1
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Abrams G, Devièse T, Pirson S, De Groote I, Flas D, Jungels C, Jadin I, Cattelain P, Bonjean D, Mathys A, Semal P, Higham T, Di Modica K. Investigating the co-occurrence of Neanderthals and modern humans in Belgium through direct radiocarbon dating of bone implements. J Hum Evol 2024; 186:103471. [PMID: 38043357 DOI: 10.1016/j.jhevol.2023.103471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 11/13/2023] [Accepted: 11/18/2023] [Indexed: 12/05/2023]
Affiliation(s)
- Grégory Abrams
- Department of Archaeology, Ghent University, B-9000, Gent, Belgium; Scientific Department, Espace Muséal d'Andenne, B-5300, Andenne, Belgium; Faculty of Archaeology, Archaeological Sciences, Bio-Archaeology, Leiden University, 2333 CC, Leiden, the Netherlands.
| | - Thibaut Devièse
- Centre Européen de Recherche et d'Enseignement des Géosciences de l'Environnement, Aix-Marseille Université, CNRS, IRD, INRAE, BP80-13545, Aix-en-Provence, cedex 4, France.
| | - Stéphane Pirson
- Direction scientifique et technique, Agence wallonne du Patrimoine, B-5100, Namur, Belgium
| | - Isabelle De Groote
- Department of Archaeology, Ghent University, B-9000, Gent, Belgium; School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, L3 3AF, UK
| | - Damien Flas
- Laboratoire Méditerranéen de Préhistoire Europe Afrique, Aix-Marseille University, CNRS, 13097, Aix-en-Provence, cedex 2, France; Department of Prehistory, University of Liège, B-4000, Liège, Belgium
| | - Cécile Jungels
- Scientific Department, Préhistomuseum, B-4400, Flémalle, Belgium; Les Chercheurs de la Wallonie, B-4400, Flémalle, Belgium
| | - Ivan Jadin
- Operational Direction Earth and History of Life, Quaternary Environments & Humans, Anthropology & Prehistory, Royal Belgium Institute of Natural Sciences, B-1000, Brussels, Belgium
| | - Pierre Cattelain
- Department of Prehistory, University of Liège, B-4000, Liège, Belgium; Cedarc-Musée du Malgré-Tout, B-5670, Belgium; Centre de Recherches en Archéologie et Patrimoine, Université Libre de Bruxelles, B-1150, Brussels, Belgium
| | - Dominique Bonjean
- Scientific Department, Espace Muséal d'Andenne, B-5300, Andenne, Belgium
| | - Aurore Mathys
- Biological Collection and Data Management, Royal Museum for Central Africa, B-3080, Tervuren, Belgium; Scientific Heritage Service, Royal Belgian Institute of Natural Sciences, B-1000, Brussels, Belgium; Art, Archaeology and Heritage Unit, University of Liège, B-4000, Liège, Belgium
| | - Patrick Semal
- Scientific Heritage Service, Royal Belgian Institute of Natural Sciences, B-1000, Brussels, Belgium
| | - Thomas Higham
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, A-1030, Vienna, Austria
| | - Kévin Di Modica
- Scientific Department, Espace Muséal d'Andenne, B-5300, Andenne, Belgium
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2
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Bergman J, Pedersen RØ, Lundgren EJ, Lemoine RT, Monsarrat S, Pearce EA, Schierup MH, Svenning JC. Worldwide Late Pleistocene and Early Holocene population declines in extant megafauna are associated with Homo sapiens expansion rather than climate change. Nat Commun 2023; 14:7679. [PMID: 37996436 PMCID: PMC10667484 DOI: 10.1038/s41467-023-43426-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 11/09/2023] [Indexed: 11/25/2023] Open
Abstract
The worldwide extinction of megafauna during the Late Pleistocene and Early Holocene is evident from the fossil record, with dominant theories suggesting a climate, human or combined impact cause. Consequently, two disparate scenarios are possible for the surviving megafauna during this time period - they could have declined due to similar pressures, or increased in population size due to reductions in competition or other biotic pressures. We therefore infer population histories of 139 extant megafauna species using genomic data which reveal population declines in 91% of species throughout the Quaternary period, with larger species experiencing the strongest decreases. Declines become ubiquitous 32-76 kya across all landmasses, a pattern better explained by worldwide Homo sapiens expansion than by changes in climate. We estimate that, in consequence, total megafauna abundance, biomass, and energy turnover decreased by 92-95% over the past 50,000 years, implying major human-driven ecosystem restructuring at a global scale.
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Affiliation(s)
- Juraj Bergman
- Center for Ecological Dynamics in a Novel Biosphere (ECONOVO), Department of Biology, Aarhus University, DK-8000, Aarhus C, Denmark.
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of Biology, Aarhus University, DK-8000, Aarhus C, Denmark.
| | - Rasmus Ø Pedersen
- Center for Ecological Dynamics in a Novel Biosphere (ECONOVO), Department of Biology, Aarhus University, DK-8000, Aarhus C, Denmark
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of Biology, Aarhus University, DK-8000, Aarhus C, Denmark
| | - Erick J Lundgren
- Center for Ecological Dynamics in a Novel Biosphere (ECONOVO), Department of Biology, Aarhus University, DK-8000, Aarhus C, Denmark
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of Biology, Aarhus University, DK-8000, Aarhus C, Denmark
- School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD, Australia
| | - Rhys T Lemoine
- Center for Ecological Dynamics in a Novel Biosphere (ECONOVO), Department of Biology, Aarhus University, DK-8000, Aarhus C, Denmark
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of Biology, Aarhus University, DK-8000, Aarhus C, Denmark
| | - Sophie Monsarrat
- Center for Ecological Dynamics in a Novel Biosphere (ECONOVO), Department of Biology, Aarhus University, DK-8000, Aarhus C, Denmark
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of Biology, Aarhus University, DK-8000, Aarhus C, Denmark
- Rewilding Europe, Toernooiveld 1, 6525 ED, Nijmegen, The Netherlands
| | - Elena A Pearce
- Center for Ecological Dynamics in a Novel Biosphere (ECONOVO), Department of Biology, Aarhus University, DK-8000, Aarhus C, Denmark
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of Biology, Aarhus University, DK-8000, Aarhus C, Denmark
| | - Mikkel H Schierup
- Bioinformatics Research Centre, Aarhus University, DK-8000, Aarhus C, Denmark
| | - Jens-Christian Svenning
- Center for Ecological Dynamics in a Novel Biosphere (ECONOVO), Department of Biology, Aarhus University, DK-8000, Aarhus C, Denmark
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of Biology, Aarhus University, DK-8000, Aarhus C, Denmark
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3
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Baca M, Popović D, Agadzhanyan AK, Baca K, Conard NJ, Fewlass H, Filek T, Golubiński M, Horáček I, Knul MV, Krajcarz M, Krokhaleva M, Lebreton L, Lemanik A, Maul LC, Nagel D, Noiret P, Primault J, Rekovets L, Rhodes SE, Royer A, Serdyuk NV, Soressi M, Stewart JR, Strukova T, Talamo S, Wilczyński J, Nadachowski A. Ancient DNA of narrow-headed vole reveal common features of the Late Pleistocene population dynamics in cold-adapted small mammals. Proc Biol Sci 2023; 290:20222238. [PMID: 36787794 PMCID: PMC9928523 DOI: 10.1098/rspb.2022.2238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023] Open
Abstract
The narrow-headed vole, collared lemming and common vole were the most abundant small mammal species across the Eurasian Late Pleistocene steppe-tundra environment. Previous ancient DNA studies of the collared lemming and common vole have revealed dynamic population histories shaped by climatic fluctuations. To investigate the extent to which species with similar adaptations share common evolutionary histories, we generated a dataset comprised the mitochondrial genomes of 139 ancient and 6 modern narrow-headed voles from several sites across Europe and northwestern Asia covering approximately the last 100 thousand years (kyr). We inferred Bayesian time-aware phylogenies using 11 radiocarbon-dated samples to calibrate the molecular clock. Divergence of the main mtDNA lineages across the three species occurred during marine isotope stages (MIS) 7 and MIS 5, suggesting a common response of species adapted to open habitat during interglacials. We identified several time-structured mtDNA lineages in European narrow-headed vole, suggesting lineage turnover. The timing of some of these turnovers was synchronous across the three species, allowing us to identify the main drivers of the Late Pleistocene dynamics of steppe- and cold-adapted species.
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Affiliation(s)
- Mateusz Baca
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Danijela Popović
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | | | - Katarzyna Baca
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Nicholas J Conard
- Department of Early Prehistory and Quaternary Ecology and.,Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany
| | - Helen Fewlass
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Thomas Filek
- Department of Palaeontology, University of Vienna, Vienna, Austria
| | | | - Ivan Horáček
- Department of Zoology, Charles University, Prague, Czechia
| | - Monika V Knul
- Department of Archaeology, Anthropology and Geography, University of Winchester, Winchester, UK
| | - Magdalena Krajcarz
- Institute of Archaeology, Nicolaus Copernicus University in Toruń, Toruń, Poland
| | - Maria Krokhaleva
- Institute of Plant and Animal Ecology, Ural Branch, Russian Academy of Sciences, Yekaterinburg, Russia
| | - Loïc Lebreton
- Department of Human and Environment, (HNHP) UMR 7194MNHN-CNRS-UPVD, National Museum of Natural History, Paris, France.,Catalan Institute of Human Paleoecology and Social Evolution (IPHES-CERCA), Tarragona, Spain.,Department of History and Art History, Rovira i Virgili University, Tarragona, Spain
| | - Anna Lemanik
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Cracow, Poland
| | - Lutz C Maul
- Senckenberg Research Station of Quaternary Palaeontology, Weimar, Germany
| | - Doris Nagel
- Department of Palaeontology, University of Vienna, Vienna, Austria
| | - Pierre Noiret
- Research Group Prehistory, University of Liège, Liège, Belgium
| | - Jérome Primault
- DRAC/SRA Poitou-Charentes, Ministry of Culture and Communications, Poitiers, France
| | - Leonid Rekovets
- Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Sara E Rhodes
- Interdisciplinary Center for Archaeology and Evolution of Human Behavior, University of Algavre, Faro, Portugal
| | - Aurélien Royer
- Biogéosciences, UMR 6282 CNRS, University of Burgundy, Dijon, France
| | - Natalia V Serdyuk
- Borissiak Paleontological Institute, Russian Academy of Sciences, Moscow, Russia
| | - Marie Soressi
- Faculty of Archaeology, Leiden University, Leiden, The Netherlands
| | - John R Stewart
- Faculty of Science and Technology, Bournemouth University, Poole, UK
| | - Tatiana Strukova
- Institute of Plant and Animal Ecology, Ural Branch, Russian Academy of Sciences, Yekaterinburg, Russia
| | - Sahra Talamo
- Department of Chemistry G. Ciamician, Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Jarosław Wilczyński
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Cracow, Poland
| | - Adam Nadachowski
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Cracow, Poland
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4
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Sanisidro O, Arganda Carreras I, Cantalapiedra JL. Folded
: A toolkit to describe mammalian herbivore dentition from
2D
images. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.14042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Oscar Sanisidro
- Universidad de Alcalá, GloCEE ‐ Global Change Ecology and Evolution Research Group Departamento Ciencias de la Vida Madrid Spain
| | - Ignacio Arganda Carreras
- Department of Computer Science and Artificial Intelligence University of the Basque Country (UPV/EHU) San Sebastian Spain
- Ikerbasque, Basque Foundation for Science Bilbao Spain
- Donostia International Physics Center (DIPC) San Sebastian Spain
| | - Juan L. Cantalapiedra
- Universidad de Alcalá, GloCEE ‐ Global Change Ecology and Evolution Research Group Departamento Ciencias de la Vida Madrid Spain
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5
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Magyari EK, Gasparik M, Major I, Lengyel G, Pál I, Virág A, Korponai J, Haliuc A, Szabó Z, Pazonyi P. Mammal extinction facilitated biome shift and human population change during the last glacial termination in East-Central Europe. Sci Rep 2022; 12:6796. [PMID: 35474321 PMCID: PMC9043214 DOI: 10.1038/s41598-022-10714-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 04/01/2022] [Indexed: 11/16/2022] Open
Abstract
The study of local extinction times, together with the associated environmental and human population changes in the last glacial termination, provides insights into the causes of mega- and microfauna extinctions. In East-Central (EC) Europe, groups of Palaeolithic humans were present throughout the last glacial maximum, but disappeared suddenly around 15,200 cal BP. In this study cave sediment profiles dated using radiocarbon techniques and a large set of mammal bones dated directly by AMS 14C were used to determine local extinction times. These were, in turn, compared to changes in the total megafauna population of EC Europe derived from coprophilous fungi, the Epigravettian population decline, quantitative climate models, pollen and plant macrofossil inferred climate, as well as to biome reconstructions. The results suggest that the population size of large herbivores decreased in the area after 17,700 cal BP, when temperate tree abundance and warm continental steppe cover both increased in the lowlands. Boreal forest expansion started around 16,200 cal BP. Cave sediments show the decline of narrow-headed vole and arctic lemming populations specifically associated with a tundra environment at the same time and the expansion of the common vole, an inhabitant of steppes. The last dated appearance of arctic lemming was at ~ 16,640 cal BP, while that of the narrow-headed vole at ~ 13,340, and the estimated extinction time of woolly mammoth was either at 13,830 (GRIWM) or 15,210 (PHASE), and reindeer at 11,860 (GRIWM) or 12,550 cal BP (PHASE). The population decline of the large herbivore fauna slightly preceded changes in terrestrial vegetation, and likely facilitated it via a reduction in the intensity of grazing and the concomitant accumulation of plant biomass. Furthermore, it is possible to conclude that the Late Epigravettian population had high degree of quarry-fidelity; they left the basin when these mammals vanished.
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Affiliation(s)
- Enikő Katalin Magyari
- MTA-MTM-ELTE Research Group for Palaeontology, Budapest, Ludovika tér 2, 1083, Hungary. .,Department of Environmental and Landscape Geography, Eötvös Loránd University, Budapest, Pázmány Péter stny 1/c, 1117, Hungary. .,Isotope Climatology and Environmental Research Centre (ICER), Institute for Nuclear Research, Hungarian Academy of Science, Debrecen, Bem tér 18/c, 4026, Hungary.
| | - Mihály Gasparik
- Department of Palaeontology and Geology, Hungarian Natural History Museum, Budapest, Ludovika tér 2, 1083, Hungary
| | - István Major
- Isotope Climatology and Environmental Research Centre (ICER), Institute for Nuclear Research, Hungarian Academy of Science, Debrecen, Bem tér 18/c, 4026, Hungary
| | - György Lengyel
- Department of Prehistory and Archaeology, University of Miskolc, Miskolc-Egyetemváros, 3515, Hungary
| | - Ilona Pál
- Isotope Climatology and Environmental Research Centre (ICER), Institute for Nuclear Research, Hungarian Academy of Science, Debrecen, Bem tér 18/c, 4026, Hungary
| | - Attila Virág
- MTA-MTM-ELTE Research Group for Palaeontology, Budapest, Ludovika tér 2, 1083, Hungary.,Department of Mineralogy and Geology, University of Debrecen, Debrecen, Egyetem tér 1, 4032, Hungary
| | - János Korponai
- Department of Water Supply and Sewerage, University of Public Service, Baja, Bajcsy-Zsilinszky utca 12-14, 6500, Hungary.,Department of Environmental Sciences, Sapientia Hungarian University of Transylvania, Calea Turzii str. 4, 400193, Cluj-Napoca, Romania.,Department of Danube's Diversity, Institute of Aquatic Ecology, Centre for Ecological Research, Budapest, Karolina út 29, 1113, Hungary
| | - Aritina Haliuc
- Institute of Speleology, Romanian Academy, 5 Clinicilor str, 400006, Cluj-Napoca, Romania.,EPOC, UMR 5805, Université de Bordeaux, Allée Geoffroy St Hilaire Bat B18N, CS 50023, 33615, Pessac Cedex, France
| | - Zoltán Szabó
- Department of Environmental and Landscape Geography, Eötvös Loránd University, Budapest, Pázmány Péter stny 1/c, 1117, Hungary
| | - Piroska Pazonyi
- MTA-MTM-ELTE Research Group for Palaeontology, Budapest, Ludovika tér 2, 1083, Hungary
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6
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Kirillova IV, Vershinina AO, Zazovskaya EP, Zanina OG, Cutler S, Kosintsev PA, Lapteva EG, Chernova OF, Shapiro B. On Time and Environment of Stephanorhinus kirchbergensis Jäger 1839 (Mammalia, Rhinoceratidae) in Altai and Northeastern Russia. BIOL BULL+ 2021. [DOI: 10.1134/s1062359021090077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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7
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Matschiner M. Museum specimens tell the history of rhinoceroses. Cell 2021; 184:4841-4842. [PMID: 34499855 DOI: 10.1016/j.cell.2021.08.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Rhinoceroses are facing an uncertain future due to human-induced population-size reductions. In this issue of Cell, Liu et al. analyze rhinoceros genomes to study their past and find support for an early divergence between African and Asian species, signatures of past hybridization, and evidence of loss of genetic diversity.
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8
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Liu S, Westbury MV, Dussex N, Mitchell KJ, Sinding MHS, Heintzman PD, Duchêne DA, Kapp JD, von Seth J, Heiniger H, Sánchez-Barreiro F, Margaryan A, André-Olsen R, De Cahsan B, Meng G, Yang C, Chen L, van der Valk T, Moodley Y, Rookmaaker K, Bruford MW, Ryder O, Steiner C, Bruins-van Sonsbeek LGR, Vartanyan S, Guo C, Cooper A, Kosintsev P, Kirillova I, Lister AM, Marques-Bonet T, Gopalakrishnan S, Dunn RR, Lorenzen ED, Shapiro B, Zhang G, Antoine PO, Dalén L, Gilbert MTP. Ancient and modern genomes unravel the evolutionary history of the rhinoceros family. Cell 2021; 184:4874-4885.e16. [PMID: 34433011 DOI: 10.1016/j.cell.2021.07.032] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 06/16/2021] [Accepted: 07/23/2021] [Indexed: 12/27/2022]
Abstract
Only five species of the once-diverse Rhinocerotidae remain, making the reconstruction of their evolutionary history a challenge to biologists since Darwin. We sequenced genomes from five rhinoceros species (three extinct and two living), which we compared to existing data from the remaining three living species and a range of outgroups. We identify an early divergence between extant African and Eurasian lineages, resolving a key debate regarding the phylogeny of extant rhinoceroses. This early Miocene (∼16 million years ago [mya]) split post-dates the land bridge formation between the Afro-Arabian and Eurasian landmasses. Our analyses also show that while rhinoceros genomes in general exhibit low levels of genome-wide diversity, heterozygosity is lowest and inbreeding is highest in the modern species. These results suggest that while low genetic diversity is a long-term feature of the family, it has been particularly exacerbated recently, likely reflecting recent anthropogenic-driven population declines.
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Affiliation(s)
- Shanlin Liu
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China; The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark.
| | - Michael V Westbury
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Nicolas Dussex
- Centre for Palaeogenetics, Svante Arrhenius vag 20C, Stockholm 10691, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm 10405, Sweden; Department of Zoology, Stockholm University, Stockholm 10691, Sweden
| | - Kieren J Mitchell
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide 5005, Australia
| | - Mikkel-Holger S Sinding
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Peter D Heintzman
- The Arctic University Museum of Norway, UiT The Arctic University of Norway, Tromsø 9037, Norway
| | - David A Duchêne
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Joshua D Kapp
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Johanna von Seth
- Centre for Palaeogenetics, Svante Arrhenius vag 20C, Stockholm 10691, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm 10405, Sweden; Department of Zoology, Stockholm University, Stockholm 10691, Sweden
| | - Holly Heiniger
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide 5005, Australia
| | - Fátima Sánchez-Barreiro
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Ashot Margaryan
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Remi André-Olsen
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 17121 Solna, Sweden
| | - Binia De Cahsan
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Guanliang Meng
- China National Genebank, BGI Shenzhen, Shenzhen 518083, China
| | - Chentao Yang
- China National Genebank, BGI Shenzhen, Shenzhen 518083, China
| | - Lei Chen
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an 710072, China
| | - Tom van der Valk
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Yoshan Moodley
- Department of Zoology, University of Venda, Thohoyandou 0950, Republic of South Africa
| | - Kees Rookmaaker
- Editor of the Rhino Resource Center, Utrecht, the Netherlands
| | - Michael W Bruford
- School of Biosciences, Sir Martin Evans Building, Cardiff University, Cardiff CF10 3AX, UK; Sustainable Places Research Institute, Cardiff University, Cardiff CF10 3BA, UK
| | - Oliver Ryder
- San Diego Zoo Wildlife Alliance, Beckman Center for Conservation Research, San Diego, CA 92027, USA
| | - Cynthia Steiner
- San Diego Zoo Wildlife Alliance, Beckman Center for Conservation Research, San Diego, CA 92027, USA
| | | | - Sergey Vartanyan
- N.A. Shilo North-East Interdisciplinary Scientific Research Institute, Far East Branch, Russian Academy of Sciences (NEISRI FEB RAS), Magadan 685000, Russia
| | - Chunxue Guo
- China National Genebank, BGI Shenzhen, Shenzhen 518083, China
| | - Alan Cooper
- South Australian Museum, Adelaide, SA 5000, Australia
| | - Pavel Kosintsev
- Institute of Plant and Animal Ecology, Ural Branch of the Russian Academy of Sciences, Yekaterinburg, Russia; Ural Federal University, Yekaterinburg, Russia
| | - Irina Kirillova
- Institute of Geography, Russian Academy of Sciences, Moscow 119017, Russia
| | - Adrian M Lister
- Department of Earth Sciences, Natural History Museum, London, UK
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), Barcelona, Spain; Centre Nacional d'Anàlisi Genòmica, Centre for Genomic Regulation (CNAG-CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain; Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Shyam Gopalakrishnan
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Robert R Dunn
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark; Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA
| | - Eline D Lorenzen
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA; Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA 96050, USA
| | - Guojie Zhang
- China National Genebank, BGI Shenzhen, Shenzhen 518083, China; Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Pierre-Olivier Antoine
- Institut des Sciences de l'Évolution, Université Montpellier, CNRS, IRD, EPHE, Montpellier 34095, France
| | - Love Dalén
- Centre for Palaeogenetics, Svante Arrhenius vag 20C, Stockholm 10691, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm 10405, Sweden; Department of Zoology, Stockholm University, Stockholm 10691, Sweden.
| | - M Thomas P Gilbert
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark; Norwegian University of Science and Technology (NTNU) University Museum, Trondheim 7012, Norway.
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9
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Antoine PO, Reyes MC, Amano N, Bautista AP, Chang CH, Claude J, De Vos J, Ingicco T. A new rhinoceros clade from the Pleistocene of Asia sheds light on mammal dispersals to the Philippines. Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlab009] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Rhinoceroses are among the most endangered mammalian species today. Their past diversity is well documented from the Eocene onward, although their evolutionary history is far from being fully understood. Here, we elucidate the systematic affinities of a Pleistocene rhinoceros species represented by a partial skeleton from 709 ± 68 kya archaeological deposits in Luzon Island, Philippines. We perform a comprehensive phylogenetic analysis, including all living species and a wide array of extinct rhinocerotid species. We confirm the early split between Elasmotheriinae and Rhinocerotinae at c. 35.5 Mya and constrain the divergence between recent Asian and African rhinoceroses at c. 24 Mya, with contrasting phenotypic evolutionary rates in Diceroti and Rhinoceroti. Dental features reveal the existence of an unsuspected Asian Pleistocene clade, referred to as Nesorhinus gen. nov.. It includes the rhinoceros from the Philippines and another extinct species from Taiwan, N. hayasakai. Nesorhinus is the sister-group to a cluster comprising Dicerorhinus and Rhinoceros. Our phylogenetic results strongly suggest an island-hopping dispersal for Nesorhinus, from the Asian mainland towards Luzon via Taiwan by the Late Miocene or later, and Pleistocene dispersals for representatives of Rhinoceros. Nesorhinus philippinensis would be the first perissodactyl species supporting the island-rule hypothesis, with decreased body weight and limb-bone robustness.
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Affiliation(s)
- Pierre-Olivier Antoine
- Institut des Sciences de l’Évolution de Montpellier, Université de Montpellier, CNRS, IRD, EPHE, Place Eugène Bataillon, 34095 Montpellier Cedex 05, France
| | - Marian C Reyes
- Archaeology Division, National Museum of the Philippines, P. Burgos Drive, Rizal Park, Manila, Philippines
| | - Noel Amano
- Department of Archaeology, Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany
| | - Angel P Bautista
- Cultural Properties Division, National Museum of the Philippines, P. Burgos Drive, Rizal Park, Manila, Philippines
| | | | - Julien Claude
- Institut des Sciences de l’Évolution de Montpellier, Université de Montpellier, CNRS, IRD, EPHE, Place Eugène Bataillon, 34095 Montpellier Cedex 05, France
| | - John De Vos
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands
| | - Thomas Ingicco
- Histoire naturelle de l’Homme préhistorique, Département Homme et Environnement, Muséum National d’Histoire Naturelle, Université de Perpignan Via Domitia, Centre National de la Recherche Scientifique (UMR7194), Institut de Paléontologie Humaine 1, rue René Panhard 75013 Paris, France
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10
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Reevaluating the timing of Neanderthal disappearance in Northwest Europe. Proc Natl Acad Sci U S A 2021; 118:2022466118. [PMID: 33798098 DOI: 10.1073/pnas.2022466118] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Elucidating when Neanderthal populations disappeared from Eurasia is a key question in paleoanthropology, and Belgium is one of the key regions for studying the Middle to Upper Paleolithic transition. Previous radiocarbon dating placed the Spy Neanderthals among the latest surviving Neanderthals in Northwest Europe with reported dates as young as 23,880 ± 240 B.P. (OxA-8912). Questions were raised, however, regarding the reliability of these dates. Soil contamination and carbon-based conservation products are known to cause problems during the radiocarbon dating of bulk collagen samples. Employing a compound-specific approach that is today the most efficient in removing contamination and ancient genomic analysis, we demonstrate here that previous dates produced on Neanderthal specimens from Spy were inaccurately young by up to 10,000 y due to the presence of unremoved contamination. Our compound-specific radiocarbon dates on the Neanderthals from Spy and those from Engis and Fonds-de-Forêt demonstrate that they disappeared from Northwest Europe at 44,200 to 40,600 cal B.P. (at 95.4% probability), much earlier than previously suggested. Our data contribute significantly to refining models for Neanderthal disappearance in Europe and, more broadly, show that chronometric models regarding the appearance or disappearance of animal or hominin groups should be based only on radiocarbon dates obtained using robust pretreatment methods.
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11
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Lundgren EJ, Schowanek SD, Rowan J, Middleton O, Pedersen RØ, Wallach AD, Ramp D, Davis M, Sandom CJ, Svenning JC. Functional traits of the world's late Quaternary large-bodied avian and mammalian herbivores. Sci Data 2021; 8:17. [PMID: 33473149 PMCID: PMC7817692 DOI: 10.1038/s41597-020-00788-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 11/30/2020] [Indexed: 01/29/2023] Open
Abstract
Prehistoric and recent extinctions of large-bodied terrestrial herbivores had significant and lasting impacts on Earth's ecosystems due to the loss of their distinct trait combinations. The world's surviving large-bodied avian and mammalian herbivores remain among the most threatened taxa. As such, a greater understanding of the ecological impacts of large herbivore losses is increasingly important. However, comprehensive and ecologically-relevant trait datasets for extinct and extant herbivores are lacking. Here, we present HerbiTraits, a comprehensive functional trait dataset for all late Quaternary terrestrial avian and mammalian herbivores ≥10 kg (545 species). HerbiTraits includes key traits that influence how herbivores interact with ecosystems, namely body mass, diet, fermentation type, habitat use, and limb morphology. Trait data were compiled from 557 sources and comprise the best available knowledge on late Quaternary large-bodied herbivores. HerbiTraits provides a tool for the analysis of herbivore functional diversity both past and present and its effects on Earth's ecosystems.
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Affiliation(s)
- Erick J Lundgren
- Centre for Compassionate Conservation, School of Life Sciences, University of Technology Sydney, Ultimo, Australia.
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of Biology, Aarhus University, Aarhus, Denmark.
- Section for Ecoinformatics and Biodiversity, Department of Biology, Aarhus University, Aarhus, Denmark.
| | - Simon D Schowanek
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of Biology, Aarhus University, Aarhus, Denmark.
- Section for Ecoinformatics and Biodiversity, Department of Biology, Aarhus University, Aarhus, Denmark.
| | - John Rowan
- Department of Anthropology, University at Albany, Albany, NY, 12222, USA
| | - Owen Middleton
- School of Life Sciences, University of Sussex, Sussex, UK
| | - Rasmus Ø Pedersen
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of Biology, Aarhus University, Aarhus, Denmark
- Section for Ecoinformatics and Biodiversity, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Arian D Wallach
- Centre for Compassionate Conservation, School of Life Sciences, University of Technology Sydney, Ultimo, Australia
| | - Daniel Ramp
- Centre for Compassionate Conservation, School of Life Sciences, University of Technology Sydney, Ultimo, Australia
| | - Matt Davis
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of Biology, Aarhus University, Aarhus, Denmark
- Section for Ecoinformatics and Biodiversity, Department of Biology, Aarhus University, Aarhus, Denmark
- Natural History Museum of Los Angeles County, Los Angeles, CA, 90007, USA
| | | | - Jens-Christian Svenning
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of Biology, Aarhus University, Aarhus, Denmark
- Section for Ecoinformatics and Biodiversity, Department of Biology, Aarhus University, Aarhus, Denmark
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12
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Herrando-Pérez S. Bone need not remain an elephant in the room for radiocarbon dating. ROYAL SOCIETY OPEN SCIENCE 2021; 8:201351. [PMID: 33614076 PMCID: PMC7890471 DOI: 10.1098/rsos.201351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 12/08/2020] [Indexed: 06/12/2023]
Abstract
Radiocarbon (14C) analysis of skeletal remains by accelerator mass spectrometry is an essential tool in multiple branches of science. However, bone 14C dating results can be inconsistent and not comparable due to disparate laboratory pretreatment protocols that remove contamination. And, pretreatments are rarely discussed or reported by end-users, making it an 'elephant in the room' for Quaternary scientists. Through a questionnaire survey, I quantified consensus on the reliability of collagen pretreatments for 14C dating across 132 experts (25 countries). I discovered that while more than 95% of the audience was wary of contamination and would avoid gelatinization alone (minimum pretreatment used by most 14C facilities), 52% asked laboratories to choose the pretreatment method for them, and 58% could not rank the reliability of at least one pretreatment. Ultrafiltration was highly popular, and purification by XAD resins seemed restricted to American researchers. Isolating and dating the amino acid hydroxyproline was perceived as the most reliable pretreatment, but is expensive, time-consuming and not widely available. Solid evidence supports that only molecular-level dating accommodates all known bone contaminants and guarantees complete removal of humic and fulvic acids and conservation substances, with three key areas of progress: (i) innovation and more funded research is required to develop affordable analytical chemistry that can handle low-mass samples of collagen amino acids, (ii) a certification agency overseeing dating-quality control is needed to enhance methodological reproducibility and dating accuracy among laboratories, and (iii) more cross-disciplinary work with better 14C reporting etiquette will promote the integration of 14C dating across disciplines. Those developments could conclude long-standing debates based on low-accuracy data used to build chronologies for animal domestications, human/megafauna extirpations and migrations, archaeology, palaeoecology, palaeontology and palaeoclimate models.
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Bai B, Meng J, Zhang C, Gong YX, Wang YQ. The origin of Rhinocerotoidea and phylogeny of Ceratomorpha (Mammalia, Perissodactyla). Commun Biol 2020; 3:509. [PMID: 32929169 PMCID: PMC7490376 DOI: 10.1038/s42003-020-01205-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 08/04/2020] [Indexed: 11/09/2022] Open
Abstract
Rhinoceroses have been considered to have originated from tapiroids in the middle Eocene; however, the transition remains controversial, and the first unequivocal rhinocerotoids appeared about 4 Ma later than the earliest tapiroids of the Early Eocene. Here we describe 5 genera and 6 new species of rhinoceroses recently discovered from the early Eocene to the early middle Eocene deposits of the Erlian Basin of Inner Mongolia, China. These new materials represent the earliest members of rhinocerotoids, forstercooperiids, and/or hyrachyids, and bridge the evolutionary gap between the early Eocene ceratomorphs and middle Eocene rhinocerotoids. The phylogenetic analyses using parsimony and Bayesian inference methods support their affinities with rhinocerotoids, and also illuminate the phylogenetic relationships and biogeography of Ceratomorpha, although some discrepancies are present between the two criteria. The nearly contemporary occurrence of various rhinocerotoids indicates that the divergence of different rhinocerotoid groups occurred no later than the late early Eocene, which is soon after the split between the rhinocerotoids and the tapiroids in the early early Eocene. However, the Bayesian tip-dating estimate suggests that the divergence of different ceratomorph groups occurred in the middle Paleocene.
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Affiliation(s)
- Bin Bai
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, 100044, China. .,CAS Center for Excellence in Life and Paleoenvironment, Beijing, 100044, China.
| | - Jin Meng
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, 100044, China.,Division of Paleontology, American Museum of Natural History, New York, NY, 10024, USA.,Earth and Environmental Sciences, Graduate Center, City University of New York, New York, NY, 10016, USA
| | - Chi Zhang
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, 100044, China.,CAS Center for Excellence in Life and Paleoenvironment, Beijing, 100044, China
| | - Yan-Xin Gong
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, 100044, China.,CAS Center for Excellence in Life and Paleoenvironment, Beijing, 100044, China.,College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuan-Qing Wang
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, 100044, China. .,CAS Center for Excellence in Life and Paleoenvironment, Beijing, 100044, China. .,College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
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14
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Heavy reliance on plants for Romanian cave bears evidenced by amino acid nitrogen isotope analysis. Sci Rep 2020; 10:6612. [PMID: 32313007 PMCID: PMC7170912 DOI: 10.1038/s41598-020-62990-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 03/19/2020] [Indexed: 12/13/2022] Open
Abstract
Heavy reliance on plants is rare in Carnivora and mostly limited to relatively small species in subtropical settings. The feeding behaviors of extinct cave bears living during Pleistocene cold periods at middle latitudes have been intensely studied using various approaches including isotopic analyses of fossil collagen. In contrast to cave bears from all other regions in Europe, some individuals from Romania show exceptionally high δ15N values that might be indicative of meat consumption. Herbivory on plants with high δ15N values cannot be ruled out based on this method, however. Here we apply an approach using the δ15N values of individual amino acids from collagen that offsets the baseline δ15N variation among environments. The analysis yielded strong signals of reliance on plants for Romanian cave bears based on the δ15N values of glutamate and phenylalanine. These results could suggest that the high variability in bulk collagen δ15N values observed among cave bears in Romania reflects niche partitioning but in a general trophic context of herbivory.
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Abstract
Single-compound analysis of stable or radioactive isotopes has found application in a number of fields ranging from archaeology to forensics. Often, the most difficult part of these analyses is the development of a method for isolating the compound(s) of interest, which can derive from a wide range of sample types including the hair, nails, and bone.Here we describe three complementary preparative HPLC techniques suitable for separating and isolating amino acids from bone collagen and hair keratin. Using preparative reversed-phase, ion-pair, or mixed-mode chromatography in aqueous carbon-free mobile phases, or those from which carbon can easily be removed, underivatized single amino acids can be isolated and further analyzed using mass spectrometric techniques.
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16
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Margaryan A, Sinding MHS, Liu S, Vieira FG, Chan YL, Nathan SKSS, Moodley Y, Bruford MW, Gilbert MTP. Recent mitochondrial lineage extinction in the critically endangered Javan rhinoceros. Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Abstract
The Javan rhinoceros (Rhinoceros sondaicus) is one of five extant rhinoceros species and among the rarest large mammals on Earth. Once widespread across Southeast Asia, it is now on the verge of extinction, with only one wild population remaining (estimated at ~60 individuals) on the island of Java, Indonesia. To assess the past genetic diversity of the female lineage of R. sondaicus, we generated mitochondrial genome data from eight museum specimens dating back to the 19th century, before the range of the Javan rhinoceros was dramatically reduced, for comparison against mitochondrial DNA (mtDNA) sequences of current R. sondaicus and other rhinoceros species. We succeeded in reconstructing five full and three partial ancient mitogenomes from the eight samples. We used BEAST to assess the phylogenetic relationship of the five extant rhinoceros species and the historical samples. The results show that the oldest and most diverse mtDNA lineages of R. sondaicus are found in historical samples, indicating a significant reduction of mtDNA diversity in modern Javan rhinos. We anticipate that the newly sequenced data will represent a useful resource for improving our understanding of evolutionary history of this species, should future studies be able to increase the available dataset. We hope this information may help in conservation efforts for this species.
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Affiliation(s)
- Ashot Margaryan
- Section for Evolutionary Genomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- Institute of Molecular Biology, National Academy of Sciences, Yerevan, Armenia
| | - Mikkel-Holger S Sinding
- Section for Evolutionary Genomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- Greenland Institute of Natural Resources, Nuuk, Greenland
| | - Shanlin Liu
- Section for Evolutionary Genomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- BGI-Shenzhen, Shenzhen, China
| | - Filipe Garrett Vieira
- Section for Evolutionary Genomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Yvonne L Chan
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE, Sweden
| | | | - Yoshan Moodley
- Department of Zoology, University of Venda, Thohoyandou, Republic of South Africa
| | - Michael W Bruford
- School of Biosciences and Sustainable Places Institute, Cardiff University, Cardiff, UK
| | - M Thomas P Gilbert
- Section for Evolutionary Genomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- Norwegian University of Science and Technology, University Museum, Norway
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17
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Ballare KM, Pope NS, Castilla AR, Cusser S, Metz RP, Jha S. Utilizing field collected insects for next generation sequencing: Effects of sampling, storage, and DNA extraction methods. Ecol Evol 2019; 9:13690-13705. [PMID: 31938475 PMCID: PMC6953651 DOI: 10.1002/ece3.5756] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 08/20/2019] [Accepted: 09/15/2019] [Indexed: 01/04/2023] Open
Abstract
DNA sequencing technologies continue to advance the biological sciences, expanding opportunities for genomic studies of non-model organisms for basic and applied questions. Despite these opportunities, many next generation sequencing protocols have been developed assuming a substantial quantity of high molecular weight DNA (>100 ng), which can be difficult to obtain for many study systems. In particular, the ability to sequence field-collected specimens that exhibit varying levels of DNA degradation remains largely unexplored. In this study we investigate the influence of five traditional insect capture and curation methods on Double-Digest Restriction Enzyme Associated DNA (ddRAD) sequencing success for three wild bee species. We sequenced a total of 105 specimens (between 7-13 specimens per species and treatment). We additionally investigated how different DNA quality metrics (including pre-sequence concentration and contamination) predicted downstream sequencing success, and also compared two DNA extraction methods. We report successful library preparation for all specimens, with all treatments and extraction methods producing enough highly reliable loci for population genetic analyses. Although results varied between species, we found that specimens collected by net sampling directly into 100% EtOH, or by passive trapping followed by 100% EtOH storage before pinning tended to produce higher quality ddRAD assemblies, likely as a result of rapid specimen desiccation. Surprisingly, we found that specimens preserved in propylene glycol during field sampling exhibited lower-quality assemblies. We provide recommendations for each treatment, extraction method, and DNA quality assessment, and further encourage researchers to consider utilizing a wider variety of specimens for genomic analyses.
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Affiliation(s)
- Kimberly M. Ballare
- Department of Integrative BiologyThe University of Texas at AustinAustinTXUSA
- Present address:
Department of Ecology and Evolutionary BiologyUniversity of California Santa CruzSanta CruzCAUSA
| | - Nathaniel S. Pope
- Department of Integrative BiologyThe University of Texas at AustinAustinTXUSA
- Present address:
Department of EntomologyPennsylvania State UniversityUniversity ParkPAUSA
| | - Antonio R. Castilla
- Department of Integrative BiologyThe University of Texas at AustinAustinTXUSA
- Present address:
Centre for Applied Ecology “Prof. Baeta Neves”/INBIOInstitutoSuperior of AgronomyUniversity of LisbonLisbonPortugal
| | - Sarah Cusser
- Department of Integrative BiologyThe University of Texas at AustinAustinTXUSA
- Present address:
Kellogg Biological StationMichigan State UniversityHickory CornersMIUSA
| | - Richard P. Metz
- Genomics and Bioinformatics ServiceTexas A&M AgriLife ResearchCollege StationTXUSA
| | - Shalene Jha
- Department of Integrative BiologyThe University of Texas at AustinAustinTXUSA
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18
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Swift JA, Bunce M, Dortch J, Douglass K, Faith JT, Fellows Yates JA, Field J, Haberle SG, Jacob E, Johnson CN, Lindsey E, Lorenzen ED, Louys J, Miller G, Mychajliw AM, Slon V, Villavicencio NA, Waters MR, Welker F, Wood R, Petraglia M, Boivin N, Roberts P. Micro Methods for Megafauna: Novel Approaches to Late Quaternary Extinctions and Their Contributions to Faunal Conservation in the Anthropocene. Bioscience 2019; 69:877-887. [PMID: 31719710 PMCID: PMC6829010 DOI: 10.1093/biosci/biz105] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Drivers of Late Quaternary megafaunal extinctions are relevant to modern conservation policy in a world of growing human population density, climate change, and faunal decline. Traditional debates tend toward global solutions, blaming either dramatic climate change or dispersals of Homo sapiens to new regions. Inherent limitations to archaeological and paleontological data sets often require reliance on scant, poorly resolved lines of evidence. However, recent developments in scientific technologies allow for more local, context-specific approaches. In the present article, we highlight how developments in five such methodologies (radiocarbon approaches, stable isotope analysis, ancient DNA, ancient proteomics, microscopy) have helped drive detailed analysis of specific megafaunal species, their particular ecological settings, and responses to new competitors or predators, climate change, and other external phenomena. The detailed case studies of faunal community composition, extinction chronologies, and demographic trends enabled by these methods examine megafaunal extinctions at scales appropriate for practical understanding of threats against particular species in their habitats today.
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Affiliation(s)
- Jillian A Swift
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
- Anthropology Department of Bernice Pauahi Bishop Museum, Honolulu, Hawai’i
| | - Michael Bunce
- Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Joe Dortch
- Centre for Rock Art Research and Management, University of Western Australia, Perth, Australia
| | - Kristina Douglass
- Department of Anthropology and with the Institutes for Energy and the Environment, The Pennsylvania State University, State College, Pennsylvania
| | - J Tyler Faith
- Natural History Museum of Utah and with the Department of Anthropology, University of Utah, Salt Lake City, Utah
| | - James A Fellows Yates
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Judith Field
- School of Biological, Earth, and Environmental Science, University of New South Wales, Sydney, Australia
| | - Simon G Haberle
- College of Asia and the Pacific and the School of Culture, History, and Language, Australian National University, Canberra, Australia
- Australian Research Council Centre of Excellence, Australian Biodiversity and Heritage, Wollongong, New South Wales, Australia
| | - Eileen Jacob
- Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, England
| | - Chris N Johnson
- Australian Research Council Centre of Excellence, Australian Biodiversity and Heritage, Wollongong, New South Wales, Australia
- School of Natural Sciences, University of Tasmania, Hobart, Australia
| | - Emily Lindsey
- La Brea Tar Pits and Museum, part of the Natural History Museum, Los Angeles County, Los Angeles, California
| | - Eline D Lorenzen
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Julien Louys
- Australian Research Center for Human Evolution, Environmental Futures Research Institute, Griffith University, Brisbane, Queensland, Australia
| | - Gifford Miller
- INSTAAR and Department of Geological Sciences, University of Colorado, Boulder
| | - Alexis M Mychajliw
- La Brea Tar Pits and Museum, part of the Natural History Museum, Los Angeles County, Los Angeles, California
| | - Viviane Slon
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Natalia A Villavicencio
- Departamento de Ecología, in the Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Instituto de Ecología and Biodiversidad, Santiago, Chile
| | - Michael R Waters
- Center for the Study of the First Americans, the Department of Anthropology, Texas A&M University, College Station, Texas
| | - Frido Welker
- Evolutionary Genomics Section of the GLOBE Institute, University of Copenhagen, Copenhagen, Denmark, and with the Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Rachel Wood
- Research School of Earth Sciences, Australian National University, Canberra, Australia
| | - Michael Petraglia
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Nicole Boivin
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Patrick Roberts
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
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19
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Lord E, Pathmanathan JS, Corel E, Makarenkov V, Lopez P, Bouchard F, Bhattacharya D, Antoine PO, Le Guyader H, Lapointe FJ, Bapteste E. Introducing Trait Networks to Elucidate the Fluidity of Organismal Evolution Using Palaeontological Data. Genome Biol Evol 2019; 11:2653-2665. [PMID: 31504500 PMCID: PMC6761957 DOI: 10.1093/gbe/evz182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/03/2019] [Indexed: 11/25/2022] Open
Abstract
Explaining the evolution of animals requires ecological, developmental, paleontological, and phylogenetic considerations because organismal traits are affected by complex evolutionary processes. Modeling a plurality of processes, operating at distinct time-scales on potentially interdependent traits, can benefit from approaches that are complementary treatments to phylogenetics. Here, we developed an inclusive network approach, implemented in the command line software ComponentGrapher, and analyzed trait co-occurrence of rhinocerotoid mammals. We identified stable, unstable, and pivotal traits, as well as traits contributing to complexes, that may follow to a common developmental regulation, that point to an early implementation of the postcranial Bauplan among rhinocerotoids. Strikingly, most identified traits are highly dissociable, used repeatedly in distinct combinations and in different taxa, which usually do not form clades. Therefore, the genes encoding these traits are likely recruited into novel gene regulation networks during the course of evolution. Our evo-systemic framework, generalizable to other evolved organizations, supports a pluralistic modeling of organismal evolution, including trees and networks.
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Affiliation(s)
- Etienne Lord
- Département d'informatique, Université du Québec à Montréal, Montréal, Québec, Canada
- Département de sciences biologiques, Université de Montréal, Montréal, Québec, Canada
| | - Jananan S Pathmanathan
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, Paris, France
| | - Eduardo Corel
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, Paris, France
| | - Vladimir Makarenkov
- Département d'informatique, Université du Québec à Montréal, Montréal, Québec, Canada
| | - Philippe Lopez
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, Paris, France
| | - Frédéric Bouchard
- Département de Philosophie, Université de Montreal, Montréal, Quebec, Canada
| | | | - Pierre-Olivier Antoine
- Institut des Sciences de l'Evolution, cc64, Université de Montpellier, CNRS, Université des Antilles, IRD, EPHE, Montpellier, France
| | - Hervé Le Guyader
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, Paris, France
| | - François-Joseph Lapointe
- Département de sciences biologiques, Université de Montréal, Montréal, Québec, Canada
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, Paris, France
| | - Eric Bapteste
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, Paris, France
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Palaeogenomics of the Hydrocarbon Producing Microalga Botryococcus braunii. Sci Rep 2019; 9:1776. [PMID: 30742038 PMCID: PMC6370823 DOI: 10.1038/s41598-018-38236-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 12/17/2018] [Indexed: 11/16/2022] Open
Abstract
Botryococcus braunii is a colonial microalga that appears early in the fossil record and is a sensitive proxy of environmental and hydroclimatic conditions. Palaeozoic Botryococcus fossils which contribute up to 90% of oil shales and approximately 1% of crude oil, co-localise with diagnostic geolipids from the degradation of source-signature hydrocarbons. However more recent Holocene sediments demonstrate no such association. Consequently, Botryococcus are identified in younger sediments by morphology alone, where potential misclassifications could lead to inaccurate paleoenvironmental reconstructions. Here we show that a combination of flow cytometry and ancient DNA (aDNA) sequencing can unambiguously identify Botryococcus microfossils in Holocene sediments with hitherto unparalleled accuracy and rapidity. The application of aDNA sequencing to microfossils offers a far-reaching opportunity for understanding environmental change in the recent geological record. When allied with other high-resolution palaeoenvironmental information such as aDNA sequencing of humans and megafauna, aDNA from microfossils may allow a deeper and more precise understanding of past environments, ecologies and migrations.
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Devièse T, Massilani D, Yi S, Comeskey D, Nagel S, Nickel B, Ribechini E, Lee J, Tseveendorj D, Gunchinsuren B, Meyer M, Pääbo S, Higham T. Compound-specific radiocarbon dating and mitochondrial DNA analysis of the Pleistocene hominin from Salkhit Mongolia. Nat Commun 2019; 10:274. [PMID: 30700710 PMCID: PMC6353915 DOI: 10.1038/s41467-018-08018-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 12/04/2018] [Indexed: 12/04/2022] Open
Abstract
A skullcap found in the Salkhit Valley in northeast Mongolia is, to our knowledge, the only Pleistocene hominin fossil found in the country. It was initially described as an individual with possible archaic affinities, but its ancestry has been debated since the discovery. Here, we determine the age of the Salkhit skull by compound-specific radiocarbon dating of hydroxyproline to 34,950-33,900 Cal. BP (at 95% probability), placing the Salkhit individual in the Early Upper Paleolithic period. We reconstruct the complete mitochondrial genome (mtDNA) of the specimen. It falls within a group of modern human mtDNAs (haplogroup N) that is widespread in Eurasia today. The results now place the specimen into its proper chronometric and biological context and allow us to begin integrating it with other evidence for the human occupation of this region during the Paleolithic, as well as wider Pleistocene sequences across Eurasia.
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Affiliation(s)
- Thibaut Devièse
- Oxford Radiocarbon Accelerator Unit, Research Laboratory for Archaeology and the History of Art, University of Oxford, Dyson Perrins Building, South Parks Road, Oxford, OX1 3QY, UK.
| | - Diyendo Massilani
- Max-Planck-Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103, Leipzig, Germany.
| | - Seonbok Yi
- Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul, 08826, Korea
| | - Daniel Comeskey
- Oxford Radiocarbon Accelerator Unit, Research Laboratory for Archaeology and the History of Art, University of Oxford, Dyson Perrins Building, South Parks Road, Oxford, OX1 3QY, UK
| | - Sarah Nagel
- Max-Planck-Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103, Leipzig, Germany
| | - Birgit Nickel
- Max-Planck-Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103, Leipzig, Germany
| | - Erika Ribechini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, Pisa, 56124, Italy
| | - Jungeun Lee
- Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul, 08826, Korea
| | - Damdinsuren Tseveendorj
- Institute of History and Archaeology, Mongolian Academy of Sciences, Jucov St 77, Ulaanbaatar, 13343, Mongolia
| | - Byambaa Gunchinsuren
- Institute of History and Archaeology, Mongolian Academy of Sciences, Jucov St 77, Ulaanbaatar, 13343, Mongolia
| | - Matthias Meyer
- Max-Planck-Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103, Leipzig, Germany
| | - Svante Pääbo
- Max-Planck-Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103, Leipzig, Germany
| | - Tom Higham
- Oxford Radiocarbon Accelerator Unit, Research Laboratory for Archaeology and the History of Art, University of Oxford, Dyson Perrins Building, South Parks Road, Oxford, OX1 3QY, UK
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