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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
general
Recalibrating equus evolution using the genome sequence of an early Middle Pleistocene horse
Nature, Volume 499, No. 7456, Year 2013
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Description
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. © 2013 Macmillan Publishers Limited. All rights reserved.
Authors & Co-Authors
Orlando, Ludovic A.A.
Denmark, Copenhagen
Statens Naturhistoriske Museum
Ginolhac, Aurélien
Denmark, Copenhagen
Statens Naturhistoriske Museum
Zhang, Guojie
China, Shenzhen
Bgi-shenzhen
Froese, Duane
Canada, Edmonton
University of Alberta
Albrechtsen, Anders
Denmark, Copenhagen
Københavns Universitet
Stiller, Mathias
United States, Santa Cruz
University of California, Santa Cruz
Schubert, Mikkel
Denmark, Copenhagen
Statens Naturhistoriske Museum
Cappellini, Enrico
Denmark, Copenhagen
Statens Naturhistoriske Museum
Petersen, Bent
Denmark, Lyngby
Technical University of Denmark
Moltke, Ida
Denmark, Copenhagen
Københavns Universitet
United States, Chicago
The University of Chicago
Johnson, Philip L.F.
United States, Atlanta
Emory University
Fumagalli, Matteo
United States, Berkeley
University of California, Berkeley
Vilstrup, Julia T.
Denmark, Copenhagen
Statens Naturhistoriske Museum
Raghavan, Maanasa
Denmark, Copenhagen
Statens Naturhistoriske Museum
Korneliussen, Thorfinn Sand
Denmark, Copenhagen
Statens Naturhistoriske Museum
Malaspinas, Anna Sapfo
Denmark, Copenhagen
Statens Naturhistoriske Museum
Vogt, Josef Korbinian
Denmark, Lyngby
Technical University of Denmark
Szklarczyk, Damian
Denmark, Copenhagen
Novo Nordisk Foundation Center for Protein Research
Macao, Taipa
Macau University of Science and Technology
Kelstrup, Christian Dahl
Denmark, Copenhagen
Novo Nordisk Foundation Center for Protein Research
Vinther, Jakob
United States, Austin
Jackson School of Geosciences
Switzerland, Zurich
Universität Zürich
Dolocan, Andrei
United States, Austin
The University of Texas at Austin
Stenderup, Jesper
Denmark, Copenhagen
Statens Naturhistoriske Museum
Velazquez, Amhed M.V.
Denmark, Copenhagen
Statens Naturhistoriske Museum
Cahill, James
United States, Santa Cruz
University of California, Santa Cruz
Rasmussen, Morten
Denmark, Copenhagen
Statens Naturhistoriske Museum
Wang, Xiaoli
China, Shenzhen
Bgi-shenzhen
Min, Jiumeng
China, Shenzhen
Bgi-shenzhen
Zazula, Grant D.
Canada, Whitehorse
Gouvernement du Yukon
Seguin-Orlando, Andaine
Denmark, Copenhagen
Statens Naturhistoriske Museum
Denmark, Copenhagen
Københavns Universitet
Mortensen, Cecilie D.
Denmark, Copenhagen
Statens Naturhistoriske Museum
Denmark, Copenhagen
Københavns Universitet
Magnussen, Kim
Denmark, Copenhagen
Statens Naturhistoriske Museum
Denmark, Copenhagen
Københavns Universitet
Thompson, John F.
United States, Providence
Nabsys 2.0 Llc
Weinstock, Jacobo
United Kingdom, Southampton
University of Southampton
Gregersen, Kristian
Denmark, Copenhagen
Statens Naturhistoriske Museum
Røed, Knut H.
Norway, As
Norges Miljø- og Biovitenskapelige Universitet
Eisenmann, Véra
France, Paris
Centre de Recherche en Paléontologie - Paris
Rubin, Carl J.
Sweden, Uppsala
Uppsala Universitet
Miller, Donald C.
United States, Ithaca
Cornell University
Antczak, Douglas F.
United States, Ithaca
Cornell University
Bertelsen, Mads F.
Denmark, Frederiksberg
Copenhagen Zoo
Brunak, Søren B.
Denmark, Lyngby
Technical University of Denmark
Denmark, Lyngby
The Novo Nordisk Foundation Center for Biosustainability
Al-Rasheid, Khaled A.S.
Saudi Arabia, Riyadh
College of Sciences
Ryder, Oliver A.
United States, San Diego
San Diego Zoo Wildlife Alliance
Andersson, Leif S.
Sweden, Uppsala
Uppsala Universitet
Mundy, John
Denmark, Copenhagen
Københavns Universitet
Krogh, Anders
Denmark, Copenhagen
Statens Naturhistoriske Museum
Denmark, Copenhagen
Københavns Universitet
Gilbert, Thomas M.P.
Denmark, Copenhagen
Statens Naturhistoriske Museum
Kjær, Kurt
Denmark, Copenhagen
Statens Naturhistoriske Museum
Sicheritz-Pontén, Thomas E.
Denmark, Lyngby
Technical University of Denmark
Denmark, Lyngby
The Novo Nordisk Foundation Center for Biosustainability
Jensen, Lars Juhl
Denmark, Copenhagen
Novo Nordisk Foundation Center for Protein Research
Olsen, Jesper Velgaard
Denmark, Copenhagen
Novo Nordisk Foundation Center for Protein Research
Hofreiter, Michael
United Kingdom, York
University of York
Nielsen, Rasmus Wedel
United States, Berkeley
University of California, Berkeley
Shapiro, Beth
United States, Santa Cruz
University of California, Santa Cruz
Wang, Jun
China, Shenzhen
Bgi-shenzhen
Denmark, Copenhagen
Københavns Universitet
Saudi Arabia, Jeddah
King Abdulaziz University
Macao, Taipa
Macau University of Science and Technology
Willerslev, Eske
Denmark, Copenhagen
Statens Naturhistoriske Museum
United Kingdom, Bristol
University of Bristol
Statistics
Citations: 733
Authors: 56
Affiliations: 28
Identifiers
Doi:
10.1038/nature12323
ISSN:
00280836
e-ISSN:
14764687
Research Areas
Environmental
Genetics And Genomics
Health System And Policy
Study Design
Cross Sectional Study