Genome‐wide population affinities and signatures of adaptation in hydruntines, sussemiones and Asian wild asses

The extremely rich palaeontological record of the horse family, also known as equids, has provided many examples of macroevolutionary change over the last ~55 Mya. This family is also one of the most documented at the palaeogenomic level, with hundreds of ancient genomes sequenced. While these data have advanced understanding of the domestication history of horses and donkeys, the palaeogenomic record of other equids remains limited. In this study, we have generated genome-wide data for 25 ancient equid specimens spanning over 44 Ky and spread across Anatolia, the Caucasus, Central Asia and Mongolia. Our dataset includes the genomes from two extinct species, the European wild ass, Equus hydruntinus, and the sussemione Equus ovodovi. We document, for the first time, the presence of sussemiones in Mongolia and their survival around ~3.9 Kya, a finding that should be considered when discussing the timing of the first arrival of the domestic horse in the region. We also identify strong spatial differentiation within the historical ecological range of Asian wild asses, Equus hemionus, and incomplete reproductive isolation in several groups yet considered as different species. Finally, we find common selection signatures at ANTXR2 gene in European, Asian and African wild asses. This locus, which encodes a receptor for bacterial toxins, shows no selection signal in E. ovodovi, but a 5.4-kb deletion within intron 7. Whether such genetic modifications played any role in the sussemione extinction remains unknown.

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Publication Details

Journal
Molecular Ecology
Published
2024-09-16
DOI
https://doi.org/10.1111/mec.17527
Citations
3
Primary Topic
Genetic diversity and population structure
Type
article
Field-Weighted Citation Impact
1.65

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article

Genome‐wide population affinities and signatures of adaptation in hydruntines, sussemiones and Asian wild asses

Jean‐Luc Houle, Taylor R. Hermes, Paweł Mackiewicz, Danijela Popović et al.
3 citations
Molecular Ecology
Genetic diversity and population structure
1.65
article

Genome‐wide population affinities and signatures of adaptation in hydruntines, sussemiones and Asian wild asses

Jean‐Luc Houle, Taylor R. Hermes, Paweł Mackiewicz, Danijela Popović, Patrick Wincker, Hossein Davoudi, Christina Warinner, David Lordkipanidze, Kristine Korzow Richter, Azadeh Fatemeh Mohaseb, Aida Abdykanova, Andrey B. Belinskiy, Jianfei Pan, Rémi Berthon, Svend Hansen, Ludovic Orlando, Nikoloz Vanishvili, Jamsranjav Bayarsaikhan, Eudald Carbonell, Beth Shapiro, Evon Hekkala, Aude Perdereau, Loreleï Chauvey, John Southon, Mateusz Baca, Stéphanie Schiavinato, Marjan Mashkour, Gaétan Tressières, Jaime Lira Garrido, William Taylor, Eline N. van Asperen, Krzysztof Stefaniak, Pavel Kuznetsov, Alexey Kalmykov, Светлана Шнайдер, Laure Calvière‐Tonasso, Nuritdin Sayfullaev, Allan S. Gilbert, Juan Luís Arsuaga, Jean‐Marc Aury, Pedro H. Oliveira, Xuexue Liu, Geoffrey D. Summers, Eden Hill, Sabine Reinhold
article en
3 citations

Abstract

The extremely rich palaeontological record of the horse family, also known as equids, has provided many examples of macroevolutionary change over the last ~55 Mya. This family is also one of the most documented at the palaeogenomic level, with hundreds of ancient genomes sequenced. While these data have advanced understanding of the domestication history of horses and donkeys, the palaeogenomic record of other equids remains limited. In this study, we have generated genome-wide data for 25 ancient equid specimens spanning over 44 Ky and spread across Anatolia, the Caucasus, Central Asia and Mongolia. Our dataset includes the genomes from two extinct species, the European wild ass, Equus hydruntinus, and the sussemione Equus ovodovi. We document, for the first time, the presence of sussemiones in Mongolia and their survival around ~3.9 Kya, a finding that should be considered when discussing the timing of the first arrival of the domestic horse in the region. We also identify strong spatial differentiation within the historical ecological range of Asian wild asses, Equus hemionus, and incomplete reproductive isolation in several groups yet considered as different species. Finally, we find common selection signatures at ANTXR2 gene in European, Asian and African wild asses. This locus, which encodes a receptor for bacterial toxins, shows no selection signal in E. ovodovi, but a 5.4-kb deletion within intron 7. Whether such genetic modifications played any role in the sussemione extinction remains unknown.

Molecular EcologyVol. 33(19)
Tbilisi State University (GE), Universidad Complutense de Madrid (ES), Centre National de la Recherche Scientifique (FR), Université Toulouse III - Paul Sabatier (FR), Tarbiat Modares University (IR), Fordham University (US), University of California, Santa Cruz (US), University of Colorado Boulder (US), University of California, Irvine (US), University of Wrocław (PL), American University of Central Asia (KG), University of Tehran (IR), Commissariat à l'Énergie Atomique et aux Énergies Alternatives (FR), Université Paris-Saclay (FR), Deutsches Archäologisches Institut, Zentrale (DE), Harvard University Press (US), Georgian National Museum (GE), Samara State University of Social Sciences and Education (RU), Museum of Boulder (US), Institut Català de Paleoecologia Humana i Evolució Social (ES), Genoscope (FR), Max Planck Institute for Evolutionary Anthropology (DE), Archéozoologie et Archéobotanique (FR), CEA Paris-Saclay (FR), Chinese Academy of Agricultural Sciences (CN), Chicago College of Oriental Medicine (US), Max Planck Institute for the Science of Human History (DE), Institute of Archaeology and Ethnography (RU), National Museum of Mongolia (MN), Centre d'Anthropobiologie et de Génomique de Toulouse (FR), University of Warsaw (PL), Universitat Rovira i Virgili (ES), National University of Mongolia (MN), University of Arkansas at Fayetteville (US), Newcastle University (GB), Western Kentucky University (US)
European Commission, Agence Nationale de la Recherche, Ministerio de Educación, Cultura y Deporte, Centre National de la Recherche Scientifique, Russian Science Foundation, HORIZON EUROPE Framework Programme, Agricultural Science and Technology Innovation Program, HORIZON EUROPE European Research Council
Life in Land
Openalex Percentile: Top 15%
Genetic diversity and population structure
1.65
DOIOpen Access PDFOpenAlex
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