Orlando, Ludovic Antoine Alexandre5; Ginolhac, Aurélien5; Zhang, Guojie6; Froese, Duane7; Albrechtsen, Anders5; Stiller, Mathias8; Schubert, Mikkel5; Cappellini, Enrico5; Petersen, Bent1; Moltke, Ida5; Johnson, Philip L F23; Fumagalli, Matteo8; Vilstrup, Julia T5; Raghavan, Maanasa5; Korneliussen, Thorfinn Sand5; Malaspinas, Anna Sapfo5; Vogt, Josef Korbinian1; Szklarczyk, Damian5; Kelstrup, Christian5; Vinther, Jakob10; Dolocan, Andrei10; Stenderup, Jesper5; Velazquez, Amhed M. V.5; Cahill, James8; Rasmussen, Morten5; Wang, Xiaoli6; Min, Jiumeng6; Zazula, Grant D11; Seguin-Orlando, Andaine5; Mortensen, Cecilie5; Magnussen, Kim5; Thompson, John F12; Weinstock, Jacobo13; Gregersen, Magnus Kristian5; Røed, Knut H14; Eisenmann, Véra15; Rubin, Carl J16; Miller, Donald C24; Antczak, Douglas F24; Bertelsen, Mads18; Brunak, Søren1; Al-Rasheid, Khaled A S25; Ryder, Oliver20; Andersson, Leif16; Mundy, John5; Krogh, Anders5; Gilbert, Marcus Thomas Pius5; Kjær, Kurt H.5; Sicheritz-Pontén, Thomas1; Jensen, Lars Juhl5; Olsen, Jesper5; Hofreiter, Michael21; Nielsen, Rasmus8; Shapiro, Beth8; Wang, Jun26; Willerslev, Eske5
1 Department of Systems Biology, Technical University of Denmark2 Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark3 Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark4 CFB - Metagenomic Systems Biology, Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark5 University of Copenhagen6 BGI-Shenzhen7 University of Alberta8 University of California9 Emory University10 University of Texas11 Government of Yukon12 NABsys Inc13 University of Southampton14 Norwegian School of Veterinary Science15 Centre National de la Recherche Scientifique16 Uppsala University17 Cornell University18 Copenhagen Zoo19 King Saud University20 San Diego Zoo’s Institute for Conservation Research21 University of York22 King Abdulaziz University23 Emory University24 Cornell University25 King Saud University26 King Abdulaziz University
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.