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Librado P, Tressières G, Chauvey L, Fages A, Khan N, Schiavinato S, Calvière-Tonasso L, Kusliy MA, Gaunitz C, Liu X, Wagner S, Der Sarkissian C, Seguin-Orlando A, Perdereau A, Aury JM, Southon J, Shapiro B, Bouchez O, Donnadieu C, Collin YRH, Gregersen KM, Jessen MD, Christensen K, Claudi-Hansen L, Pruvost M, Pucher E, Vulic H, Novak M, Rimpf A, Turk P, Reiter S, Brem G, Schwall C, Barrey É, Robert C, Degueurce C, Horwitz LK, Klassen L, Rasmussen U, Kveiborg J, Johannsen NN, Makowiecki D, Makarowicz P, Szeliga M, Ilchyshyn V, Rud V, Romaniszyn J, Mullin VE, Verdugo M, Bradley DG, Cardoso JL, Valente MJ, Telles Antunes M, Ameen C, Thomas R, Ludwig A, Marzullo M, Prato O, Bagnasco Gianni G, Tecchiati U, Granado J, Schlumbaum A, Deschler-Erb S, Mráz MS, Boulbes N, Gardeisen A, Mayer C, Döhle HJ, Vicze M, Kosintsev PA, Kyselý R, Peške L, O'Connor T, Ananyevskaya E, Shevnina I, Logvin A, Kovalev AA, Iderkhangai TO, Sablin MV, Dashkovskiy PK, Graphodatsky AS, Merts I, Merts V, Kasparov AK, Pitulko VV, Onar V, Öztan A, Arbuckle BS, McColl H, Renaud G, Khaskhanov R, Demidenko S, Kadieva A, Atabiev B, Sundqvist M, Lindgren G, López-Cachero FJ, Albizuri S, Trbojević Vukičević T, Rapan Papeša A, Burić M, Rajić Šikanjić P, Weinstock J, Asensio Vilaró D, Codina F, García Dalmau C, Morer de Llorens J, Pou J, de Prado G, Sanmartí J, Kallala N, Torres JR, Maraoui-Telmini B, Belarte Franco MC, Valenzuela-Lamas S, Zazzo A, Lepetz S, Duchesne S, Alexeev A, Bayarsaikhan J, Houle JL, Bayarkhuu N, Turbat T, Crubézy É, Shingiray I, Mashkour M, Berezina NY, Korobov DS, Belinskiy A, Kalmykov A, Demoule JP, Reinhold S, Hansen S, Wallner B, Roslyakova N, Kuznetsov PF, Tishkin AA, Wincker P, Kanne K, Outram A, Orlando L. Widespread horse-based mobility arose around 2200 BCE in Eurasia. Nature 2024; 631:819-825. [PMID: 38843826 PMCID: PMC11269178 DOI: 10.1038/s41586-024-07597-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 05/23/2024] [Indexed: 07/19/2024]
Abstract
Horses revolutionized human history with fast mobility1. However, the timeline between their domestication and their widespread integration as a means of transport remains contentious2-4. Here we assemble a collection of 475 ancient horse genomes to assess the period when these animals were first reshaped by human agency in Eurasia. We find that reproductive control of the modern domestic lineage emerged around 2200 BCE, through close-kin mating and shortened generation times. Reproductive control emerged following a severe domestication bottleneck starting no earlier than approximately 2700 BCE, and coincided with a sudden expansion across Eurasia that ultimately resulted in the replacement of nearly every local horse lineage. This expansion marked the rise of widespread horse-based mobility in human history, which refutes the commonly held narrative of large horse herds accompanying the massive migration of steppe peoples across Europe around 3000 BCE and earlier3,5. Finally, we detect significantly shortened generation times at Botai around 3500 BCE, a settlement from central Asia associated with corrals and a subsistence economy centred on horses6,7. This supports local horse husbandry before the rise of modern domestic bloodlines.
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Affiliation(s)
- Pablo Librado
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France.
- Institut de Biologia Evolutiva (CSIC - Universitat Pompeu Fabra), Barcelona, Spain.
| | - Gaetan Tressières
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
| | - Lorelei Chauvey
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
| | - Antoine Fages
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
- Zoological institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Naveed Khan
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
- Department of Biotechnology, Abdul Wali Khan University, Mardan, Pakistan
| | - Stéphanie Schiavinato
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
| | - Laure Calvière-Tonasso
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
| | - Mariya A Kusliy
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology, Novosibirsk, Russia
| | - Charleen Gaunitz
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Xuexue Liu
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
| | - Stefanie Wagner
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
- INRAE Division Ecology and Biodiversity (ECODIV), Plant Genomic Resources Center (CNRGV), Castanet Tolosan Cedex, France
| | - Clio Der Sarkissian
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
| | - Andaine Seguin-Orlando
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
| | - Aude Perdereau
- Genoscope, Institut de Biologie François Jacob, CEA, CNRS, Université d'Évry, Université Paris-Saclay, Évry, France
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université d'Évry, Université Paris-Saclay, Évry, France
| | - John Southon
- Department of Earth System Science, University of California, Irvine, CA, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | | | | | - Yvette Running Horse Collin
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
- Taku Skan Skan Wasakliyapi: Global Institute for Traditional Sciences, Rapid City, SD, USA
| | | | - Mads Dengsø Jessen
- Department for Prehistory Middle Ages and Renaissance, National Museum of Denmark, Copenhagen K, Denmark
| | | | | | - Mélanie Pruvost
- UMR 5199 De la Préhistoire à l'Actuel: Culture, Environnement et Anthropologie (PACEA), CNRS, Université de Bordeaux, Pessac Cédex, France
| | | | | | - Mario Novak
- Centre for Applied Bioanthropology, Institute for Anthropological Research, Zagreb, Croatia
| | | | - Peter Turk
- Narodni muzej Slovenije, Ljubljana, Slovenia
| | - Simone Reiter
- Institute of Animal Breeding and Genetics, Department of Biomedical Sciences, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Gottfried Brem
- Institute of Animal Breeding and Genetics, Department of Biomedical Sciences, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Christoph Schwall
- Leibniz-Zentrum für Archäologie (LEIZA), Mainz, Germany
- Department of Prehistory & Western Asian/Northeast African Archaeology, Austrian Archaeological Institute (OeAI), Austrian Academy of Sciences (OeAW), Vienna, Austria
| | - Éric Barrey
- Université Paris-Saclay, AgroParisTech, INRAE GABI UMR1313, Jouy-en-Josas, France
| | - Céline Robert
- Université Paris-Saclay, AgroParisTech, INRAE GABI UMR1313, Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d'Alfort, Maisons-Alfort, France
| | | | - Liora Kolska Horwitz
- National Natural History Collections, Edmond J. Safra Campus, Givat Ram, The Hebrew University, Jerusalem, Israel
| | | | - Uffe Rasmussen
- Department of Archaeology, Moesgaard Museum, Højbjerg, Denmark
| | - Jacob Kveiborg
- Department of Archaeological Science and Conservation, Moesgaard Museum, Højbjerg, Denmark
| | | | - Daniel Makowiecki
- Institute of Archaeology, Faculty of History, Nicolaus Copernicus University, Toruń, Poland
| | | | - Marcin Szeliga
- Institute of Archaeology, Maria Curie-Skłodowska University, Lublin, Poland
| | - Vasyl Ilchyshyn
- Kremenetsko-Pochaivskii Derzhavnyi Istoriko-arkhitekturnyi Zapovidnik, Kremenets, Ukraine
| | - Vitalii Rud
- Institute of Archaeology, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Jan Romaniszyn
- Faculty of Archaeology, Adam Mickiewicz University, Poznań, Poland
| | - Victoria E Mullin
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Marta Verdugo
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Daniel G Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - João L Cardoso
- ICArEHB, Campus de Gambelas, University of Algarve, Faro, Portugal
- Universidade Aberta, Lisbon, Portugal
| | - Maria J Valente
- Faculdade de Ciências Humanas e Sociais, Centro de Estudos de Arqueologia, Artes e Ciências do Património, Universidade do Algarve, Faro, Portugal
| | - Miguel Telles Antunes
- Centre for Research on Science and Geological Engineering, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Carly Ameen
- Department of Archaeology and History, University of Exeter, Exeter, UK
| | - Richard Thomas
- School of Archaeology and Ancient History, University of Leicester, Leicester, UK
| | - Arne Ludwig
- Department of Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research, Berlin, Germany
- Albrecht Daniel Thaer-Institute, Faculty of Life Sciences, Humboldt University Berlin, Berlin, Germany
| | - Matilde Marzullo
- Dipartimento di Beni Culturali e Ambientali, Università degli Studi di Milano, Milan, Italy
| | - Ornella Prato
- Dipartimento di Beni Culturali e Ambientali, Università degli Studi di Milano, Milan, Italy
| | | | - Umberto Tecchiati
- Dipartimento di Beni Culturali e Ambientali, Università degli Studi di Milano, Milan, Italy
| | - José Granado
- Department of Environmental Sciences, Integrative Prehistory and Archaeological Science, Basel University, Basel, Switzerland
| | - Angela Schlumbaum
- Department of Environmental Sciences, Integrative Prehistory and Archaeological Science, Basel University, Basel, Switzerland
| | - Sabine Deschler-Erb
- Department of Environmental Sciences, Integrative Prehistory and Archaeological Science, Basel University, Basel, Switzerland
| | - Monika Schernig Mráz
- Department of Environmental Sciences, Integrative Prehistory and Archaeological Science, Basel University, Basel, Switzerland
| | - Nicolas Boulbes
- Institut de Paléontologie Humaine, Fondation Albert Ier, Paris/UMR 7194 HNHP, MNHN-CNRS-UPVD/EPCC Centre Européen de Recherche Préhistorique, Tautavel, France
| | - Armelle Gardeisen
- Archéologie des Sociétés Méditeranéennes, Archimède IA-ANR-11-LABX-0032-01, CNRS UMR 5140, Université Paul Valéry, Montpellier, France
| | - Christian Mayer
- Department for Digitalization and Knowledge Transfer, Federal Monuments Authority Austria, Vienna, Austria
| | - Hans-Jürgen Döhle
- Landesamt für Denkmalpflege und Archäologie Sachsen-Anhalt - Landesmuseum für Vorgeschichte, Halle (Saale), Germany
| | - Magdolna Vicze
- National Institute of Archaeology, Hungarian National Museum, Budapest, Hungary
| | - Pavel A Kosintsev
- Paleoecology Laboratory, Institute of Plant and Animal Ecology, Ural Branch of the Russian Academy of Sciences, Ekaterinburg, Russia
- Department of History of the Institute of Humanities, Ural Federal University, Ekaterinburg, Russia
| | - René Kyselý
- Department of Natural Sciences and Archaeometry, Institute of Archaeology of the Czech Academy of Sciences, Prague, Czechia
| | | | | | - Elina Ananyevskaya
- Department of Archaeology, History Faculty, Vilnius University, Vilnius, Lithuania
| | - Irina Shevnina
- Laboratory for Archaeological Research, Akhmet Baitursynuly Kostanay Regional University, Kostanay, Kazakhstan
| | - Andrey Logvin
- Laboratory for Archaeological Research, Akhmet Baitursynuly Kostanay Regional University, Kostanay, Kazakhstan
| | - Alexey A Kovalev
- Department of Archaeological Heritage Preservation, Institute of Archaeology of the Russian Academy of Sciences, Moscow, Russia
| | - Tumur-Ochir Iderkhangai
- Department of Innovation and Technology, Ulaanbaatar Science and Technology Park, National University of Mongolia, Ulaanbaatar, Mongolia
| | - Mikhail V Sablin
- Zoological Institute, Russian Academy of Sciences, St Petersburg, Russia
| | - Petr K Dashkovskiy
- Department of Russian Regional Studies, National and State-confessional Relations, Altai State University, Barnaul, Russia
| | - Alexander S Graphodatsky
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology, Novosibirsk, Russia
| | - Ilia Merts
- Toraighyrov University, Joint Research Center for Archeological Studies, Pavlodar, Kazakhstan
- Department of Archaeology, Ethnography and Museology, Altai State University, Barnaul, Russia
| | - Viktor Merts
- Toraighyrov University, Joint Research Center for Archeological Studies, Pavlodar, Kazakhstan
| | - Aleksei K Kasparov
- Institute of the History of Material Culture, Russian Academy of Sciences, St. Petersburg, Russia
| | - Vladimir V Pitulko
- Institute of the History of Material Culture, Russian Academy of Sciences, St. Petersburg, Russia
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Sciences, St Petersburg, Russia
| | - Vedat Onar
- Osteoarchaeology Practice and Research Center and Department of Anatomy, Faculty of Veterinary Medicine, Istanbul University-Cerrahpaşa, Istanbul, Türkiye
| | - Aliye Öztan
- Archaeology Department, Ankara University, Ankara, Türkiye
| | - Benjamin S Arbuckle
- Department of Anthropology, Alumni Building, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Hugh McColl
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Gabriel Renaud
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
- Department of Health Technology, Section for Bioinformatics, Technical University of Denmark (DTU), Copenhagen, Denmark
| | - Ruslan Khaskhanov
- Kh. Ibragimov Complex Institute of the Russian Academy of Sciences (CI RAS), Grozny, Russia
| | - Sergey Demidenko
- Institute of Archaeology, Russian Academy of Sciences, Moscow, Russia
| | - Anna Kadieva
- Department of Archaeological Monuments, State Historical Museum, Moscow, Russian Federation
| | | | | | - Gabriella Lindgren
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Center for Animal Breeding and Genetics, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - F Javier López-Cachero
- Institut d'Arqueologia de la Universitat de Barcelona (IAUB), Seminari d'Estudis i Recerques Prehistoriques (SERP-UB), Universitat de Barcelona (UB), Barcelona, Spain
| | - Silvia Albizuri
- Institut d'Arqueologia de la Universitat de Barcelona (IAUB), Seminari d'Estudis i Recerques Prehistoriques (SERP-UB), Universitat de Barcelona (UB), Barcelona, Spain
| | - Tajana Trbojević Vukičević
- Department of Anatomy, Histology and Embryology, Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia
| | | | - Marcel Burić
- Department of Archaeology, Faculty of Humanities and Social Sciences, University of Zagreb, Zagreb, Croatia
| | | | - Jaco Weinstock
- Faculty of Arts and Humanities (Archaeology), University of Southampton, Southampton, UK
| | - David Asensio Vilaró
- Secció de Prehistòria i Arqueologia, IAUB Institut d'Arqueologia de la Universitat de Barcelona, Barcelona, Spain
| | - Ferran Codina
- C/Major, 20, Norfeu, Arqueologia Art i Patrimoni S.C., La Tallada d'Empordà, Spain
| | | | | | - Josep Pou
- Ajuntament de Calafell, Calafell (Tarragona), Spain
| | - Gabriel de Prado
- Museu d'Arqueologia de Catalunya (MAC-Ullastret), Ullastret, Spain
| | - Joan Sanmartí
- IEC-Institut d'Estudis Catalans (Union Académique Internationale), Barcelona, Spain
- Departament d'Història i Arqueologia, Facultat de Geografia i Història, Universitat de Barcelona, Barcelona, Spain
| | - Nabil Kallala
- Ecole Tunisienne d'Histoire et d'Anthropologie, Tunis, Tunisia
- University of Tunis, Institut National du Patrimoine, Tunis, Tunisia
| | | | | | - Maria-Carme Belarte Franco
- IEC-Institut d'Estudis Catalans (Union Académique Internationale), Barcelona, Spain
- ICREA, Catalan Institution for Research and Advanced Studies, Barcelona, Spain
- ICAC (Catalan Institute of Classical Archaeology), Tarragona, Spain
| | - Silvia Valenzuela-Lamas
- Archaeology of Social Dynamics (ASD), Institució Milà i Fontanals, Consejo Superior de Investigaciones Científicas (IMF-CSIC), Barcelona, Spain
- UNIARQ - Unidade de Arqueologia, Universidade de Lisboa, Alameda da Universidade, Lisboa, Portugal
| | - Antoine Zazzo
- Centre National de Recherche Scientifique, Muséum national d'Histoire naturelle, Archéozoologie, Archéobotanique (AASPE), CP 56, Paris, France
| | - Sébastien Lepetz
- Centre National de Recherche Scientifique, Muséum national d'Histoire naturelle, Archéozoologie, Archéobotanique (AASPE), CP 56, Paris, France
| | - Sylvie Duchesne
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
| | - Anatoly Alexeev
- Institute for Humanities Research and Indigenous Studies of the North (IHRISN), Yakutsk, Russia
| | - Jamsranjav Bayarsaikhan
- Max Planck Institute of Geoanthropology, Jena, Germany
- Institute of Archaeology, Mongolian Academy of Science, Ulaanbaatar, Mongolia
| | - Jean-Luc Houle
- Department of Folk Studies and Anthropology, Western Kentucky University, Bowling Green, KY, USA
| | - Noost Bayarkhuu
- Archaeological Research Center and Department of Anthropology and Archaeology, National University of Mongolia, Ulaanbaatar, Mongolia
| | - Tsagaan Turbat
- Archaeological Research Center and Department of Anthropology and Archaeology, National University of Mongolia, Ulaanbaatar, Mongolia
| | - Éric Crubézy
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
| | | | - Marjan Mashkour
- Centre National de Recherche Scientifique, Muséum national d'Histoire naturelle, Archéozoologie, Archéobotanique (AASPE), CP 56, Paris, France
- Central Laboratory, Bioarchaeology Laboratory, Archaeozoology section, University of Tehran, Tehran, Iran
| | - Natalia Ya Berezina
- Research Institute and Museum of Anthropology, Lomonosov Moscow State University, Moscow, Russia
| | - Dmitriy S Korobov
- Institute of Archaeology, Russian Academy of Sciences, Moscow, Russia
| | | | | | - Jean-Paul Demoule
- UMR du CNRS 8215 Trajectoires, Institut d'Art et Archéologie, Paris, France
| | - Sabine Reinhold
- Eurasia Department of the German Archaeological Institute, Berlin, Germany
| | - Svend Hansen
- Eurasia Department of the German Archaeological Institute, Berlin, Germany
| | - Barbara Wallner
- Institute of Animal Breeding and Genetics, Department of Biomedical Sciences, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Natalia Roslyakova
- Department of Russian History and Archaeology, Samara State University of Social Sciences and Education, Samara, Russia
| | - Pavel F Kuznetsov
- Department of Russian History and Archaeology, Samara State University of Social Sciences and Education, Samara, Russia
| | - Alexey A Tishkin
- Department of Archaeology, Ethnography and Museology, Altai State University, Barnaul, Russia
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université d'Évry, Université Paris-Saclay, Évry, France
| | - Katherine Kanne
- Department of Archaeology and History, University of Exeter, Exeter, UK
- School of Archaeology, University College Dublin, Dublin, Ireland
| | - Alan Outram
- Department of Archaeology and History, University of Exeter, Exeter, UK
| | - Ludovic Orlando
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France.
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2
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Billenstein RJ, Höhna S. Comparison of Bayesian Coalescent Skyline Plot Models for Inferring Demographic Histories. Mol Biol Evol 2024; 41:msae073. [PMID: 38630635 PMCID: PMC11068272 DOI: 10.1093/molbev/msae073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 02/16/2024] [Accepted: 04/01/2024] [Indexed: 04/19/2024] Open
Abstract
Bayesian coalescent skyline plot models are widely used to infer demographic histories. The first (non-Bayesian) coalescent skyline plot model assumed a known genealogy as data, while subsequent models and implementations jointly inferred the genealogy and demographic history from sequence data, including heterochronous samples. Overall, there exist multiple different Bayesian coalescent skyline plot models which mainly differ in two key aspects: (i) how changes in population size are modeled through independent or autocorrelated prior distributions, and (ii) how many change-points in the demographic history are used, where they occur and if the number is pre-specified or inferred. The specific impact of each of these choices on the inferred demographic history is not known because of two reasons: first, not all models are implemented in the same software, and second, each model implementation makes specific choices that the biologist cannot influence. To facilitate a detailed evaluation of Bayesian coalescent skyline plot models, we implemented all currently described models in a flexible design into the software RevBayes. Furthermore, we evaluated models and choices on an empirical dataset of horses supplemented by a small simulation study. We find that estimated demographic histories can be grouped broadly into two groups depending on how change-points in the demographic history are specified (either independent of or at coalescent events). Our simulations suggest that models using change-points at coalescent events produce spurious variation near the present, while most models using independent change-points tend to over-smooth the inferred demographic history.
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Affiliation(s)
- Ronja J Billenstein
- GeoBio-Center, Ludwig-Maximilians-Universität München, Munich 80333, Germany
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Munich 80333, Germany
| | - Sebastian Höhna
- GeoBio-Center, Ludwig-Maximilians-Universität München, Munich 80333, Germany
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Munich 80333, Germany
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3
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Musiał AD, Ropka-Molik K, Stefaniuk-Szmukier M, Myćka G, Bieniek A, Yasynetska N. Characteristic of Przewalski horses population from Askania-Nova reserve based on genetic markers. Mol Biol Rep 2023; 50:7121-7126. [PMID: 37365410 PMCID: PMC10374732 DOI: 10.1007/s11033-023-08581-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 06/02/2023] [Indexed: 06/28/2023]
Abstract
Przewalski horses are considered the last living population of wild horses, however, they are secondarily feral offspring of herds domesticated ~ 5000 years ago by the Botai culture. After Przewalski horses were almost extinct at the beginning of the twentieth century, their population is about 2500 individuals worldwide, with one of the largest breeding centers in Askania-Nova Biosphere Reserve (Ukraine). The research aimed to establish the maternal variation of Przewalski horses population maintained in Askania-Nova Reserve based on mitochondrial DNA hypervariable 1 and hypervariable 2 regions profiling, as well as, analysis of Y chromosome single nucleotide polymorphism unique for Przewalski horses, and coat color markers: MC1R and TBX3. The mtDNA hypervariable regions analysis in 23 Przewalski horses allowed assigning them to three distinctly different haplotypes, showing the greatest similarity to the Equus caballus reference, the Equus przewalskii reference, and to extinct species-Haringtonhippus. The Y chromosome analysis using fluorescently labelled assays differentiated horses in terms of polymorphism (g731821T>C) characteristic of Equus przewalskii. All male individuals presented genotype C characteristics for Przewalski horses. The polymorphisms within the coat color genes indicated only native, wild genotypes. The Y chromosome and coat color analysis denied admixtures of the tested horses with other Equidae.
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Affiliation(s)
- Adrianna D Musiał
- Department of Animal Molecular Biology, National Research Institute of Animal Production, 32-083, Balice, Poland.
| | - Katarzyna Ropka-Molik
- Department of Animal Molecular Biology, National Research Institute of Animal Production, 32-083, Balice, Poland
| | - Monika Stefaniuk-Szmukier
- Department of Animal Molecular Biology, National Research Institute of Animal Production, 32-083, Balice, Poland
| | - Grzegorz Myćka
- Department of Animal Molecular Biology, National Research Institute of Animal Production, 32-083, Balice, Poland
| | - Agnieszka Bieniek
- Department of Animal Molecular Biology, National Research Institute of Animal Production, 32-083, Balice, Poland
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4
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Batcher K, Varney S, Raudsepp T, Jevit M, Dickinson P, Jagannathan V, Leeb T, Bannasch D. Ancient segmentally duplicated LCORL retrocopies in equids. PLoS One 2023; 18:e0286861. [PMID: 37289743 PMCID: PMC10249811 DOI: 10.1371/journal.pone.0286861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 05/25/2023] [Indexed: 06/10/2023] Open
Abstract
LINE-1 is an active transposable element encoding proteins capable of inserting host gene retrocopies, resulting in retro-copy number variants (retroCNVs) between individuals. Here, we performed retroCNV discovery using 86 equids and identified 437 retrocopy insertions. Only 5 retroCNVs were shared between horses and other equids, indicating that the majority of retroCNVs inserted after the species diverged. A large number (17-35 copies) of segmentally duplicated Ligand Dependent Nuclear Receptor Corepressor Like (LCORL) retrocopies were present in all equids but absent from other extant perissodactyls. The majority of LCORL transcripts in horses and donkeys originate from the retrocopies. The initial LCORL retrotransposition occurred 18 million years ago (17-19 95% CI), which is coincident with the increase in body size, reduction in digit number, and changes in dentition that characterized equid evolution. Evolutionary conservation of the LCORL retrocopy segmental amplification in the Equidae family, high expression levels and the ancient timeline for LCORL retrotransposition support a functional role for this structural variant.
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Affiliation(s)
- Kevin Batcher
- Department of Population Health and Reproduction, University of California Davis, Davis, CA, United States of America
| | - Scarlett Varney
- Department of Population Health and Reproduction, University of California Davis, Davis, CA, United States of America
| | - Terje Raudsepp
- Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Matthew Jevit
- Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Peter Dickinson
- Department of Surgical and Radiological Sciences, University of California Davis, Davis, CA, United States of America
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Danika Bannasch
- Department of Population Health and Reproduction, University of California Davis, Davis, CA, United States of America
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5
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Tsai CL, Lu CN, Tzeng HY, Krafsur ES, Tu WC, Yeh WB. Global population genetic structure and lineage differentiation of the stable fly, Stomoxys calcitrans. MEDICAL AND VETERINARY ENTOMOLOGY 2023; 37:371-380. [PMID: 36734022 DOI: 10.1111/mve.12637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 12/15/2022] [Indexed: 05/18/2023]
Abstract
The bloodsucking fly, Stomoxys calcitrans (Diptera: Muscidae), is a cosmopolitan pest that transmits potential pathogens mechanically. We conduct phylogeographic analyses of S. calcitrans to resolve its global population genetic structure for establishing baseline of molecular studies. Results from mitochondrial gene suggested that the major divergence of S. calcitrans predominantly occurred 0.32-0.47 million years ago (Mya) and the subsequent diversifications took place during 0.13-0.27 Mya. The Ethiopian region was deduced as the most likely origin of S. calcitrans and the Nearctic lineages were considered to have originated from Oriental or Palaearctic regions. Our results further revealed that each biogeographic region of S. calcitrans likely maintains its genetic specialty, and yet, those non-monophyletic relationships were possibly caused by ancestral retention, dispersal with mammals, long-distance migration, and the international livestock industries. Moreover, the three highly diverged Ethiopian lineages may be putative cryptic species that require clarification of their veterinary importance. Unravelling the genetic structure of stable fly and preventing gene flow among biogeographic regions through anthropogenic activities are thus pivotal in livestock industry administration, particularly genetic exchange among differentiated lineages that might lead to the consequence of ecological trait alterations.
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Affiliation(s)
- Cheng-Lung Tsai
- Department of Entomology, National Chung Hsing University, Taichung City, Taiwan
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung City, Taiwan
| | - Chia-Ning Lu
- Department of Entomology, National Chung Hsing University, Taichung City, Taiwan
| | - Hau-You Tzeng
- Department of Entomology, National Chung Hsing University, Taichung City, Taiwan
| | - Elliot S Krafsur
- Department of Entomology, Iowa State University, Ames, Iowa, USA
| | - Wu-Chun Tu
- Department of Entomology, National Chung Hsing University, Taichung City, Taiwan
| | - Wen-Bin Yeh
- Department of Entomology, National Chung Hsing University, Taichung City, Taiwan
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6
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Yurchenko AA, Naumenko AN, Artemov GN, Karagodin DA, Hodge JM, Velichevskaya AI, Kokhanenko AA, Bondarenko SM, Abai MR, Kamali M, Gordeev MI, Moskaev AV, Caputo B, Aghayan SA, Baricheva EM, Stegniy VN, Sharakhova MV, Sharakhov IV. Phylogenomics revealed migration routes and adaptive radiation timing of Holarctic malaria mosquito species of the Maculipennis Group. BMC Biol 2023; 21:63. [PMID: 37032389 PMCID: PMC10084679 DOI: 10.1186/s12915-023-01538-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 02/08/2023] [Indexed: 04/11/2023] Open
Abstract
BACKGROUND Phylogenetic analyses of closely related species of mosquitoes are important for better understanding the evolution of traits contributing to transmission of vector-borne diseases. Six out of 41 dominant malaria vectors of the genus Anopheles in the world belong to the Maculipennis Group, which is subdivided into two Nearctic subgroups (Freeborni and Quadrimaculatus) and one Palearctic (Maculipennis) subgroup. Although previous studies considered the Nearctic subgroups as ancestral, details about their relationship with the Palearctic subgroup, and their migration times and routes from North America to Eurasia remain controversial. The Palearctic species An. beklemishevi is currently included in the Nearctic Quadrimaculatus subgroup adding to the uncertainties in mosquito systematics. RESULTS To reconstruct historic relationships in the Maculipennis Group, we conducted a phylogenomic analysis of 11 Palearctic and 2 Nearctic species based on sequences of 1271 orthologous genes. The analysis indicated that the Palearctic species An. beklemishevi clusters together with other Eurasian species and represents a basal lineage among them. Also, An. beklemishevi is related more closely to An. freeborni, which inhabits the Western United States, rather than to An. quadrimaculatus, a species from the Eastern United States. The time-calibrated tree suggests a migration of mosquitoes in the Maculipennis Group from North America to Eurasia about 20-25 million years ago through the Bering Land Bridge. A Hybridcheck analysis demonstrated highly significant signatures of introgression events between allopatric species An. labranchiae and An. beklemishevi. The analysis also identified ancestral introgression events between An. sacharovi and its Nearctic relative An. freeborni despite their current geographic isolation. The reconstructed phylogeny suggests that vector competence and the ability to enter complete diapause during winter evolved independently in different lineages of the Maculipennis Group. CONCLUSIONS Our phylogenomic analyses reveal migration routes and adaptive radiation timing of Holarctic malaria vectors and strongly support the inclusion of An. beklemishevi into the Maculipennis Subgroup. Detailed knowledge of the evolutionary history of the Maculipennis Subgroup provides a framework for examining the genomic changes related to ecological adaptation and susceptibility to human pathogens. These genomic variations may inform researchers about similar changes in the future providing insights into the patterns of disease transmission in Eurasia.
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Affiliation(s)
- Andrey A Yurchenko
- Department of Entomology, the Fralin Life Sciences Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
- Kurchatov Genomics Center, the Federal Research Center, Institute of Cytology and Genetics, Novosibirsk, Russia
- Current Address: INSERM U981, Gustave Roussy Institute, Université Paris-Saclay, Villejuif, France
| | - Anastasia N Naumenko
- Department of Entomology, the Fralin Life Sciences Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Gleb N Artemov
- Department of Genetics and Cell Biology and the Laboratory of Ecology, Genetics and Environmental Protection, Tomsk State University, Tomsk, Russia
| | - Dmitry A Karagodin
- Laboratory of Cell Differentiation Mechanisms, the Federal Research Center, Institute of Cytology and Genetics, Novosibirsk, Russia
| | - James M Hodge
- Department of Entomology, the Fralin Life Sciences Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Alena I Velichevskaya
- Department of Genetics and Cell Biology and the Laboratory of Ecology, Genetics and Environmental Protection, Tomsk State University, Tomsk, Russia
| | - Alina A Kokhanenko
- Department of Genetics and Cell Biology and the Laboratory of Ecology, Genetics and Environmental Protection, Tomsk State University, Tomsk, Russia
| | - Semen M Bondarenko
- Department of Entomology, the Fralin Life Sciences Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
- Department of Genetics and Cell Biology and the Laboratory of Ecology, Genetics and Environmental Protection, Tomsk State University, Tomsk, Russia
| | - Mohammad R Abai
- Department of Medical Entomology and Vector Control, Tehran University of Medical Sciences, Tehran, Iran
| | - Maryam Kamali
- Department of Medical Entomology and Parasitology, Tarbiat Modares University, Tehran, Iran
| | - Mikhail I Gordeev
- Department of General Biology and Ecology, State University of Education, Mytishchi, Russia
| | - Anton V Moskaev
- Department of General Biology and Ecology, State University of Education, Mytishchi, Russia
| | - Beniamino Caputo
- Dipartimento Di Sanità Pubblica E Malattie Infettive, Università Sapienza, Rome, Italy
| | - Sargis A Aghayan
- Scientific Center of Zoology and Hydroecology, National Academy of Sciences of the Republic of Armenia, Yerevan, Armenia
- Department of Zoology, Yerevan State University, Yerevan, Armenia
| | - Elina M Baricheva
- Laboratory of Cell Differentiation Mechanisms, the Federal Research Center, Institute of Cytology and Genetics, Novosibirsk, Russia
| | - Vladimir N Stegniy
- Department of Genetics and Cell Biology and the Laboratory of Ecology, Genetics and Environmental Protection, Tomsk State University, Tomsk, Russia
| | - Maria V Sharakhova
- Department of Entomology, the Fralin Life Sciences Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA.
- Laboratory of Cell Differentiation Mechanisms, the Federal Research Center, Institute of Cytology and Genetics, Novosibirsk, Russia.
| | - Igor V Sharakhov
- Department of Entomology, the Fralin Life Sciences Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA.
- Department of Genetics and Cell Biology and the Laboratory of Ecology, Genetics and Environmental Protection, Tomsk State University, Tomsk, Russia.
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7
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DNA methylation-based profiling of horse archaeological remains for age-at-death and castration. iScience 2023; 26:106144. [PMID: 36843848 PMCID: PMC9950528 DOI: 10.1016/j.isci.2023.106144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 01/02/2023] [Accepted: 02/01/2023] [Indexed: 02/07/2023] Open
Abstract
Age profiling of archaeological bone assemblages can inform on past animal management practices, but is limited by the fragmentary nature of the fossil record and the lack of universal skeletal markers for age. DNA methylation clocks offer new, albeit challenging, alternatives for estimating the age-at-death of ancient individuals. Here, we take advantage of the availability of a DNA methylation clock based on 31,836 CpG sites and dental age markers in horses to assess age predictions in 84 ancient remains. We evaluate our approach using whole-genome sequencing data and develop a capture assay providing reliable estimates for only a fraction of the cost. We also leverage DNA methylation patterns to assess castration practice in the past. Our work opens for a deeper characterization of past husbandry and ritual practices and holds the potential to reveal age mortality profiles in ancient societies, once extended to human remains.
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8
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Gaughran SJ, vonHoldt B. Pleistocene parades of carnivores into North America. Mol Ecol 2022; 31:6387-6389. [PMID: 36373266 DOI: 10.1111/mec.16783] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022]
Abstract
The distribution and movement of species, broadly known as biogeography, is one of the fundamental subfields of ecology and evolutionary biology. However, significant mysteries remain about the processes that gave rise to the modern distribution of biodiversity across the globe. Over the last several decades, the genetic study of ancient and subfossil specimens has started to shed light on past migrations of some species, with a particular focus on humans and megafauna. In this issue of Molecular Ecology, Salis et al. (2021) use ancient mitogenomes and a new phylogeographic method to add an important new piece of evidence to the mystery of megafaunal migrations into North America during the Pleistocene. They found a striking synchronicity of brown bear (Ursus arctos) and lion (Panthera spp.) migrations across the Bering Land Bridge at several time points during the late Pleistocene, which highlights the lasting impact of sea level change on the prehistoric and modern dispersal of terrestrial carnivores across continents.
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Affiliation(s)
- Stephen J Gaughran
- Department of Ecology & Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
| | - Bridgett vonHoldt
- Department of Ecology & Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
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9
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Salis AT, Bray SCE, Lee MSY, Heiniger H, Barnett R, Burns JA, Doronichev V, Fedje D, Golovanova L, Harington CR, Hockett B, Kosintsev P, Lai X, Mackie Q, Vasiliev S, Weinstock J, Yamaguchi N, Meachen JA, Cooper A, Mitchell KJ. Lions and brown bears colonized North America in multiple synchronous waves of dispersal across the Bering Land Bridge. Mol Ecol 2022; 31:6407-6421. [PMID: 34748674 DOI: 10.1111/mec.16267] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 10/15/2021] [Accepted: 10/25/2021] [Indexed: 01/13/2023]
Abstract
The Bering Land Bridge connecting North America and Eurasia was periodically exposed and inundated by oscillating sea levels during the Pleistocene glacial cycles. This land connection allowed the intermittent dispersal of animals, including humans, between Western Beringia (far northeast Asia) and Eastern Beringia (northwest North America), changing the faunal community composition of both continents. The Pleistocene glacial cycles also had profound impacts on temperature, precipitation and vegetation, impacting faunal community structure and demography. While these palaeoenvironmental impacts have been studied in many large herbivores from Beringia (e.g., bison, mammoths, horses), the Pleistocene population dynamics of the diverse guild of carnivorans present in the region are less well understood, due to their lower abundances. In this study, we analyse mitochondrial genome data from ancient brown bears (Ursus arctos; n = 103) and lions (Panthera spp.; n = 39), two megafaunal carnivorans that dispersed into North America during the Pleistocene. Our results reveal striking synchronicity in the population dynamics of Beringian lions and brown bears, with multiple waves of dispersal across the Bering Land Bridge coinciding with glacial periods of low sea levels, as well as synchronous local extinctions in Eastern Beringia during Marine Isotope Stage 3. The evolutionary histories of these two taxa underline the crucial biogeographical role of the Bering Land Bridge in the distribution, turnover and maintenance of megafaunal populations in North America.
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Affiliation(s)
- Alexander T Salis
- Australian Centre for Ancient DNA (ACAD), School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia.,Division of Vertebrate Zoology, American Museum of Natural History, New York, New York, USA
| | - Sarah C E Bray
- Australian Centre for Ancient DNA (ACAD), School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia.,Registry of Senior Australians (ROSA), South Australian Health and Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia
| | - Michael S Y Lee
- College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia.,South Australian Museum, Adelaide, South Australia, Australia
| | - Holly Heiniger
- Australian Centre for Ancient DNA (ACAD), School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Ross Barnett
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - James A Burns
- Curator Emeritus, Royal Alberta Museum, Edmonton, Alberta, Canada
| | | | - Daryl Fedje
- Department of Anthropology, University of Victoria, Victoria, B.C, Canada
| | | | - C Richard Harington
- Curator Emeritus and Research Associate, Research Division (Paleobiology), Canadian Museum of Nature, Ottawa, Canada
| | - Bryan Hockett
- US Department of Interior, Bureau of Land Management, Nevada State Office, Reno, Nevada, USA
| | - Pavel Kosintsev
- Institute of Plant and Animal Ecology, Ural Branch of the Russian Academy of Sciences, Yekaterinburg, Russia.,Department of History, Ural Federal University, Yekaterinburg, Russia
| | - Xulong Lai
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, Hubei, China
| | - Quentin Mackie
- Department of Anthropology, University of Victoria, Victoria, B.C, Canada
| | - Sergei Vasiliev
- Institute of Archaeology and Ethnography, Russian Academy of Sciences, Russia
| | - Jacobo Weinstock
- Faculty of Humanities (Archaeology), University of Southampton, UK
| | - Nobuyuki Yamaguchi
- Institute of Tropical Biodiversity and Sustainable Development, University Malaysia Terengganu, Kuala Nerus, Malaysia
| | - Julie A Meachen
- Anatomy Department, Des Moines University, Des Moines, Iowa, USA
| | - Alan Cooper
- South Australian Museum, Adelaide, South Australia, Australia
| | - Kieren J Mitchell
- Australian Centre for Ancient DNA (ACAD), School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia.,Department of Zoology, Otago Palaeogenetics Laboratory, University of Otago, Dunedin, New Zealand
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10
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Wiens BJ, Combe FJ, Dickerson B, Divine LM, Padula VM, Sage GK, Talbot SL, Hope AG. Genetic drift drives rapid speciation of an Arctic insular endemic shrew (Sorex pribilofensis). Mol Ecol 2022; 31:5231-5248. [PMID: 35972323 DOI: 10.1111/mec.16658] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 08/08/2022] [Accepted: 08/11/2022] [Indexed: 12/15/2022]
Abstract
Episodes of Quaternary environmental change shaped the genomes of extant species, influencing their response to contemporary environments, which are changing rapidly. Island endemics are among the most vulnerable to such change, accounting for a disproportionate number of recent extinctions. To prevent extinctions and conserve island biodiversity it is vital to combine knowledge of species' ecologies with their complex evolutionary histories. The Bering Sea has a history of cyclical island isolation and reconnection, coupled with modern rates of climate change that exceed global averages. The endangered Pribilof Island shrew (Sorex pribilofensis) is endemic to St. Paul Island, Alaska, which was isolated from mainland Beringia ~14,000 years ago by rising sea levels. Using ~11,000 single nucleotide polymorphisms, 17 microsatellites and mitochondrial sequence data, we test predictions about the evolutionary processes driving shrew speciation across Beringia. Our data show considerable differentiation of S. pribilofensis from mainland sibling species, relative to levels of divergence between mainland shrews. We also find a genome-wide loss of diversity and extremely low Ne for S. pribilofensis. We then show that intraspecific genetic diversity is significantly related to interspecific divergence, and that differentiation between S. pribilofensis and other Beringian shrews is highest across loci that are fixed in S. pribilofensis, indicating that strong drift has driven differentiation of this island species. Our findings show that drift as a consequence of Arctic climate cycling can rapidly reshape insular biodiversity. Arctic island species that lack genomic diversity and have evolved in response to past climate may have limited ability to respond to modern environmental changes.
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Affiliation(s)
- Ben J Wiens
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Fraser J Combe
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | | | - Lauren M Divine
- Aleut Community of St. Paul Island, Ecosystem Conservation Office, St. Paul, Alaska, USA
| | - Veronica M Padula
- Aleut Community of St. Paul Island, Ecosystem Conservation Office, St. Paul, Alaska, USA
| | - George K Sage
- Far Northwestern Institute of Art and Science, Anchorage, Alaska, USA
| | - Sandra L Talbot
- Far Northwestern Institute of Art and Science, Anchorage, Alaska, USA
| | - Andrew G Hope
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
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11
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Investigating the reliability of metapodials as taxonomic Indicators for Beringian horses. J MAMM EVOL 2022; 29:863-875. [PMID: 36438779 PMCID: PMC9684255 DOI: 10.1007/s10914-022-09626-4] [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] [Accepted: 08/17/2022] [Indexed: 11/30/2022]
Abstract
The metapodials of extinct horses have long been regarded as one of the most useful skeletal elements to determine taxonomic identity. However, recent research on both extant and extinct horses has revealed the possibility for plasticity in metapodial morphology, leading to notable variability within taxa. This calls into question the reliability of metapodials in species identification, particularly for species identified from fragmentary remains. Here, we use ten measurements of metapodials from 203 specimens of four Pleistocene horse species from eastern Beringia to test whether there are significant differences in metapodial morphology that support the presence of multiple species. We then reconstruct the body masses for every specimen to assess the range in body size within each species and determine whether species differ significantly from one another in mean body mass. We find that that taxonomic groups are based largely on the overall size of the metapodial, and that all metapodial measurements are highly autocorrelated. We also find that mean body mass differs significantly among most, but not all, species. We suggest that metapodial measurements are unreliable taxonomic indicators for Beringian horses given evidence for plasticity in metapodial morphology and their clear reflection of differences in body mass. We recommend future studies use more reliable indicators of taxonomy to identify Beringian horse species, particularly from localities from which fossils of several species have been recovered.
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12
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Evolution of the Family Equidae, Subfamily Equinae, in North, Central and South America, Eurasia and Africa during the Plio-Pleistocene. BIOLOGY 2022; 11:biology11091258. [PMID: 36138737 PMCID: PMC9495906 DOI: 10.3390/biology11091258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/17/2022] [Accepted: 08/19/2022] [Indexed: 11/17/2022]
Abstract
Studies of horse evolution arose during the middle of the 19th century, and several hypotheses have been proposed for their taxonomy, paleobiogeography, paleoecology and evolution. The present contribution represents a collaboration of 19 multinational experts with the goal of providing an updated summary of Pliocene and Pleistocene North, Central and South American, Eurasian and African horses. At the present time, we recognize 114 valid species across these continents, plus 4 North African species in need of further investigation. Our biochronology and biogeography sections integrate Equinae taxonomic records with their chronologic and geographic ranges recognizing regional biochronologic frameworks. The paleoecology section provides insights into paleobotany and diet utilizing both the mesowear and light microscopic methods, along with calculation of body masses. We provide a temporal sequence of maps that render paleoclimatic conditions across these continents integrated with Equinae occurrences. These records reveal a succession of extinctions of primitive lineages and the rise and diversification of more modern taxa. Two recent morphological-based cladistic analyses are presented here as competing hypotheses, with reference to molecular-based phylogenies. Our contribution represents a state-of-the art understanding of Plio-Pleistocene Equus evolution, their biochronologic and biogeographic background and paleoecological and paleoclimatic contexts.
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13
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Pacheco C, Stronen AV, Jędrzejewska B, Plis K, Okhlopkov IM, Mamaev NV, Drovetski SV, Godinho R. Demography and evolutionary history of grey wolf populations around the Bering Strait. Mol Ecol 2022; 31:4851-4865. [PMID: 35822863 PMCID: PMC9545117 DOI: 10.1111/mec.16613] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 06/16/2022] [Accepted: 07/04/2022] [Indexed: 11/28/2022]
Abstract
Glacial and interglacial periods throughout the Pleistocene have been substantial drivers of change in species distributions. Earlier analyses suggested that modern grey wolves (Canis lupus) trace their origin to a single Late Pleistocene Beringian population that expanded east and westwards, starting c. 25,000 years ago (ya). Here, we examined the demographic and phylogeographic histories of extant populations around the Bering Strait with wolves from two inland regions of the Russian Far East (RFE) and one coastal and two inland regions of North‐western North America (NNA), genotyped for 91,327 single nucleotide polymorphisms. Our results indicated that RFE and NNA wolves had a common ancestry until c. 34,400 ya, suggesting that these populations started to diverge before the previously proposed expansion out of Beringia. Coastal and inland NNA populations diverged c. 16,000 ya, concordant with the minimum proposed date for the ecological viability of the migration route along the Pacific Northwest coast. Demographic reconstructions for inland RFE and NNA populations reveal spatial and temporal synchrony, with large historical effective population sizes that declined throughout the Pleistocene, possibly reflecting the influence of broadscale climatic changes across continents. In contrast, coastal NNA wolves displayed a consistently lower effective population size than the inland populations. Differences between the demographic history of inland and coastal wolves may have been driven by multiple ecological factors, including historical gene flow patterns, natural landscape fragmentation, and more recent anthropogenic disturbance.
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Affiliation(s)
- Carolina Pacheco
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Astrid Vik Stronen
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia.,Department of Biotechnology and Life Sciences, Insubria University, Varese, Italy.,Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | | | - Kamila Plis
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
| | - Innokentiy M Okhlopkov
- Institute of Biological Problems of Cryolithozone, Siberian Branch of Russian Academy of Sciences, Yakutsk, Russia
| | - Nikolay V Mamaev
- Institute of Biological Problems of Cryolithozone, Siberian Branch of Russian Academy of Sciences, Yakutsk, Russia
| | - Sergei V Drovetski
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Raquel Godinho
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
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14
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Bergström A, Stanton DWG, Taron UH, Frantz L, Sinding MHS, Ersmark E, Pfrengle S, Cassatt-Johnstone M, Lebrasseur O, Girdland-Flink L, Fernandes DM, Ollivier M, Speidel L, Gopalakrishnan S, Westbury MV, Ramos-Madrigal J, Feuerborn TR, Reiter E, Gretzinger J, Münzel SC, Swali P, Conard NJ, Carøe C, Haile J, Linderholm A, Androsov S, Barnes I, Baumann C, Benecke N, Bocherens H, Brace S, Carden RF, Drucker DG, Fedorov S, Gasparik M, Germonpré M, Grigoriev S, Groves P, Hertwig ST, Ivanova VV, Janssens L, Jennings RP, Kasparov AK, Kirillova IV, Kurmaniyazov I, Kuzmin YV, Kosintsev PA, Lázničková-Galetová M, Leduc C, Nikolskiy P, Nussbaumer M, O'Drisceoil C, Orlando L, Outram A, Pavlova EY, Perri AR, Pilot M, Pitulko VV, Plotnikov VV, Protopopov AV, Rehazek A, Sablin M, Seguin-Orlando A, Storå J, Verjux C, Zaibert VF, Zazula G, Crombé P, Hansen AJ, Willerslev E, Leonard JA, Götherström A, Pinhasi R, Schuenemann VJ, Hofreiter M, Gilbert MTP, Shapiro B, Larson G, Krause J, Dalén L, Skoglund P. Grey wolf genomic history reveals a dual ancestry of dogs. Nature 2022; 607:313-320. [PMID: 35768506 PMCID: PMC9279150 DOI: 10.1038/s41586-022-04824-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 04/28/2022] [Indexed: 01/01/2023]
Abstract
The grey wolf (Canis lupus) was the first species to give rise to a domestic population, and they remained widespread throughout the last Ice Age when many other large mammal species went extinct. Little is known, however, about the history and possible extinction of past wolf populations or when and where the wolf progenitors of the present-day dog lineage (Canis familiaris) lived1–8. Here we analysed 72 ancient wolf genomes spanning the last 100,000 years from Europe, Siberia and North America. We found that wolf populations were highly connected throughout the Late Pleistocene, with levels of differentiation an order of magnitude lower than they are today. This population connectivity allowed us to detect natural selection across the time series, including rapid fixation of mutations in the gene IFT88 40,000–30,000 years ago. We show that dogs are overall more closely related to ancient wolves from eastern Eurasia than to those from western Eurasia, suggesting a domestication process in the east. However, we also found that dogs in the Near East and Africa derive up to half of their ancestry from a distinct population related to modern southwest Eurasian wolves, reflecting either an independent domestication process or admixture from local wolves. None of the analysed ancient wolf genomes is a direct match for either of these dog ancestries, meaning that the exact progenitor populations remain to be located. DNA from ancient wolves spanning 100,000 years sheds light on wolves’ evolutionary history and the genomic origin of dogs.
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Affiliation(s)
- Anders Bergström
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK.
| | - David W G Stanton
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Centre for Palaeogenetics, Stockholm, Sweden.,School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Ulrike H Taron
- Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Laurent Frantz
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK.,Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich, Germany
| | - Mikkel-Holger S Sinding
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland.,The Qimmeq Project, University of Greenland, Nuuk, Greenland.,Greenland Institute of Natural Resources, Nuuk, Greenland
| | - Erik Ersmark
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Centre for Palaeogenetics, Stockholm, Sweden
| | - Saskia Pfrengle
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany.,Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland
| | - Molly Cassatt-Johnstone
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Ophélie Lebrasseur
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Linus Girdland-Flink
- Department of Archaeology, School of Geosciences, University of Aberdeen, Aberdeen, UK.,School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, UK
| | - Daniel M Fernandes
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.,CIAS, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Morgane Ollivier
- University of Rennes, CNRS, ECOBIO (Ecosystèmes, biodiversité, évolution)-UMR 6553, Rennes, France
| | - Leo Speidel
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK.,Genetics Institute, University College London, London, UK
| | | | - Michael V Westbury
- Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany.,The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Tatiana R Feuerborn
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,The Qimmeq Project, University of Greenland, Nuuk, Greenland.,Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
| | - Ella Reiter
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
| | - Joscha Gretzinger
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany.,Max Planck Institute for the Science of Human History, Jena, Germany
| | - Susanne C Münzel
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
| | - Pooja Swali
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK
| | - Nicholas J Conard
- Department of Early Prehistory and Quaternary Ecology, University of Tübingen, Tübingen, Germany.,Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany
| | - Christian Carøe
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - James Haile
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Anna Linderholm
- Centre for Palaeogenetics, Stockholm, Sweden.,The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK.,Texas A&M University, College Station, TX, USA.,Department of Geological Sciences, Stockholm University, Stockholm, Sweden
| | | | - Ian Barnes
- Department of Earth Sciences, Natural History Museum, London, UK
| | - Chris Baumann
- Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany.,Department of Geosciences and Geography, Faculty of Science, University of Helsinki, Helsinki, Finland
| | | | - Hervé Bocherens
- Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany.,Biogeology, Department of Geosciences, University of Tübingen, Tübingen, Germany
| | - Selina Brace
- Department of Earth Sciences, Natural History Museum, London, UK
| | - Ruth F Carden
- School of Archaeology, University College Dublin, Dublin, Ireland
| | - Dorothée G Drucker
- Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany
| | - Sergey Fedorov
- North-Eastern Federal University, Yakutsk, Russian Federation
| | | | | | | | - Pam Groves
- University of Alaska, Fairbanks, AK, USA
| | - Stefan T Hertwig
- Naturhistorisches Museum Bern, Bern, Switzerland.,Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | | | | | - Richard P Jennings
- School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, UK
| | - Aleksei K Kasparov
- Institute for the History of Material Culture, Russian Academy of Sciences, St Petersburg, Russian Federation
| | - Irina V Kirillova
- Ice Age Museum, Shidlovskiy National Alliance 'Ice Age', Moscow, Russian Federation
| | - Islam Kurmaniyazov
- Department of Archaeology, Ethnology and Museology, Al-Farabi Kazakh State University, Almaty, Kazakhstan
| | - Yaroslav V Kuzmin
- Sobolev Institute of Geology and Mineralogy, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | | | | | | | - Pavel Nikolskiy
- Geological Institute, Russian Academy of Sciences, Moscow, Russian Federation
| | | | - Cóilín O'Drisceoil
- National Monuments Service, Department of Housing, Local Government and Heritage, Dublin, Ireland
| | - Ludovic Orlando
- Centre d'Anthropobiologie et de Génomique de Toulouse UMR 5288, CNRS, Faculté de Médecine Purpan, Université Paul Sabatier, Toulouse, France
| | - Alan Outram
- Department of Archaeology, University of Exeter, Exeter, UK
| | - Elena Y Pavlova
- Arctic & Antarctic Research Institute, St Petersburg, Russian Federation
| | - Angela R Perri
- PaleoWest, Henderson, NV, USA.,Department of Anthropology, University of Nevada, Las Vegas, Las Vegas, NV, USA
| | - Małgorzata Pilot
- Museum & Institute of Zoology, Polish Academy of Sciences, Gdańsk, Poland
| | - Vladimir V Pitulko
- Institute for the History of Material Culture, Russian Academy of Sciences, St Petersburg, Russian Federation
| | | | | | | | - Mikhail Sablin
- Zoological Institute of the Russian Academy of Sciences, St. Petersburg, Russian Federation
| | - Andaine Seguin-Orlando
- Centre d'Anthropobiologie et de Génomique de Toulouse UMR 5288, CNRS, Faculté de Médecine Purpan, Université Paul Sabatier, Toulouse, France
| | - Jan Storå
- Stockholm University, Stockholm, Sweden
| | | | - Victor F Zaibert
- Institute of Archaeology and Steppe Civilizations, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Grant Zazula
- Yukon Palaeontology Program, Whitehorse, Yukon Territories, Canada.,Collections and Research, Canadian Museum of Nature, Ottawa, Ontario, Canada
| | | | - Anders J Hansen
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Eske Willerslev
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Department of Zoology, University of Cambridge, Cambridge, UK
| | | | - Anders Götherström
- Centre for Palaeogenetics, Stockholm, Sweden.,Stockholm University, Stockholm, Sweden
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.,Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria
| | - Verena J Schuenemann
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany.,Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland.,Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Michael Hofreiter
- Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - M Thomas P Gilbert
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,University Museum, NTNU, Trondheim, Norway
| | - 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
| | - Greger Larson
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Johannes Krause
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Centre for Palaeogenetics, Stockholm, Sweden
| | - Pontus Skoglund
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK.
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15
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Wang MS, Murray GGR, Mann D, Groves P, Vershinina AO, Supple MA, Kapp JD, Corbett-Detig R, Crump SE, Stirling I, Laidre KL, Kunz M, Dalén L, Green RE, Shapiro B. A polar bear paleogenome reveals extensive ancient gene flow from polar bears into brown bears. Nat Ecol Evol 2022; 6:936-944. [PMID: 35711062 DOI: 10.1038/s41559-022-01753-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 03/30/2022] [Indexed: 11/09/2022]
Abstract
Polar bears (Ursus maritimus) and brown bears (Ursus arctos) are sister species possessing distinct physiological and behavioural adaptations that evolved over the last 500,000 years. However, comparative and population genomics analyses have revealed that several extant and extinct brown bear populations have relatively recent polar bear ancestry, probably as the result of geographically localized instances of gene flow from polar bears into brown bears. Here, we generate and analyse an approximate 20X paleogenome from an approximately 100,000-year-old polar bear that reveals a massive prehistoric admixture event, which is evident in the genomes of all living brown bears. This ancient admixture event was not visible from genomic data derived from living polar bears. Like more recent events, this massive admixture event mainly involved unidirectional gene flow from polar bears into brown bears and occurred as climate changes caused overlap in the ranges of the two species. These findings highlight the complex reticulate paths that evolution can take within a regime of radically shifting climate.
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Affiliation(s)
- Ming-Shan Wang
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, USA.,Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Gemma G R Murray
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Daniel Mann
- Department of Geosciences, University of Alaska, Fairbanks, AK, USA.,Institute of Arctic Biology, University of Alaska, Fairbanks, AK, USA
| | - Pamela Groves
- Institute of Arctic Biology, University of Alaska, Fairbanks, AK, USA
| | - Alisa O Vershinina
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Megan A Supple
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, USA.,Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Joshua D Kapp
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Russell Corbett-Detig
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Sarah E Crump
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Ian Stirling
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada.,Wildlife Research Division, Environment and Climate Change Canada Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Kristin L Laidre
- Polar Science Center, Applied Physics Laboratory, University of Washington, Seattle, WA, USA
| | - Michael Kunz
- University of Alaska Museum of the North, Fairbanks, AK, USA
| | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Centre for Palaeogenetics, Stockholm, Sweden
| | - Richard E Green
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Beth Shapiro
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, USA. .,Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA.
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16
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Cai D, Zhu S, Gong M, Zhang N, Wen J, Liang Q, Sun W, Shao X, Guo Y, Cai Y, Zheng Z, Zhang W, Hu S, Wang X, Tian H, Li Y, Liu W, Yang M, Yang J, Wu D, Orlando L, Jiang Y. Radiocarbon and genomic evidence for the survival of Equus Sussemionus until the late Holocene. eLife 2022; 11:73346. [PMID: 35543411 PMCID: PMC9142152 DOI: 10.7554/elife.73346] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 05/11/2022] [Indexed: 12/02/2022] Open
Abstract
The exceptionally rich fossil record available for the equid family has provided textbook examples of macroevolutionary changes. Horses, asses, and zebras represent three extant subgenera of Equus lineage, while the Sussemionus subgenus is another remarkable Equus lineage ranging from North America to Ethiopia in the Pleistocene. We sequenced 26 archaeological specimens from Northern China in the Holocene that could be assigned morphologically and genetically to Equus ovodovi, a species representative of Sussemionus. We present the first high-quality complete genome of the Sussemionus lineage, which was sequenced to 13.4× depth of coverage. Radiocarbon dating demonstrates that this lineage survived until ~3500 years ago, despite continued demographic collapse during the Last Glacial Maximum and the great human expansion in East Asia. We also confirmed the Equus phylogenetic tree and found that Sussemionus diverged from the ancestor of non-caballine equids ~2.3–2.7 million years ago and possibly remained affected by secondary gene flow post-divergence. We found that the small genetic diversity, rather than enhanced inbreeding, limited the species’ chances of survival. Our work adds to the growing literature illustrating how ancient DNA can inform on extinction dynamics and the long-term resilience of species surviving in cryptic population pockets.
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Affiliation(s)
- Dawei Cai
- Bioarchaeology Laboratory, Jilin University, Changchun, China
| | - Siqi Zhu
- Bioarchaeology Laboratory, Jilin University, Changchun, China
| | - Mian Gong
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Naifan Zhang
- Bioarchaeology Laboratory, Jilin University, Changchuin, China
| | - Jia Wen
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Qiyao Liang
- Bioarchaeology Laboratory, Jilin University, Changchun, China
| | - Weilu Sun
- Bioarchaeology Laboratory, Jilin University, Changchun, China
| | - Xinyue Shao
- Bioarchaeology Laboratory, Jilin University, Changchun, China
| | - Yaqi Guo
- Bioarchaeology Laboratory, Jilin University, Changchun, China
| | - Yudong Cai
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Zhuqing Zheng
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Wei Zhang
- Heilongjiang Provincial Institute of Cultural Relics and Archaeology, Harbin, China
| | - Songmei Hu
- Shaanxi Provincial Institute of Archaeology, Xi'an, China
| | - Xiaoyang Wang
- Ningxia Institute of Cultural Relics and Archaeology, Yinchuan, China
| | - He Tian
- Heilongjiang Provincial Institute of Cultural Relics and Archaeology, Harbin, China
| | - Youqian Li
- Heilongjiang Provincial Institute of Cultural Relics and Archaeology, Harbin, China
| | - Wei Liu
- Heilongjiang Provincial Institute of Cultural Relics and Archaeology, Harbin, China
| | - Miaomiao Yang
- Shaanxi Provincial Institute of Archaeology, Xi'an, China
| | - Jian Yang
- Ningxia Institute of Cultural Relics and Archaeology, Yinchuan, China
| | - Duo Wu
- College of Earth and Environmental Sciences, Lanzhou University, Lanzhou, China
| | - Ludovic Orlando
- 7Centre d'Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier, CNRS UMR 5288, Toulouse, France
| | - Yu Jiang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
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17
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Murchie TJ, Karpinski E, Eaton K, Duggan AT, Baleka S, Zazula G, MacPhee RDE, Froese D, Poinar HN. Pleistocene mitogenomes reconstructed from the environmental DNA of permafrost sediments. Curr Biol 2022; 32:851-860.e7. [PMID: 35016010 DOI: 10.1016/j.cub.2021.12.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 10/20/2021] [Accepted: 12/08/2021] [Indexed: 11/17/2022]
Abstract
Traditionally, paleontologists have relied on the morphological features of bones and teeth to reconstruct the evolutionary relationships of extinct animals.1 In recent decades, the analysis of ancient DNA recovered from macrofossils has provided a powerful means to evaluate these hypotheses and develop novel phylogenetic models.2 Although a great deal of life history data can be extracted from bones, their scarcity and associated biases limit their information potential. The paleontological record of Beringia3-the unglaciated areas and former land bridge between northeast Eurasia and northwest North America-is relatively robust thanks to its perennially frozen ground favoring fossil preservation.4,5 However, even here, the macrofossil record is significantly lacking in small-bodied fauna (e.g., rodents and birds), whereas questions related to migration and extirpation, even among well-studied taxa, remain crudely resolved. The growing sophistication of ancient environmental DNA (eDNA) methods have allowed for the identification of species within terrestrial/aquatic ecosystems,6-12 in paleodietary reconstructions,13-19 and facilitated genomic reconstructions from cave contexts.8,20-22 Murchie et al.6,23 used a capture enrichment approach to sequence a diverse range of faunal and floral DNA from permafrost silts deposited during the Pleistocene-Holocene transition.24 Here, we expand on their work with the mitogenomic assembly and phylogenetic placement of Equus caballus (caballine horse), Bison priscus (steppe bison), Mammuthus primigenius (woolly mammoth), and Lagopus lagopus (willow ptarmigan) eDNA from multiple permafrost cores spanning the last 30,000 years. We identify a diverse metagenomic spectra of Pleistocene fauna and identify the eDNA co-occurrence of distinct Eurasian and American mitogenomic lineages.
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Affiliation(s)
- Tyler J Murchie
- McMaster Ancient DNA Centre, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada; Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada.
| | - Emil Karpinski
- McMaster Ancient DNA Centre, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada; Department of Biology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
| | - Katherine Eaton
- McMaster Ancient DNA Centre, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada; Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
| | - Ana T Duggan
- McMaster Ancient DNA Centre, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada; Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
| | - Sina Baleka
- McMaster Ancient DNA Centre, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
| | - Grant Zazula
- Yukon Government, Palaeontology Program, Department of Tourism and Culture, Box 2703, Whitehorse, YT Y1A 2C6, Canada; Collections and Research, Canadian Museum of Nature, PO Box 3443, Station D, Ottawa, ON K1P 6P4, Canada
| | - Ross D E MacPhee
- Division of Vertebrate Zoology/Mammalogy, American Museum of Natural History, 200 Central Park West, New York, NY 10024, USA
| | - Duane Froese
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, AB T6G 2E3, Canada.
| | - Hendrik N Poinar
- McMaster Ancient DNA Centre, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada; Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada; Department of Biochemistry, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada; CIFAR, Humans and the Microbiome Program, MaRS Centre, West Tower, 661 University Avenue, Suite 505, Toronto, ON M5G 1M1, Canada.
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18
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Rieseberg L, Warschefsky E, O'Boyle B, Taberlet P, Ortiz-Barrientos D, Kane NC, Sibbett B. Editorial 2022. Mol Ecol 2021; 31:1-30. [PMID: 34957606 DOI: 10.1111/mec.16328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 12/10/2021] [Indexed: 11/30/2022]
Affiliation(s)
- Loren Rieseberg
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | | | | | - Pierre Taberlet
- Laboratoire d'Ecologie Alpine, CNRS UMR 5553, Université Univ. Grenoble Alpes, Grenoble Cedex 9, France
| | - Daniel Ortiz-Barrientos
- School of Biological Sciences, The University of Queenland, St. Lucia, Queensland, Australia
| | - Nolan C Kane
- University of Colorado at Boulder, Boulder, Colorado, USA
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19
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The Sequence Analysis of Mitochondrial DNA Revealed Some Major Centers of Horse Domestications: The Archaeologist's Cut. J Equine Vet Sci 2021; 109:103830. [PMID: 34871751 DOI: 10.1016/j.jevs.2021.103830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 11/28/2021] [Accepted: 11/29/2021] [Indexed: 11/22/2022]
Abstract
The question about the time and the place of horse domestication, a process which had a profound impact on the progress of mankind, is disputable. According to the most widely accepted hypothesis, the earliest domestication of the horse happened in the western parts of the Eurasian steppes, between the Northern Black Sea region and present-day Kazakhstan and Turkmenistan. It seems that it occurred not earlier than the first half and most probably during the middle (even the last third) of the fourth millennium BC (from ∼ 5.5 kya). The next steps of large-scale horse breeding occurred almost simultaneously in Eurasia and North Africa due to the development of the social structure of human communities. On the other hand, the morphological differences between wild and domestic animals are rather vague and the genetic introgression between them is speculative. In this review, we have tried to gather all available scientific data on the existing possible hypotheses for the earliest domestication of the horse, as well as to highlight some data on the most plausible ones. This is due to the frequency of some significant data on the frequency of strictly defined mitotypes in different historical periods of human civilizations existing in the same periods.
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20
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Taylor RS, Jensen EL, Coltman DW, Foote AD, Lamichhaney S. Seeing the whole picture: What molecular ecology is gaining from whole genomes. Mol Ecol 2021; 30:5917-5922. [PMID: 34845797 DOI: 10.1111/mec.16282] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 11/12/2021] [Accepted: 11/15/2021] [Indexed: 12/12/2022]
Affiliation(s)
- Rebecca S Taylor
- Biology Department, Trent University, Peterborough, Ontario, Canada
| | - Evelyn L Jensen
- School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne, UK
| | - David W Coltman
- Department of Biological Sciences, University of Alberta, Edmonton, Canada.,Biology Department, Western University, London, Ontario, Canada
| | - Andrew D Foote
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
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21
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Britton K, Crowley BE, Bataille CP, Miller JH, Wooller MJ. Silver Linings at the Dawn of a “Golden Age”. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.748938] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Nearly four decades after the first applications of strontium isotope analyses in archaeology and paleoecology research, it could be said that we are entering a “Golden Age”. Here, we reflect on major past developments and current strengths in strontium isotope research, as well as speculate on future directions. We review (1) the currently limited number of (but much needed) controlled feeding experiments, (2) recent advances in isoscape mapping and spatial assignment, and (3) the strength of multi-proxy approaches (including both the integration of strontium isotopes with other isotope systems and complementary techniques such as ancient DNA analyses). We also explore the integration of strontium isotope research with other types of paleoecological or archaeology data, as well as with evidence and interpretative frameworks from other fields (such as conservation ecology, conservation paleobiology or history). This blending is critical as we seek to advance the field beyond simply distinguishing local or relatively sedentary individuals from those that were non-local or highly mobile. We finish with a call for future research centered on balancing methodological developments and novel applications with critical self-reflection, deeper theoretical considerations and cross-disciplinarity.
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Ancient Faunal History Revealed by Interdisciplinary Biomolecular Approaches. DIVERSITY 2021. [DOI: 10.3390/d13080370] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Starting four decades ago, studies have examined the ecology and evolutionary dynamics of populations and species using short mitochondrial DNA fragments and stable isotopes. Through technological and analytical advances, the methods and biomolecules at our disposal have increased significantly to now include lipids, whole genomes, proteomes, and even epigenomes. At an unprecedented resolution, the study of ancient biomolecules has made it possible for us to disentangle the complex processes that shaped the ancient faunal diversity across millennia, with the potential to aid in implicating probable causes of species extinction and how humans impacted the genetics and ecology of wild and domestic species. However, even now, few studies explore interdisciplinary biomolecular approaches to reveal ancient faunal diversity dynamics in relation to environmental and anthropogenic impact. This review will approach how biomolecules have been implemented in a broad variety of topics and species, from the extinct Pleistocene megafauna to ancient wild and domestic stocks, as well as how their future use has the potential to offer an enhanced understanding of drivers of past faunal diversity on Earth.
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