Refining the evolutionary tree of the horse Y chromosome
Bozlak E. Radovic L. Remer V. Rigler D. Allen L. Brem G. Stalder G. Castaneda C. Cothran G. Raudsepp T. Okuda Y. Moe K.K. Moe H.H. Kounnavongsa B. Keonouchanh S. Van N.H. Vu V.H. Shah M.K. Nishibori M. Kazymbet P. Bakhtin M. Zhunushov A. Paul R.C. Dashnyam B. Nozawa K. Almarzook S. Brockmann G.A. Reissmann M. Antczak D.F. Miller D.C. Sadeghi R. von Butler-Wemken I. Kostaras N. Han H. Manglai D. Abdurasulov A. Sukhbaatar B. Ropka-Molik K. Stefaniuk-Szmukier M. Lopes M.S. da Câmara Machado A. Kalashnikov V.V. Kalinkova L. Zaitev A.M. Novoa‐Bravo M. Lindgren G. Brooks S. Rosa L.P. Orlando L. Juras R. Kunieda T. Wallner B.
December 2023Nature Research
Scientific Reports
2023#13Issue 1
The Y chromosome carries information about the demography of paternal lineages, and thus, can prove invaluable for retracing both the evolutionary trajectory of wild animals and the breeding history of domesticates. In horses, the Y chromosome shows a limited, but highly informative, sequence diversity, supporting the increasing breeding influence of Oriental lineages during the last 1500 years. Here, we augment the primary horse Y-phylogeny, which is currently mainly based on modern horse breeds of economic interest, with haplotypes (HT) segregating in remote horse populations around the world. We analyze target enriched sequencing data of 5 Mb of the Y chromosome from 76 domestic males, together with 89 whole genome sequenced domestic males and five Przewalski’s horses from previous studies. The resulting phylogeny comprises 153 HTs defined by 2966 variants and offers unprecedented resolution into the history of horse paternal lineages. It reveals the presence of a remarkable number of previously unknown haplogroups in Mongolian horses and insular populations. Phylogenetic placement of HTs retrieved from 163 archaeological specimens further indicates that most of the present-day Y-chromosomal variation evolved after the domestication process that started around 4200 years ago in the Western Eurasian steppes. Our comprehensive phylogeny significantly reduces ascertainment bias and constitutes a robust evolutionary framework for analyzing horse population dynamics and diversity.
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Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, 1210, Austria
Vienna Graduate School of Population Genetics, University of Veterinary Medicine Vienna, Vienna, 1210, Austria
Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Vienna, 1210, Austria
School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, 77843, TX, United States
Museum of Dinosaur Research, Okayama University of Science, Okayama, Japan
Department of Pathology and Microbiology, University of Veterinary Science, Nay Pyi Taw, Yezin, 05282, Myanmar
Department of Genetics and Animal Breeding, University of Veterinary Science, Nay Pyi Taw, Yezin, 05282, Myanmar
National Agriculture and Forestry Research Institute (Lao) Resources, Livestock Research Center, Xaythany District, Vientiane, Laos
Faculty of Animal Science and Veterinary Medicine, University of Agriculture and Forestry, Hue University, Hue, Viet Nam
Faculty of Animal Science, Veterinary Science and Fisheries, Agriculture and Forestry University, Rampur, 44209, Nepal
Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-8528, Japan
Radiobiological Research Institute, JSC Astana Medical University, Astana, 010000, Kazakhstan
Institute of Biotechnology, National Academy of Sciences of the Kyrgyz Republic, Bishkek, 720071, Kyrgyzstan
Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
Faculty of Animal Science and Veterinary Medicine, Patuakhali Science and Technology University, Barishal, Bangladesh
Institute of Biological Sciences, Mongolian Academy of Sciences, Ulaan Baator, Mongolia
Primate Research Institute, Kyoto University, Aichi, Japan
Albrecht Daniel Thaer-Institut, Humboldt-Universität zu Berlin, Berlin, 10115, Germany
Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, 14853, NY, United States
Barb Horse Breeding Organisation VFZB E. V., Verein der Freunde und Züchter Des Berberpferdes E.V., Kirchgasse 11, Schmalenberg, 67718, Germany
Amaltheia, Argirokastrou 51, Papagou, 15669, Greece
Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, College of Animal Science, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, 010018, China
Department of Agriculture, Faculty of Natural Sciences and Geography, Osh State University, Osh, 723500, Kyrgyzstan
Sector of Surveillance and Diagnosis of Infectious Diseases, State Central Veterinary Laboratory, Ulaanbaatar, 17024, Mongolia
National Research Institute of Animal Production, Animal Molecular Biology, Cracow, 31-047, Poland
Biotechnology Centre of Azores, University of Azores, Angra do Heroísmo, 9700-042, Portugal
All-Russian Research Institute for Horse Breeding, Ryazan, 391105, Russian Federation
Genética Animal de Colombia SAS., Av. Calle 26 #69-76, Bogotá, 111071, Colombia
Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, 75007, Sweden
Department of Biosystems, Center for Animal Breeding and Genetics, KU Leuven, Leuven, 3001, Belgium
Department of Animal Science, UF Genetics Institute, University of Florida, Gainesville, 32610, FL, United States
Department of Agriculture and Industry, Sul Ross State University, Alpine, 79832, TX, United States
Centre d’Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier, Toulouse, France
Faculty of Veterinary Medicine, Okayama University of Science, Imabari, Japan
Institute of Animal Breeding and Genetics
Vienna Graduate School of Population Genetics
Research Institute of Wildlife Ecology
School of Veterinary Medicine and Biomedical Sciences
Museum of Dinosaur Research
Department of Pathology and Microbiology
Department of Genetics and Animal Breeding
National Agriculture and Forestry Research Institute (Lao) Resources
Faculty of Animal Science and Veterinary Medicine
Faculty of Animal Science
Graduate School of Integrated Sciences for Life
Radiobiological Research Institute
Institute of Biotechnology
Graduate School of Environmental and Life Science
Faculty of Animal Science and Veterinary Medicine
Institute of Biological Sciences
Primate Research Institute
Albrecht Daniel Thaer-Institut
Baker Institute for Animal Health
Barb Horse Breeding Organisation VFZB E. V.
Amaltheia
Inner Mongolia Key Laboratory of Equine Genetics
Department of Agriculture
Sector of Surveillance and Diagnosis of Infectious Diseases
National Research Institute of Animal Production
Biotechnology Centre of Azores
All-Russian Research Institute for Horse Breeding
Genética Animal de Colombia SAS.
Department of Animal Breeding and Genetics
Department of Biosystems
Department of Animal Science
Department of Agriculture and Industry
Centre d’Anthropobiologie et de Génomique de Toulouse
Faculty of Veterinary Medicine
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