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Prehistoric genomes reveal the genetic foundation and cost of horse domestication.

  • Schubert M Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350K Copenhagen, Denmark;
  • Jónsson H Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350K Copenhagen, Denmark;
  • Chang D Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064;
  • Der Sarkissian C Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350K Copenhagen, Denmark;
  • Ermini L Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350K Copenhagen, Denmark;
  • Ginolhac A Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350K Copenhagen, Denmark;
  • Albrechtsen A The Bioinformatics Centre, Department of Biology, University of Copenhagen, 2200N Copenhagen, Denmark;
  • Dupanloup I Institute of Ecology and Evolution, University of Berne, 3012 Berne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland;
  • Foucal A Institute of Ecology and Evolution, University of Berne, 3012 Berne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland;
  • Petersen B Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, 2800 Lyngby, Denmark;
  • Fumagalli M UCL Genetics Institute, Department of Genetics, Evolution, and Environment, University College London, London WC1E 6BT, United Kingdom;
  • Raghavan M Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350K Copenhagen, Denmark;
  • Seguin-Orlando A Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350K Copenhagen, Denmark; National High-Throughput DNA Sequencing Center, University of Copenhagen, 1353K Copenhagen, Denmark;
  • Korneliussen TS Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350K Copenhagen, Denmark;
  • Velazquez AM Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350K Copenhagen, Denmark;
  • Stenderup J Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350K Copenhagen, Denmark;
  • Hoover CA Department of Energy Joint Genome Institute, Walnut Creek, CA 94598;
  • Rubin CJ Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23 Uppsala, Sweden;
  • Alfarhan AH Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia;
  • Alquraishi SA Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia;
  • Al-Rasheid KA Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia;
  • MacHugh DE Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland; UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland;
  • Kalbfleisch T Biochemistry and Molecular Biology, School of Medicine, University of Louisville, Louisville, KY 40292;
  • MacLeod JN Department of Veterinary Science, Gluck Equine Research Center, University of Kentucky, Lexington, KY 40546;
  • Rubin EM Department of Energy Joint Genome Institute, Walnut Creek, CA 94598;
  • Sicheritz-Ponten T Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, 2800 Lyngby, Denmark;
  • Andersson L Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23 Uppsala, Sweden;
  • Hofreiter M Institute for Biochemistry and Biology, Faculty for Mathematics and Natural Sciences, University of Potsdam, 14476 Potsdam, Germany;
  • Marques-Bonet T Instituticó Catalana de Recerca i Estudis Avançats, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/Consejo Superior de Investigaciones Cientificas), 08003 Barcelona, Spain; Centro Nacional de Análisis Genómico, 08028 Barcelona, Spain; and.
  • Gilbert MT Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350K Copenhagen, Denmark;
  • Nielsen R Departments of Integrative Biology and Statistics, University of California, Berkeley, CA 94720.
  • Excoffier L Institute of Ecology and Evolution, University of Berne, 3012 Berne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland;
  • Willerslev E Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350K Copenhagen, Denmark;
  • Shapiro B Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064;
  • Orlando L Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350K Copenhagen, Denmark; Lorlando@snm.ku.dk.
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  • 2014-12-17
Published in:
  • Proceedings of the National Academy of Sciences of the United States of America. - 2014
Przewalski’s horse
ancient DNA
cost of domestication
horse domestication
positive selection
Animals
Animals, Domestic
Cardiovascular System
Dogs
Evolution, Molecular
Genome
Hindlimb
Horses
Humans
Inbreeding
Russia
English The domestication of the horse ∼ 5.5 kya and the emergence of mounted riding, chariotry, and cavalry dramatically transformed human civilization. However, the genetics underlying horse domestication are difficult to reconstruct, given the near extinction of wild horses. We therefore sequenced two ancient horse genomes from Taymyr, Russia (at 7.4- and 24.3-fold coverage), both predating the earliest archeological evidence of domestication. We compared these genomes with genomes of domesticated horses and the wild Przewalski's horse and found genetic structure within Eurasia in the Late Pleistocene, with the ancient population contributing significantly to the genetic variation of domesticated breeds. We furthermore identified a conservative set of 125 potential domestication targets using four complementary scans for genes that have undergone positive selection. One group of genes is involved in muscular and limb development, articular junctions, and the cardiac system, and may represent physiological adaptations to human utilization. A second group consists of genes with cognitive functions, including social behavior, learning capabilities, fear response, and agreeableness, which may have been key for taming horses. We also found that domestication is associated with inbreeding and an excess of deleterious mutations. This genetic load is in line with the "cost of domestication" hypothesis also reported for rice, tomatoes, and dogs, and it is generally attributed to the relaxation of purifying selection resulting from the strong demographic bottlenecks accompanying domestication. Our work demonstrates the power of ancient genomes to reconstruct the complex genetic changes that transformed wild animals into their domesticated forms, and the population context in which this process took place.
Language
  • English
Open access status
green
Identifiers
Persistent URL
https://folia.unifr.ch/global/documents/241369
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