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Frontiers in genetics2026; 17; 1874969; doi: 10.3389/fgene.2026.1874969

Mitochondrial DNA reveals high maternal diversity within a weak breed structure in native Kazakhstani horses.

Abstract: Understanding the genetic diversity and evolutionary history of domestic horses () is essential for reconstructing their population dynamics and origins. In this study, we analyzed mitochondrial DNA variation (COI and cytb) in six Kazakhstani horse populations representing four native breeds (Kazakh, Kostanay, Adai, and Mugalzhar) to assess genetic diversity, population structure, and evolutionary relationships within a broader phylogenetic framework. High haplotype diversity combined with low nucleotide diversity revealed population expansion and admixture. Population structure analyses revealed weak genetic differentiation and a lack of breed-specific structuring, with most variation occurring within populations. Phylogenetic reconstruction and haplotype network analyses showed that Kazakhstani horses are interspersed among global domestic lineages, reflecting extensive historical connectivity and admixture. Demographic analyses based on neutrality tests and mismatch distributions support signals of ancient population expansion, while the multimodal distribution patterns suggest a complex demographic history involving population substructure and multiple expansion events rather than a single, sudden expansion. Times since expansion were calculated to be around 205 Kya. Divergence time estimates place the diversification of all caballine horses, including Kazakhstani horses, within the Pleistocene (0.89 Mya) with the majority of them grouping with different horse breeds across the world. These results indicate that the maternal genetic structure of Kazakhstani horses has been shaped by a combination of ancient evolutionary processes and more recent demographic dynamics, including recurrent gene flow across Eurasian steppe environments. Overall, this study highlights a reticulate evolutionary history of domestic horses, emphasizing the role of long-term connectivity and population expansion in shaping mitochondrial diversity.
Copyright © 2026 Ualiyeva, Dossybayev, Kapassuly, Kozhakhmet, Kozhanov, Kryukov, Arita, Torekhanov and Torekhanov.
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Publication Date: 2026-07-06 PubMed ID: 42483728PubMed Central: PMC13387962DOI: 10.3389/fgene.2026.1874969Google 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.

Mitochondrial DNA analysis of native Kazakhstani horses reveals high maternal genetic diversity but weak differentiation among breeds, indicating extensive historical mixing and population expansion linked to ancient and recent evolutionary events.

Research Objective and Background

  • Investigate the genetic diversity, population structure, and evolutionary history of native Kazakhstani horse breeds using mitochondrial DNA (mtDNA) markers.
  • Focus on four native breeds: Kazakh, Kostanay, Adai, and Mugalzhar, representing the genetic pool of horses in Kazakhstan.
  • Understand how historical gene flow and population dynamics have shaped the current genetic makeup of these horses.
  • Place Kazakhstani horses within a broader phylogenetic and evolutionary context relative to global domestic horse lineages.

Methods and Genetic Markers Used

  • Analysis of mitochondrial DNA, specifically the cytochrome oxidase I (COI) and cytochrome b (cytb) genes, which are commonly used for studying maternal lineage and evolutionary relationships.
  • Examination of genetic diversity metrics such as haplotype diversity (number and frequency of different maternal lineages) and nucleotide diversity (average genetic difference among sequences).
  • Population structure assessments to evaluate how genetic variation is partitioned within and among breeds.
  • Phylogenetic reconstruction and haplotype network analyses were performed to visualize evolutionary connections between Kazakhstani horses and global domestic horse lineages.
  • Demographic history inferred using neutrality tests and mismatch distribution analyses to detect signals of population expansion and complexity.

Key Findings: Genetic Diversity and Population Structure

  • High haplotype diversity was observed, indicating many different maternal lineages within Kazakhstani horses.
  • Low nucleotide diversity suggests these diverse lineages do not differ greatly at the sequence level, consistent with recent population expansion or admixture among related lineages.
  • Population structure analyses revealed weak genetic differentiation among the four native breeds, meaning these breeds are not genetically distinct at the mitochondrial level.
  • Most genetic variation exists within individual populations rather than between breeds, reflecting extensive gene flow and lack of strict maternal breed boundaries.

Phylogenetic and Evolutionary Insights

  • Kazakhstani horses’ mitochondrial lineages are intermingled with global domestic horse haplotypes, indicating long-term connectivity and shared ancestry across Eurasia.
  • Phylogenetic trees and haplotype networks display a reticulate evolutionary pattern—an intricate web of connections rather than linear divergence—due to historical interbreeding.
  • The divergence of all caballine (true horses) including Kazakhstani horses dates back to approximately 0.89 million years ago (Mya) during the Pleistocene epoch.
  • Most Kazakh horse haplotypes cluster alongside various horse breeds worldwide, reflecting widespread maternal gene flow and shared evolutionary backgrounds.

Demographic History and Population Dynamics

  • Neutrality tests and mismatch distributions show signs of ancient population expansions rather than recent, sudden growth, implying complex demographic events.
  • Multimodal mismatch distribution patterns suggest multiple expansion phases and/or persistent population substructure rather than a single, panmictic expansion.
  • Expansion times calculated to be around 205 thousand years ago (Kya), overlapping with late Pleistocene environmental changes.
  • The demographic complexity reflects the interplay of ancient evolutionary processes, such as glacial cycles, and more recent dynamics associated with horse domestication and human-mediated breeding.

Conclusions and Significance

  • The maternal genetic makeup of Kazakhstani horses is characterized by high diversity and weak breed differentiation.
  • Historical gene flow across the Eurasian steppe has played a major role in shaping this genetic landscape.
  • Findings emphasize that domestic horses possess a complex and reticulate evolutionary history rather than discrete, isolated breed lineages.
  • This research contributes to understanding horse domestication, population structure, and the influence of geographic and historical factors on maternal genetic diversity.
  • It also underlines the importance of preserving genetic variation in native breeds, which carry signatures of both ancient and recent evolutionary events.

Cite This Article

APA
Ualiyeva D, Dossybayev K, Kapassuly T, Kozhakhmet A, Kozhanov Z, Kryukov K, Arita M, Torekhanov M, Torekhanov A. (2026). Mitochondrial DNA reveals high maternal diversity within a weak breed structure in native Kazakhstani horses. Front Genet, 17, 1874969. https://doi.org/10.3389/fgene.2026.1874969

Publication

Frontiers in genetics
ISSN: 1664-8021
NlmUniqueID: 101560621
Country: Switzerland
Language: English
Volume: 17
Pages: 1874969
PII: 1874969

Researcher Affiliations

Ualiyeva, Daniya
  • Kazakh Research Institute of Livestock and Fodder Production, Almaty, Kazakhstan.
  • Institute of Genetics and Physiology, MSHE of the Republic of Kazakhstan, Almaty, Kazakhstan.
Dossybayev, Kairat
  • Kazakh Research Institute of Livestock and Fodder Production, Almaty, Kazakhstan.
  • Institute of Genetics and Physiology, MSHE of the Republic of Kazakhstan, Almaty, Kazakhstan.
  • Faculty of Biology and Biotechnology, Farabi University, Almaty, Kazakhstan.
Kapassuly, Tilek
  • Kazakh Research Institute of Livestock and Fodder Production, Almaty, Kazakhstan.
  • Institute of Genetics and Physiology, MSHE of the Republic of Kazakhstan, Almaty, Kazakhstan.
  • Faculty of Biology and Biotechnology, Farabi University, Almaty, Kazakhstan.
Kozhakhmet, Altynay
  • Kazakh Research Institute of Livestock and Fodder Production, Almaty, Kazakhstan.
  • Institute of Genetics and Physiology, MSHE of the Republic of Kazakhstan, Almaty, Kazakhstan.
  • Faculty of Biology and Biotechnology, Farabi University, Almaty, Kazakhstan.
Kozhanov, Zhassulan
  • Kazakh Research Institute of Livestock and Fodder Production, Almaty, Kazakhstan.
Kryukov, Kirill
  • Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Shizuoka, Japan.
  • Center for Genome Informatics, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Mishima, Shizuoka, Japan.
Arita, Masanori
  • Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Shizuoka, Japan.
  • Department of Informatics, National Institute of Genetics, Mishima, Shizuoka, Japan.
Torekhanov, Merey
  • Institute of Genetics and Physiology, MSHE of the Republic of Kazakhstan, Almaty, Kazakhstan.
Torekhanov, Aibyn
  • Kazakh Research Institute of Livestock and Fodder Production, Almaty, Kazakhstan.

Conflict of Interest Statement

The author(s) declared that this work was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

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