Spatial structure of tilapia phylogenetic diversity across five rivers in the Niger Delta states of Nigeria

• The mitochondrial DNA d -loop, a highly variable region of the mitochondrial genome, was used to delineate the phylogenetic relationships among three tilapia species sourced from five rivers (populations). • Phylogenetic analysis revealed two major clades, with species-specific subgrouping observed across the tilapia species. • Molecular variance analysis (AMOVA) indicated greater genetic variation among fish populations (86.39 %) compared to within populations (24.71 %), with a significant fixation index ( F ST = 0.743; p < 0.05). • Evidence of introgression was observed within each river population, although no introgression occurred between populations. • The findings provide valuable information for tilapia species management and selective breeding programmes, supporting efforts to enhance tilapia production in Nigeria. Understanding the phylogenetic relationships among species is crucial for effective conservation, selection, and hybridization, which can enhance economic gains through improved growth characteristics. This study aimed to assess the reliability of mtDNA d -loop in delineating the phylogenetics of three tilapia species. Blood samples were collected from tilapia across five rivers (populations) in the Niger Delta region of Nigeria. The species sampled included Oreochromis niloticus ( n = 44), Oreochromis aureus ( n = 23), and Oreochromis mossambicus ( n = 14). Phylogenetic analysis revealed two major clades, with tilapia sub-grouped by species. Within each population, the three species were genetically distinct from each other based on variations in their mtDNA d -loop. Clustering was species-specific when fish from the five populations were compared. The relationship between the tilapia from this study and those from other regions showed that O. aureus and O. niloticus from the five populations were similar to counterparts from other regions. In contrast, O. mossambicus clustered closely with Coptodon zilli and Tilapia zilli . Analysis of molecular variance (AMOVA) revealed greater variation among fish populations (86.39 %) than within populations (24.71 %), with a significant fixation index ( F ST = 0.743; p < 0.05). Demographic expansion and mismatch distribution analyses indicated no expansion within the three tilapia species. These findings are valuable for species management and selective breeding programmes to enhance tilapia production in Nigeria.