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

Research output: Research - peer-reviewJournal article – Annual report year: 2013

  • Author: Orlando, Ludovic Antoine Alexandre

    University of Copenhagen, Denmark

  • Author: Ginolhac, Aurélien

    University of Copenhagen, Denmark

  • Author: Zhang, Guojie

    BGI-Shenzhen , Denmark

  • Author: Froese, Duane

    University of Alberta, Canada

  • Author: Albrechtsen, Anders

    University of Copenhagen, Denmark

  • Author: Stiller, Mathias

    University of California, United States

  • Author: Schubert, Mikkel

    University of Copenhagen, Denmark

  • Author: Cappellini, Enrico

    University of Copenhagen, Denmark

  • Author: Petersen, Bent

    Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark

  • Author: Moltke, Ida

    University of Copenhagen, Denmark

  • Author: Johnson, Philip L F

    Emory University, United States

  • Author: Fumagalli, Matteo

    University of California, United States

  • Author: Vilstrup, Julia T.

    University of Copenhagen, Denmark

  • Author: Raghavan, Maanasa

    University of Copenhagen, Denmark

  • Author: Korneliussen, Thorfinn Sand

    University of Copenhagen, Denmark

  • Author: Malaspinas, Anna Sapfo

    University of Copenhagen, Denmark

  • Author: Vogt, Josef Korbinian

    Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark

  • Author: Szklarczyk, Damian

    University of Copenhagen, Denmark

  • Author: Kelstrup, Christian

    University of Copenhagen, Denmark

  • Author: Vinther, Jakob

    University of Texas, United States

  • Author: Dolocan, Andrei

    University of Texas, United States

  • Author: Stenderup, Jesper

    University of Copenhagen, Denmark

  • Author: Velazquez, Amhed M. V.

    University of Copenhagen, Denmark

  • Author: Cahill, James

    University of California, United States

  • Author: Rasmussen, Morten

    University of Copenhagen, Denmark

  • Author: Wang, Xiaoli

    BGI-Shenzhen , China

  • Author: Min, Jiumeng

    BGI-Shenzhen , China

  • Author: Zazula, Grant D

    Government of Yukon, Canada

  • Author: Seguin-Orlando, Andaine

    University of Copenhagen, Denmark

  • Author: Mortensen, Cecilie

    University of Copenhagen, Denmark

  • Author: Magnussen, Kim

    University of Copenhagen, Denmark

  • Author: Thompson, John F

    Nabsys 2.0 LLC, United States

  • Author: Weinstock, Jacobo

    University of Southampton, United Kingdom

  • Author: Gregersen, Magnus Kristian

    University of Copenhagen, Denmark

  • Author: Røed, Knut H

    Norwegian School of Veterinary Science, Norway

  • Author: Eisenmann, Véra

    Centre National de la Recherche Scientifique, France

  • Author: Rubin, Carl J

    Uppsala University, Sweden

  • Author: Miller, Donald C

    Cornell University, United States

  • Author: Antczak, Douglas F

    Cornell University, United States

  • Author: Bertelsen, Mads

    Copenhagen Zoo, Denmark

  • Author: Brunak, Søren

    CFB - Metagenomic Systems Biology, Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark

  • Author: Al-Rasheid, Khaled A S

    King Saud University, Saudi Arabia

  • Author: Ryder, Oliver

    San Diego Zoo’s Institute for Conservation Research, United States

  • Author: Andersson, Leif

    Uppsala University, Sweden

  • Author: Mundy, John

    University of Copenhagen, Denmark

  • Author: Krogh, Anders

    University of Copenhagen, Denmark

  • Author: Gilbert, Marcus Thomas Pius

    University of Copenhagen, Denmark

  • Author: Kjær, Kurt H.

    University of Copenhagen, Denmark

  • Author: Sicheritz-Pontén, Thomas

    Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark

  • Author: Jensen, Lars Juhl

    University of Copenhagen, Denmark

  • Author: Olsen, Jesper

    University of Copenhagen, Denmark

  • Author: Hofreiter, Michael

    University of York, United Kingdom

  • Author: Nielsen, Rasmus

    University of California, United States

  • Author: Shapiro, Beth

    University of California, United States

  • Author: Wang, Jun

    King Abdulaziz University, Saudi Arabia

  • Author: Willerslev, Eske

    University of Copenhagen, Denmark

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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.
Original languageEnglish
JournalNature
Volume499
Pages (from-to)74-78
ISSN0028-0836
DOIs
StatePublished - 2013
CitationsWeb of Science® Times Cited: 280
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