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Nature2013; 499(7456); 74-78; doi: 10.1038/nature12323

Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse.

Abstract: The rich fossil record of equids has made them a model for evolutionary processes. Here we present a 1.12-times coverage draft genome from a horse bone recovered from permafrost dated to approximately 560-780 thousand years before present (kyr BP). Our data represent the oldest full genome sequence determined so far by almost an order of magnitude. For comparison, we sequenced the genome of a Late Pleistocene horse (43 kyr BP), and modern genomes of five domestic horse breeds (Equus ferus caballus), a Przewalski's horse (E. f. przewalskii) and a donkey (E. asinus). Our analyses suggest that the Equus lineage giving rise to all contemporary horses, zebras and donkeys originated 4.0-4.5 million years before present (Myr BP), twice the conventionally accepted time to the most recent common ancestor of the genus Equus. We also find that horse population size fluctuated multiple times over the past 2 Myr, particularly during periods of severe climatic changes. We estimate that the Przewalski's and domestic horse populations diverged 38-72 kyr BP, and find no evidence of recent admixture between the domestic horse breeds and the Przewalski's horse investigated. This supports the contention that Przewalski's horses represent the last surviving wild horse population. We find similar levels of genetic variation among Przewalski's and domestic populations, indicating that the former are genetically viable and worthy of conservation efforts. We also find evidence for continuous selection on the immune system and olfaction throughout horse evolution. Finally, we identify 29 genomic regions among horse breeds that deviate from neutrality and show low levels of genetic variation compared to the Przewalski's horse. Such regions could correspond to loci selected early during domestication.
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Publication Date: 2013-06-26 PubMed ID: 23803765DOI: 10.1038/nature12323Google Scholar: Lookup
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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.

The researchers sequenced the genome of a horse fossil dating back between 560-780 thousand years ago, providing valuable data for the study of the evolution of equids. Comparing it with other horse genomes – both modern and prehistoric – they concluded that the lineage of all current horses, zebras and donkeys started 4-4.5 million years ago, much earlier than previously thought. They noted population size shifts aligning with major climate changes, analyzed the divergence time between Przewalski’s and domestic horses, and identified areas of the genome potentially affected by early domestication.

Extraction of Ancient DNA

  • The researchers obtained a preserved horse bone from permafrost dating back to the early Middle Pleistocene Era (approximately 560-780 thousand years before present). From this bone, they extracted and sequenced the genome, producing the oldest full genome sequence currently available, by almost an order of magnitude.

Comparative Genomics

  • For comparison against the ancient genome sequence, the genomes of several other horses were sequenced. These included another prehistoric Late Pleistocene horse from 43 thousand years ago, five modern domestic horse breeds (Equus ferus caballus), a Przewalski’s horse (E. f. przewalskii) and a donkey (E. asinus).
  • The scientists then analyzed the similarities and differences among these genomes. They found that the lineage of all extant horses, zebras, and donkeys likely originated 4-4.5 million years ago, which is twice the conventionally-accepted age.

Insights into Population Dynamics and Evolution

  • The research also noted that horse populations experienced numerous changes in size over the past two million years. This was especially true during periods of significant climate change.
  • The team’s estimates suggest that Przewalski’s horse and domestic horse populations diverged somewhere between 38,000 and 72,000 years before present. They found no recent genetic mingling between these two populations, enhancing the existing belief that Przewalski’s horses are the last surviving wild horse population.
  • Genetic variability within the Przewalski’s horse population was found to be similar to that observed in domestic horse populations, indicating that the Przewalski’s horse is genetically fit and should be the focus of conservation efforts.

Selection and Domestication

  • The researchers also examined the continuing selection on the horse immune system and sense of smell throughout their evolution.
  • By comparing the genome of modern domestic horses and Przewalski’s horse, they identified 29 regions that deviate from neutrality and show low genetic variation compared to the Przewalski’s horse. These regions could be the result of selection pressures during early domestication.

Cite This Article

APA
Orlando L, Ginolhac A, Zhang G, Froese D, Albrechtsen A, Stiller M, Schubert M, Cappellini E, Petersen B, Moltke I, Johnson PL, Fumagalli M, Vilstrup JT, Raghavan M, Korneliussen T, Malaspinas AS, Vogt J, Szklarczyk D, Kelstrup CD, Vinther J, Dolocan A, Stenderup J, Velazquez AM, Cahill J, Rasmussen M, Wang X, Min J, Zazula GD, Seguin-Orlando A, Mortensen C, Magnussen K, Thompson JF, Weinstock J, Gregersen K, Røed KH, Eisenmann V, Rubin CJ, Miller DC, Antczak DF, Bertelsen MF, Brunak S, Al-Rasheid KA, Ryder O, Andersson L, Mundy J, Krogh A, Gilbert MT, Kjær K, Sicheritz-Ponten T, Jensen LJ, Olsen JV, Hofreiter M, Nielsen R, Shapiro B, Wang J, Willerslev E. (2013). Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. Nature, 499(7456), 74-78. https://doi.org/10.1038/nature12323

Publication

Nature
ISSN: 1476-4687
NlmUniqueID: 0410462
Country: England
Language: English
Volume: 499
Issue: 7456
Pages: 74-78

Researcher Affiliations

Orlando, Ludovic
  • Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark. Lorlando@snm.ku.dk
Ginolhac, Aurélien
    Zhang, Guojie
      Froese, Duane
        Albrechtsen, Anders
          Stiller, Mathias
            Schubert, Mikkel
              Cappellini, Enrico
                Petersen, Bent
                  Moltke, Ida
                    Johnson, Philip L F
                      Fumagalli, Matteo
                        Vilstrup, Julia T
                          Raghavan, Maanasa
                            Korneliussen, Thorfinn
                              Malaspinas, Anna-Sapfo
                                Vogt, Josef
                                  Szklarczyk, Damian
                                    Kelstrup, Christian D
                                      Vinther, Jakob
                                        Dolocan, Andrei
                                          Stenderup, Jesper
                                            Velazquez, Amhed M V
                                              Cahill, James
                                                Rasmussen, Morten
                                                  Wang, Xiaoli
                                                    Min, Jiumeng
                                                      Zazula, Grant D
                                                        Seguin-Orlando, Andaine
                                                          Mortensen, Cecilie
                                                            Magnussen, Kim
                                                              Thompson, John F
                                                                Weinstock, Jacobo
                                                                  Gregersen, Kristian
                                                                    Røed, Knut H
                                                                      Eisenmann, Véra
                                                                        Rubin, Carl J
                                                                          Miller, Donald C
                                                                            Antczak, Douglas F
                                                                              Bertelsen, Mads F
                                                                                Brunak, Søren
                                                                                  Al-Rasheid, Khaled A S
                                                                                    Ryder, Oliver
                                                                                      Andersson, Leif
                                                                                        Mundy, John
                                                                                          Krogh, Anders
                                                                                            Gilbert, M Thomas P
                                                                                              Kjær, Kurt
                                                                                                Sicheritz-Ponten, Thomas
                                                                                                  Jensen, Lars Juhl
                                                                                                    Olsen, Jesper V
                                                                                                      Hofreiter, Michael
                                                                                                        Nielsen, Rasmus
                                                                                                          Shapiro, Beth
                                                                                                            Wang, Jun
                                                                                                              Willerslev, Eske

                                                                                                                MeSH Terms

                                                                                                                • Animals
                                                                                                                • Conservation of Natural Resources
                                                                                                                • DNA / analysis
                                                                                                                • DNA / genetics
                                                                                                                • Endangered Species
                                                                                                                • Equidae / classification
                                                                                                                • Equidae / genetics
                                                                                                                • Evolution, Molecular
                                                                                                                • Fossils
                                                                                                                • Genetic Variation / genetics
                                                                                                                • Genome / genetics
                                                                                                                • History, Ancient
                                                                                                                • Horses / classification
                                                                                                                • Horses / genetics
                                                                                                                • Phylogeny
                                                                                                                • Proteins / analysis
                                                                                                                • Proteins / chemistry
                                                                                                                • Proteins / genetics
                                                                                                                • Yukon Territory

                                                                                                                Grant Funding

                                                                                                                • R01 HG003229 / NHGRI NIH HHS
                                                                                                                • RC2 HG005598 / NHGRI NIH HHS

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