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Cell. 2019 May 2. pii: S0092-8674(19)30384-8. doi: 10.1016/j.cell.2019.03.049. [Epub ahead of print]

Tracking Five Millennia of Horse Management with Extensive Ancient Genome Time Series.

Fages A1, Hanghøj K1, Khan N2, Gaunitz C3, Seguin-Orlando A1, Leonardi M4, McCrory Constantz C5, Gamba C3, Al-Rasheid KAS6, Albizuri S7, Alfarhan AH6, Allentoft M3, Alquraishi S6, Anthony D8, Baimukhanov N9, Barrett JH10, Bayarsaikhan J11, Benecke N12, Bernáldez-Sánchez E13, Berrocal-Rangel L14, Biglari F15, Boessenkool S16, Boldgiv B17, Brem G18, Brown D8, Burger J19, Crubézy E20, Daugnora L21, Davoudi H22, de Barros Damgaard P3, de Los Ángeles de Chorro Y de Villa-Ceballos M23, Deschler-Erb S24, Detry C25, Dill N24, do Mar Oom M26, Dohr A27, Ellingvåg S28, Erdenebaatar D29, Fathi H30, Felkel S18, Fernández-Rodríguez C31, García-Viñas E32, Germonpré M33, Granado JD24, Hallsson JH34, Hemmer H19, Hofreiter M35, Kasparov A36, Khasanov M37, Khazaeli R30, Kosintsev P38, Kristiansen K39, Kubatbek T40, Kuderna L41, Kuznetsov P42, Laleh H43, Leonard JA44, Lhuillier J45, Liesau von Lettow-Vorbeck C14, Logvin A46, Lõugas L47, Ludwig A48, Luis C49, Arruda AM25, Marques-Bonet T50, Matoso Silva R51, Merz V52, Mijiddorj E29, Miller BK53, Monchalov O42, Mohaseb FA54, Morales A55, Nieto-Espinet A56, Nistelberger H16, Onar V57, Pálsdóttir AH58, Pitulko V36, Pitskhelauri K59, Pruvost M60, Rajic Sikanjic P61, Rapan Papeša A62, Roslyakova N42, Sardari A63, Sauer E64, Schafberg R65, Scheu A19, Schibler J24, Schlumbaum A24, Serrand N66, Serres-Armero A41, Shapiro B67, Sheikhi Seno S54, Shevnina I46, Shidrang S68, Southon J69, Star B16, Sykes N70, Taheri K71, Taylor W72, Teegen WR73, Trbojević Vukičević T74, Trixl S75, Tumen D76, Undrakhbold S17, Usmanova E77, Vahdati A63, Valenzuela-Lamas S78, Viegas C25, Wallner B18, Weinstock J79, Zaibert V80, Clavel B81, Lepetz S81, Mashkour M54, Helgason A82, Stefánsson K82, Barrey E83, Willerslev E3, Outram AK84, Librado P1, Orlando L85.

Author information

1
Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse, France; Lundbeck Foundation GeoGenetics Center, University of Copenhagen, 1350K Copenhagen, Denmark.
2
Lundbeck Foundation GeoGenetics Center, University of Copenhagen, 1350K Copenhagen, Denmark; Department of Biotechnology, Abdul Wali Khan University, Mardan, Pakistan.
3
Lundbeck Foundation GeoGenetics Center, University of Copenhagen, 1350K Copenhagen, Denmark.
4
Lundbeck Foundation GeoGenetics Center, University of Copenhagen, 1350K Copenhagen, Denmark; Evolutionary Ecology Group, Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK.
5
Lundbeck Foundation GeoGenetics Center, University of Copenhagen, 1350K Copenhagen, Denmark; Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA.
6
Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia.
7
Seminari d'Estudis i Recerques Prehistoriques, HAR2017-87695-P, Universitat de Barcelona, Barcelona, Spain.
8
Anthropology Department, Hartwick College 1, Oneonta, NY 13820, USA.
9
Shejire DNA project, 050046 Almaty, Kazakhstan.
10
McDonald Institute for Archaeological Research, Department of Archaeology, University of Cambridge, Cambridge CB2 3ER, UK.
11
National Museum of Mongolia, Ulaanbaatar 210646, Mongolia.
12
Deutsches Archäologisches Institut (DAI), 14195 Berlin, Germany.
13
Laboratorio de Paleontologia y Paleobiologia, Instituto Andaluz del Patrimonio Historico, Sevilla, Spain.
14
Departamento de Prehistoria y Arqueología, Universidad Autónoma de Madrid, Madrid, Spain.
15
Department of Paleolithic, National Museum of Iran, 1136918111, Tehran, Iran.
16
Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Postbox 1066, Blindern, 0316 Oslo, Norway.
17
Ecology Group, Department of Biology, School of Arts and Sciences, National University of Mongolia, Ulaanbaatar 14201, Mongolia.
18
Institute of Animal Breeding and Genetics, Department of Biomedical Sciences, Veterinary University of Vienna, 1210 Vienna, Austria.
19
Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iOME), Johannes Gutenberg-University Mainz, 55099 Mainz, Germany.
20
Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse, France.
21
Osteological material research laboratory, Klaipėda university, Klaipėda 92294, Lithuania.
22
Department of Osteology, National Museum of Iran, 1136918111, Tehran, Iran; Department of Archaeology, Faculty of Humanities, Tarbiat Modares University, Tehran, Iran.
23
Centro de Biología Molecular Severo Ochoa (CSIC-UAM), E-28049, Madrid, Spain.
24
Integrative prähistorische und naturwissenschaftliche Archäologie (IPNA), 4055 Basel, Switzerland.
25
Uniarq, Centro de Arqueologia da Universidade de Lisboa, Faculdade de Letras da Universidade de Lisboa, 1600-214 Lisboa, Portugal.
26
CE3C-Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal.
27
Institute for Pre- and Protohistoric Archaeology and Archaeology of the Roman Provinces, Ludwig-Maximilians-University Munich, 80539 München, Germany; ArchaeoBioCenter, Ludwig-Maximilians-University Munich, 80539 München, Germany; Institute of Palaeoanatomy, Domestication Research and History of Veterinary Medicine, Ludwig-Maximilians-University Munich, 80539 München, Germany.
28
Explico Foundation, 6900 Florø, Norway.
29
Department of Archaeology, Ulaanbaatar State University, Ulaanbaatar 51, Mongolia.
30
Department of Osteology, National Museum of Iran, 1136918111, Tehran, Iran; Archaezoology section, Bioarchaeology Laboratory of the Central Laboratory, University of Tehran, Tehran CP1417634934, Iran.
31
Departamento de Historia, Facultad de Filosofía y Letras, Universidad de León, León, Spain.
32
Departamento de Sistemas Físicos, Químicos y Naturales, Universidad Pablo de Olavide, 41013 Sevilla, Spain.
33
Operational Direction, Earth and History of Life, Royal Belgian Institute of Natural Sciences, 1000, Brussels, Belgium.
34
Faculty of Agricultural and Environmental Sciences, The Agricultural University of Iceland, Keldnaholti - Árleyni 22, 112 Reykjavík, Iceland.
35
University of Potsdam, Faculty of Mathematics and Natural Sciences, Institute for Biochemistry and Biology, 14476 Potsdam, Germany.
36
Institute for the History of Material Culture, Russian Academy of Sciences, St. Petersburg 191186, Russia.
37
Archaeology Institute of Samarkand, Uzbekistan.
38
Institute of Plant and Animal Ecology, Urals Branch of the Russian Academy of Sciences, Ekaterinburg 620144, Russia.
39
Department of Historical Studies, University of Gothenburg, Gothenburg, Sweden.
40
Department of History, Kyrgyz-Turkish Manas University, Bishkek, Kyrgyzstan.
41
Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, Barcelona, Catalonia 08003, Spain.
42
Samara State University of Social Science and Education, Samara, Russia.
43
Archaezoology section, Bioarchaeology Laboratory of the Central Laboratory, University of Tehran, Tehran CP1417634934, Iran; Department of Archaeology, Faculty of Humanities, University of Tehran, Iran.
44
Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), 41092 Sevilla, Spain.
45
Laboratoire Archéorient, UMR 5133, Maison de l'Orient et de la Méditerranée, 69365 Lyon Cedex 7, France.
46
Laboratory for Archaeological Research, Faculty of History and Law, Kostanay State University, Kostanay, Kazakhstan.
47
Archaeological Research Collection, Tallinn University, 10130 Tallinn, Estonia.
48
Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, 10315 Berlin, Germany; Faculty of Life Sciences, Albrecht Daniel Thaer-Institute, Humboldt University Berlin, 10115 Berlin, Germany.
49
Museu Nacional de História Natural e da Ciência, Universidade de Lisboa, Lisboa, Portugal; Centro Interuniversitário de História das Ciências e da Tecnologia (CIUHCT), Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal; Instituto Universitário de Lisboa (ISCTE-IUL), CIES-IUL, Lisboa, Portugal.
50
Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, Barcelona, Catalonia 08003, Spain; Catalan Institution of Research and Advanced Studies (ICREA), 08010 Barcelona, Spain; CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain; Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, 08193, Cerdanyola del Vallès, Barcelona, Spain.
51
Instituto Universitário de Lisboa (ISCTE-IUL), CIES-IUL, Lisboa, Portugal.
52
S.Toraighyrov Pavlodar State University, Joint Research Center for Archeological Studies, 637000 Pavlodar, Kazakhstan.
53
University of Oxford, Faculty of History, George Street, Oxford, OX1 2RL, UK.
54
Department of Osteology, National Museum of Iran, 1136918111, Tehran, Iran; Archaezoology section, Bioarchaeology Laboratory of the Central Laboratory, University of Tehran, Tehran CP1417634934, Iran; Centre National de la Recherche Scientifique, Muséum National d'Histoire Naturelle, Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements (UMR 7209), 75005 Paris, France.
55
Laboratory of Archaeozoology, Department Biología, Universidad Autónoma de Madrid, Madrid, Spain.
56
Archaeology of Social Dynamics Group (ADS), Institució Milà i Fontanals-Consejo Superior de Investigaciones Científicas (IMF-CSIC), 08001 Barcelona, Spain; Grup d'Investigació Prehistòrica, HAR2016-78277-R, Universitat de Lleida, 25003 Lleida, Spain.
57
Osteoarchaeology Practice and Research Center and Department of Anatomy, Faculty of Veterinary Medicine, Istanbul University-Cerrahpaşa, 34320, Avcılar, Istanbul, Turkey.
58
Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Postbox 1066, Blindern, 0316 Oslo, Norway; Faculty of Agricultural and Environmental Sciences, The Agricultural University of Iceland, Keldnaholti - Árleyni 22, 112 Reykjavík, Iceland.
59
Ivane Javakhishvili Tbilisi State University, Tbilisi 0179, Georgia.
60
Université de Bordeaux, CNRS, UMR 5199-PACEA, 33615 Pessac Cedex, France.
61
Institute for Anthropological Research, Gajeva 32, 10000 Zagreb, Croatia.
62
Vinkovci Municipal Museum, 32 100 Vinkovci, Croatia.
63
Iranian Center for Archaeological Research (ICAR), Iranian Cultural Heritage, Handicrafts, and Tourism Organization (ICHHTO), 1136918111, Tehran, Iran.
64
School of History, Classics and Archaeology, The University of Edinburgh, Edinburgh, EH8 9AG, UK.
65
Central Natural Science Collections (ZNS), Martin Luther University Halle-Wittenberg, Domplatz 4, 06108 Halle (Saale), Germany.
66
Centre National de la Recherche Scientifique, Muséum National d'Histoire Naturelle, Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements (UMR 7209), 75005 Paris, France; INRAP Guadeloupe, Centre de recherches archéologiques, UMR 7209 CNRS/MNHN, 97113 Gourbeyre, Guadeloupe.
67
Department of Ecology and Evolutionary Biology and Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA 95060, USA.
68
Saeedi Institute for Advanced Studies, University of Kashan, Kashan 87317-51167, Iran.
69
Department Earth System Science, University of California, Irvine, Irvine, CA 92697, USA.
70
Department of Archaeology, University of Nottingham, Nottingham, NG7 2RD, UK; Department of Archaeology, University of Exeter, Exeter, EX4 4QE, UK.
71
Kermanshah Regional Water Authority, Kermanshah 67145-1466, Iran.
72
Max Planck Institute for the Science of Human History, 07745 Jena, Germany.
73
Institute for Pre- and Protohistoric Archaeology and Archaeology of the Roman Provinces, Ludwig-Maximilians-University Munich, 80539 München, Germany; ArchaeoBioCenter, Ludwig-Maximilians-University Munich, 80539 München, Germany.
74
Department of Anatomy, Histology and Embryology, Faculty of Veterinary Medicine, University of Zagreb, 10 000 Zagreb, Croatia.
75
Institute of Palaeoanatomy, Domestication Research and History of Veterinary Medicine, Ludwig-Maximilians-University Munich, 80539 München, Germany.
76
Department of Anthropology and Archaeology, School of Arts and Sciences, National University of Mongolia, Ulaanbaatar 14201, Mongolia.
77
Saryarka Archaeological Institute of Buketov Karaganda State University, Karaganda 100074, Kazakhstan.
78
Archaeology of Social Dynamics Group (ADS), Institució Milà i Fontanals-Consejo Superior de Investigaciones Científicas (IMF-CSIC), 08001 Barcelona, Spain.
79
Faculty of Humanities (Archaeology), University of Southampton, Avenue Campus, Highfield, Southampton SO17 1BF, UK.
80
Scientific Research Institute of Archaeology and Steppe Civilizations, Al Farabi Kazakh National University, 050040 Almaty, Kazakhstan.
81
Centre National de la Recherche Scientifique, Muséum National d'Histoire Naturelle, Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements (UMR 7209), 75005 Paris, France.
82
deCODE Genetics, 101 Reykjavik, Iceland.
83
GABI UMR1313, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France.
84
Department of Archaeology, University of Exeter, Exeter, EX4 4QE, UK.
85
Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse, France; Lundbeck Foundation GeoGenetics Center, University of Copenhagen, 1350K Copenhagen, Denmark. Electronic address: ludovic.orlando@univ-tlse3.fr.

Abstract

Horse domestication revolutionized warfare and accelerated travel, trade, and the geographic expansion of languages. Here, we present the largest DNA time series for a non-human organism to date, including genome-scale data from 149 ancient animals and 129 ancient genomes (≥1-fold coverage), 87 of which are new. This extensive dataset allows us to assess the modern legacy of past equestrian civilizations. We find that two extinct horse lineages existed during early domestication, one at the far western (Iberia) and the other at the far eastern range (Siberia) of Eurasia. None of these contributed significantly to modern diversity. We show that the influence of Persian-related horse lineages increased following the Islamic conquests in Europe and Asia. Multiple alleles associated with elite-racing, including at the MSTN "speed gene," only rose in popularity within the last millennium. Finally, the development of modern breeding impacted genetic diversity more dramatically than the previous millennia of human management.

KEYWORDS:

ancient DNA; animal breeding; diversity; domestication; equestrian civilizations; extinct lineages; horses; management; mules; selection

PMID:
31056281
DOI:
10.1016/j.cell.2019.03.049
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