https://phaidra.vetmeduni.ac.at/o:2388 Refining the evolutionary tree of the horse Y chromosome Bozlak, Elif Elif Bozlak University of Veterinary Medicine Vienna Kunieda, Tetsuo Tetsuo Kunieda Okayama University Juras, Rytis Rytis Juras Texas A&M University Wallner, Barbara Barbara Wallner 0000-0003-4159-0695 University of Veterinary Medicine Vienna Orlando, Ludovic Ludovic Orlando Université Paul Sabatier Rosa, Laura Patterson Laura Patterson Rosa Sul Ross State University Brooks, Samantha Samantha Brooks University of Florida Lindgren, Gabriella Gabriella Lindgren Swedish University of Agricultural Sciences / KU Leuven Novoa-Bravo, Miguel Miguel Novoa-Bravo Genética Animal de Colombia SAS. Zaitev, Alexander M. Alexander M. Zaitev All-Russian Research Institute for Horse Breeding Kalinkova, Liliya Liliya Kalinkova All-Russian Research Institute for Horse Breeding Kalashnikov, Valery V. Valery V. Kalashnikov All-Russian Research Institute for Horse Breeding da Câmara Machado, Artur Artur da Câmara Machado University of Azores Lopes, Maria Susana Maria Susana Lopes University of Azores Lopes, Maria Susana Maria Susana Lopes University of Azores Stefaniuk-Szmukier, Monika Monika Stefaniuk-Szmukier National Research Institute of Animal Production Ropka-Molik, Katarzyna Katarzyna Ropka-Molik National Research Institute of Animal Production Sukhbaatar, Boldbaatar Boldbaatar Sukhbaatar State Central Veterinary Laboratory of Mongolia Abdurasulov, Abdugani Abdugani Abdurasulov Osh State University Manglai, Dugarjaviin Dugarjaviin Manglai Inner Mongolia Agricultural University Han, Haige Haige Han Inner Mongolia Agricultural University Kostaras, Nikos Nikos Kostaras Amaltheia von Butler-Wemken, Ines Ines von Butler-Wemken Barb Horse Breeding Organisation VFZB E. V. Sadeghi, Raheleh Raheleh Sadeghi Cornell University Miller, Donald C. Donald C. Miller Cornell University Antczak, Douglas F. Douglas F. Antczak Cornell University Reissmann, Monika Monika Reissmann Cornell University Brockmann, Gudrun A. Gudrun A. Brockmann Humboldt-Universität zu Berlin Almarzook, Saria Saria Almarzook Humboldt-Universität zu Berlin Nozawa, Ken Ken Nozawa Kyoto University Dashnyam, Bumbein Bumbein Dashnyam Mongolian Academy of Sciences Paul, Ripon Chandra Ripon Chandra Paul Okayama University / Patuakhali Science and Technology University Zhunushov, Asankadyr Asankadyr Zhunushov National Academy of Sciences of the Kyrgyz Republic Bakhtin, Meirat Meirat Bakhtin National Academy of Sciences of the Kyrgyz Republic Kazymbet, Polat Polat Kazymbet JSC Astana Medical University Nishibori, Masahide Masahide Nishibori Hiroshima University Shah, Manoj Kumar Manoj Kumar Shah Agriculture and Forestry University Rampur Vu, Van Hai Van Hai Vu Hue University Van, Nguyen Huu Nguyen Huu Van Hue University Keonouchanh, Soukanh Soukanh Keonouchanh Hue University Kounnavongsa, Bounthavone Bounthavone Kounnavongsa National Agriculture and Forestry Research Institute (Lao) Resources Moe, Hla Hla Hla Hla Moe University of Veterinary Science Yezin Moe, Kyaw Kyaw Kyaw Kyaw Moe University of Veterinary Science Yezin Okuda, Yu Yu Okuda Okayama University of Science Raudsepp, Terje Terje Raudsepp Texas A&M University Cothran, Gus Gus Cothran Texas A&M University Castaneda, Caitlin Caitlin Castaneda Texas A&M University Stalder, Gabrielle Gabrielle Stalder 0000-0002-8901-1181 University of Veterinary Medicine Vienna Brem, Gottfried Gottfried Brem 0000-0002-7522-0708 University of Veterinary Medicine Vienna Allen, Lucy Lucy Allen University of Veterinary Medicine Vienna Rigler, Doris Doris Rigler University of Veterinary Medicine Vienna Radovic, Lara Lara Radovic 0000-0003-4621-3856 University of Veterinary Medicine Vienna Remer, Viktoria Viktoria Remer University of Veterinary Medicine Vienna Nature Portfolio text eng 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. Male; Animals; Horsesgenetics; Phylogeny; Biological Evolution; Animals, Wildgenetics; Y Chromosomegenetics; Genome; Haplotypes; Genetic Variation; DNA, Mitochondrialgenetics http://creativecommons.org/licenses/by/4.0/ https://phaidra.vetmeduni.ac.at/api/object/o:2388/download 10.1038/s41598-023-35539-0 https://phaidra.vetmeduni.ac.at/o:605 application/pdf Scientific Reports 13(1) (2023) Scientific Reports 13 1 6.74 MB 2023