Article (Scientific journals)
Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse.
Orlando, Ludovic; Ginolhac, Aurélien; Zhang, Guojie et al.
2013In Nature, 499 (7456), p. 74-8
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Keywords :
Animals; Conservation of Natural Resources; DNA/analysis/genetics; Endangered Species; Equidae/classification/genetics; Evolution, Molecular; Fossils; Genetic Variation/genetics; Genome/genetics; History, Ancient; Horses/classification/genetics; Phylogeny; Proteins/analysis/chemistry/genetics; Yukon Territory
Abstract :
[en] 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.
Disciplines :
Biochemistry, biophysics & molecular biology
Author, co-author :
Orlando, Ludovic 
Ginolhac, Aurélien   ;  University of Copenhagen > Centre for Geogenetics
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
Roed, Knut H.
Eisenmann, Vera
Rubin, Carl J.
Miller, Donald C.
Antczak, Douglas F.
Bertelsen, Mads F.
Brunak, Soren
Al-Rasheid, Khaled A. S.
Ryder, Oliver
Andersson, Leif
Mundy, John
Krogh, Anders
Gilbert, M. Thomas P.
Kjaer, Kurt
Sicheritz-Ponten, Thomas
Jensen, Lars Juhl
Olsen, Jesper V.
Hofreiter, Michael
Nielsen, Rasmus
Shapiro, Beth
Willerslev, Eske
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 These authors have contributed equally to this work.
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Title :
Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse.
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Nature Publishing Group, London, United Kingdom
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Peer Reviewed verified by ORBi
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