Comparative analysis of morphometric and genetic diversity in wild populations and farmed stocks of Nile tilapia (Oreochromis niloticus) from eastern DR Congo

Nile tilapia ( Oreochromis niloticus ) is a cornerstone of aquaculture in South Kivu, eastern DR Congo, playing a vital role in food security, livelihoods, and the local economy. However, the expansion of aquaculture near natural waterbodies has led to fish escapes and interbreeding with wild populations, raising concerns about crossbreeding and its conservation impact. Understanding morphogenetic variation and population structure is therefore essential for balancing sustainable aquaculture development with the preservation of wild populations. This study assessed the morphogenetic variation and population genetic structure of wild populations and farmed stocks of Nile tilapia in South Kivu. A total of 300 individuals were sampled from wild populations (Lakes Kivu and Tanganyika, and the Ruzizi River) and farmed systems (Lake Kivu cages, Kabare ponds, and Ruzizi Plain ponds) for morphometric analysis. Based on principal component analysis and fin-clip quality, 150 representative individuals were selected for genetic analysis using seven polymorphic microsatellite loci. Morphometric analyses revealed clear differentiation among populations, forming three distinct clusters primarily driven by body size, depth-related traits, eye diameter, and anal fin length. Genetic analyses showed substantial within-population diversity, with AMOVA indicating that 60% of genetic variation occurred within individuals and 11% among populations. Genetic diversity was higher in wild populations, with Lake Kivu showing the highest observed heterozygosity (0.754 ± 0.035). Pairwise Fst values indicated low to moderate genetic differentiation, while UPGMA clustering and Mantel test results highlighted geographic isolation as a major driver of population structure. These findings provide critical insights for maintaining genetic integrity, enhancing aquaculture productivity, and guiding conservation efforts in South Kivu.