Refining the evolutionary tree of the horse Y chromosome

Bozlak, Elif; Radovic, Lara; Remer, Viktoria; Rigler, Doris; Allen, Lucy; Brem, Gottfried; Stalder, Gabrielle; Castaneda, Caitlin; Cothran, Gus; Raudsepp, Terje; Okuda, Yu; Moe, Kyaw Kyaw; Moe, Hla Hla; Kounnavongsa, Bounthavone; Keonouchanh, Soukanh; Van, Nguyen Huu; Vu, Van Hai; Shah, Manoj Kumar; Nishibori, Masahide; Kazymbet, Polat; Bakhtin, Meirat; Zhunushov, Asankadyr; Paul, Ripon Chandra; Dashnyam, Bumbein; Nozawa, Ken; Almarzook, Saria; Brockmann, Gudrun A.; Reissmann, Monika; Antczak, Douglas F.; Miller, Donald C.; Sadeghi, Raheleh; Butler-Wemken, Ines von; Kostaras, Nikos; Han, Haige; Manglai, Dugarjaviin; Abdurasulov, Abdugani; Sukhbaatar, Boldbaatar; Ropka-Molik, Katarzyna; Stefaniuk-Szmukier, Monika; Lopes, Maria Susana; Machado, Artur da Câmara; Kalashnikov, Valery V.; Kalinkova, Liliya; Zaitev, Alexander M.; Novoa-Bravo, Miguel; Lindgren, Gabriella; Brooks, Samantha; Rosa, Laura Patterson; Orlando, Ludovic; Juras, Rytis; Kunieda, Tetsuo; Wallner, Barbara

doi:10.1038/s41598-023-35539-0

Permalink : http://escholarship.lib.okayama-u.ac.jp/65545

ID	65545
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Author	Bozlak, Elif Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna Radovic, Lara Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna Remer, Viktoria Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna Rigler, Doris Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna Allen, Lucy Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna Brem, Gottfried Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna Stalder, Gabrielle Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna Castaneda, Caitlin School of Veterinary Medicine and Biomedical Sciences, Texas A&M University Cothran, Gus School of Veterinary Medicine and Biomedical Sciences, Texas A&M University Raudsepp, Terje School of Veterinary Medicine and Biomedical Sciences, Texas A&M University Okuda, Yu Museum of Dinosaur Research, Okayama University of Science Moe, Kyaw Kyaw Department of Pathology and Microbiology, University of Veterinary Science Moe, Hla Hla Department of Genetics and Animal Breeding, University of Veterinary Science Kounnavongsa, Bounthavone National Agriculture and Forestry Research Institute (Lao) Resources, Livestock Research Center Keonouchanh, Soukanh Faculty of Animal Science and Veterinary Medicine, University of Agriculture and Forestry, Hue University Van, Nguyen Huu Faculty of Animal Science and Veterinary Medicine, University of Agriculture and Forestry, Hue University Vu, Van Hai Faculty of Animal Science and Veterinary Medicine, University of Agriculture and Forestry, Hue University Shah, Manoj Kumar Faculty of Animal Science, Veterinary Science and Fisheries, Agriculture and Forestry University Nishibori, Masahide Graduate School of Integrated Sciences for Life, Hiroshima University Kazymbet, Polat Radiobiological Research Institute, JSC Astana Medical University Bakhtin, Meirat Institute of Biotechnology, National Academy of Sciences of the Kyrgyz Republic Zhunushov, Asankadyr Institute of Biotechnology, National Academy of Sciences of the Kyrgyz Republic Paul, Ripon Chandra Graduate School of Environmental and Life Science, Okayama University Dashnyam, Bumbein Institute of Biological Sciences, Mongolian Academy of Sciences Nozawa, Ken Primate Research Institute, Kyoto University Almarzook, Saria Albrecht Daniel Thaer‑Institut, Humboldt-Universität zu Berlin Brockmann, Gudrun A. Albrecht Daniel Thaer‑Institut, Humboldt-Universität zu Berlin Reissmann, Monika Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University Antczak, Douglas F. Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University Miller, Donald C. Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University Sadeghi, Raheleh Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University Butler-Wemken, Ines von Barb Horse Breeding Organisation VFZB E. V., Verein der Freunde und Züchter Des Berberpferdes E.V. Kostaras, Nikos Amaltheia Han, Haige Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, College of Animal Science, Equine Research Center, Inner Mongolia Agricultural University Manglai, Dugarjaviin Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, College of Animal Science, Equine Research Center, Inner Mongolia Agricultural University Abdurasulov, Abdugani Department of Agriculture, Faculty of Natural Sciences and Geography, Osh State University Sukhbaatar, Boldbaatar Sector of Surveillance and Diagnosis of Infectious Diseases, State Central Veterinary Laboratory Ropka-Molik, Katarzyna National Research Institute of Animal Production, Animal Molecular Biology Stefaniuk-Szmukier, Monika National Research Institute of Animal Production, Animal Molecular Biology Lopes, Maria Susana Biotechnology Centre of Azores, University of Azores Machado, Artur da Câmara Biotechnology Centre of Azores, University of Azores Kalashnikov, Valery V. All-Russian Research Institute for Horse Breeding Kalinkova, Liliya All-Russian Research Institute for Horse Breeding Zaitev, Alexander M. All-Russian Research Institute for Horse Breeding Novoa-Bravo, Miguel Genética Animal de Colombia SAS. Lindgren, Gabriella Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences Brooks, Samantha Department of Animal Science, UF Genetics Institute, University of Florida Rosa, Laura Patterson Department of Agriculture and Industry, Sul Ross State University Orlando, Ludovic Centre d’Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier Juras, Rytis School of Veterinary Medicine and Biomedical Sciences, Texas A&M University Kunieda, Tetsuo Graduate School of Environmental and Life Science, Okayama University Kaken ID researchmap Wallner, Barbara Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna
Abstract	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.
Note	The version of record of this article, first published in Scientific Reports, is available online at Publisher’s website: http://dx.doi.org/10.1038/s41598-023-35539-0
Published Date	2023-06-02
Publication Title	Scientific Reports
Volume	volume13
Issue	issue1
Publisher	Nature Portfolio
Start Page	8954
ISSN	2045-2322
Content Type	Journal Article
language	English
OAI-PMH Set	岡山大学
Copyright Holders	© The Author(s) 2023
File Version	publisher
PubMed ID	37268661
DOI	10.1038/s41598-023-35539-0
Web of Science KeyUT	001000613900036
Related Url	isVersionOf https://doi.org/10.1038/s41598-023-35539-0
License	http://creativecommons.org/licenses/by/4.0/
Citation	Bozlak, E., Radovic, L., Remer, V. et al. Refining the evolutionary tree of the horse Y chromosome. Sci Rep 13, 8954 (2023). https://doi.org/10.1038/s41598-023-35539-0