o:2388 Refining the evolutionary tree of the horse Y chromosome en 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 1552099 10.1038/s41598-023-35539-0 2023-11-29T09:02:52.932Z 44 yes 46 Elif Bozlak University of Veterinary Medicine Vienna Lara Radovic University of Veterinary Medicine Vienna person 0000-0003-4621-3856 Viktoria Remer University of Veterinary Medicine Vienna person Doris Rigler University of Veterinary Medicine Vienna person Lucy Allen University of Veterinary Medicine Vienna person Gottfried Brem University of Veterinary Medicine Vienna person 0000-0002-7522-0708 Gabrielle Stalder University of Veterinary Medicine Vienna person 0000-0002-8901-1181 Caitlin Castaneda Texas A&M University person Gus Cothran Texas A&M University person Terje Raudsepp Texas A&M University person Yu Okuda Okayama University of Science person Kyaw Kyaw Moe University of Veterinary Science Yezin person Hla Hla Moe University of Veterinary Science Yezin person Bounthavone Kounnavongsa National Agriculture and Forestry Research Institute (Lao) Resources person Soukanh Keonouchanh Hue University person Nguyen Huu Van Hue University person Van Hai Vu Hue University person Manoj Kumar Shah Agriculture and Forestry University Rampur person Masahide Nishibori Hiroshima University person Polat Kazymbet JSC Astana Medical University person Meirat Bakhtin National Academy of Sciences of the Kyrgyz Republic person Asankadyr Zhunushov National Academy of Sciences of the Kyrgyz Republic person Ripon Chandra Paul Okayama University / Patuakhali Science and Technology University person Bumbein Dashnyam Mongolian Academy of Sciences person Ken Nozawa Kyoto University person Saria Almarzook Humboldt-Universität zu Berlin person Gudrun A. Brockmann Humboldt-Universität zu Berlin person Monika Reissmann Cornell University person Douglas F. Antczak Cornell University person Donald C. Miller Cornell University person Raheleh Sadeghi Cornell University person Ines von Butler-Wemken Barb Horse Breeding Organisation VFZB E. V. person Nikos Kostaras Amaltheia person Haige Han Inner Mongolia Agricultural University person Dugarjaviin Manglai Inner Mongolia Agricultural University person Abdugani Abdurasulov Osh State University person Boldbaatar Sukhbaatar State Central Veterinary Laboratory of Mongolia person Katarzyna Ropka-Molik National Research Institute of Animal Production person Monika Stefaniuk-Szmukier National Research Institute of Animal Production person Maria Susana Lopes University of Azores person Maria Susana Lopes University of Azores person Artur da Câmara Machado University of Azores person Valery V. Kalashnikov All-Russian Research Institute for Horse Breeding person Liliya Kalinkova All-Russian Research Institute for Horse Breeding person Alexander M. Zaitev All-Russian Research Institute for Horse Breeding person Miguel Novoa-Bravo Genética Animal de Colombia SAS. person Gabriella Lindgren Swedish University of Agricultural Sciences / KU Leuven person Samantha Brooks University of Florida person Laura Patterson Rosa Sul Ross State University person Ludovic Orlando Université Paul Sabatier person Rytis Juras Texas A&M University person Tetsuo Kunieda Okayama University person Barbara Wallner University of Veterinary Medicine Vienna person 0000-0003-4159-0695 application/pdf 7067318 https://phaidra.vetmeduni.ac.at/o:2388 no yes 16 70 1552253 Scientific Reports 13 13 1 Nature Portfolio 2023