Margot Schenesse, Guylaine H. L. Nuijten, Ellen C. Hopmans, Muhammad Farhan Ul Haque, J. Colin Murrell, Sabine K. Lengger, Université Claude Bernard Lyon 1 (UCBL), Université de Lyon, Newcastle University [Newcastle], Institut de Chimie de Strasbourg, Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Utrecht University [Utrecht], Royal Netherlands Institute for Sea Research (NIOZ), University of East Anglia [Norwich] (UEA), University of the Punjab, Radboud university [Nijmegen], School of Geography, Earth and Environmental Sciences [Plymouth] (SoGEES), Plymouth University, School of Environmental Sciences [Norwich], Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Departments of Archaeology [York] (BioArch), University of York [York, UK], and Natural Environment Research Council (NERC), United Kingdom project ANAMMARKS NE/N011112/1SIAM, Netherlands 024002002EAOG, Netherlands Research Award Rubicon fellowship from the Netherlands Organization for Scientific Research (NWO), Netherlands 825.14.014European Research Council (ERC) European Union under the European Union's Horizon 2020 research and innovation program 694569 -MICROLIPIDSLeverhulme TrustRPG2016-050

Subjects
bepress|Physical Sciences and Mathematics, Komagataeibacter xylinus, Bacteriohopanetetrols, 010504 meteorology & atmospheric sciences, bepress|Physical Sciences and Mathematics|Earth Sciences, EarthArXiv|Physical Sciences and Mathematics|Earth Sciences, 010502 geochemistry & geophysics, 01 natural sciences, High-performance liquid chromatography, Anammox, Geochemistry and Petrology, [SDU.STU.GC]Sciences of the Universe [physics]/Earth Sciences/Geochemistry, Bacteriohopanepolyols, Stereoisomers, 14. Life underwater, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], 0105 earth and related environmental sciences, Chromatography, Bacteriohopanetetrol, biology, Chemistry, Anaerobic ammonium oxidation, biology.organism_classification, EarthArXiv|Physical Sciences and Mathematics, Biomarker (petroleum), EarthArXiv|Physical Sciences and Mathematics|Earth Sciences|Biogeochemistry, 13. Climate action, Ecological Microbiology, [SDE]Environmental Sciences, Scalindua, bepress|Physical Sciences and Mathematics|Earth Sciences|Biogeochemistry, Bacteria, Biomarkers
Abstract

Anaerobic ammonium oxidation (anammox) is a significant process for bioavailable nitrogen removal from marine systems. A bacteriohopanetetrol (BHT) isomer, with unknown stereochemistry, eluting later than BHT using high performance liquid chromatography (HPLC), was detected in ‘Ca. Scalindua profunda’ and proposed as a biomarker for anammox in marine paleo-environments. Four non-marine, non-anammox genera also produce late-eluting BHT stereoisomers. Of these, the stereochemistry in Acetobacter pasteurianus, Komagataeibacter xylinus and Frankia sp. was shown to be 17β, 21β(H), 22R, 32R, 33R, 34R (BHT-34R), while the stereochemistry of the late-eluting BHT in Methylocella palustris was unknown. We studied the BHT distributions and stereochemistry of these known BHT isomer producers and of previously unscreened marine (‘Ca. Scalindua brodeae’) and freshwater (‘Ca. Brocadia sp.’) anammox species and genera using HPLC and gas chromatographic (GC) analysis of acetylated BHTs and ultra high performance liquid chromatography (UHPLC)-High Resolution Mass Spectrometry (HRMS) analysis of non-acetylated BHTs. The 34R stereochemistry was confirmed for the BHT isomers in Ca. Brocadia sp., and Methylocella palustris. However, ‘Ca. Scalindua sp.’ synthesise a stereochemically distinct BHT isomer, with a still unconfirmed stereochemistry (BHT-x). ‘Ca. Kuenenia sp.’ was confirmed not to produce any late-eluting BHT stereoisomers. Only GC analysis of acetylated BHT and UHPLC analysis of non-acetylated BHT distinguished between late-eluting BHT isomers. Acetylated BHT-x and BHT-34R co-elute by HPLC. As BHT-x is so far only known to be produced by ‘Ca. Scalindua spp.’, it may be applied as a biomarker for marine anammox. As ‘Ca. Brocadia sp.’ produces BHT-34R, this BHT isomer is a potential, albeit less specific, biomarker for anammox in non-marine settings.

Published
2020
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3. Forgotten Mediterranean calving grounds of grey and North Atlantic right whales: evidence from Roman archaeological records

Author

Krista McGrath, Carlos Nores, Darío Bernal-Casasola, Camilla Speller, Ana S. L. Rodrigues, Armelle Gardeisen, José Antonio Pis Millán, Anne Charpentier, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut de Recherche pour le Développement (IRD [France-Sud]), Archéologie des Sociétés Méditerranéennes (ASM), Université Paul-Valéry - Montpellier 3 (UPVM)-Centre National de la Recherche Scientifique (CNRS)-Ministère de la Culture (MC), INDUROT, University of Oviedo, Departments of Archaeology [York] (BioArch), University of York [York, UK], Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut de Recherche pour le Développement (IRD [France-Sud]), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Paul-Valéry - Montpellier 3 (UM3), and Université Paul-Valéry - Montpellier 3 (UM3)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, Mediterranean climate, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, Range (biology), North Atlantic right whale, [SDV.BID]Life Sciences [q-bio]/Biodiversity, 010603 evolutionary biology, 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, Predation, Sexual Behavior, Animal, Mediterranean sea, Homing Behavior, biology.animal, Mediterranean Sea, Animals, DNA Barcoding, Taxonomic, 0601 history and archaeology, Whaling, 14. Life underwater, General Environmental Science, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, Global Change and Conservation, 060102 archaeology, General Immunology and Microbiology, biology, Whale, collagen fingerprinting (ZooMS), Whales, 06 humanities and the arts, General Medicine, ancient DNA barcoding, Archaeology, antiquity, Geography, Ancient DNA, Shifting baseline, Atlantic grey whale, shifting baseline, General Agricultural and Biological Sciences
Abstract

Right whales ( Eubalaena glacialis ) were extirpated from the eastern North Atlantic by commercial whaling. Grey whales ( Eschrichtius robustus ) disappeared from the entire North Atlantic in still-mysterious circumstances. Here, we test the hypotheses that both species previously occurred in the Mediterranean Sea, an area not currently considered part of their historical range. We used ancient DNA barcoding and collagen fingerprinting methods to taxonomically identify a rare set of 10 presumed whale bones from Roman and pre-Roman archaeological sites in the Strait of Gibraltar region, plus an additional bone from the Asturian coast. We identified three right whales, and three grey whales, demonstrating that the ranges of both of these species historically encompassed the Gibraltar region, probably including the Mediterranean Sea as calving grounds. Our results significantly extend the known range of the Atlantic grey whale, and suggest that 2000 years ago, right and grey whales were common when compared with other whale species. The disappearance of right and grey whales from the Mediterranean region is likely to have been accompanied by broader ecosystem impacts, including the disappearance of their predators (killer whales) and a reduction in marine primary productivity. The evidence that these two coastal and highly accessible species were present along the shores of the Roman Empire raises the hypothesis that they may have formed the basis of a forgotten whaling industry.

Published
2018
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4. The role of birds at Çatalhöyük revealed by the analysis of eggshell

Author

Julia Best, Beatrice Demarchi, Roman Fischer, Jorune Sakalauskaite, Samantha Presslee, Department of Life Sciences and Systems Biology [University of Turin], University of Turin, Departments of Archaeology [York] (BioArch), University of York [York, UK], Biogéosciences [UMR 6282] [Dijon] (BGS), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS), Nuffield Department of Clinical Medicine [Oxford], University of Oxford [Oxford], Department of Archaeology and Conservation, Cardiff University, Italian Ministry of Education, University and Research ('Young Researchers - Rita Levi Montalcini' programme) and the UK Engineering and Physical Sciences Research Council (EPSRC) under Grant [EP/I001514/1]., Università degli studi di Torino = University of Turin (UNITO), and Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Eggshell, Taxonomy, Birds, Morphology, Microscopy, Ancient proteins, Mass spectrometry, Çatalhöyük, Neolithic, Morphology, 010506 paleontology, Ancient proteins, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, Zoology, Biology, Q1, 010502 geochemistry & geophysics, 01 natural sciences, Birds, Eggshell, Neolithic, [SDV.IB.BIO]Life Sciences [q-bio]/Bioengineering/Biomaterials, 0105 earth and related environmental sciences, Earth-Surface Processes, Taxonomy, Microscopy, Osteology, Mass spectrometry, Çatalhöyük, Biological classification, 15. Life on land, Integrated approach, CC, Anseriformes, biology.organism_classification, Taxonomy (biology)
Abstract

11 pages; International audience; The exceptional eggshell assemblage from Çatalhöyük was studied using an integrated approach combining morphology (by optical and scanning electron microscopy) and palaeoproteomics (by mass spectrometry). We provide taxonomic classification for 90 fragments, of which only 11 remain undetermined. The striking predominance of Anseriformes (probably including greylag geese, as well as ducks and swans) in all types of deposits examined, particularly middens and burial fills, suggests that these eggs were exploited as food and, at the same time, had a special significance for the inhabitants of the site. We detected the presence of crane eggshell in contexts associated with both the world of the living and the world of the dead (consistent with the well-known importance of this bird at Çatalhöyük), as well as the possible but infrequent occurrence of bustards and herons. Overall, we suggest that eggshell analysis, together with osteological data and the archaeological context, can provide the basis for a nuanced understanding of the relationship between humans and birds in the past.

Published
2018
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5. Genomic and proteomic identification of Late Holocene remains: Setting baselines for Black Sea odontocetes

Author

Vincent Biard, Nathan Wales, Michael C. Fontaine, Filipe G. Vieira, E. V. Gladilina, Krista McGrath, Pavel Gol'din, Karina Vishnyakova, Morten Tange Olsen, Camilla Speller, Departments of Archaeology [York] (BioArch), University of York [York, UK], University of Copenhagen = Københavns Universitet (KU), Diversity, ecology, evolution & Adaptation of arthropod vectors (MIVEGEC-DEEVA), Evolution des Systèmes Vectoriels (ESV), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Groningen Institute for Evolutionary Life Sciences [Groningen] (GELIFES), and University of Groningen [Groningen]

Subjects
0301 basic medicine, Sanger sequencing, Archeology, education.field_of_study, biology, Ecology, Shotgun sequencing, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Population, Context (language use), 15. Life on land, 03 medical and health sciences, symbols.namesake, 030104 developmental biology, Ancient DNA, 13. Climate action, biology.animal, symbols, Identification (biology), 14. Life underwater, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, education, Porpoise, Zooarchaeology, ComputingMilieux_MISCELLANEOUS
Abstract

A critical challenge of the 21st century is to understand and minimise the effects of human activities on biodiversity. Cetaceans are a prime concern in biodiversity research, as many species still suffer from human impacts despite decades of management and conservation efforts. Zooarchaeology constitutes a valuable approach for informing conservation and management decisions by providing baseline information on the past distribution and human uses of species. However, traditional morphological species identification of mixed assemblage bones can be challenging, particularly in the case of cetaceans. To address this issue, we applied and evaluated the performance of three biomolecular approaches – Sanger sequencing, shotgun sequencing and collagen peptide fingerprinting (ZooMS) – for species identification in a mixed assemblage of 800 to 1600 years old odontocete (toothed whale) samples from the site of Chersonesus in Crimea, Ukraine. We found that ZooMS allowed for identification to the taxonomic level for 28 of our 30 samples (> 90%), identifying them as either “porpoise” or “dolphin”, and approximately half of those samples could be further identified to species level with the shotgun sequencing approach. In addition, shotgun sequencing produced several complete ancient odontocete mitogenomes and auxiliary nuclear genomic data for further exploration in a population genetic context. In contrast, both morphological identification and Sanger sequencing lacked taxonomic resolution and/or resulted in misclassification of samples. We found that the combination of ZooMS and shotgun sequencing provides a powerful tool in zooarchaeology, and here allowed for a deeper understanding of past marine resource use and its implication for current management and conservation of Black Sea odontocetes.

Published
2017
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6. Open data and digital morphology

Author

Timothy B. Rowe, Zongjun Yin, Chris Stringer, Thomas G. Davies, Brian D. Metscher, Alistair R. Evans, Stephen Wroe, John R. Hutchinson, Russell J. Garwood, Nathan Jeffery, Jesús Marugán-Lobón, Lawrence M. Witmer, Adam P. Summers, Selena Y. Smith, Emily J. Rayfield, Philip C. J. Donoghue, Peter L. Falkingham, Martin Rücklin, Stephan Lautenschlager, Maeva J. Orliac, Vera Weisbecker, Stig A. Walsh, Imran A. Rahman, Mark D. Sutton, Xi Ping Dong, Paul O'Higgins, Stefan Bengtson, Marcelo R. Sánchez-Villagra, Renaud Lebrun, Robert J. Asher, Neil H. Shubin, John A. Cunningham, Paul M. Barrett, Philip G. Cox, Carlos Martínez-Pérez, Matt Friedman, José Braga, Doug M. Boyer, J. Matthias Starck, Zerina Johanson, Jen A. Bright, Leon P. A. M. Claessens, Anjali Goswami, Roger B. J. Benson, Karl T. Bates, Natural Environment Research Council (NERC), School of Earth Sciences [Bristol], University of Bristol [Bristol], Oxford University Museum of Natural History, University of Oxford [Oxford], School of Geography, Earth and Environmental Sciences [Birmingham], University of Birmingham [Birmingham], Museum of Zoology, University of Cambridge, Department of Earth Sciences [NHM London] (DES-NHM), The Natural History Museum [London] (NHM), Institute of Ageing and Chronic Disease, University of Liverpool, Department of Palaeobiology [Stockholm], Swedish Museum of Natural History (NRM), Department of Earth Sciences [Oxford], Department of Evolutionary Anthropology Durham, Duke University [Durham], Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), School of Geosciences, University of South Florida, Florida, Tampa, USA, University of South Florida [Tampa] (USF), College of the Holy Cross, Departments of Archaeology [York] (BioArch), University of York [York, UK], School of Earth and Space Sciences [Beijing], Peking University [Beijing], School of Biological Sciences, VIC, Monash University, Faculty of Science/School of Natural Sciences and Psychology, Liverpool John Moores University (LJMU), Department of Earth and Environmental Sciences [Ann Arbor], University of Michigan [Ann Arbor], University of Michigan System-University of Michigan System, Museum of Paleontology [Ann Arbor], School of Earth and Environmental Sciences [Manchester] (SEES), University of Manchester [Manchester], Department of Genetics, Evolution and Environment, Centre for Biodiversity and Environment, Research, University College of London [London] (UCL), Structure and Motion Laboratory, Royal Veterinary College, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, Unidad de Paleontologia, Departamento de Biologia, Facultad de Ciencias, Universidad Autonoma de Madrid, Department of theoretical biology, University of Vienna, Jackson School of Geosciences (JSG), University of Texas at Austin [Austin], Naturalis Biodiversity Center [Leiden], Paläontologisches Institut und Museum der Universität Zürich, Paläontologisches Institut und Museum der Univer sität Zürich, University of Chicago, Oxford University Museum of Natural History (OUMNH), University of Oxford, Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), and Universität Wien

Subjects
0106 biological sciences, 0301 basic medicine, Life Sciences & Biomedicine - Other Topics, DYNAMICS, Computer science, Datasets as Topic, Reuse, 01 natural sciences, FOSSILS, three-dimensional models, Naturvetenskap, Data Curation, General Environmental Science, Ecology, palaeontology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], General Medicine, 11 Medical And Health Sciences, CC, biomechanics Keywords: digital data, Open data, Perspective, Computer data storage, [SDU.STU.PG]Sciences of the Universe [physics]/Earth Sciences/Paleontology, General Agricultural and Biological Sciences, Natural Sciences, Life Sciences & Biomedicine, TISSUES, phenotype, Best practice, Digital data, Library science, Environmental Sciences & Ecology, 010603 evolutionary biology, Biological Science Disciplines, General Biochemistry, Genetics and Molecular Biology, QA76, functional analysis, Set (abstract data type), 03 medical and health sciences, PALEONTOLOGY, Biology, Subject Category: Morphology and biomechanics Subject Areas: evolution, visualization, digital data, Evolutionary Biology, Science & Technology, TOMOGRAPHIC MICROSCOPY, Morphology and Biomechanics, General Immunology and Microbiology, business.industry, Research, QH, Reproducibility of Results, computed tomography, PERFORMANCE, 06 Biological Sciences, Data science, EVOLUTION, Visualization, 030104 developmental biology, VISUALIZATION, 07 Agricultural And Veterinary Sciences, business
Abstract

International audience; Over the past two decades, the development of methods for visualizing and analysing specimens digitally, in three and even four dimensions, has transformed the study of living and fossil organisms. However, the initial promise that the widespread application of such methods would facilitate access to the underlying digital data has not been fully achieved. The underlying datasets for many published studies are not readily or freely available, introducing a barrier to verification and reproducibility, and the reuse of data. There is no current agreement or policy on the amount and type of data that should be made available alongside studies that use, and in some cases are wholly reliant on, digital morphology. Here, we propose a set of recommendations for minimum standards and additional best practice for three-dimensional digital data publication, and review the issues around data storage, management and accessibility.

Published
2017
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7. Barcoding the largest animals on Earth: ongoing challenges and molecular solutions in the taxonomic identification of ancient cetaceans

Author

Barbara Wilkens, Luke Spindler, Krista McGrath, Keri Rowsell, Michael Hofreiter, Ana S. L. Rodrigues, Matthew J. Collins, Anne Charpentier, Youri van den Hurk, Camilla Speller, Armelle Gardeisen, Departments of Archaeology [York] (BioArch), University of York [York, UK], Institute of Biochemistry and Biology University of Potsdam, Institute of archaeology (UCL), University College of London [London] (UCL), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Paul-Valéry - Montpellier 3 (UM3), Archéologie des Sociétés Méditerranéennes (ASM), Centre National de la Recherche Scientifique (CNRS)-Université Paul-Valéry - Montpellier 3 (UM3)-Ministère de la Culture et de la Communication (MCC), Dipartimento di Scienze della Natura e del Territorio, University of Sassari, Université Paul-Valéry - Montpellier 3 (UPVM)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Université Paul-Valéry - Montpellier 3 (UPVM)-Centre National de la Recherche Scientifique (CNRS)-Ministère de la Culture (MC), Università degli Studi di Sassari = University of Sassari [Sassari] (UNISS), Archaeology of Northwestern Europe, Hofreiter, Michael [0000-0003-0441-4705], Apollo - University of Cambridge Repository, Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut de Recherche pour le Développement (IRD [France-Sud]), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut de Recherche pour le Développement (IRD [France-Sud])

Subjects
0301 basic medicine, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, Biome, species identification, species, Review Article, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Biology, DNA barcoding, General Biochemistry, Genetics and Molecular Biology, zooarchaeology by mass spectrometry, spectrometry, cetaceans, 03 medical and health sciences, Abundance (ecology), biology.animal, Animals, DNA Barcoding, Taxonomic, 14. Life underwater, Baseline (configuration management), ancient DNA, Zooarchaeology, Institut für Biochemie und Biologie, zooarchaeology by mass, Whale, Ecology, High-Throughput Nucleotide Sequencing, Articles, Biodiversity, Classification, collagen peptide mass fingerprinting, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, 030104 developmental biology, Ancient DNA, Archaeology, 13. Climate action, archaeozoology, identification, Identification (biology), Cetacea, Collagen, North Sea, General Agricultural and Biological Sciences
Abstract

International audience; One contribution of 16 to a theme issue 'From DNA barcodes to biomes'. Over the last few centuries, many cetacean species have witnessed dramatic global declines due to industrial overharvesting and other anthropogenic influences, and thus are key targets for conservation. Whale bones recovered from archaeological and palaeontological contexts can provide essential baseline information on the past geographical distribution and abundance of species required for developing informed conservation policies. Here we review the challenges with identifying whale bones through traditional anatomical methods, as well as the opportunities provided by new molecular analyses. Through a case study focused on the North Sea, we demonstrate how the utility of this (pre)historic data is currently limited by a lack of accurate taxonomic information for the majority of ancient cetacean remains. We then discuss current opportunities presented by molecular identification methods such as DNA barcoding and collagen peptide mass fingerprinting (zooarchaeology by mass spectrometry), and highlight the importance of molecular identifications in assessing ancient species' distributions through a case study focused on the Mediterranean. We conclude by considering high-throughput molecular approaches such as hybridization capture followed by next-generation sequencing as cost-effective approaches for enhancing the ecological informativeness of these ancient sample sets. This article is part of the themed issue 'From DNA barcodes to biomes'.

Published
2016
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8. Another brick in the wall: fifth millennium BC earthen-walled architecture on the Channel shores

Author

Elise Werthe, Nancy Marcoux, Véronique Guitton, Catherine Bizien-Jaglin, David Aoustin, Gwenaëlle Hamon, Ludovic Soler, Jean-Noël Guyodo, Julia Wattez, Luc Laporte, Emmanuel Mens, Alexandre Lucquin, Ramiro March, Jean-Baptiste Barreau, Luc Jallot, Yann Bernard, Centre de Recherche en Archéologie, Archéosciences, Histoire (CReAAH), Le Mans Université (UM)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Université de Nantes - UFR Histoire, Histoire de l'Art et Archéologie (UFR HHAA), Université de Nantes (UN)-Université de Nantes (UN)-Ministère de la Culture (MC), Centre Régional d'Archéologie d'Alet [Saint-Malo], Archéologie des Sociétés Méditerranéennes (ASM), Centre National de la Recherche Scientifique (CNRS)-Ministère de la Culture (MC)-Université Paul-Valéry - Montpellier 3 (UPVM), 3D interaction with virtual environments using body and mind (Hybrid), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-MEDIA ET INTERACTIONS (IRISA-D6), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS), Institut national de recherches archéologiques préventives, centre archéologique de Cesson-Sévigné (Inrap, Cesson-Sévigné), Institut national de recherches archéologiques préventives (Inrap), Departments of Archaeology [York] (BioArch), University of York [York, UK], Préhistoire et Technologie (PréTech), Université Paris Nanterre (UPN)-Centre National de la Recherche Scientifique (CNRS), De la Préhistoire à l'Actuel : Culture, Environnement et Anthropologie (PACEA), Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB), Université de Nantes (UN)-Le Mans Université (UM)-Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Ministère de la Culture (MC), Université Paul-Valéry - Montpellier 3 (UPVM)-Centre National de la Recherche Scientifique (CNRS)-Ministère de la Culture (MC), CentraleSupélec-Télécom Bretagne-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Université de Bretagne Sud (UBS)-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-CentraleSupélec-Télécom Bretagne-Université de Rennes 1 (UR1), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Université de Bretagne Sud (UBS)-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Le Mans Université (UM)-Université de Rennes (UR)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Université de Nantes - UFR Histoire, Histoire de l'Art et Archéologie (UFR HHAA), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS), Institut national de recherches archéologiques préventives - Centre de recherches archéologiques de Cesson-Sévigné (Inrap, Cesson-Sévigné), Nantes Université (NU)-Ministère de la Culture (MC)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Le Mans Université (UM), and Centre National de la Recherche Scientifique (CNRS)-Université Paul-Valéry - Montpellier 3 (UPVM)-Ministère de la Culture (MC)

Subjects
Shore, causewayed enclosure, 010506 paleontology, Archeology, geography, geography.geographical_feature_category, Marsh, 060102 archaeology, biology, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, General Arts and Humanities, Agrochola circellaris, Context (language use), 06 humanities and the arts, Ancient history, biology.organism_classification, 01 natural sciences, Archaeology, 0601 history and archaeology, wetland archaeology, Architecture, Channel (geography), 0105 earth and related environmental sciences
Abstract

International audience; The west European Neolithic is famed for its funerary and ceremonial monuments, but the evidence for houses is sparse. Can this be explained by the materials of which they were built? On the northern coast of Brittany, the site of Lillemer rises from the surrounding marshes and presents abundant evidence of Middle Neolithic occupation, contemporary with the passage graves of the region. Surprisingly, their evidence includes the remains of collapsed earthen-walled structures, providing the northernmost example of this type of architecture in a Neolithic context and a possible explanation for the invisibility of much Neolithic domestic architecture

Published
2015
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9. Ancient biomolecules from deep ice cores reveal a forested Southern Greenland

Author

Antonella Casoli, Hendrik N. Poinar, J. D. Barker, Roger Nathan, Juerg Beer, Michael Bunce, Enrico Cappellini, Vasily Alfimov, Raimund Muscheler, M. Thomas P. Gilbert, Rasmus Nielsen, Kirsty Penkman, Martin B. Hebsgaard, Wouter Boomsma, Tina B. Brand, Cees-Jan de Hoog, Elisa Campani, Sigfus J Johnsen, Pierre Taberlet, Ole Bennike, Matthew J. Collins, James Haile, Eske Willerslev, Jørgen Peder Steffensen, Martin Sharp, Simon J. Armitage, Marcus Christl, Jean-Luc Schwenninger, Dorthe Dahl-Jensen, Michael Hofreiter, Center for Ancient Genetics, University of Copenhagen = Københavns Universitet (KU), Departments of Archaeology [York] (BioArch), University of York [York, UK], Section of Biostatistics [Copenhagen], Department of Public Health [Copenhagen], Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Centre for Comparative Genomics, Max Planck Institute for Evolutionary Anthropology [Leipzig], Max-Planck-Gesellschaft, Ancient DNA Research Laboratory, Murdoch University, McMaster Ancient DNA Center, McMaster University [Hamilton, Ontario], Centre for Ice and Climate [Copenhagen], Niels Bohr Institute [Copenhagen] (NBI), Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Science [Copenhagen], Geological Survey of Denmark and Greenland (GEUS), Research Laboratory for Archaeology and the History of Art [Oxford], University of Oxford [Oxford], Department of Geography, University College of London [London] (UCL), Department of Earth Sciences [Oxford], Laboratory for Ion Beam Physics, Institute for Particle Physics, Swiss Federal Insitute of Aquatic Science and Technology [Dübendorf] (EAWAG), GeoBiosphere Science Center, Lund University [Lund], Department of Earth and Atmospheric Sciences [Edmonton], University of Alberta, Ancient Biomolecules Centre, Laboratoire d'Ecologie Alpine (LECA), Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), Dipartimento di Chimica Generale e Inorganica, and University of Parma = Università degli studi di Parma [Parme, Italie]

Subjects
010504 meteorology & atmospheric sciences, Fauna, Greenland, ELLESMERE ISLAND, Polymerase Chain Reaction, 01 natural sciences, Proxy (climate), Trees, Ice core, HOLOCENE, Ice Cover, Amino Acids, History, Ancient, Holocene, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, 0303 health sciences, Multidisciplinary, geography.geographical_feature_category, Geography, biology, Fossils, POLLEN, RECORD, Plants, Oceanography, GLACIER, SEDIMENTS, INSTABILITY, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Article, Time, 03 medical and health sciences, Paleontology, CHRONOLOGY, Animals, Ecosystem, Dye 3, 030304 developmental biology, 0105 earth and related environmental sciences, geography, Bayes Theorem, Glacier, DNA, 15. Life on land, biology.organism_classification, Invertebrates, CLIMATE, 13. Climate action, Groenlandia, Ice sheet, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract

Times Cited: 1; International audience; It is difficult to obtain fossil data from the 10% of Earth's terrestrial surface that is covered by thick glaciers and ice sheets, and hence, knowledge of the paleoenvironments of these regions has remained limited. We show that DNA and amino acids from buried organisms can be recovered from the basal sections of deep ice cores, enabling reconstructions of past flora and fauna. We show that high-altitude southern Greenland, currently lying below more than 2 kilometers of ice, was inhabited by a diverse array of conifer trees and insects within the past million years. The results provide direct evidence in support of a forested southern Greenland and suggest that many deep ice cores may contain genetic records of paleoenvironments in their basal sections.

Published
2007
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10. A Gray Whale in Magdalenian Perigord. Species identification of a bone projectile point from La Madeleine (Dordogne, France) using collagen fingerprinting

Author

François Baleux, Krista McGrath, Camilla Speller, François-Xavier Chauvière, Anne Charpentier, Jean-Marc Pétillon, Ana S. L. Rodrigues, Travaux et recherches archéologiques sur les cultures, les espaces et les sociétés (TRACES), École des hautes études en sciences sociales (EHESS)-Université Toulouse - Jean Jaurès (UT2J)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Office et Musée d'Archéologie de Neuchâtel, Latenium, Université de Neuchâtel (UNINE), University of Britsh Columbia [Vancouver], Departments of Archaeology [York] (BioArch), University of York [York, UK], Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut de Recherche pour le Développement (IRD [France-Sud]), ANR-18-CE27-0018,PaleoCet,L'exploitation des cétacés dans le Paléolithique de l'Europe atlantique(2018), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut de Recherche pour le Développement (IRD [France-Sud]), École des hautes études en sciences sociales (EHESS)-Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université de Toulouse (UT)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), University of British Columbia [Vancouver], Université Paul-Valéry - Montpellier 3 (UPVM)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École Pratique des Hautes Études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)

Subjects
0106 biological sciences, 010506 paleontology, Baleine grise (Eschrichtius robustus), bone tool, Pleistocene, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, La Madeleine, Magdalénien, pointe de projectile, Context (language use), 010603 evolutionary biology, 01 natural sciences, law.invention, law, biology.animal, projectile point, 14. Life underwater, Radiocarbon dating, Magdalenian, Bone industry, 0105 earth and related environmental sciences, Gray Whale (Eschrichtius robustus), Artifact (archaeology), biology, Whale, Bone tool, Projectile point, General Engineering, Whales, collagen peptide mass fingerprinting, Archaeology, Collagen peptide mass fingerprinting, industrie osseuse, analyse Zooms, Geology
Abstract

The Cetacean bone artifact described in this paper is the result of excavations carried out in La Madeleine (Tursac, Dordogne) under the direction of D. Peyrony, between 1910-1913. It was discovered in the middle layer (“couche moyenne”) of the stratigraphy described by Capitan and Peyrony and subsequently attributed to the “Magdalenian V” by H. Breuil (i.e the beginning of the Upper Magdalenian). This layer corresponds to layers C25 to C20 of the stratigraphy established later by J.-M. Bouvier. Two radiocarbon dates are currently available (C21: 12750 ± 240 BP, Ly 920; and C25: 13070 ± 190 BP, Ly 921). The artifact was recently identified as Cetacean bone during an integrated study of the bones and reindeer antlers kept at the Musée National de Préhistoire (Peyrony and Bouvier collections). It is a fully worked object, elongated in shape (129 X 13.2 X 12.8 mm; 18.6 g) with straight outline and profile, a circular cross-section and parallel sides. It is interpreted as a mesio-proximal fragment of projectile point. Collagen peptide mass fingerprinting (PMF) was applied to taxonomically identify the bone artefact, as a part of the PaleoCet project. Also known as ZooMS, collagen PMF discriminates taxonomic groups based on differences in the collagen protein sequence observed through Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. The bone subsamples from the exterior and interior of the artifact produced similar MALDI-TOF spectra, both of which could be confidently identified as gray whale (Eschrichtius robustus). The artifact from La Madeleine is the first evidence of the presence of this species in Atlantic waters at the end of MIS2, suggesting continuity between the Pleistocene and Holocene populations of this species. Moreover, to our knowledge, this gray whale bone artifact represents the oldest identified gray whale in an archaeological context, thus first witness of the millennia-old interactions between humans and this highly coastal whale species. The manufacturing of the La Madeleine artifact on the Basque coast, followed by its circulation through the western Pyrenees and then towards the north at the east of Landes and Gironde up to Périgord (a travel distance of roughly 350 km), might be the most plausible route taken by this artifact to reach La Madeleine. L’artefact en os de cétacé décrit dans cet article provient des fouilles effectuées entre 1910 et 1913 à La Madeleine (Tursac, Dordogne) sous la direction de D. Peyrony. Il a été découvert dans la couche moyenne de la stratigraphie décrite par Capitan et Peyrony («Magdalenien V» de H. Breuil, c’est-à-dire le début du Magdalénien supérieur), et qui correspond aux couches C25 à C20 de la stratigraphie établie ultérieurement par J.-M. Bouvier. Deux dates radiocarbone sont actuellement disponibles (C21: 12750 ± 240 BP, Ly 920 ; et C25: 13070 ± 190 BP, Ly 921). La pièce a récemment été identifiée comme os de cétacé lors d’une étude intégrée des os et bois de rennes conservés au Musée national de Préhistoire (collections Peyrony et Bouvier). Il s’agit d’un objet entièrement façonné, de forme allongée (longueur X largeur X épaisseur : 129 X 13,2 X 12,8 mm ; masse 18,6 g) avec un contour et un profil droits, une section circulaire et des bords parallèles. Il est interprété comme un fragment mésio-proximal de pointe de projectile. Dans le cadre du projet PaleoCet, l’identification taxinomique de l’artefact osseux a fait l’objet d’une empreinte peptidique de masse de collagène (PMF). Aussi connu sous le nom de ZooMS, le collagène PMF discrimine les groupes taxinomiques en fonction des différences dans la séquence protéique du collagène observées par spectrométrie de masse MALDI-TOF. Les sous-échantillons osseux de l’extérieur et de l’intérieur de l’objet ont produit des spectres MALDI-TOF similaires, que l’on peut rapporter à la baleine grise (Eschrichtius robustus). La pièce de La Madeleine est la première preuve de la présence de cette espèce dans les eaux atlantiques à la fin du MIS2, ce qui suggère une continuité entre les populations pléistocènes et holocènes de cette espèce. Elle constitue la plus ancienne trace de baleine grise identifiée en contexte archéologique, et est donc le plus ancien indice des interactions millénaires entre les humains et cette espèce de baleine très côtière. Une fabrication sur la côte basque, puis une circulation à travers les Pyrénées occidentales, le nord-est des Landes et la Gironde, jusqu’au Périgord (environ 350 km de trajet), pourrait être la voie la plus plausible suivie par la pièce de La Madeleine.

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