Comparative Population Genetics of Rutilus rutilus and Perca fluviatilis in Lithuanian Freshwater Ecosystems

Understanding how co-occurring freshwater species respond to the same hydrological landscape is important for interpreting genetic diversity and population connectivity. We compared the population genetic structure of two widespread freshwater fishes, Rutilus rutilus (Linnaeus, 1758) and Perca fluviatilis Linnaeus, 1758, across major Lithuanian river basins using mitochondrial ATP6 and D-loop sequences. Both species exhibited high haplotype diversity but differed markedly in genetic structure. R. rutilus showed weak differentiation, widespread haplotype sharing among basins, and demographic signals compatible with population expansion. By contrast, P. fluviatilis exhibited stronger, more spatially heterogeneous structuring, with less consistent demographic signals and more localized differentiation. Contrary to expectations, genetic variation was not consistently associated with major drainage-basin boundaries in either species. Instead, the observed patterns suggest that species-specific ecological traits, particularly differences in dispersal capacity and habitat use, may play a greater role in shaping population structure than contemporary hydrological boundaries alone. These findings demonstrate that co-occurring freshwater fishes can exhibit contrasting patterns of genetic diversity even within shared hydrological systems. Although nuclear or genome-wide markers would strengthen these mitochondrial inferences, the study highlights the value of comparative approaches for understanding population connectivity and informing freshwater biodiversity conservation and management.