Genetic Differentiation of Nelma Stenodus nelma (Coregoninae) from the Irtysh River Basin (Central Asia, Kazakhstan) as a Consequence of Pleistocene Migrations

Background/Objectives: The genetic structure and phylogeographic history of nelma (Stenodus leucichthys) populations across Eurasia remain incompletely understood. This study aimed to investigate genome-wide genetic differentiation among populations from seven Eurasian localities, with particular attention to the genetic distinctiveness and conservation significance of the middle Irtysh population. Methods: Genome-wide single nucleotide polymorphism (SNP) data from 41 specimens representing seven Eurasian localities, including 11 specimens from the middle reaches of the Irtysh River, were analysed. Genetic structure and admixture were assessed using ADMIXTURE with leave-one-out cross-validation (LOOCV), principal component analysis (PCA), discriminant principal component analysis (DPCA), and f2-statistics. Phylogeographic relationships and divergence times were also investigated. Results: ADMIXTURE analysis indicated the lowest LOOCV error at K = 2–4. Across all K values, the Irtysh population remained genetically homogeneous and distinct, whereas other populations exhibited varying degrees of admixture. The Volga population clustered with Arctic Ocean basin populations at K = 2 but formed a separate genetic cluster at K = 3–4; the Indigirka population was also distinguished at K = 4. PCA, DPCA, ancestry estimation, and f2-statistics consistently supported genetic differentiation among populations. The Volga, Irtysh, and Ob populations were approximately equidistant from one another, while the remaining populations showed closer genetic relationships to the Ob lineage, with increasing differentiation towards the east. The three major lineages (Volga, Irtysh, and Ob) diverged between the penultimate and last glacial periods. The Volga population was estimated to have diverged approximately 108–84 thousand years ago (MIS 5c–MIS 5a), while the Ob semi-anadromous population diverged approximately 90–60 thousand years ago (late MIS 5–MIS 4). Eastern populations subsequently diverged from the Ob lineage during MIS 4–3, whereas the Kubena population diverged during MIS 2. Conclusions: The Irtysh population represents a genetically distinct and homogeneous lineage of Stenodus leucichthys. Its pronounced genetic differentiation highlights its conservation importance and suggests that population decline associated with river regulation may have serious consequences for the preservation of its unique genetic diversity.