Molecular Phylogenetics and Evolutionary Relationships Among Freshwater Fish Populations

Abstract

Understanding evolutionary relationships among freshwater fish populations is essential for biodiversity assessment, conservation planning, and taxonomic clarification. Traditional morphological classification has often been limited by phenotypic plasticity and convergent evolution, leading to uncertainties in species boundaries and lineage divergence. Molecular phylogenetics provides a powerful framework for resolving these ambiguities by analyzing genetic variation at the DNA level. the application of molecular markers, including mitochondrial DNA sequences such as cytochrome b and cytochrome oxidase I, along with nuclear gene markers, to reconstruct phylogenetic relationships among selected freshwater fish populations. Comparative sequence analysis and phylogenetic tree construction reveal patterns of genetic divergence, historical dispersal, and population structuring across different river basins. The results indicate significant genetic differentiation among geographically isolated populations, suggesting the influence of vicariance events, habitat fragmentation, and historical climatic fluctuations on evolutionary trajectories. Molecular data further highlight instances of cryptic speciation and previously unrecognized lineages within morphologically similar taxa. Genetic distance measures and haplotype diversity analyses provide insights into population connectivity and gene flow. These findings underscore the importance of integrating molecular tools with ecological and morphological data to achieve accurate taxonomic resolution.