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