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Genes2026; 17(1); 95; doi: 10.3390/genes17010095

Sequencing and Analysis of mtDNA Genomes from the Teeth of Early Medieval Horses in Poland.

Abstract: This study presents the sequencing and analysis of mitochondrial DNA (mtDNA) genomes from nine early medieval horse remains excavated across archaeological sites in Silesia region in present day Poland. Methods: Using aDNA extraction protocols optimized for short fragments, combined with target enrichment and high-throughput sequencing, we reconstructed partial mtDNA sequences for seven of the specimens. Results: The authenticity of the aDNA was confirmed through damage pattern analysis. Phylogenetic reconstruction revealed that the specimens belonged to six distinct mtDNA lineages (B, D, E, G, L, and M), indicating a high level of mitochondrial diversity within medieval Silesian horse population. Conclusions: These findings highlight the extensive mtDNA variability among domestic horses, reflecting the diversity of their ancestral populations rather than modern breed differentiation. This research enhances our understanding of horse population structure in medieval Europe, emphasizing the genetic complexity present during this period.
Publication Date: 2026-01-18 PubMed ID: 41595516PubMed Central: PMC12841091DOI: 10.3390/genes17010095Google Scholar: Lookup
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  • Journal Article
  • Historical Article

Summary

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Research Overview

  • This study sequenced mitochondrial DNA from medieval horse teeth excavated in Poland and found high genetic diversity, providing insights into the population structure of horses in early medieval Europe.

Introduction and Objectives

  • The study focused on analyzing mitochondrial DNA (mtDNA) extracted from horse remains discovered at archaeological sites in the Silesia region of present-day Poland.
  • The primary aim was to reconstruct mtDNA genomes to understand the genetic diversity and population structure of horses during the early medieval period.

Materials and Methods

  • Samples were taken from nine horse teeth remains excavated across multiple early medieval archaeological sites.
  • Ancient DNA (aDNA) extraction protocols optimized for short DNA fragments were employed to ensure maximal recovery of degraded genetic material.
  • Target enrichment techniques were applied to selectively capture mtDNA sequences before sequencing.
  • High-throughput sequencing technologies were used to generate partial mitochondrial genome sequences from the samples.
  • Damage pattern analysis was conducted to authenticate the ancient origin of the DNA sequences, ensuring the results were not contaminated by modern DNA.

Results

  • Partial mtDNA sequences were successfully reconstructed for seven out of the nine specimens.
  • Phylogenetic analysis identified six distinct mtDNA lineages among the specimens: B, D, E, G, L, and M.
  • The presence of these six lineages indicated a high degree of mitochondrial genetic diversity within the early medieval Silesian horse population.

Discussion and Conclusions

  • The high mtDNA variability suggests that medieval domestic horses in this region descended from a wide variety of ancestral populations rather than being limited to narrow breed lines.
  • This diversity predates the modern classification and differentiation of horse breeds, highlighting a complex population structure during medieval times.
  • The study contributes to a better understanding of the genetic makeup and historical population dynamics of horses in medieval Europe.
  • These findings emphasize the importance of ancient DNA studies in revealing genetic complexity not evident from modern horse populations alone.

Cite This Article

APA
Pasicka E, Baca M, Popović D, Makowiecki D, Janeczek M. (2026). Sequencing and Analysis of mtDNA Genomes from the Teeth of Early Medieval Horses in Poland. Genes (Basel), 17(1), 95. https://doi.org/10.3390/genes17010095

Publication

ISSN: 2073-4425
NlmUniqueID: 101551097
Country: Switzerland
Language: English
Volume: 17
Issue: 1
PII: 95

Researcher Affiliations

Pasicka, Edyta
  • Department of Biostructure and Animal Physiology, Wrocław University of Environmental and Life Sciences, Kożuchowska 1, 51-631 Wrocław, Poland.
Baca, Mateusz
  • Centre of New Technologies, University of Warsaw, S. Banacha 2c, 02-097 Warsaw, Poland.
Popović, Danijela
  • Centre of New Technologies, University of Warsaw, S. Banacha 2c, 02-097 Warsaw, Poland.
Makowiecki, Daniel
  • Institute of Archaeology, Nicolaus Copernicus University in Toruń, Szosa Bydgoska 44/48, 87-100 Toruń, Poland.
Janeczek, Maciej
  • Department of Biostructure and Animal Physiology, Wrocław University of Environmental and Life Sciences, Kożuchowska 1, 51-631 Wrocław, Poland.

MeSH Terms

  • Horses / genetics
  • Animals
  • Poland
  • DNA, Mitochondrial / genetics
  • Genome, Mitochondrial / genetics
  • Phylogeny
  • Tooth / chemistry
  • DNA, Ancient / analysis
  • History, Medieval
  • Sequence Analysis, DNA
  • High-Throughput Nucleotide Sequencing

Conflict of Interest Statement

The authors declare no conflicts of interest.

References

This article includes 56 references
  1. Reitz E, Wing E. Zooarchaeology. 2nd ed. Cambridge University Press; Cambridge, UK: 2008.
  2. Gifford-Gonzalez D. An Introduction to Zooarchaeology. Springer International Publishing; New York, NY, USA: 2018. p. 604.
  3. Bartosiewicz L, Gal E. Shuffling Nags, Lame Ducks. The Archaeology of Animals Disease. Oxbow Books; Oxford, UK: 2013. Pathological lesions in working animals; pp. 130–154.
  4. Bartosiewicz L, Gal E. Care or Neglect? Evidence of Animal Disease in Archaeology. Proceedings of the 6th Meeting of the Animal Palaeopathology Working Group of the International Council for Archaeozoology (ICAZ); Budapest, Hungary. 26–29 May 2016; Oxford, UK: Oxbow Books; 2018. p. 288.
  5. Makowiecki D, Chudziak W, Szczepanik P, Janeczek M, Pasicka E. Horses in the Early Medieval (10th–13th c.) Religious Rituals of Slavs in Polish Areas—An Archaeozoological, Archaeological and Historical Overview. Animals 2022;12:2282.
    doi: 10.3390/ani12172282pmc: PMC9454541pubmed: 36078002google scholar: lookup
  6. Makowiecki D, Janeczek M, Pasicka E, Rozwadowska A, Ciaputa R, Kocińska K. Pathologies on a horse skeleton from the early medieval stronghold in Gdańsk (Poland). Int. J. Osteoarchaeol. 2022;32:866–877.
    doi: 10.1002/oa.3114google scholar: lookup
  7. Janeczek M, Makowiecki D, Rozwadowska A, Chudziak W, Pasicka E. Pathological Changes in Early Medieval Horses from Different Archaeological Sites in Poland. Animals 2024;14:490.
    doi: 10.3390/ani14030490pmc: PMC10854896pubmed: 38338132google scholar: lookup
  8. Pawlak J, Kowalik N, Anczkiewicz R, Krajcarz M, Makowiecki D, Krajcarz M.T. The application of a genetic algorithm in the correlation of intra-individual isotopic Sr dental records for archaeological and palaeontological reconstruction of years-long mobility. Archaeometry 2025;67:1619–1635.
    doi: 10.1111/arcm.70010google scholar: lookup
  9. Achilli A, Olivieri A, Soares P, Lancioni H, Kashani B.H, Perego U.A, Nergadze S.G, Carossa V, Santagostino M, Capomaccio S. Mitochondrial genomes from modern horses reveal the major haplogroups that underwent domestication. Proc. Natl. Acad. Sci. USA 2012;109:2449–2454.
    doi: 10.1073/pnas.1111637109pmc: PMC3289334pubmed: 22308342google scholar: lookup
  10. Schubert M, Mashkour M, Gaunitz C, Fages A, Seguin-Orlando A, Sheikhi S, Alfarhan A.H, Alquraishi S.A, Al-Rasheid K.A, Chuang R. Zonkey: A simple, accurate and sensitive pipeline to genetically identify equine F1-hybrids in archaeological assemblages. J. Archaeol. Sci. 2017;78:147–157.
    doi: 10.1016/j.jas.2016.12.005google scholar: lookup
  11. Agbani A, Aminou O, Machmoum M, Germot A, Badaoui B, Petit D, Piro M. A Systematic Literature Review of Mitochondrial DNA Analysis for Horse Genetic Diversity. Animals 2025;15:885.
    doi: 10.3390/ani15060885pmc: PMC11939364pubmed: 40150414google scholar: lookup
  12. Orlando L. Ancient Genomes Reveal Unexpected Horse Domestication and Management Dynamics. BioEssays 2020;42:e1900164.
    doi: 10.1002/bies.201900164pubmed: 31808562google scholar: lookup
  13. Clutton-Brock J. A History of the Horse and Donkey in Human Societies. Oxbow; Oxford, UK: 1992. Horse Power.
  14. Levine M.A. The origins of horse husbandry on the Eurasian steppe. In: Levine M.A., Rassamakin Y.Y., Kislenko A.M., Tatarintseva N.S., editors. Late Prehistoric Exploitation of the Eurasian Steppe. McDonald Institute; Cambridge, UK: 1999. pp. 5–58.
  15. Makowiecki D, Chudziak W, Wiejacka M. Preliminary reflections on horse-human relationship in early medieval Poland on the basis of history and archaeozoology. In: Niinimäki S., Salmi A.-K., editors. Archaeologies of Animal Movement, Animals on the Move, Seria: Themes in Contemporary Archaeology. Springer; Cham, Switzerland: 2021. pp. 21–32.
  16. Brzóstkowska A, Swoboda W. Testimonia Najdawniejszych Dziejów Słowian: Pisarze z V–X Wieku. Zakład Narodowy im Ossolińskich; Wrocław, Poland: 1989.
  17. Wołek A. Obraz Słowian w dziełach Prokopiusza z Cezarei. Iuvenilia Philol. Crac. 2012;5:219–238.
  18. Kurnatowska Z. Słowiańszczyzna Południowa. Zakład Narodowy im Ossolińskich; Wrocław, Poland: 1977.
  19. Labuda G. Antologia Tekstów Źródłowych. Sorus; Poznań, Poland: 1999. Słowiańszczyzna starożytna i wczesnośredniowieczna.
  20. Kowalski T. Relacja Ibrahima Ibn Jakuba z Podróży do Krajów Słowiańskich w Przekazie Al–Bekriego. Wydawnictwa Komisji Historycznej PAU; Warszawa, Poland: 1946.
  21. Anonim G. Kronika polska. Zakład Narodowy Im. Ossolińskich; Wrocław, Poland: 2008.
  22. Radek T. Morphological investigation into species belonging of tanned animal skins coming from Nakło on Noteć. In: Kubasiewicz M., editor. Archaeozoology, Proceedings of the IIIrd International Archaeozoological, Agricultural Academy Szczecin, Poland, 23–26 April 1978. Volume 1. Agricultural Academy; Szczecin, Poland: 1979. pp. 142–150.
  23. Jaworski K. Wyroby z Kości i Poroża w Kulturze Wczesnośredniowiecznego Ostrowa Tumskiego we Wrocławiu. Uniwersytet Wrocławski Volumen; Wrocław, Poland: 1990.
  24. Popović D, Baca M, Wiejacka M, Chudziak W, Makowiecki D. Genetic Characterization of Horses in Early Medieval Poland. J. Archaeol. Sci. Rep. 2024;56:1–10.
  25. Makowiecki D, Wiejacka M. The Horse (Equus Caballus) in Early Medieval Poland (8th–13th/14th Century); According to Zooarchaeological Records. Wydawnictwo Uniwerstytetu Mikołaja Kopernika; Toruń, Poland: 2023.
  26. Kaźmierczyk J, Kramarek J, Lasota C. Badania na Ostrowie Tumskim we Wrocławiu w 1977 roku. Sil. Antiq. 1979;21:119–182.
  27. Mackiewicz M, Marcinkiewicz K, Piekalski J. Plac Nowy Targ we Wrocławiu w świetle badań wykopaliskowych w latach 2010–2012. Archaeol. Hist. Pol. 2014;22:167.
    doi: 10.12775/AHP.2014.008google scholar: lookup
  28. Ramsey C.B. Bayesian Analysis of Radiocarbon Dates. Radiocarbon 2009;51:337–360.
    doi: 10.1017/S0033822200033865google scholar: lookup
  29. Reimer P.J, Austin W.E.N, Bard E, Bayliss A, Blackwell P.G, Bronk Ramsey C, Butzin M, Cheng H, Edwards R.L, Friedrich M. The IntCal20 northern hemisphere radiocarbon age calibration curve (0–55 cal kBP). Radiocarbon 2020;62:725–757.
    doi: 10.1017/RDC.2020.41google scholar: lookup
  30. Dabney J, Knapp M, Glocke I, Gansauge M.-T, Weihmann A, Nickel B, Valdiosera C, García N, Pääbo S, Arsuaga J.-L. Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments. Proc. Natl. Acad. Sci. USA 2013;110:15758–15763.
    doi: 10.1073/pnas.1314445110pmc: PMC3785785pubmed: 24019490google scholar: lookup
  31. Meyer M, Kircher M. Illumina sequencing library preparation for highly multiplexed target capture and sequencing.. Cold Spring Harb. Protoc. 2010;2010:t5448.
    doi: 10.1101/pdb.prot5448pubmed: 20516186google scholar: lookup
  32. Horn S. Ancient DNA: Methods and Protocols. Springer; Berlin/Heidelberg, Germany: 2012. Target enrichment via DNA hybridization capture.
    pubmed: 22237535
  33. Schubert M, Lindgreen S, Orlando L. AdapterRemoval v2: Rapid adapter trimming, identification, and read merging.. BMC Res. Notes 2016;9:88.
    doi: 10.1186/s13104-016-1900-2pmc: PMC4751634pubmed: 26868221google scholar: lookup
  34. Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform.. Bioinformatics 2010;26:589–595.
  35. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools.. Bioinformatics 2009;25:2078–2079.
  36. Milne I, Stephen G, Bayer M, Cock P.J.A., Pritchard L, Cardle L, Shaw P.D, Marshall D. Using Tablet for visual exploration of second-generation sequencing data.. Brief. Bioinform. 2013;14:193–202.
    doi: 10.1093/bib/bbs012pubmed: 22445902google scholar: lookup
  37. Jónsson H, Ginolhac A, Schubert M, Johnson P.L.F., Orlando L. MapDamage2.0: Fast approximate Bayesian estimates of ancient DNA damage parameters.. Bioinformatics 2013;29:1682–1684.
  38. Lippold S, Matzke N.J., Reissmann M, Hofreiter M. Whole mitochondrial genome sequencing of domestic horses reveals incorporation of extensive wild horse diversity during domestication.. BMC Evol. Biol. 2011;11:328.
    doi: 10.1186/1471-2148-11-328pmc: PMC3247663pubmed: 22082251google scholar: lookup
  39. Stamatakis A. RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies.. Bioinformatics 2014;30:1312–1313.
  40. Rozas J, Ferrer-Mata A, Sánchez-DelBarrio J.C., Guirao-Rico S, Librado P, Ramos-Onsins S.E., Sánchez-Gracia A. DnaSP 6: DNA Sequence Polymorphism Analysis of Large Datasets.. Mol. Biol. Evol. 2017;34:3299–3302.
    doi: 10.1093/molbev/msx248pubmed: 29029172google scholar: lookup
  41. Wiens J.J. Missing Data and the Design of Phylogenetic Analyses.. J. Biomed. Inform. 2006;39:34–42.
    doi: 10.1016/j.jbi.2005.04.001pubmed: 15922672google scholar: lookup
  42. Fages A, Seguin-Orlando A, Germonpré M, Orlando L. Horse males became over-represented in archaeological assemblages during the Bronze Age.. J. Archaeol. Sci. Rep. 2020;31:102364.
  43. Peng M.-S, Fan L, Shi N.-N, Ning T, Yao Y.-G, Murphy R.W, Wang W.-Z, Zhang Y.-P. DomeTree: A canonical toolkit for mitochondrial DNA analyses in domesticated animals.. Mol. Ecol. Resour. 2015;15:1238–1242.
    doi: 10.1111/1755-0998.12386pubmed: 25655564google scholar: lookup
  44. Cieślak M, Pruvost M, Benecke N, Hofreiter M, Morales A, Reissmann M, Ludwig A. Origin and history of mitochondrial DNA lineages in domestic horses.. PLoS ONE 2010;5:e15311.
  45. Jansen T, Forster P, Levine M.A., Oelke H, Hurles M, Renfrew C, Weber J, Olek K. Mitochondrial DNA and the Origins of the Domestic Horse.. Proc. Natl. Acad. Sci. USA 2002;99:10905–10910.
    doi: 10.1073/pnas.152330099pmc: PMC125071pubmed: 12130666google scholar: lookup
  46. Pycińska N, Cieślak J. Wykorzystanie badań genetycznych w rekonstrukcji historii gatunku koń domowy.. Przegląd Hod. 2024;3:7–12.
  47. Ma H, Wu Y, Xiang H, Yang Y, Wang M, Zhao C, Wu C. Some maternal lineages of domestic horses may have origins in East Asia revealed with further evidence of mitochondrial genomes and HVR-1 sequences.. PeerJ 2018;6:e4896.
    doi: 10.7717/peerj.4896pmc: PMC5985762pubmed: 29868288google scholar: lookup
  48. Maroń J. Legnica 1241. Bellona; Warszawa, Poland: 2008.
  49. Welsh W.E. The Battle of Legnica: The Mongol Devastation of Poland.. JSTOR 2016;5:26–34.
  50. Pankiewicz A. Między centrum, zapleczem a szlakiem handlowym. Wymiana i obieg pieniężny w tzw. ośrodkach centralnych we wczesnym średniowieczu na przykładzie Wrocławia.. Archeol. Pol. 2022;LXVII:159–198.
    doi: 10.23858/APol67.2022.006google scholar: lookup
  51. Ramsey B.C. OxCal v4.4.2. Oxford. 2020. [(accessed on 4 November 2025)]. Available online: https://c14.arch.ox.ac.uk.
  52. Myczkowski K. Ogólne wyniki badań szczątków kostnych i skorup zwierzęcych z wczesnego średniowiecza, wydobytych na Ostrowie Tumskim we Wrocławiu w latach 1950–1957.. Przegląd Archeol. 1960;12:150–171.
  53. Alexander D.H, Novembre J, Lange K. Fast model-based estimation of ancestry in unrelated individuals.. Genome Res. 2009;19:1655–1664.
    doi: 10.1101/gr.094052.109pmc: PMC2752134pubmed: 19648217google scholar: lookup
  54. Pickrell J.K, Pritchard J.K. Inference of population splits and mixtures from genome-wide allele frequency data.. PLoS Genet. 2012;8:e1002967.
  55. Neale B, Todd-Brown K, Thomas L, Ferreira M.A.R., Bender D, Maller J, Sklar P, de Bakker P.I.W., Daly M.J., Sham P.C. PLINK: A tool set for whole- genome association and population-based linkage analyses.. Am. J. Hum. Genet. 2007;81:559–575.
    pmc: PMC1950838pubmed: 17701901
  56. Stamatakis A. RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models.. Bioinformatics 2006;22:2688–2690.
    doi: 10.1093/bioinformatics/btl446pubmed: 16928733google scholar: lookup

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