Scientific Reports (Jun 2023)
Refining the evolutionary tree of the horse Y chromosome
- Elif Bozlak,
- Lara Radovic,
- Viktoria Remer,
- Doris Rigler,
- Lucy Allen,
- Gottfried Brem,
- Gabrielle Stalder,
- Caitlin Castaneda,
- Gus Cothran,
- Terje Raudsepp,
- Yu Okuda,
- Kyaw Kyaw Moe,
- Hla Hla Moe,
- Bounthavone Kounnavongsa,
- Soukanh Keonouchanh,
- Nguyen Huu Van,
- Van Hai Vu,
- Manoj Kumar Shah,
- Masahide Nishibori,
- Polat Kazymbet,
- Meirat Bakhtin,
- Asankadyr Zhunushov,
- Ripon Chandra Paul,
- Bumbein Dashnyam,
- Ken Nozawa,
- Saria Almarzook,
- Gudrun A. Brockmann,
- Monika Reissmann,
- Douglas F. Antczak,
- Donald C. Miller,
- Raheleh Sadeghi,
- Ines von Butler-Wemken,
- Nikos Kostaras,
- Haige Han,
- Dugarjaviin Manglai,
- Abdugani Abdurasulov,
- Boldbaatar Sukhbaatar,
- Katarzyna Ropka-Molik,
- Monika Stefaniuk-Szmukier,
- Maria Susana Lopes,
- Artur da Câmara Machado,
- Valery V. Kalashnikov,
- Liliya Kalinkova,
- Alexander M. Zaitev,
- Miguel Novoa‐Bravo,
- Gabriella Lindgren,
- Samantha Brooks,
- Laura Patterson Rosa,
- Ludovic Orlando,
- Rytis Juras,
- Tetsuo Kunieda,
- Barbara Wallner
Affiliations
- Elif Bozlak
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna
- Lara Radovic
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna
- Viktoria Remer
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna
- Doris Rigler
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna
- Lucy Allen
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna
- Gottfried Brem
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna
- Gabrielle Stalder
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna
- Caitlin Castaneda
- School of Veterinary Medicine and Biomedical Sciences, Texas A&M University
- Gus Cothran
- School of Veterinary Medicine and Biomedical Sciences, Texas A&M University
- Terje Raudsepp
- School of Veterinary Medicine and Biomedical Sciences, Texas A&M University
- Yu Okuda
- Museum of Dinosaur Research, Okayama University of Science
- Kyaw Kyaw Moe
- Department of Pathology and Microbiology, University of Veterinary Science
- Hla Hla Moe
- Department of Genetics and Animal Breeding, University of Veterinary Science
- Bounthavone Kounnavongsa
- National Agriculture and Forestry Research Institute (Lao) Resources, Livestock Research Center
- Soukanh Keonouchanh
- Faculty of Animal Science and Veterinary Medicine, University of Agriculture and Forestry, Hue University
- Nguyen Huu Van
- Faculty of Animal Science and Veterinary Medicine, University of Agriculture and Forestry, Hue University
- Van Hai Vu
- Faculty of Animal Science and Veterinary Medicine, University of Agriculture and Forestry, Hue University
- Manoj Kumar Shah
- Faculty of Animal Science, Veterinary Science and Fisheries, Agriculture and Forestry University
- Masahide Nishibori
- Graduate School of Integrated Sciences for Life, Hiroshima University
- Polat Kazymbet
- Radiobiological Research Institute, JSC Astana Medical University
- Meirat Bakhtin
- Institute of Biotechnology, National Academy of Sciences of the Kyrgyz Republic
- Asankadyr Zhunushov
- Institute of Biotechnology, National Academy of Sciences of the Kyrgyz Republic
- Ripon Chandra Paul
- Graduate School of Environmental and Life Science, Okayama University
- Bumbein Dashnyam
- Institute of Biological Sciences, Mongolian Academy of Sciences
- Ken Nozawa
- Primate Research Institute, Kyoto University
- Saria Almarzook
- Albrecht Daniel Thaer-Institut, Humboldt-Universität zu Berlin
- Gudrun A. Brockmann
- Albrecht Daniel Thaer-Institut, Humboldt-Universität zu Berlin
- Monika Reissmann
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University
- Douglas F. Antczak
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University
- Donald C. Miller
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University
- Raheleh Sadeghi
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University
- Ines von Butler-Wemken
- Barb Horse Breeding Organisation VFZB E. V., Verein der Freunde und Züchter Des Berberpferdes E.V.
- Nikos Kostaras
- Amaltheia
- Haige Han
- Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, College of Animal Science, Equine Research Center, Inner Mongolia Agricultural University
- Dugarjaviin Manglai
- Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, College of Animal Science, Equine Research Center, Inner Mongolia Agricultural University
- Abdugani Abdurasulov
- Department of Agriculture, Faculty of Natural Sciences and Geography, Osh State University
- Boldbaatar Sukhbaatar
- Sector of Surveillance and Diagnosis of Infectious Diseases, State Central Veterinary Laboratory
- Katarzyna Ropka-Molik
- National Research Institute of Animal Production, Animal Molecular Biology
- Monika Stefaniuk-Szmukier
- National Research Institute of Animal Production, Animal Molecular Biology
- Maria Susana Lopes
- Biotechnology Centre of Azores, University of Azores
- Artur da Câmara Machado
- Biotechnology Centre of Azores, University of Azores
- Valery V. Kalashnikov
- All-Russian Research Institute for Horse Breeding
- Liliya Kalinkova
- All-Russian Research Institute for Horse Breeding
- Alexander M. Zaitev
- All-Russian Research Institute for Horse Breeding
- Miguel Novoa‐Bravo
- Genética Animal de Colombia SAS.
- Gabriella Lindgren
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences
- Samantha Brooks
- Department of Animal Science, UF Genetics Institute, University of Florida
- Laura Patterson Rosa
- Department of Agriculture and Industry, Sul Ross State University
- Ludovic Orlando
- Centre d’Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier
- Rytis Juras
- School of Veterinary Medicine and Biomedical Sciences, Texas A&M University
- Tetsuo Kunieda
- Graduate School of Environmental and Life Science, Okayama University
- Barbara Wallner
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna
- DOI
- https://doi.org/10.1038/s41598-023-35539-0
- Journal volume & issue
-
Vol. 13,
no. 1
pp. 1 – 13
Abstract
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.
