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Home / Equine Research Bank / Nat Ecol Evol / Mitochondrial genomes of Middle Pleistocene horses from the ...
Nature ecology & evolution2025; 9(12); 2248-2258; doi: 10.1038/s41559-025-02859-5

Mitochondrial genomes of Middle Pleistocene horses from the open-air site complex of Schöningen.

Abstract: Deep-time palaeogenomics offers rare insights into macroevolutionary events for both extant and extinct species. Aside from a Middle Pleistocene genome from North American permafrost (780-560 ka) and a number of Late Pleistocene specimens, most ancient horse DNA studies have focused on tracing the origins of domestication and subsequent periods. Here we present mitochondrial genomes from two Equus mosbachensis specimens from Schöningen, Germany, a Middle Pleistocene archaeological site complex with direct and repeated evidence of hominin-horse interactions on the shore of a palaeolake. Using petrous bone sampling, targeted enrichment and damage-aware and polarization-free mitochondrial DNA reconstruction methods, we extend the range of genome recovery in open-air sites to ~300,000 years ago. Phylogenetic analyses position these mitochondrial DNAs in two distinct, deeply divergent lineages, basal to both previously sequenced ancient Eurasian specimens and all modern-day horses. The Schöningen horse mitochondrial DNA data reveal a previously unrecognized diversification event within the clade, ultimately giving rise to modern-day horses, that is molecularly dated to ~570 ka and provides genetic support for the morphological species assignment. By extending the recoverable limits of ancient DNA from Middle Pleistocene open-air sites, our molecular findings bridge a temporal and geographic gap, providing insights on early evolutionary events within the genus Equus.
© 2025. The Author(s).
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Publication Date: 2025-10-01 PubMed ID: 41034648PubMed Central: PMC12680542DOI: 10.1038/s41559-025-02859-5Google Scholar: Lookup
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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 study reports the recovery and analysis of mitochondrial genomes from Middle Pleistocene horses (~300,000 years old) found at the open-air archaeological site complex of Schöningen, Germany.
  • The findings reveal new insights into the evolutionary history and diversification of horses, identifying ancient lineages that predate previously known ancient and modern horses.

Background and Importance of the Study

  • Ancient DNA studies typically focus on relatively recent specimens, especially those relating to domestication or Late Pleistocene eras.
  • Middle Pleistocene DNA data are very rare, especially from open-air archaeological sites, due to DNA degradation over time and environmental exposure.
  • Before this research, only a few ancient horse genomes were available, notably one from North American permafrost dated between 780,000 to 560,000 years ago.
  • The Schöningen site is significant for its repeated evidence of early humans (hominins) interacting with horses near an ancient lake shore, providing a valuable ecological and anthropological context.

Methodology

  • Two specimens identified as Equus mosbachensis (an extinct Middle Pleistocene horse species) were sampled.
  • Sampling focused on the petrous bone, known to preserve DNA better due to its dense structure.
  • Targeted enrichment techniques were used to isolate mitochondrial DNA (mtDNA) from the samples.
  • The researchers employed damage-aware and polarization-free methods for reconstructing the mtDNA, enhancing the accuracy of sequences from highly degraded ancient DNA.

Key Findings

  • Successfully recovered mitochondrial genomes date back around 300,000 years, extending the known range for DNA recovery from open-air sites.
  • Phylogenetic analysis revealed two distinct and deeply divergent mitochondrial lineages in the Schöningen horses.
  • These lineages are basal, meaning that they appear at the root of the evolutionary tree, prior to all previously sequenced ancient Eurasian horses and all modern horses.
  • The Schöningen mtDNA indicates a previously unrecognized diversification event within the horse lineage approximately 570,000 years ago.
  • This diversification is consistent with the morphology-based species identification of the specimens, confirming that the genetic data supports the species classification of Equus mosbachensis.

Implications and Significance

  • The study bridges a critical temporal and geographical gap in the horse evolutionary record by providing genomic data from a Middle Pleistocene, European open-air site.
  • The discovery of distinct, basal horse lineages increases understanding of early horse evolution and population dynamics before the Late Pleistocene and domestication phases.
  • Provides a molecular timeline for early diversification events within genus Equus, contributing to the broader field of macroevolutionary studies of mammals.
  • Demonstrates that ancient DNA can be successfully retrieved from challenging contexts like open-air sites, not only permafrost or caves, potentially expanding the scope of future palaeogenomic research.

Summary

  • This research advances paleo-genomics by successfully extracting and analyzing mitochondrial genomes from Middle Pleistocene horses at Schöningen, an open-air site in Germany.
  • It uncovers ancient evolutionary lineages, deepening our understanding of horse ancestry and evolution that occurred hundreds of thousands of years ago.
  • The methodological innovations and findings highlight the potential for future studies to explore ancient DNA across wider temporal and environmental settings, offering new perspectives on extinct and extant species’ history.

Cite This Article

APA
Weingarten A, Häusler M, Serangeli J, Verheijen I, Reiter E, Radzevičiūtė R, Stoessel A, Krause J, Spyrou MA, Conard NJ, Nieselt K, Posth C. (2025). Mitochondrial genomes of Middle Pleistocene horses from the open-air site complex of Schöningen. Nat Ecol Evol, 9(12), 2248-2258. https://doi.org/10.1038/s41559-025-02859-5

Publication

Nature ecology & evolution
ISSN: 2397-334X
NlmUniqueID: 101698577
Country: England
Language: English
Volume: 9
Issue: 12
Pages: 2248-2258

Researcher Affiliations

Weingarten, Arianna
  • Archaeo- and Palaeogenetics, Institute for Archaeological Sciences, Department of Geosciences, University of Tübingen, Tübingen, Germany. arianna.weingarten@uni-tuebingen.de.
  • Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany. arianna.weingarten@uni-tuebingen.de.
  • Senckenberg Centre for Human Evolution and Palaeoenvironment, Schöningen, Germany. arianna.weingarten@uni-tuebingen.de.
Häusler, Meret
  • Archaeo- and Palaeogenetics, Institute for Archaeological Sciences, Department of Geosciences, University of Tübingen, Tübingen, Germany.
  • Integrative Transcriptomics, Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany.
Serangeli, Jordi
  • Senckenberg Centre for Human Evolution and Palaeoenvironment, Schöningen, Germany.
  • Early Prehistory and Quaternary Ecology, Department of Geosciences, University of Tübingen, Tübingen, Germany.
Verheijen, Ivo
  • Senckenberg Centre for Human Evolution and Palaeoenvironment, Schöningen, Germany.
  • Early Prehistory and Quaternary Ecology, Department of Geosciences, University of Tübingen, Tübingen, Germany.
  • Cultural Heritage Office of Lower Saxony, Hanover, Germany.
Reiter, Ella
  • Archaeo- and Palaeogenetics, Institute for Archaeological Sciences, Department of Geosciences, University of Tübingen, Tübingen, Germany.
Radzevičiūtė, Rita
  • Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
Stoessel, Alexander
  • Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
  • Institute of Zoology and Evolutionary Research, Friedrich Schiller University Jena, Jena, Germany.
Krause, Johannes
  • Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
Spyrou, Maria A
  • Archaeo- and Palaeogenetics, Institute for Archaeological Sciences, Department of Geosciences, University of Tübingen, Tübingen, Germany.
  • Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany.
  • Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
Conard, Nicholas J
  • Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany.
  • Early Prehistory and Quaternary Ecology, Department of Geosciences, University of Tübingen, Tübingen, Germany.
Nieselt, Kay
  • Integrative Transcriptomics, Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany.
Posth, Cosimo
  • Archaeo- and Palaeogenetics, Institute for Archaeological Sciences, Department of Geosciences, University of Tübingen, Tübingen, Germany. cosimo.posth@uni-tuebingen.de.
  • Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany. cosimo.posth@uni-tuebingen.de.

MeSH Terms

  • Animals
  • Horses / genetics
  • Genome, Mitochondrial
  • Phylogeny
  • Fossils
  • DNA, Ancient / analysis
  • Germany
  • DNA, Mitochondrial / genetics
  • Biological Evolution

Conflict of Interest Statement

Competing interests: The authors declare no competing interests.

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Citations

This article has been cited 1 times.
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