Analyze Diet
Nature communications2025; 16(1); 7098; doi: 10.1038/s41467-025-62266-z

The genomic history of Iberian horses since the last Ice Age.

Abstract: Horses have inhabited Iberia (present-day Spain and Portugal) since the Middle Pleistocene, shaping a complex history in the region. Iberia has been proposed as a potential domestication centre and is renowned for producing world-class bloodlines. Here, we generate genome-wide sequence data from 87 ancient horse specimens (median coverage = 0.97X) from Iberia and the broader Mediterranean to reconstruct their genetic history over the last ~26,000 years. Here, we report that wild horses of the divergent IBE lineage inhabited Iberia from the Late Pleistocene, while domesticated DOM2 horses, native from the Pontic-Caspian steppes, already arrived ~1850 BCE. Admixture dating suggests breeding practices involving continued wild restocking until at least ~350 BCE, with IBE disappearing shortly after. Patterns of genetic affinity highlight the far-reaching influence of Iberian bloodlines across Europe and north Africa during the Iron Age and Antiquity, with continued impact extending thereafter, particularly during the colonization of the Americas.
Publication Date: 2025-08-02 PubMed ID: 40753154PubMed Central: PMC12317975DOI: 10.1038/s41467-025-62266-zGoogle Scholar: Lookup
The Equine Research Bank provides access to a large database of publicly available scientific literature. Inclusion in the Research Bank does not imply endorsement of study methods or findings by Mad Barn.
  • Journal Article
  • Historical 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.

This research focused on exploring the genetic history of horses in Iberia, present-day Spain and Portugal, across the past roughly 26,000 years. Data was collected from 87 ancient horse specimens from Iberia and the Mediterranean region, revealing a complex lineage and suggesting that domesticated horses arrived around 1850 BCE.

Overview of the Research

  • The study involved extracting genetic data from 87 ancient horse samples and analysing this to learn more about the origins and evolution of horses in Iberia, a region covering present-day Spain and Portugal.
  • The specimens used in the study ranged across about 26,000 years, allowing for a comprehensive view of horse lineage over a substantial period.
  • The aim was to understand more about the complex history of horses in this region, including insights into the timelines of wild and domesticated populations, breeding practices, influence on European and African bloodlines, and significant impacts across various historical periods.

Key Findings

  • The research revealed that wild horses from a distinct lineage, named the IBE lineage, inhabited Iberia from the Late Pleistocene Epoch.
  • The analysis also suggested that a breed of domesticated horses, known as DOM2 horses which originated from the Pontic-Caspian steppes, arrived in Iberia around 1850 BCE.
  • Admixture dating was used to suggest that local breeding practices may have involved reintroduction of wild horses into the gene pool until as recently as 350 BCE.
  • The IBE lineage appears to have disappeared shortly after this restocking ceased.

Impact and Influence of Iberian Horses

  • The study’s findings suggest that the bloodlines of Iberian horses had a significant impact across Europe and north Africa during the Iron Age and Antiquity, the periods roughly covering 1200 BCE to 500 CE.
  • Iberian horse bloodlines also had a notable influence during the colonization of the Americas, demonstrating a far-reaching influence geographically and over a long span of time.
  • The research provides a more comprehensive understanding of the extensive history and influence of Iberian horses, informing our understanding of equine evolution and human-horse relationships over time.

Cite This Article

APA
(2025). The genomic history of Iberian horses since the last Ice Age. Nat Commun, 16(1), 7098. https://doi.org/10.1038/s41467-025-62266-z

Publication

ISSN: 2041-1723
NlmUniqueID: 101528555
Country: England
Language: English
Volume: 16
Issue: 1
Pages: 7098
PII: 7098

Researcher Affiliations

MeSH Terms

  • Animals
  • Horses / genetics
  • Spain
  • Portugal
  • Genome
  • Genomics
  • Breeding
  • Phylogeny
  • History, Ancient
  • DNA, Ancient / analysis
  • Domestication

Grant Funding

  • 681605-PEGASUS / EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)
  • 101071707 Synergy Grant Horsepower / EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)
  • 101062645 - ZEPHYRUS / EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)

Conflict of Interest Statement

Competing interests: The authors declare no competing interests.

References

This article includes 70 references
  1. Kelekna, P. (Cambridge University Press, 2009).
  2. Fages A et al. Tracking five millennia of horse management with extensive ancient genome time series. 1419–1435.e1431 (2019).
    pmc: PMC6547883pubmed: 31056281
  3. Iborra Eres M P et al. Mass animal sacrifice at casas del Turuñuelo (Guareña, Spain): a unique Tartessian (Iron Age) site in the southwest of the Iberian Peninsula. e0293654 (2023).
    pmc: PMC10664939pubmed: 37992004
  4. Librado P et al. The origins and spread of domestic horses from the Western Eurasian steppes. 634–640 (2021).
    pmc: PMC8550961pubmed: 34671162
  5. Librado P et al. Widespread horse-based mobility arose around 2200 BCE in Eurasia. 819–825 (2024).
    pmc: PMC11269178pubmed: 38843826
  6. Outram A. Horse domestication as a multi-centered, multi-stage process: Botai and the role of specialized Eneolithic horse pastoralism in the development of human-equine relationships. 1134068 (2023).
  7. Gaunitz C et al. Ancient genomes revisit the ancestry of domestic and Przewalski’s horses. 111–114 (2018).
    pubmed: 29472442
  8. Librado P et al. Tracking the origins of Yakutian horses and the genetic basis for their fast adaptation to subarctic environments. E6889–E6897 (2015).
    pmc: PMC4687531pubmed: 26598656
  9. Bernáldez-Sánchez E et al. Equids ( sp.) in southern Spain from the Palaeolithic to the Bronze Age. 261–276 (2024).
  10. Sánchez-Hernández C et al. Dietary traits of ungulates in northeastern Iberian Peninsula: Did these Neanderthal preys show adaptive behaviour to local habitats during the Middle Palaeolithic?. 47–62 (2020).
  11. Sanz-Royo A, Sanz M, Daura J. Upper Pleistocene equids from Terrasses de la Riera dels Canyars (NE Iberian Peninsula): The presence of and based on dental criteria and their implications for palaeontological identification and palaeoenvironmental reconstruction. 78–90 (2020).
  12. Juan Cabanilles J, Martínez Valle R. Fuente Flores (Requena, Valencia). Nuevos datos sobre el poblamiento y la economía del Neo-eneolítico valenciano. 181–231 (1988).
  13. Martínez Valle, R., Iborra Eres, M. P. & Calatayud, P. M. In (ed. Coimbra, F. A.) 63–73 (Cordero Editore, 2016).
  14. Uerpmann H P. Die domestikation des pferdes im Chalkolithikum West und Mitteleuropas. 109–153 (1990).
  15. Librado P, Orlando L. Genomics and the evolutionary history of equids. 81–101 (2021).
    pubmed: 33197207
  16. Pascual Barea, J. In (ed. Santamaría Hernández, M. T.), 117–202 (Ediciones de la Universidad de Castilla-La Mancha, 2008).
  17. Seco Serra, I. & de la Villa, J. In (eds. Quesada Sanz, F. & Zamora Merchán, M.), 125–140 (Real Academia de la Historia & Universidad Autónoma de Madrid, 2003).
  18. Guichard, P. (Hachette Pluriel Reference, 2011).
  19. Taylor W T T et al. Early dispersal of domestic horses into the Great Plains and northern Rockies. 1316–1323 (2023).
    pubmed: 36996225
  20. Jónsson H, Ginolhac A, Schubert M, Johnson P L F, Orlando L. mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters. 1682–1684 (2013).
    pmc: PMC3694634pubmed: 23613487
  21. Skoglund P et al. Separating endogenous ancient DNA from modern day contamination in a Siberian Neandertal. 2229–2234 (2014).
    pmc: PMC3926038pubmed: 24469802
  22. Orlando L et al. Ancient DNA analysis. 14 (2021).
  23. Clark P U et al. The Last Glacial Maximum. 710–714 (2009).
    pubmed: 19661421
  24. Cieslak M et al. Origin and history of mitochondrial DNA lineages in domestic horses. e15311 (2010).
    pmc: PMC3004868pubmed: 21187961
  25. Sala N et al. Nobody’s land? The oldest evidence of early Upper Paleolithic settlements in inland Iberia. eado3807 (2024).
    pmc: PMC11809639pubmed: 38924409
  26. Leonardi M et al. Late Quaternary horses in Eurasia in the face of climate and vegetation change. eaar5589 (2018).
    pmc: PMC6059734pubmed: 30050986
  27. Szpak P. Complexities of nitrogen isotope biogeochemistry in plant-soil systems: implications for the study of ancient agricultural and animal management practices. 288 (2014).
    pmc: PMC4066317pubmed: 25002865
  28. Bonafini M, Pellegrini M, Ditchfield P, Pollard A M. Investigation of the ‘canopy effect’ in the isotope ecology of temperate woodlands. 3926–3935 (2013).
  29. Nielsen S V et al. Bayesian inference of admixture graphs on Native American and Arctic populations. e1010410 (2023).
    pmc: PMC9956672pubmed: 36780565
  30. Sommer R S, Benecke N, Lõugas L, Nelle O, Schmölcke U. Holocene survival of the wild horse in Europe: a matter of open landscape?. 805–812 (2011).
  31. Patterson N et al. Ancient admixture in human history. 1065–1093 (2012).
    pmc: PMC3522152pubmed: 22960212
  32. Alexander D H, Novembre J, Lange K. Fast model-based estimation of ancestry in unrelated individuals. 1655–1664 (2009).
    pmc: PMC2752134pubmed: 19648217
  33. Librado P, Orlando L. Struct-f4: a Rcpp package for ancestry profile and population structure inference from f4-statistics. 2070–2071 (2022).
    pmc: PMC8963280pubmed: 35080599
  34. Harney É, Patterson N, Reich D, Wakeley J. Assessing the performance of qpAdm: a statistical tool for studying population admixture. iyaa045 (2021).
    pmc: PMC8049561pubmed: 33772284
  35. Molloy E K, Durvasula A, Sankararaman S. Advancing admixture graph estimation via maximum likelihood network orientation. i142–i150 (2021).
    pmc: PMC8336447pubmed: 34252951
  36. Chintalapati M, Patterson N, Moorjani P. The spatiotemporal patterns of major human admixture events during the European Holocene. e77625 (2022).
    pmc: PMC9293011pubmed: 35635751
  37. Altamirano, J. C. (Ediciones Ecuestres, 1998).
  38. Altamirano, J. C. (Ediciones Ecuestres, 2003).
  39. Costa Ferreira, J. & Henriques, P. C. (ICONOM, 2001).
  40. García-Gelabert Pérez M P. Movilidad entre África y la península ibérica en la Antigüedad. 7–26 (2005).
  41. Nieto Espinet A. Porcs, cavalls, ovelles i infants. Noves aportacions a les pràctiques rituals de la fortalesa dels Vilars (Arbeca, les Garrigues). 127–162 (2013).
  42. Nieto Espinet, A., López, J. B. & Junyent, E. In (ed. Coimbra, F. A.), 117–134 (Cordero Editore, 2016).
  43. Celestino Pérez, S. & López-Ruiz, C. (Oxford University Press, 2016).
  44. Olalde I et al. The genomic history of the Iberian Peninsula over the past 8000 years. 1230–1234 (2019).
    pmc: PMC6436108pubmed: 30872528
  45. Morillo Á, Adroher A M, Dobson M, Martín Hernández E. Constructing the archaeology of the Roman conquest of Hispania: new evidence, perspectives and challenges. 36–52 (2020).
  46. Sousa da Mota B et al. Imputation of ancient human genomes. 3660 (2023).
    pmc: PMC10282092pubmed: 37339987
  47. Ringbauer H et al. Accurate detection of identity-by-descent segments in human ancient DNA. 143–151 (2024).
    pmc: PMC10786714pubmed: 38123640
  48. Allentoft M E et al. 100 ancient genomes show repeated population turnovers in Neolithic Denmark. 329–337 (2024).
    pmc: PMC10781617pubmed: 38200294
  49. Todd E T et al. Imputed genomes of historical horses provide insights into modern breeding. 107104 (2023).
    pmc: PMC10319840pubmed: 37416458
  50. Antonio M L et al. Ancient Rome: A genetic crossroads of Europe and the Mediterranean. 708–714 (2019).
    pmc: PMC7093155pubmed: 31699931
  51. Antonio M L et al. Stable population structure in Europe since the Iron Age, despite high mobility. e79714 (2024).
    pmc: PMC10827293pubmed: 38288729
  52. Todd E T et al. The genomic history and global expansion of domestic donkeys. 1172–1180 (2022).
    pubmed: 36074859
  53. Lepetz S et al. Historical management of equine resources in France from the Iron Age to the Modern Period. 103250 (2021).
  54. Bronk Ramsey C. Bayesian analysis of radiocarbon dates. 337–360 (2009).
  55. Reimer P J et al. The IntCal20 Northern Hemisphere Radiocarbon Age Calibration Curve (0–55 cal kBP). 725–757 (2020).
  56. Gamba C et al. Comparing the performance of three ancient DNA extraction methods for high-throughput sequencing. 459–469 (2016).
    pubmed: 26401836
  57. Schubert M, Lindgreen S, Orlando L. AdapterRemoval v2: rapid adapter trimming, identification, and read merging. 88 (2016).
    pmc: PMC4751634pubmed: 26868221
  58. Kalbfleisch T S et al. Improved reference genome for the domestic horse increases assembly contiguity and composition. 197 (2018).
    pmc: PMC6240028pubmed: 30456315
  59. Felkel S et al. The horse Y chromosome as an informative marker for tracing sire lines. 6095 (2019).
    pmc: PMC6465346pubmed: 30988347
  60. Xu X, Árnason Ú. The complete mitochondrial DNA sequence of the horse, : extensive heteroplasmy of the control region. 357–362 (1994).
    pubmed: 7958969
  61. Schubert M et al. Prehistoric genomes reveal the genetic foundation and cost of horse domestication. E5661–E5669 (2014).
    pmc: PMC4284583pubmed: 25512547
  62. Langmead B, Salzberg S L. Fast gapped-read alignment with Bowtie 2. 357–359 (2012).
    pmc: PMC3322381pubmed: 22388286
  63. Poullet M, Orlando L. Assessing DNA sequence alignment methods for characterizing ancient genomes and methylomes. 105 (2020).
  64. Danecek P et al. Twelve years of SAMtools and BCFtools. giab008 (2021).
    pmc: PMC7931819pubmed: 33590861
  65. Wang C et al. Donkey genomes provide new insights into domestication and selection for coat color. 6014 (2020).
    pmc: PMC7723042pubmed: 33293529
  66. Nguyen L-T, Schmidt H A, von Haeseler A, Minh B Q. IQ-TREE: A fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. 268–274 (2015).
    pmc: PMC4271533pubmed: 25371430
  67. Lefort V, Desper R, Gascuel O. FastME 2.0: A comprehensive, accurate, and fast distance-based phylogeny inference program. 2798–2800 (2015).
    pmc: PMC4576710pubmed: 26130081
  68. Chang C C et al. Second-generation PLINK: rising to the challenge of larger and richer datasets. s13742-13015-10047-13748 (2015).
    pmc: PMC4342193pubmed: 25722852
  69. Junier T, Zdobnov E M. The Newick utilities: high-throughput phylogenetic tree processing in the Unix shell. 1669–1670 (2010).
    pmc: PMC2887050pubmed: 20472542
  70. Patterson N, Price A L, Reich D. Population structure and eigenanalysis. e190 (2006).
    pmc: PMC1713260pubmed: 17194218

Citations

This article has been cited 0 times.