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

Understanding the genetic diversity and evolutionary history of domestic horses (Equus caballus) 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.