Population genetics of the Cichlid Oreochromis shiranus in Malawi

Abstract

Oreochromis shiranus is an important cichlid both in capture fisheries and aquaculture. However, in Malawi, biomass yield for the species has declined. Sustainable strategies to increase in yield from capture fisheries and aquaculture would require sound knowledge of the population genetics of the species. In this study, 20 microsatellite markers developed from various Oreochromis spp. were used for cross-species amplification to evaluate allelic diversity, population structure and past demography of O. shiranus in the entire natural distribution range in Malawi. This study involved 306 fish sampled from Lake Malawi, Lake Malombe, Lake Chilwa, Lake Chiuta and the Lower Shire River. Thirty-eight fish from an experimental stock at Bunda College were also included. The study concluded that there were no significant differences in genetic diversity among and within the main water bodies which were also not different from the experimental population. Analysis of molecular variance (AMOVA), pairwise FST values, model-based clustering and multivariate discriminant analysis of principal components (DAPC) revealed that there was limited gene flow resulting in five meta-populations. There was evidence of population bottlenecks that corresponded to small effective population sizes (Ne < 500). The results emphasize that there is enough genetic diversity but management and conservation strategies of O. shiranus in Malawi should consider that the species is structured within the water bodies and possibly recovering from or experiencing genetic bottlenecks. In aquaculture, care should be taken when recruiting fish for breeding programmes to avoid mixing genetic material from different populations without proper regard.