Evolutionary genomics and conservation of the endangered Przewalski's horse

Clio Der Sarkissian, Luca Ermini, Mikkel Schubert, Melinda A. Yang, Pablo Librado, Matteo Fumagalli, Hákon Jónsson, Gila Kahila Bar-Gal, Anders Albrechtsen, Filipe G. Vieira, Bent Petersen, Aurélien Ginolhac, Andaine Seguin-Orlando, Kim Magnussen, Antoine Fages, Cristina Gamba, Belen Lorente-Galdos, Sagi Polani, Cynthia Steiner, Markus NeuditschkoVidhya Jagannathan, Claudia Feh, Charles L. Greenblatt, Arne Ludwig, Natalia I. Abramson, Waltraut Zimmermann, Renate Schafberg, Alexei Tikhonov, Thomas Sicheritz-Ponten, Eske Willerslev, Tomas Marques-Bonet, Oliver A. Ryder, Molly McCue, Stefan Rieder, Tosso Leeb, Montgomery Slatkin, Ludovic Orlando

Research output: Contribution to journalArticlepeer-review

104 Scopus citations

Abstract

Przewalski's horses (PHs, Equus ferus ssp. przewalskii) were discovered in the Asian steppes in the 1870s and represent the last remaining true wild horses. PHs became extinct in the wild in the 1960s but survived in captivity, thanks to major conservation efforts. The current population is still endangered, with just 2,109 individuals, one-quarter of which are in Chinese and Mongolian reintroduction reserves [1]. These horses descend from a founding population of 12 wild-caught PHs and possibly up to four domesticated individuals [2-4]. With a stocky build, an erect mane, and stripped and short legs, they are phenotypically and behaviorally distinct from domesticated horses (DHs, Equus caballus). Here, we sequenced the complete genomes of 11 PHs, representing all founding lineages, and five historical specimens dated to 1878-1929 CE, including the Holotype. These were compared to the hitherto-most-extensive genome dataset characterized for horses, comprising 21 new genomes. We found that loci showing the most genetic differentiation with DHs were enriched in genes involved in metabolism, cardiac disorders, muscle contraction, reproduction, behavior, and signaling pathways. We also show that DH and PH populations split ∼45,000 years ago and have remained connected by gene-flow thereafter. Finally, we monitor the genomic impact of ∼110 years of captivity, revealing reduced heterozygosity, increased inbreeding, and variable introgression of domestic alleles, ranging from non-detectable to as much as 31.1%. This, together with the identification of ancestry informative markers and corrections to the International Studbook, establishes a framework for evaluating the persistence of genetic variation in future reintroduced populations.

Original languageEnglish (US)
Pages (from-to)2577-2583
Number of pages7
JournalCurrent Biology
Volume25
Issue number19
DOIs
StatePublished - Oct 5 2015

Bibliographical note

Funding Information:
We thank the staff of the Danish National High-Throughput DNA Sequencing Center for technical assistance. This work was supported by the Danish Council for Independent Research, Natural Sciences (FNU-4002-00152B); the Danish National Research Foundation (DNFR94); the Villum Fonden Blokstipendium (2014); the Lundbeck Foundation (R52-A5062); the Israel Science Foundation (1365/10); the German Research Council (DFG-LU852/7-4); the NIH (R01-GM40282); the Caesar Kleberg Foundation for Wildlife Conservation; the John and Beverly Stauffer Foundation; FP7 European Marie-Curie programs (CIG-293845, ITN-290344, IEF-328024, IEF-299176, and IEF-302617); a National Science Foundation Graduate Research Fellowship; and the Human Frontier Science Program (LT000320/2014).

Publisher Copyright:
© 2015 Elsevier Ltd All rights reserved.

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