title: Evolutionary Genomics and Conservation of the Endangered Przewalski's Horse.
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.
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350K, Denmark.
authors.forename: Clio
authors.initials: C
authors.lastname: Der Sarkissian
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350K, Denmark.
authors.forename: Luca
authors.initials: L
authors.lastname: Ermini
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350K, Denmark.
authors.forename: Mikkel
authors.initials: M
authors.lastname: Schubert
authors.affiliation: Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720-3140, USA.
authors.forename: Melinda A
authors.initials: MA
authors.lastname: Yang
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350K, Denmark.
authors.forename: Pablo
authors.initials: P
authors.lastname: Librado
authors.affiliation: Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, London WC1E 6BT, UK.
authors.forename: Matteo
authors.initials: M
authors.lastname: Fumagalli
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350K, Denmark.
authors.forename: Hákon
authors.initials: H
authors.lastname: Jónsson
authors.affiliation: The Robert H. Smith Faculty of Agriculture, Food and Environment, The Koret School of Veterinary Medicine, The Hebrew University, Rehovot 76100, Israel.
authors.forename: Gila Kahila
authors.initials: GK
authors.lastname: Bar-Gal
authors.affiliation: Department of Biology, The Bioinformatics Centre, University of Copenhagen, Copenhagen 2200N, Denmark.
authors.forename: Anders
authors.initials: A
authors.lastname: Albrechtsen
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350K, Denmark.
authors.forename: Filipe G
authors.initials: FG
authors.lastname: Vieira
authors.affiliation: Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby 2800, Denmark.
authors.forename: Bent
authors.initials: B
authors.lastname: Petersen
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350K, Denmark.
authors.forename: Aurélien
authors.initials: A
authors.lastname: Ginolhac
authors.affiliation: National High-Throughput DNA Sequencing Centre, University of Copenhagen, Copenhagen 1353K, Denmark.
authors.forename: Andaine
authors.initials: A
authors.lastname: Seguin-Orlando
authors.affiliation: National High-Throughput DNA Sequencing Centre, University of Copenhagen, Copenhagen 1353K, Denmark.
authors.forename: Kim
authors.initials: K
authors.lastname: Magnussen
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350K, Denmark.
authors.forename: Antoine
authors.initials: A
authors.lastname: Fages
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350K, Denmark.
authors.forename: Cristina
authors.initials: C
authors.lastname: Gamba
authors.affiliation: ICREA at the Institut de Biologia Evolutiva (CSIC-University Pompeu Fabra), Barcelona 08003, Spain.
authors.forename: Belen
authors.initials: B
authors.lastname: Lorente-Galdos
authors.affiliation: The Robert H. Smith Faculty of Agriculture, Food and Environment, The Koret School of Veterinary Medicine, The Hebrew University, Rehovot 76100, Israel.
authors.forename: Sagi
authors.initials: S
authors.lastname: Polani
authors.affiliation: San Diego Zoo Institute for Conservation Research, Escondido, CA 92027, USA.
authors.forename: Cynthia
authors.initials: C
authors.lastname: Steiner
authors.affiliation: Agroscope, Swiss National Stud Farm, Avenches 1580, Switzerland.
authors.forename: Markus
authors.initials: M
authors.lastname: Neuditschko
authors.affiliation: Institute of Genetics, University of Bern, Bern 3001, Switzerland.
authors.forename: Vidhya
authors.initials: V
authors.lastname: Jagannathan
authors.affiliation: Station Biologique de la Tour du Valat, Arles 13200, France.
authors.forename: Claudia
authors.initials: C
authors.lastname: Feh
authors.affiliation: Department of Microbiology and Molecular Genetics, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel.
authors.forename: Charles L
authors.initials: CL
authors.lastname: Greenblatt
authors.affiliation: Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin 10315, Germany.
authors.forename: Arne
authors.initials: A
authors.lastname: Ludwig
authors.affiliation: Zoological Institute of the Russian Academy of Sciences, Saint-Petersburg 199034, Russia.
authors.forename: Natalia I
authors.initials: NI
authors.lastname: Abramson
authors.affiliation: EAZA Equid TAG, Köln 50668, Germany.
authors.forename: Waltraut
authors.initials: W
authors.lastname: Zimmermann
authors.affiliation: Martin-Luther-University Halle-Wittenberg, Museum of Domesticated Animals "Julius Kühn", Halle 06108, Germany.
authors.forename: Renate
authors.initials: R
authors.lastname: Schafberg
authors.affiliation: Zoological Institute of the Russian Academy of Sciences, Saint-Petersburg 199034, Russia; Institute of Applied Ecology of the North, North-Eastern Federal University, Yakutsk 677980, Russia.
authors.forename: Alexei
authors.initials: A
authors.lastname: Tikhonov
authors.affiliation: Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby 2800, Denmark.
authors.forename: Thomas
authors.initials: T
authors.lastname: Sicheritz-Ponten
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350K, Denmark.
authors.forename: Eske
authors.initials: E
authors.lastname: Willerslev
authors.affiliation: ICREA at the Institut de Biologia Evolutiva (CSIC-University Pompeu Fabra), Barcelona 08003, Spain; Centro Nacional de Analisis Genomico (CNAG-CRG), Barcelona 08023, Spain.
authors.forename: Tomas
authors.initials: T
authors.lastname: Marques-Bonet
authors.affiliation: San Diego Zoo Institute for Conservation Research, Escondido, CA 92027, USA.
authors.forename: Oliver A
authors.initials: OA
authors.lastname: Ryder
authors.affiliation: College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55108, USA.
authors.forename: Molly
authors.initials: M
authors.lastname: McCue
authors.affiliation: Agroscope, Swiss National Stud Farm, Avenches 1580, Switzerland.
authors.forename: Stefan
authors.initials: S
authors.lastname: Rieder
authors.affiliation: Institute of Genetics, University of Bern, Bern 3001, Switzerland.
authors.forename: Tosso
authors.initials: T
authors.lastname: Leeb
authors.affiliation: Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720-3140, USA.
authors.forename: Montgomery
authors.initials: M
authors.lastname: Slatkin
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350K, Denmark; Université de Toulouse, University Paul Sabatier (UPS), Laboratoire AMIS, CNRS UMR 5288, 37 Allées Jules Guesde, 31000 Toulouse, France. Electronic address: lorlando@snm.ku.dk.
authors.forename: Ludovic
authors.initials: L
authors.lastname: Orlando
mesh_terms: D000818:Animals; D000835:Animals, Wild / Q000235:genetics; D005075:Biological Evolution; D015415:Biomarkers / Q000097:blood; D001947:Breeding; D003247:Conservation of Natural Resources; D056727:Endangered Species; D014644:Genetic Variation; D023281:Genomics; D006736:Horses / Q000235:genetics*; D010802:Phylogeny; D017422:Sequence Analysis, DNA
chemical_list: D015415:Biomarkers