Population structure and historical demography of a widespread salmonid fish (Thymallus baicalensis) shaped by Lake Baikal’s late Pleistocene outlet history

Palaeohydrological changes can profoundly shape biological diversification and are key to reconstructing the biogeographic history of ancient lakes. In Lake Baikal, the Pleistocene formation of the Irkut/Angara outlets connected the lake to the Arctic-draining Yenisei River, potentially leading to profound changes in the lake’s faunal development. Here, we investigated population structure, demographic history, and colonization of a widely distributed salmonid fish ( Thymallus baicalensis ) across the Yenisei River system, including Lake Baikal, using genome-wide single nucleotide polymorphism (SNP) data. We found strong population structure with three major genetic groups across the river system and, for the first time, evidence of population substructure within Lake Baikal, possibly reflecting distinct phenotypes. While population expansion of T. baicalensis within Lake Baikal (∼125 ka) coincides with a late Pleistocene formation of the Irkut/Angara outlet, divergence time estimates among the three groups (536–804 ka) substantially predate this event and may reflect earlier phases of hydrological connectivity between Lake Baikal and the Angara–Yenisei system, consistent with previously estimated mitochondrial dates. The most likely scenario of gene flow suggested migration following outlet formation, with gene flow between Lake Baikal and riverine populations both upstream and downstream. Overall, the results support an initial colonization of Lake Baikal by T. baicalensis from the Yenisei River system, followed by a subsequent upstream expansion into the Selenga River and Lake Chovsgul. Notably, this relatively recent colonization stands in contrast to the lake’s ancient age, underscoring the complexity of its biogeographic history and the need for comparative studies across its diverse taxonomic groups.