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Molecular ecology2024; 33(19); e17527; doi: 10.1111/mec.17527

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

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.
© 2024 The Author(s). Molecular Ecology published by John Wiley & Sons Ltd.
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Publication Date: 2024-09-16 PubMed ID: 39279684DOI: 10.1111/mec.17527Google Scholar: Lookup
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  • Journal Article

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.

Overview

  • This research investigates the genetic history and adaptation of extinct and extant wild equids, including hydruntines, sussemiones, and Asian wild asses, through genome-wide analysis of ancient specimens.
  • It uncovers new findings about the geographic distribution, evolutionary relationships, and genetic adaptations of these species, contributing to our understanding of their evolution and extinction.

Background

  • The horse family (equids) has a rich fossil and palaeontological record spanning approximately 55 million years, showing extensive macroevolutionary changes.
  • Equids are among the best-documented mammals in terms of palaeogenomics, with hundreds of ancient genomes sequenced, primarily focusing on the domestication histories of horses and donkeys.
  • Prior to this study, the genomic data for other equid species beyond domesticated horses and donkeys were sparse, limiting understanding of their population affinities and evolutionary history.

Study Design and Methods

  • Researchers generated genome-wide data from 25 ancient equid specimens dating back up to approximately 44,000 years (44 Ky).
  • The specimens came from various geographic regions including Anatolia, the Caucasus, Central Asia, and Mongolia, providing broad spatial coverage.
  • The dataset included genomes of two extinct species:
    • Equus hydruntinus (European wild ass, known as hydruntines)
    • Equus ovodovi (sussemione)

Key Findings

  • New Distribution and Survival Data for Sussemiones:
    • For the first time, sussemione genomes were identified in Mongolia, extending their known geographic range eastwards.
    • Evidence suggests that sussemiones survived until about 3,900 years ago around Mongolia, which overlaps with periods previously thought to signify the arrival of domestic horses in that region.
  • Population Structure and Reproductive Isolation:
    • There is strong spatial genetic differentiation among populations of the Asian wild asses (Equus hemionus) throughout their historical range.
    • The study detected incomplete reproductive isolation among groups previously classified as distinct species, highlighting the complexity of equid taxonomy and evolutionary relationships.
  • Genetic Adaptations and Selection Signatures:
    • A common signature of natural selection was detected at the ANTXR2 gene across European, Asian, and African wild asses.
    • The ANTXR2 gene encodes a receptor that binds bacterial toxins, indicating possible adaptive evolution to environmental pathogens.
    • Interestingly, the extinct sussemione (E. ovodovi) showed no such selection signal but possessed a 5.4-kilobase deletion within intron 7 of ANTXR2.
    • The functional implications of this deletion and whether it contributed to the extinction of the sussemione species remain unknown.

Significance and Implications

  • This study expands the knowledge of equid evolutionary history beyond previously focused domesticated species to include extinct wild species with new genomic data.
  • The presence of sussemiones in Mongolia later than previously thought suggests a need to reconsider the timeline for horse domestication and introduction in Central Asia.
  • Findings of incomplete reproductive isolation challenge the strict species boundaries of Asian wild asses, implying gene flow among groups with conservation and evolutionary implications.
  • Identification of shared and unique genetic adaptations, especially involving immunity-related genes like ANTXR2, opens avenues for exploring how wild equids adapted to their environments and pathogens.
  • Understanding genetic changes linked to extinction events in extinct species like the sussemione may help unravel factors contributing to their demise, relevant for conserving extant equid species.

Cite This Article

APA
(2024). Genome-wide population affinities and signatures of adaptation in hydruntines, sussemiones and Asian wild asses. Mol Ecol, 33(19), e17527. https://doi.org/10.1111/mec.17527

Publication

Molecular ecology
ISSN: 1365-294X
NlmUniqueID: 9214478
Country: England
Language: English
Volume: 33
Issue: 19
Pages: e17527

Researcher Affiliations

MeSH Terms

  • Animals
  • Equidae / genetics
  • Genetics, Population
  • Mongolia
  • Genome / genetics
  • Phylogeny
  • Fossils
  • Horses / genetics
  • Adaptation, Physiological / genetics

Grant Funding

  • 101027750 / European Union's Horizon 2020 research and innovation programme
  • 101062645 / European Union's Horizon 2020 research and innovation programme
  • Agricultural Science and Technology Innovation Program (ASTIP-05)
  • CNRS and University Paul Sabatier (AnimalFarm IRP)
  • Spanish Ministerio de Educación, Cultura y Deporte (Archaeological Projects Abroad 2017)
  • Wroclaw Centre of Biotechnology programme ('The Leading National Research Center [KNOW]')
  • 681605 / HORIZON EUROPE European Research Council
  • 834616 / HORIZON EUROPE European Research Council
  • 101071707 / HORIZON EUROPE European Research Council
  • ANR-10-INBS-09 / Agence Nationale pour la Recherche
  • 19-78-10053 / Russian Science Foundation
  • 22-18-00194 / Russian Science Foundation

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