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Scientific reports2023; 13(1); 8954; doi: 10.1038/s41598-023-35539-0

Refining the evolutionary tree of the horse Y chromosome.

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.
© 2023. The Author(s).
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Publication Date: 2023-06-02 PubMed ID: 37268661PubMed Central: PMC10238413DOI: 10.1038/s41598-023-35539-0Google Scholar: Lookup
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  • Journal Article
  • Research Support
  • Non-U.S. Gov't

Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

The research studied the Y chromosome present in horses to gain insights into the evolution and breeding history of horses. It noted the influence of Oriental lineages in the past 1500 years and identified previously unknown genetic attributes in Mongolian and insular horse populations. The study also suggested that many variations in the horse Y chromosome started after horse domestication began roughly 4200 years ago.

Objectives of the Study

  • The research aims to enhance the understanding of the horse Y chromosome’s evolutionary path.
  • It endeavors to gain information about the paternal lineage of horses by studying the Y chromosome.
  • The study aims to detect the influence of Oriental lineages on horse breeding in the past 1500 years.

Methodology of the Research

  • The researchers analyzed 5 Mb of enriched sequencing data from 76 domestic horse Y chromosomes.
  • This data was compared with whole genome sequences from 89 domestic horses and five Przewalski’s horses.
  • The team also studied haplotypes (HT), the groups of genes in an organism inherited from one parent, in horses across different global populations.

Findings from the Study

  • The analysis led to the development of a phylogeny comprising 153 HTs, defined through 2966 variants. This phylogeny presents a detailed view of the history of horse paternal lineages.
  • They discovered previously unknown haplogroups in horses from Mongolia and isolated populations.
  • By placing 163 archaeological specimens in the phylogenetic tree, the researchers suggest that most variations in the horse Y chromosome came about after domestication started around 4200 years ago in Western Eurasian steppes.

Implications of the Research

  • The findings provide a better comprehension of horse population dynamics and diversity.
  • The results of the study assist in reducing ascertainment bias, thereby improving the accuracy of related research in the future.
  • This extensive phylogeny serves as a strong evolutionary structure for studying the history and development of horses.

Cite This Article

APA
Bozlak E, Radovic L, Remer V, Rigler D, Allen L, Brem G, Stalder G, Castaneda C, Cothran G, Raudsepp T, Okuda Y, Moe KK, Moe HH, Kounnavongsa B, Keonouchanh S, Van NH, Vu VH, Shah MK, Nishibori M, Kazymbet P, Bakhtin M, Zhunushov A, Paul RC, Dashnyam B, Nozawa K, Almarzook S, Brockmann GA, Reissmann M, Antczak DF, Miller DC, Sadeghi R, von Butler-Wemken I, Kostaras N, Han H, Manglai D, Abdurasulov A, Sukhbaatar B, Ropka-Molik K, Stefaniuk-Szmukier M, Lopes MS, da Câmara Machado A, Kalashnikov VV, Kalinkova L, Zaitev AM, Novoa-Bravo M, Lindgren G, Brooks S, Rosa LP, Orlando L, Juras R, Kunieda T, Wallner B. (2023). Refining the evolutionary tree of the horse Y chromosome. Sci Rep, 13(1), 8954. https://doi.org/10.1038/s41598-023-35539-0

Publication

Scientific reports
ISSN: 2045-2322
NlmUniqueID: 101563288
Country: England
Language: English
Volume: 13
Issue: 1
Pages: 8954

Researcher Affiliations

Bozlak, Elif
  • Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, 1210, Vienna, Austria.
  • Vienna Graduate School of Population Genetics, University of Veterinary Medicine Vienna, 1210, Vienna, Austria.
Radovic, Lara
  • Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, 1210, Vienna, Austria.
  • Vienna Graduate School of Population Genetics, University of Veterinary Medicine Vienna, 1210, Vienna, Austria.
Remer, Viktoria
  • Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, 1210, Vienna, Austria.
Rigler, Doris
  • Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, 1210, Vienna, Austria.
Allen, Lucy
  • Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, 1210, Vienna, Austria.
Brem, Gottfried
  • Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, 1210, Vienna, Austria.
Stalder, Gabrielle
  • Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, 1210, Vienna, Austria.
Castaneda, Caitlin
  • School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA.
Cothran, Gus
  • School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA.
Raudsepp, Terje
  • School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA.
Okuda, Yu
  • Museum of Dinosaur Research, Okayama University of Science, Okayama, Japan.
Moe, Kyaw Kyaw
  • Department of Pathology and Microbiology, University of Veterinary Science, Yezin, Nay Pyi Taw, 05282, Myanmar.
Moe, Hla Hla
  • Department of Genetics and Animal Breeding, University of Veterinary Science, Yezin, Nay Pyi Taw, 05282, Myanmar.
Kounnavongsa, Bounthavone
  • National Agriculture and Forestry Research Institute (Lao) Resources, Livestock Research Center, Xaythany District, Vientiane, Laos.
Keonouchanh, Soukanh
  • Faculty of Animal Science and Veterinary Medicine, University of Agriculture and Forestry, Hue University, Hue, Vietnam.
Van, Nguyen Huu
  • Faculty of Animal Science and Veterinary Medicine, University of Agriculture and Forestry, Hue University, Hue, Vietnam.
Vu, Van Hai
  • Faculty of Animal Science and Veterinary Medicine, University of Agriculture and Forestry, Hue University, Hue, Vietnam.
Shah, Manoj Kumar
  • Faculty of Animal Science, Veterinary Science and Fisheries, Agriculture and Forestry University, Rampur, 44209, Nepal.
Nishibori, Masahide
  • Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-8528, Japan.
Kazymbet, Polat
  • Radiobiological Research Institute, JSC Astana Medical University, Astana, 010000, Republic of Kazakhstan.
Bakhtin, Meirat
  • Institute of Biotechnology, National Academy of Sciences of the Kyrgyz Republic, Bishkek, 720071, Kyrgyz Republic.
Zhunushov, Asankadyr
  • Institute of Biotechnology, National Academy of Sciences of the Kyrgyz Republic, Bishkek, 720071, Kyrgyz Republic.
Paul, Ripon Chandra
  • Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan.
  • Faculty of Animal Science and Veterinary Medicine, Patuakhali Science and Technology University, Barishal, Bangladesh.
Dashnyam, Bumbein
  • Institute of Biological Sciences, Mongolian Academy of Sciences, Ulaan Baator, Mongolia.
Nozawa, Ken
  • Primate Research Institute, Kyoto University, Aichi, Japan.
Almarzook, Saria
  • Albrecht Daniel Thaer-Institut, Humboldt-Universität zu Berlin, 10115, Berlin, Germany.
Brockmann, Gudrun A
  • Albrecht Daniel Thaer-Institut, Humboldt-Universität zu Berlin, 10115, Berlin, Germany.
Reissmann, Monika
  • Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA.
Antczak, Douglas F
  • Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA.
Miller, Donald C
  • Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA.
Sadeghi, Raheleh
  • Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA.
von Butler-Wemken, Ines
  • Barb Horse Breeding Organisation VFZB E. V., Verein der Freunde und Züchter Des Berberpferdes E.V., Kirchgasse 11, 67718, Schmalenberg, Germany.
Kostaras, Nikos
  • Amaltheia, Argirokastrou 51, 15669, Papagou, Greece.
Han, Haige
  • Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, College of Animal Science, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, 010018, China.
Manglai, Dugarjaviin
  • Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, College of Animal Science, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, 010018, China.
Abdurasulov, Abdugani
  • Department of Agriculture, Faculty of Natural Sciences and Geography, Osh State University, 723500, Osh, Kyrgyzstan.
Sukhbaatar, Boldbaatar
  • Sector of Surveillance and Diagnosis of Infectious Diseases, State Central Veterinary Laboratory, Ulaanbaatar, 17024, Mongolia.
Ropka-Molik, Katarzyna
  • National Research Institute of Animal Production, Animal Molecular Biology, 31-047, Cracow, Poland.
Stefaniuk-Szmukier, Monika
  • National Research Institute of Animal Production, Animal Molecular Biology, 31-047, Cracow, Poland.
Lopes, Maria Susana
  • Biotechnology Centre of Azores, University of Azores, 9700-042, Angra do Heroísmo, Portugal.
da Câmara Machado, Artur
  • Biotechnology Centre of Azores, University of Azores, 9700-042, Angra do Heroísmo, Portugal.
Kalashnikov, Valery V
  • All-Russian Research Institute for Horse Breeding, Ryazan, 391105, Russia.
Kalinkova, Liliya
  • All-Russian Research Institute for Horse Breeding, Ryazan, 391105, Russia.
Zaitev, Alexander M
  • All-Russian Research Institute for Horse Breeding, Ryazan, 391105, Russia.
Novoa-Bravo, Miguel
  • Genética Animal de Colombia SAS., Av. Calle 26 #69-76, 111071, Bogotá, Colombia.
Lindgren, Gabriella
  • Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 75007, Uppsala, Sweden.
  • Department of Biosystems, Center for Animal Breeding and Genetics, KU Leuven, 3001, Leuven, Belgium.
Brooks, Samantha
  • Department of Animal Science, UF Genetics Institute, University of Florida, Gainesville, FL, 32610, USA.
Rosa, Laura Patterson
  • Department of Agriculture and Industry, Sul Ross State University, Alpine, TX, 79832, USA.
Orlando, Ludovic
  • Centre d'Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier, Toulouse, France.
Juras, Rytis
  • School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA. rjuras@cvm.tamu.edu.
Kunieda, Tetsuo
  • Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan. t-kunieda@vet.ous.ac.jp.
  • Faculty of Veterinary Medicine, Okayama University of Science, Imabari, Japan. t-kunieda@vet.ous.ac.jp.
Wallner, Barbara
  • Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, 1210, Vienna, Austria. barbara.wallner@vetmeduni.ac.at.

MeSH Terms

  • Male
  • Animals
  • Horses / genetics
  • Phylogeny
  • Biological Evolution
  • Animals, Wild / genetics
  • Y Chromosome / genetics
  • Genome
  • Haplotypes
  • Genetic Variation
  • DNA, Mitochondrial / genetics

Grant Funding

  • W 1225 / Austrian Science Fund FWF

Conflict of Interest Statement

The authors declare no competing interests.

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