Abstract
To assess the genetic diversity and matrilineal differentiation between the Betpak-Dala (BD) and Volga–Ural (VU) populations of Saiga tatarica in Kazakhstan, this study sequenced and comparatively analyzed the complete mitochondrial genomes of both populations. Phylogenetic analyses showed that Saiga tatarica clustered with the genera Gazella, Nanger, and Eudorcas, indicating a close evolutionary relationship. Genetic diversity analysis revealed that the BD population exhibited higher nucleotide diversity than the VU population. A total of 22 haplotypes were identified based on complete mitochondrial genome sequences, and no haplotypes were shared between the two populations, indicating pronounced matrilineal genetic differentiation. Synonymous mutations predominated among protein-coding genes, with the NADH dehydrogenase subunit 2 gene (nd2) and NADH dehydrogenase subunit 5 gene (nd5) genes exhibiting high levels of variation and serving as key regions for the accumulation of genetic diversity within the mitochondrial genome. These findings enhance the understanding of the genetic diversity and matrilineal genetic structure of Saiga tatarica populations in Kazakhstan and provide valuable information for their conservation and management.