Genetic Diversity and Population Structure of Nigerian Sea Bass (Lates niloticus) Across Lake Kainji and River Niger Using Microsatellite Markers

Understanding the genetic structure of inland fish populations is essential for designing effective management units and avoiding outbreeding depression in stocking programmes. This study assessed the genetic diversity and population structure of Nile perch (Lates niloticus) across Lake Kainji, the upper River Niger, and the lower River Niger in Nigeria using polymorphic microsatellite markers. Fin clip tissue samples were collected from 180 individuals at six sampling locations. Eight microsatellite loci were amplified by polymerase chain reaction, and allelic data were scored using capillary electrophoresis. Genetic diversity statistics including expected heterozygosity, allelic richness, and inbreeding coefficient were calculated. Population structure was assessed using FST, STRUCTURE Bayesian clustering, and discriminant analysis of principal components. All populations showed moderate to high levels of genetic diversity with mean expected heterozygosity ranging from 0.58 to 0.76. FST values indicated significant genetic differentiation between Lake Kainji and lower River Niger populations (FST = 0.094, p less than 0.001), while populations within the continuous river section showed low differentiation. STRUCTURE analysis identified two genetic clusters corresponding to the lake population and the river populations. The observed differentiation is consistent with the genetic structuring effect of the Kainji Dam as a barrier to gene flow since its completion in 1968. Effective population size estimates were below minimum viable population thresholds for the lake population, raising conservation concerns. The study recommends that Lake Kainji and River Niger populations be managed as separate conservation units. Keywords: Lates niloticus, microsatellites, population genetics, Kainji Lake, gene flow.