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Proceedings of the National Academy of Sciences of the United States of America2014; 111(52); E5661-E5669; doi: 10.1073/pnas.1416991111

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

Abstract: 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.
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Publication Date: 2014-12-15 PubMed ID: 25512547PubMed Central: PMC4284583DOI: 10.1073/pnas.1416991111Google Scholar: Lookup
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  • Journal Article
  • Research Support
  • Non-U.S. Gov't

Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

This research investigates the genetic changes underlying horse domestication, using ancient genomes from pre-domestication horses. The study also examines the adverse effects of domestication — a phenomenon known as the “cost of domestication”.

Methodology and Results

  • The researchers sequenced the genomes of two prehistoric horses from Taymyr, Russia which predate the first evidence of horse domestication.
  • They then compared these genomes with those of domesticated horses and the wild Przewalski’s horse.
  • The comparison revealed genetic structure within Eurasia during the Late Pleistocene, and showed that the ancient population greatly influenced the genetic variation in domesticated horse breeds.

Identification of Potential Domestication Targets

  • Through four different scans for genes that exhibited positive selection, the researchers identified 125 potential domestication targets.
  • These genes belong to two major groups. The first group is associated with muscular and limb development, articular junctions, and cardiac system. These may represent physiological adaptations for human utilization.
  • The second group consists of genes related to cognitive functions, such as learning capabilities, social behavior, fear response, and agreeableness. These genes could have played important roles in the taming of horses.

“Cost of Domestication”

  • The study also found that domestication is related to inbreeding and an increase in deleterious mutations, consistent with the “cost of domestication” hypothesis.
  • This genetic load, a result of the decrease in purifying selection due to the strong demographic shifts during domestication, has also been reported in other domesticated species such as rice, tomatoes, and dogs.

Conclusion

  • The researchers concluded that the study of ancient genomes could provide significant insights into the complex genetic changes that led to the domestication of wild animals, and reveal the population context in which this transformation occurred.

Cite This Article

APA
Schubert M, Jónsson H, Chang D, Der Sarkissian C, Ermini L, Ginolhac A, Albrechtsen A, Dupanloup I, Foucal A, Petersen B, Fumagalli M, Raghavan M, Seguin-Orlando A, Korneliussen TS, Velazquez AM, Stenderup J, Hoover CA, Rubin CJ, Alfarhan AH, Alquraishi SA, Al-Rasheid KA, MacHugh DE, Kalbfleisch T, MacLeod JN, Rubin EM, Sicheritz-Ponten T, Andersson L, Hofreiter M, Marques-Bonet T, Gilbert MT, Nielsen R, Excoffier L, Willerslev E, Shapiro B, Orlando L. (2014). Prehistoric genomes reveal the genetic foundation and cost of horse domestication. Proc Natl Acad Sci U S A, 111(52), E5661-E5669. https://doi.org/10.1073/pnas.1416991111

Publication

Proceedings of the National Academy of Sciences of the United States of America
ISSN: 1091-6490
NlmUniqueID: 7505876
Country: United States
Language: English
Volume: 111
Issue: 52
Pages: E5661-E5669

Researcher Affiliations

Schubert, Mikkel
  • Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350K Copenhagen, Denmark;
Jónsson, Hákon
  • Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350K Copenhagen, Denmark;
Chang, Dan
  • Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064;
Der Sarkissian, Clio
  • Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350K Copenhagen, Denmark;
Ermini, Luca
  • Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350K Copenhagen, Denmark;
Ginolhac, Aurélien
  • Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350K Copenhagen, Denmark;
Albrechtsen, Anders
  • The Bioinformatics Centre, Department of Biology, University of Copenhagen, 2200N Copenhagen, Denmark;
Dupanloup, Isabelle
  • Institute of Ecology and Evolution, University of Berne, 3012 Berne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland;
Foucal, Adrien
  • Institute of Ecology and Evolution, University of Berne, 3012 Berne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland;
Petersen, Bent
  • Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, 2800 Lyngby, Denmark;
Fumagalli, Matteo
  • UCL Genetics Institute, Department of Genetics, Evolution, and Environment, University College London, London WC1E 6BT, United Kingdom;
Raghavan, Maanasa
  • Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350K Copenhagen, Denmark;
Seguin-Orlando, Andaine
  • 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, Thorfinn S
  • Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350K Copenhagen, Denmark;
Velazquez, Amhed M V
  • Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350K Copenhagen, Denmark;
Stenderup, Jesper
  • Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350K Copenhagen, Denmark;
Hoover, Cindi A
  • Department of Energy Joint Genome Institute, Walnut Creek, CA 94598;
Rubin, Carl-Johan
  • Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23 Uppsala, Sweden;
Alfarhan, Ahmed H
  • Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia;
Alquraishi, Saleh A
  • Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia;
Al-Rasheid, Khaled A S
  • Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia;
MacHugh, David E
  • 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, Ted
  • Biochemistry and Molecular Biology, School of Medicine, University of Louisville, Louisville, KY 40292;
MacLeod, James N
  • Department of Veterinary Science, Gluck Equine Research Center, University of Kentucky, Lexington, KY 40546;
Rubin, Edward M
  • Department of Energy Joint Genome Institute, Walnut Creek, CA 94598;
Sicheritz-Ponten, Thomas
  • Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, 2800 Lyngby, Denmark;
Andersson, Leif
  • Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23 Uppsala, Sweden;
Hofreiter, Michael
  • Institute for Biochemistry and Biology, Faculty for Mathematics and Natural Sciences, University of Potsdam, 14476 Potsdam, Germany;
Marques-Bonet, Tomas
  • 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, M Thomas P
  • Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350K Copenhagen, Denmark;
Nielsen, Rasmus
  • Departments of Integrative Biology and Statistics, University of California, Berkeley, CA 94720.
Excoffier, Laurent
  • Institute of Ecology and Evolution, University of Berne, 3012 Berne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland;
Willerslev, Eske
  • Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350K Copenhagen, Denmark;
Shapiro, Beth
  • Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064;
Orlando, Ludovic
  • Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350K Copenhagen, Denmark; Lorlando@snm.ku.dk.

MeSH Terms

  • Animals
  • Animals, Domestic / genetics
  • Cardiovascular System / anatomy & histology
  • Dogs
  • Evolution, Molecular
  • Genome / physiology
  • Hindlimb / anatomy & histology
  • Hindlimb / physiology
  • Horses / anatomy & histology
  • Horses / genetics
  • Humans
  • Inbreeding
  • Russia

Grant Funding

  • 260372 / European Research Council

Conflict of Interest Statement

The authors declare no conflict of interest.

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