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

Jianfei Pan^{1

2}, Xuexue Liu¹, Mateusz Baca³, Laure Calvière-Tonasso¹, Stéphanie Schiavinato¹, Loreleï Chauvey¹, Gaétan Tressières¹, Aude Perdereau⁴, Jean-Marc Aury⁴, Pedro H Oliveira⁴, Patrick Wincker⁴, Aida Abdykanova⁵, Juan Luis Arsuaga^{6

7}, Jamsranjav Bayarsaikhan^{8

9}, Andrey B Belinskiy¹⁰, Eudald Carbonell^{11

12}, Hossein Davoudi¹³, Jaime Lira Garrido¹, Allan S Gilbert¹⁴, Taylor Hermes^{15

16}, Christina Warinner^{16

17}, Alexey A Kalmykov¹⁰, David Lordkipanidze^{18

19}, Paweł Mackiewicz²⁰, Azadeh F Mohaseb²¹, Kristine Richter¹⁷, Nuritdin Sayfullaev²², Beth Shapiro²³, Svetlana Shnaider²⁴, John Southon²⁵, Krzysztof Stefaniak²⁶, Geoffrey D Summers^{27

28}, Eline Naomi van Asperen²⁹, Nikoloz Vanishvili³⁰, Eden A Hill¹⁶, Pavel Kuznetsov³¹, Sabine Reinhold³², Svend Hansen³², Marjan Mashkour²¹, Rémi Berthon²¹, William Timothy Treal Taylor^{33

34}, Jean-Luc Houle³⁵, Evon Hekkala³⁶, Danijela Popović³, Ludovic Orlando¹

Affiliations

¹ Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR5288, Université Paul Sabatier, Toulouse, France.
² State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.
³ Centre of New Technologies, University of Warsaw, Warsaw, Poland.
⁴ Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France.
⁵ Anthropology Department, American University of Central Asia, Bishkek, Kyrgyzstan.
⁶ Centro Mixto UCM-ISCIII de Evolución y Comportamiento Humanos, Madrid, Spain.
⁷ Departamento de Geodinámica, Estratigrafía y Paleontología. Facultad de Ciencias Geológicas, Universidad Complutense de Madrid, Madrid, Spain.
⁸ Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany.
⁹ National Museum of Mongolia, Ulaanbaatar, Mongolia.
¹⁰ Nasledie Cultural Heritage Unit, Stavropol, Russia.
¹¹ Departament d'Història i Història de l'Art, Universitat Rovira i Virgili, Tarragona, Spain.
¹² Institut Català de Paleoecologia Humana I Evolució Social (IPHES-CERCA), Tarragona, Spain.
¹³ Bioarchaeology Laboratory, Central Laboratory, University of Tehran, Tehran, Iran.
¹⁴ Department of Sociology and Anthropology, Fordham University, New York, New York, USA.
¹⁵ Department of Anthropology, University of Arkansas, Fayetteville, Arkansas, USA.
¹⁶ Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
¹⁷ Department of Anthropology, Harvard University, Cambridge, Massachusetts, USA.
¹⁸ Georgian National Museum, Tbilisi, Tbilisi, Georgia.
¹⁹ Tbilisi State University Tbilisi I. Chavchavadze Avenue 1, Tbilisi, Georgia.
²⁰ Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland.
²¹ UMR 7209 'Archéozoologie, Archéobotanique: sociétés, Pratiques et Environnements', CNRS, Muséum National d'Histoire Naturelle, Paris, France.
²² Donish Institute of History, Archaeology and Ethnography, Dushanbe, Tajikistan.
²³ Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, California, USA.
²⁴ International Laboratory "Archaeozoology in Siberia and Central Asia" ZooSCAn, IRL 2013, National Center for Scientific Research - Institute of Archeology and Ethnography SB RAS, Novosibirsk, Russia.
²⁵ Earth System Science Department, University of California, Irvine, California, USA.
²⁶ Department of Palaeozoology, University of Wrocław, Wrocław, Poland.
²⁷ Ecole Nationale Supérieure d'Architecture de Nantes-Mauritius, Pierrefonds, Mauritius.
²⁸ The Oriental Institute, Chicago University, Chicago, Illinois, USA.
²⁹ School of History, Classics and Archaeology Newcastle University, Newcastle-upon-Tyne, UK.
³⁰ Department of Vertebrate Paleontology, L. Davitashvili Institute of Paleobiology, Georgian National Museum, Tbilisi, Georgia.
³¹ The Museum of Archeology of the Volga Region Samara State University of Social Sciences and Education, Samara, Russia.
³² Eurasia Department, German Archaeological Institute, Berlin, Germany.
³³ Museum of Natural History, University of Colorado Boulder, Boulder, Colorado, USA.
³⁴ Department of Anthropology, University of Colorado Boulder, Boulder, Colorado, USA.
³⁵ Department of Folk Studies and Anthropology, Western Kentucky University, Bowling Green, Kentucky, USA.
³⁶ Department Biological Sciences, Fordham University, New York, New York, USA.

PMID: 39279684
DOI: 10.1111/mec.17527

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

Jianfei Pan et al. Mol Ecol. 2024 Oct.

. 2024 Oct;33(19):e17527.

doi: 10.1111/mec.17527. Epub 2024 Sep 16.

Authors

Affiliations

¹ Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR5288, Université Paul Sabatier, Toulouse, France.
² State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.
³ Centre of New Technologies, University of Warsaw, Warsaw, Poland.
⁴ Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France.
⁵ Anthropology Department, American University of Central Asia, Bishkek, Kyrgyzstan.
⁶ Centro Mixto UCM-ISCIII de Evolución y Comportamiento Humanos, Madrid, Spain.
⁷ Departamento de Geodinámica, Estratigrafía y Paleontología. Facultad de Ciencias Geológicas, Universidad Complutense de Madrid, Madrid, Spain.
⁸ Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany.
⁹ National Museum of Mongolia, Ulaanbaatar, Mongolia.
¹⁰ Nasledie Cultural Heritage Unit, Stavropol, Russia.
¹¹ Departament d'Història i Història de l'Art, Universitat Rovira i Virgili, Tarragona, Spain.
¹² Institut Català de Paleoecologia Humana I Evolució Social (IPHES-CERCA), Tarragona, Spain.
¹³ Bioarchaeology Laboratory, Central Laboratory, University of Tehran, Tehran, Iran.
¹⁴ Department of Sociology and Anthropology, Fordham University, New York, New York, USA.
¹⁵ Department of Anthropology, University of Arkansas, Fayetteville, Arkansas, USA.
¹⁶ Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
¹⁷ Department of Anthropology, Harvard University, Cambridge, Massachusetts, USA.
¹⁸ Georgian National Museum, Tbilisi, Tbilisi, Georgia.
¹⁹ Tbilisi State University Tbilisi I. Chavchavadze Avenue 1, Tbilisi, Georgia.
²⁰ Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland.
²¹ UMR 7209 'Archéozoologie, Archéobotanique: sociétés, Pratiques et Environnements', CNRS, Muséum National d'Histoire Naturelle, Paris, France.
²² Donish Institute of History, Archaeology and Ethnography, Dushanbe, Tajikistan.
²³ Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, California, USA.
²⁴ International Laboratory "Archaeozoology in Siberia and Central Asia" ZooSCAn, IRL 2013, National Center for Scientific Research - Institute of Archeology and Ethnography SB RAS, Novosibirsk, Russia.
²⁵ Earth System Science Department, University of California, Irvine, California, USA.
²⁶ Department of Palaeozoology, University of Wrocław, Wrocław, Poland.
²⁷ Ecole Nationale Supérieure d'Architecture de Nantes-Mauritius, Pierrefonds, Mauritius.
²⁸ The Oriental Institute, Chicago University, Chicago, Illinois, USA.
²⁹ School of History, Classics and Archaeology Newcastle University, Newcastle-upon-Tyne, UK.
³⁰ Department of Vertebrate Paleontology, L. Davitashvili Institute of Paleobiology, Georgian National Museum, Tbilisi, Georgia.
³¹ The Museum of Archeology of the Volga Region Samara State University of Social Sciences and Education, Samara, Russia.
³² Eurasia Department, German Archaeological Institute, Berlin, Germany.
³³ Museum of Natural History, University of Colorado Boulder, Boulder, Colorado, USA.
³⁴ Department of Anthropology, University of Colorado Boulder, Boulder, Colorado, USA.
³⁵ Department of Folk Studies and Anthropology, Western Kentucky University, Bowling Green, Kentucky, USA.
³⁶ Department Biological Sciences, Fordham University, New York, New York, USA.

PMID: 39279684
DOI: 10.1111/mec.17527

Erratum in

Correction to "Genome-wide population affinities and signatures of adaptation in hydruntines, sussemiones and Asian wild asses".
[No authors listed] [No authors listed] Mol Ecol. 2025 Mar;34(5):e17674. doi: 10.1111/mec.17674. Epub 2025 Jan 29. Mol Ecol. 2025. PMID: 39888080 No abstract available.

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.

Keywords: ANTXR2; Asian wild ass; European wild ass; Sussemione; ancient DNA; extinction.

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References

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

Affiliations

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

Authors

Affiliations

Erratum in

Abstract

References

REFERENCES

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Miscellaneous