1
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Winter RM, de Kock W, Mackie M, Ramsøe M, Desiderà E, Collins M, Guidetti P, Presslee S, Alegre MM, Oueslati T, Muniz AM, Michailidis D, van den Hurk Y, Taurozzi AJ, Çakirlar C. Grouping groupers in the Mediterranean: Ecological baselines revealed by ancient proteins. Ecol Evol 2023; 13:e10625. [PMID: 37877101 PMCID: PMC10591212 DOI: 10.1002/ece3.10625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 09/29/2023] [Accepted: 10/04/2023] [Indexed: 10/26/2023] Open
Abstract
Marine historical ecology provides a means to establish baselines to inform current fisheries management. Groupers (Epinephelidae) are key species for fisheries in the Mediterranean, which have been heavily overfished. Species abundance and distribution prior to the 20th century in the Mediterranean remains poorly known. To reconstruct the past biogeography of Mediterranean groupers, we investigated whether Zooarchaeology by Mass Spectrometry (ZooMS) can be used for identifying intra-genus grouper bones to species level. We discovered 22 novel, species-specific ZooMS biomarkers for groupers. Applying these biomarkers to Kinet Höyük, a Mediterranean archaeological site, demonstrated 4000 years of regional Epinephelus aeneus dominance and resiliency through millennia of fishing pressures, habitat degradation and climatic changes. Combining ZooMS identifications with catch size reconstructions revealed the Epinephelus aeneus capacity for growing 30 cm larger than hitherto documented, revising the maximum Total Length from 120 to 150 cm. Our results provide ecological baselines for a key Mediterranean fishery which could be leveraged to define and assess conservation targets.
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Affiliation(s)
- Rachel M. Winter
- Groningen Institute of ArchaeologyUniversity of GroningenGroningenThe Netherlands
| | - Willemien de Kock
- Groningen Institute of ArchaeologyUniversity of GroningenGroningenThe Netherlands
- Marine Evolution and Conservation, Groningen Institute for Evolutionary Life SciencesUniversity of GroningenGroningenThe Netherlands
| | - Meaghan Mackie
- Faculty of Health and Medical Science, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
- Faculty of Health and Medical Science, Novo Nordisk Foundation Center for Protein ResearchUniversity of CopenhagenCopenhagenDenmark
| | - Max Ramsøe
- Faculty of Health and Medical Science, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
| | - Elena Desiderà
- Department of Integrative Marine Ecology (EMI)Stazione Zoologica Anton Dohrn–National Institute of Marine Biology, Ecology and Biotechnology—Genoa Marine CentreGenoaItaly
| | - Matthew Collins
- Faculty of Health and Medical Science, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
- Department of ArchaeologyUniversity of CambridgeCambridgeUK
| | - Paolo Guidetti
- Department of Integrative Marine Ecology (EMI)Stazione Zoologica Anton Dohrn–National Institute of Marine Biology, Ecology and Biotechnology—Genoa Marine CentreGenoaItaly
| | | | | | - Tarek Oueslati
- Centre National de la Recherche ScientifiqueUniversity of LilleLilleFrance
| | | | - Dimitris Michailidis
- Malcolm H. Wiener Lab, American School of Classical Studies at AthensAthensGreece
| | - Youri van den Hurk
- Department of Archaeology and Cultural HistoryNorwegian University of Science and TechnologyTrondheimNorway
| | - Alberto J. Taurozzi
- Faculty of Health and Medical Science, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
| | - Canan Çakirlar
- Groningen Institute of ArchaeologyUniversity of GroningenGroningenThe Netherlands
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2
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Sierra A, Balasse M, Radović S, Orton D, Fiorillo D, Presslee S. Early Dalmatian farmers specialized in sheep husbandry. Sci Rep 2023; 13:10355. [PMID: 37365303 DOI: 10.1038/s41598-023-37516-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 06/22/2023] [Indexed: 06/28/2023] Open
Abstract
The spread of farming in the central and western Mediterranean took place rapidly, linked to the Impressa Ware. The Impressa Ware originated somewhere in the southern Adriatic and spread westwards across the Mediterranean. These early farmers had an economy based on cereal agriculture and caprine husbandry, but there is still little information on how this agropastoral system functioned. This study aims to unravel the farming practices of the early Dalmatian farmers linked to the Impressa culture by using an integrated analysis, combining archaeozoology, palaeoproteomics and stable isotopes, applied to the faunal assemblages of Tinj-Podlivade and Crno Vrilo. The results show: (1) the composition of the flocks was overwhelmingly sheep; (2) sheep exploitation at both sites was similar, focusing on milk and meat; (3) sheep reproduction was concentrated at the beginning of winter, with no reproduction in autumn as in later sites in the western Mediterranean. We conclude that a common animal economy existed at both sites, which could be related to the mobility practiced by these early farming societies throughout the Mediterranean.
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Affiliation(s)
- A Sierra
- AASPE «Archéozoologie, Archéobotanique: Sociétés, Pratiques, Environnements» CNRS, MNHN, 75005, Paris, France.
- Departament de Prehistoria, Facultat de Lletres, Universitat Autonoma de Barcelona, Bellaterra, Barcelona, Spain.
| | - M Balasse
- AASPE «Archéozoologie, Archéobotanique: Sociétés, Pratiques, Environnements» CNRS, MNHN, 75005, Paris, France
| | - S Radović
- Croatian Academy of Sciences and Arts, Institute for Quaternary Palaeontology and Geology, Ante Kovačića 5, 10000, Zagreb, Croatia
| | - D Orton
- BioArCh, Department of Archaeology, Environment Building, University of York, Heslington, York, YO10 5NG, UK
| | - D Fiorillo
- AASPE «Archéozoologie, Archéobotanique: Sociétés, Pratiques, Environnements» CNRS, MNHN, 75005, Paris, France
| | - S Presslee
- BioArCh, Department of Archaeology, Environment Building, University of York, Heslington, York, YO10 5NG, UK
- Department of Chemistry, University of York, Heslington, York, YO10 5NG, UK
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3
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Dierickx K, Presslee S, Harvey VL. Rapid collagen peptide mass fingerprinting as a tool to authenticate Pleuronectiformes in the food industry. Food Control 2023. [DOI: 10.1016/j.foodcont.2023.109680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
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4
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Dierickx K, Presslee S, Hagan R, Oueslati T, Harland J, Hendy J, Orton D, Alexander M, Harvey VL. Peptide mass fingerprinting of preserved collagen in archaeological fish bones for the identification of flatfish in European waters. R Soc Open Sci 2022; 9:220149. [PMID: 35911190 PMCID: PMC9326269 DOI: 10.1098/rsos.220149] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 07/06/2022] [Indexed: 06/15/2023]
Abstract
Bones of Pleuronectiformes (flatfish) are often not identified to species due to the lack of diagnostic features on bones that allow adequate distinction between taxa. This hinders in-depth understanding of archaeological fish assemblages and particularly flatfish fisheries throughout history. This is especially true for the North Sea region, where several commercially significant species have been exploited for centuries, yet their archaeological remains continue to be understudied. In this research, eight peptide biomarkers for 18 different species of Pleuronectiformes from European waters are described using MALDI-TOF MS and liquid chromatography tandem mass spectrometry data obtained from modern reference specimens. Bone samples (n = 202) from three archaeological sites in the UK and France dating to the medieval period (ca seventh-sixteenth century CE) were analysed using zooarchaeology by mass spectrometry (ZooMS). Of the 201 that produced good quality spectra, 196 were identified as flatfish species, revealing a switch in targeted species through time and indicating that ZooMS offers a more reliable and informative approach for species identification than osteological methods alone. We recommend this approach for future studies of archaeological flatfish remains as the precise species uncovered from a site can tell much about the origin of the fish, where people fished and whether they traded between regions.
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Affiliation(s)
- Katrien Dierickx
- Department of Archaeology, University of York, Heslington YO10 5DD, York, UK
| | - Samantha Presslee
- Department of Archaeology, University of York, Heslington YO10 5DD, York, UK
| | - Richard Hagan
- Department of Archaeology, University of York, Heslington YO10 5DD, York, UK
| | - Tarek Oueslati
- Centre National de la Recherche Scientifique, University of Lille, Lille, France
| | - Jennifer Harland
- Department of Archaeology, University of York, Heslington YO10 5DD, York, UK
- Archaeology Institute, University of the Highlands and Islands, Kirkwall, UK
| | - Jessica Hendy
- Department of Archaeology, University of York, Heslington YO10 5DD, York, UK
| | - David Orton
- Department of Archaeology, University of York, Heslington YO10 5DD, York, UK
| | - Michelle Alexander
- Department of Archaeology, University of York, Heslington YO10 5DD, York, UK
| | - Virginia L. Harvey
- Department of Archaeology, University of York, Heslington YO10 5DD, York, UK
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5
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Perri AR, Mitchell KJ, Mouton A, Álvarez-Carretero S, Hulme-Beaman A, Haile J, Jamieson A, Meachen J, Lin AT, Schubert BW, Ameen C, Antipina EE, Bover P, Brace S, Carmagnini A, Carøe C, Samaniego Castruita JA, Chatters JC, Dobney K, Dos Reis M, Evin A, Gaubert P, Gopalakrishnan S, Gower G, Heiniger H, Helgen KM, Kapp J, Kosintsev PA, Linderholm A, Ozga AT, Presslee S, Salis AT, Saremi NF, Shew C, Skerry K, Taranenko DE, Thompson M, Sablin MV, Kuzmin YV, Collins MJ, Sinding MHS, Gilbert MTP, Stone AC, Shapiro B, Van Valkenburgh B, Wayne RK, Larson G, Cooper A, Frantz LAF. Dire wolves were the last of an ancient New World canid lineage. Nature 2021; 591:87-91. [PMID: 33442059 DOI: 10.1038/s41586-020-03082-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 11/12/2020] [Indexed: 11/09/2022]
Abstract
Dire wolves are considered to be one of the most common and widespread large carnivores in Pleistocene America1, yet relatively little is known about their evolution or extinction. Here, to reconstruct the evolutionary history of dire wolves, we sequenced five genomes from sub-fossil remains dating from 13,000 to more than 50,000 years ago. Our results indicate that although they were similar morphologically to the extant grey wolf, dire wolves were a highly divergent lineage that split from living canids around 5.7 million years ago. In contrast to numerous examples of hybridization across Canidae2,3, there is no evidence for gene flow between dire wolves and either North American grey wolves or coyotes. This suggests that dire wolves evolved in isolation from the Pleistocene ancestors of these species. Our results also support an early New World origin of dire wolves, while the ancestors of grey wolves, coyotes and dholes evolved in Eurasia and colonized North America only relatively recently.
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Affiliation(s)
- Angela R Perri
- Department of Archaeology, Durham University, Durham, UK.
| | - Kieren J Mitchell
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia.
| | - Alice Mouton
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | | | - Ardern Hulme-Beaman
- Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool, UK.,School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool, UK
| | - James Haile
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, The University of Oxford, Oxford, UK
| | - Alexandra Jamieson
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, The University of Oxford, Oxford, UK
| | - Julie Meachen
- Department of Anatomy, Des Moines University, Des Moines, IA, USA
| | - Audrey T Lin
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, The University of Oxford, Oxford, UK.,Department of Zoology, University of Oxford, Oxford, UK.,Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Blaine W Schubert
- Center of Excellence in Paleontology & Department of Geosciences, East Tennessee State University, Johnson City, TN, USA
| | - Carly Ameen
- Department of Archaeology, University of Exeter, Exeter, UK
| | | | - Pere Bover
- ARAID Foundation, Instituto Universitario de Investigación en Ciencias Ambientales (IUCA) - Aragosaurus Group, Universidad de Zaragoza, Zaragoza, Spain
| | - Selina Brace
- Department of Earth Sciences, Natural History Museum, London, UK
| | - Alberto Carmagnini
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Christian Carøe
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Keith Dobney
- Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool, UK.,Department of Archaeology, University of Sydney, Sydney, New South Wales, Australia.,Department of Archaeology, University of Aberdeen, Aberdeen, UK.,Department of Archaeology, Simon Fraser University, Burnaby, Canada
| | - Mario Dos Reis
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Allowen Evin
- Institut des Sciences de l'Evolution - Montpellier, CNRS, Université de Montpellier, IRD, EPHE, Montpellier, France
| | - Philippe Gaubert
- Laboratoire Evolution & Diversité Biologique, UPS/CNRS/IRD, Université Paul Sabatier, Toulouse, France
| | - Shyam Gopalakrishnan
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Graham Gower
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Holly Heiniger
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Kristofer M Helgen
- Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia
| | - Josh Kapp
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Pavel A Kosintsev
- Institute of Plant and Animal Ecology, Urals Branch of the Russian Academy of Sciences, Yekaterinburg, Russia.,Ural Federal University, Yekaterinburg, Russia
| | - Anna Linderholm
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, The University of Oxford, Oxford, UK.,Department of Anthropology, Texas A&M University, College Station, TX, USA
| | - Andrew T Ozga
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA.,School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA.,Halmos College of Arts and Sciences, Nova Southeastern University, Fort Lauderdale, FL, USA
| | | | - Alexander T Salis
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Nedda F Saremi
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Colin Shew
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - Katherine Skerry
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA
| | - Dmitry E Taranenko
- Institute of Systematics and Ecology of Animals, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Mary Thompson
- Idaho Museum of Natural History, Idaho State University, Pocatello, ID, USA
| | - Mikhail V Sablin
- Zoological Institute of the Russian Academy of Sciences, St Petersburg, Russia
| | - Yaroslav V Kuzmin
- Sobolev Institute of Geology and Mineralogy, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Tomsk State University, Tomsk, Russia
| | - Matthew J Collins
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
| | - Mikkel-Holger S Sinding
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Greenland Institute of Natural Resources, Nuuk, Greenland
| | - M Thomas P Gilbert
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,NTNU University Museum, Trondheim, Norway
| | - Anne C Stone
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA.,School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA.,Institute of Human Origins, Arizona State University, Tempe, AZ, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA.,Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Blaire Van Valkenburgh
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - Greger Larson
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, The University of Oxford, Oxford, UK
| | - Alan Cooper
- South Australian Museum, Adelaide, South Australia, Australia
| | - Laurent A F Frantz
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK. .,Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich, Germany.
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6
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Presslee S, Penkman K, Fischer R, Richards-Slidel E, Southon J, Hospitaleche CA, Collins M, MacPhee R. Assessment of different screening methods for selecting palaeontological bone samples for peptide sequencing. J Proteomics 2020; 230:103986. [PMID: 32941991 DOI: 10.1016/j.jprot.2020.103986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 07/24/2020] [Accepted: 09/10/2020] [Indexed: 10/23/2022]
Abstract
Ancient proteomics is being applied to samples dating further and further back in time, with many palaeontological specimens providing protein sequence data for phylogenetic analysis as well as protein degradation studies. However, fossils are a precious material and proteomic analysis is destructive and costly. In this paper we consider three different techniques (ATR-FTIR, MALDI-ToF MS and chiral AA analysis) to screen fossil material for potential protein preservation, aiming to maximise the proteomic information recovered and saving costly time consuming analyses which may produce low quality results. It was found that splitting factor and C/P indices from ATR-FTIR were not a reliable indicator of protein survival as they are confounded by secondary mineralisation of the fossil material. Both MALDI-ToF MS and chiral AA analysis results were able to successfully identify samples with surviving proteins, and it is suggested that one or both of these analyses be used for screening palaeontological specimens. SIGNIFICANCE: This study has shown both chiral amino acid analysis and MALDI-ToF MS are reliable screening methods for predicting protein survival in fossils. Both these methods are quick, cheap, minimally destructive (1 mg and 15 mg respectively) and can provide crucial additional information about the endogeneity of the surviving proteins. It is hoped that the use of these screening methods will encourage the examination of a wide range of palaeontological specimens for potential proteomic analysis. This in turn will give us a better understanding of protein survival far back in time and under different environmental conditions.
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Affiliation(s)
- Samantha Presslee
- BioArCh, Department of Archaeology, University of York, York, UK; BioArCh, Department of Chemistry, University of York, York, UK.
| | - Kirsty Penkman
- BioArCh, Department of Chemistry, University of York, York, UK
| | - Roman Fischer
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Eden Richards-Slidel
- BioArCh, Department of Archaeology, University of York, York, UK; Section for Evolutionary Genomics, The Globe Institute, Faculty of Health, University of Copenhagen, Copenhagen, Denmark
| | - John Southon
- Department of Earth System Science, University of California, Irvine, USA
| | | | - Matthew Collins
- Section for Evolutionary Genomics, The Globe Institute, Faculty of Health, University of Copenhagen, Copenhagen, Denmark; McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
| | - Ross MacPhee
- Department of Mammalogy, American Museum of Natural History, New York, NY, USA
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7
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Presslee S, Slater GJ, Pujos F, Forasiepi AM, Fischer R, Molloy K, Mackie M, Olsen JV, Kramarz A, Taglioretti M, Scaglia F, Lezcano M, Lanata JL, Southon J, Feranec R, Bloch J, Hajduk A, Martin FM, Salas Gismondi R, Reguero M, de Muizon C, Greenwood A, Chait BT, Penkman K, Collins M, MacPhee RDE. Palaeoproteomics resolves sloth relationships. Nat Ecol Evol 2019; 3:1121-1130. [PMID: 31171860 DOI: 10.1038/s41559-019-0909-z] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 04/28/2019] [Indexed: 01/16/2023]
Abstract
The living tree sloths Choloepus and Bradypus are the only remaining members of Folivora, a major xenarthran radiation that occupied a wide range of habitats in many parts of the western hemisphere during the Cenozoic, including both continents and the West Indies. Ancient DNA evidence has played only a minor role in folivoran systematics, as most sloths lived in places not conducive to genomic preservation. Here we utilize collagen sequence information, both separately and in combination with published mitochondrial DNA evidence, to assess the relationships of tree sloths and their extinct relatives. Results from phylogenetic analysis of these datasets differ substantially from morphology-based concepts: Choloepus groups with Mylodontidae, not Megalonychidae; Bradypus and Megalonyx pair together as megatherioids, while monophyletic Antillean sloths may be sister to all other folivorans. Divergence estimates are consistent with fossil evidence for mid-Cenozoic presence of sloths in the West Indies and an early Miocene radiation in South America.
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Affiliation(s)
- Samantha Presslee
- Department of Archaeology and BioArCh, University of York, Heslington, UK.,Department of Mammalogy, American Museum of Natural History, New York, NY, USA.,Paleoproteomics Group, Natural History Museum of Denmark and University of Copenhagen, Copenhagen, Denmark
| | - Graham J Slater
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, USA
| | - François Pujos
- Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales, CCT-CONICET-Mendoza, Mendoza, Argentina
| | - Analía M Forasiepi
- Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales, CCT-CONICET-Mendoza, Mendoza, Argentina
| | - Roman Fischer
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Kelly Molloy
- Chait Laboratory and National Resource for the Mass Spectrometric Analysis of Biological Macromolecules, The Rockefeller University, New York, NY, USA
| | - Meaghan Mackie
- Paleoproteomics Group, Natural History Museum of Denmark and University of Copenhagen, Copenhagen, Denmark.,Novo Nordisk Foundation Center for Protein Research, Copenhagen, Denmark
| | - Jesper V Olsen
- Novo Nordisk Foundation Center for Protein Research, Copenhagen, Denmark
| | - Alejandro Kramarz
- Sección Paleovertebrados, Museo Argentino de Ciencias Naturales 'Bernardino Rivadavia', Buenos Aires, Argentina
| | - Matías Taglioretti
- Museo Municipal de Ciencias Naturales 'Lorenzo Scaglia', Mar del Plata, Argentina
| | - Fernando Scaglia
- Museo Municipal de Ciencias Naturales 'Lorenzo Scaglia', Mar del Plata, Argentina
| | - Maximiliano Lezcano
- Instituto de Investigaciones en Diversidad Cultural y Procesos de Cambio, CONICET and Universidad Nacional de Río Negro, Bariloche, Argentina
| | - José Luis Lanata
- Instituto de Investigaciones en Diversidad Cultural y Procesos de Cambio, CONICET and Universidad Nacional de Río Negro, Bariloche, Argentina
| | - John Southon
- Keck-CCAMS Group, Earth System Science Department, University of California, Irvine, Irvine, CA, USA
| | | | - Jonathan Bloch
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - Adam Hajduk
- Museo de la Patagonia 'F. P. Moreno', Bariloche, Argentina
| | - Fabiana M Martin
- Centro de Estudios del Hombre Austral, Instituto de la Patagonia, Universidad de Magallanes, Punta Arenas, Chile
| | - Rodolfo Salas Gismondi
- BioGeoCiencias Lab, Facultad de Ciencias y Filosofía/CIDIS, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Marcelo Reguero
- CONICET and División Paleontología de Vertebrados, Museo de La Plata. Facultad de Ciencias Naturales, Universidad Nacional de La Plata, La Plata, Argentina
| | - Christian de Muizon
- Centre de Recherches sur la Paléobiodiversité et les Paléoenvironnements, Muséum national d'Histoire naturelle, Paris, France
| | - Alex Greenwood
- Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany.,Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Brian T Chait
- Chait Laboratory and National Resource for the Mass Spectrometric Analysis of Biological Macromolecules, The Rockefeller University, New York, NY, USA
| | - Kirsty Penkman
- Department of Chemistry, University of York, Heslington, UK
| | - Matthew Collins
- Paleoproteomics Group, Natural History Museum of Denmark and University of Copenhagen, Copenhagen, Denmark.,McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
| | - Ross D E MacPhee
- Department of Mammalogy, American Museum of Natural History, New York, NY, USA.
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8
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Demarchi B, Hall S, Roncal-Herrero T, Freeman CL, Woolley J, Crisp MK, Wilson J, Fotakis A, Fischer R, Kessler BM, Rakownikow Jersie-Christensen R, Olsen JV, Haile J, Thomas J, Marean CW, Parkington J, Presslee S, Lee-Thorp J, Ditchfield P, Hamilton JF, Ward MW, Wang CM, Shaw MD, Harrison T, Domínguez-Rodrigo M, MacPhee RDE, Kwekason A, Ecker M, Kolska Horwitz L, Chazan M, Kröger R, Thomas-Oates J, Harding JH, Cappellini E, Penkman K, Collins MJ. Protein sequences bound to mineral surfaces persist into deep time. eLife 2016; 5. [PMID: 27668515 PMCID: PMC5039028 DOI: 10.7554/elife.17092] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 08/17/2016] [Indexed: 12/14/2022] Open
Abstract
Proteins persist longer in the fossil record than DNA, but the longevity, survival mechanisms and substrates remain contested. Here, we demonstrate the role of mineral binding in preserving the protein sequence in ostrich (Struthionidae) eggshell, including from the palaeontological sites of Laetoli (3.8 Ma) and Olduvai Gorge (1.3 Ma) in Tanzania. By tracking protein diagenesis back in time we find consistent patterns of preservation, demonstrating authenticity of the surviving sequences. Molecular dynamics simulations of struthiocalcin-1 and -2, the dominant proteins within the eggshell, reveal that distinct domains bind to the mineral surface. It is the domain with the strongest calculated binding energy to the calcite surface that is selectively preserved. Thermal age calculations demonstrate that the Laetoli and Olduvai peptides are 50 times older than any previously authenticated sequence (equivalent to ~16 Ma at a constant 10°C). DOI:http://dx.doi.org/10.7554/eLife.17092.001 The pattern of chemical reactions that break down the molecules that make our bodies is still fairly mysterious. Archaeologists and geologists hope that dead organisms (or artefacts made from them) might not decay entirely, leaving behind clues to their lives. We know that some molecules are more resistant than others; for example, fats are tough and survive for a long time while DNA is degraded very rapidly. Proteins, which are made of chains of smaller molecules called amino acids, are usually sturdier than DNA. Since the amino acid sequence of a protein reflects the DNA sequence that encodes it, proteins in fossils can help researchers to reconstruct how extinct organisms are related in cases where DNA cannot be retrieved. Time, temperature, burial environment and the chemistry of the fossil all influence how quickly a protein decays. However, it is not clear what mechanisms slow down decay so that full protein sequences can be preserved and identified after millions of years. As a result, it is difficult to know where to look for these ancient sequences. In the womb of ostriches, several proteins are responsible for assembling the minerals that make up the ostrich eggshell. These proteins become trapped tightly within the mineral crystals themselves. In this situation, proteins can potentially be preserved over geological time. Demarchi et al. have now studied 3.8 million-year-old eggshells found close to the equator and, despite the extent to which the samples have degraded, discovered fully preserved protein sequences. Using a computer simulation method called molecular dynamics, Demarchi et al. calculated that the protein sequences that are able to survive the longest are stabilized by strong binding to the surface of the mineral crystals. The authenticity of these sequences was tested thoroughly using a combination of several approaches that Demarchi et al. recommend using as a standard for ancient protein studies. Overall, it appears that biominerals are an excellent source of ancient protein sequences because mineral binding ensures survival. A systematic survey of fossil biominerals from different environments is now needed to assess whether these biomolecules have the potential to act as barcodes for interpreting the evolution of organisms. DOI:http://dx.doi.org/10.7554/eLife.17092.002
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Affiliation(s)
- Beatrice Demarchi
- BioArCh, Department of Archaeology, University of York, York, United Kingdom
| | - Shaun Hall
- Department of Material Science and Engineering, University of Sheffield, Sheffield, United Kingdom
| | | | - Colin L Freeman
- Department of Material Science and Engineering, University of Sheffield, Sheffield, United Kingdom
| | - Jos Woolley
- BioArCh, Department of Archaeology, University of York, York, United Kingdom
| | - Molly K Crisp
- Department of Chemistry, University of York, York, United Kingdom
| | - Julie Wilson
- Department of Chemistry, University of York, York, United Kingdom.,Department of Mathematics, University of York, York, United Kingdom
| | - Anna Fotakis
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Roman Fischer
- Advanced Proteomics Facility, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Benedikt M Kessler
- Advanced Proteomics Facility, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | | | - Jesper V Olsen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - James Haile
- Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, United Kingdom
| | - Jessica Thomas
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Bangor, United Kingdom
| | - Curtis W Marean
- Institute of Human Origins, SHESC, Arizona State University, Tempe, United States.,Centre for Coastal Palaeoscience, Nelson Mandela Metropolitan University, Port Elizabeth, South Africa
| | - John Parkington
- Department of Archaeology, University of Cape Town, Cape Town, South Africa
| | - Samantha Presslee
- BioArCh, Department of Archaeology, University of York, York, United Kingdom
| | - Julia Lee-Thorp
- Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, United Kingdom
| | - Peter Ditchfield
- Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, United Kingdom
| | - Jacqueline F Hamilton
- Wolfson Atmospheric Chemistry Laboratories, Department of Chemistry, University of York, York, United Kingdom
| | - Martyn W Ward
- Wolfson Atmospheric Chemistry Laboratories, Department of Chemistry, University of York, York, United Kingdom
| | - Chunting Michelle Wang
- Wolfson Atmospheric Chemistry Laboratories, Department of Chemistry, University of York, York, United Kingdom
| | - Marvin D Shaw
- Wolfson Atmospheric Chemistry Laboratories, Department of Chemistry, University of York, York, United Kingdom
| | - Terry Harrison
- Center for the Study of Human Origins, Department of Anthropology, New York University, New York, United States
| | | | - Ross DE MacPhee
- Department of Mammalogy, American Museum of Natural History, New York, United States
| | | | - Michaela Ecker
- Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, United Kingdom
| | - Liora Kolska Horwitz
- National Natural History Collections, Faculty of Life Sciences, The Hebrew University, Jerusalem, Israel
| | - Michael Chazan
- Department of Anthropology, University of Toronto, Toronto, Canada.,Evolutionary Studies Institute, University of the Witwatersrand, Braamfontein, South Africa
| | - Roland Kröger
- Department of Physics, University of York, York, United Kingdom
| | - Jane Thomas-Oates
- Department of Chemistry, University of York, York, United Kingdom.,Centre of Excellence in Mass Spectrometry, University of York, New York, United States
| | - John H Harding
- Department of Material Science and Engineering, University of Sheffield, Sheffield, United Kingdom
| | - Enrico Cappellini
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Kirsty Penkman
- Department of Chemistry, University of York, York, United Kingdom
| | - Matthew J Collins
- BioArCh, Department of Archaeology, University of York, York, United Kingdom
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