The need for improved aquaculture productivity has led to widespread pressure to introduce the Genetically Improved Farmed Tilapia (GIFT) strains of Nile tilapia (Oreochromis niloticus) into Africa. However, the physical and regulatory infrastructures for preventing the escape of farmed stocks into wild populations and ecosystems are generally lacking. This study characterized the genetic background of O. niloticus being farmed in Ghana and assessed the genetic effects of aquaculture on wild populations. We characterized O. niloticus collected in 2017 using mitochondrial and microsatellite DNA markers from 140 farmed individuals sampled from five major aquaculture facilities on the Volta Lake, and from 72 individuals sampled from the wild in the Lower Volta River downstream of the lake and the Black Volta tributary upstream of the lake. Our results revealed that two farms were culturing non-native O. niloticus stocks, which were distinct from the native Akosombo strain. The non-native tilapia stocks were identical to several GIFT strains, some of which showed introgression of mitochondrial DNA from non-native Oreochromis mossambicus. We also found that the non-native cultured tilapias have escaped into the wild and interbred with local populations, and also observed potentially admixed individuals on some farms. Our results highlight aquaculture as a vector in the spread of invasive non-native species and strains, and underscore the importance of genetic baseline studies to guide conservation planning for wild populations.

Despite the global importance of the Nile tilapia Oreochromis niloticus, especially to aquaculture, knowledge of genetic variability within native populations is still limited. While several studies have assessed genetic differentiation across the major drainage basins of Africa, relatively little effort has focused on characterizing genetic differentiation at finer scales. We assessed genetic variation in O. niloticus within and among nine drainage basins in Ghana using nuclear microsatellite DNA markers as the basis for identifying potential units of conservation among wild populations. We screened 312 wild individuals using eight nuclear microsatellite DNA markers. We found moderate genetic diversity within and differentiation among all wild populations studied, with strong signals of recent demographic bottlenecks in several populations. Genetic structure among 11 populations suggested the presence of up to ten management units (MUs). In particular, the Black Volta and the Tano–Asuhyea populations, which were the most genetically distinct and geographically isolated and may be most at risk of loss of genetic diversity over time, may well represent evolutionary significant units. Therefore, at the minimum, the Black Volta and Tano–Asuhyea populations should be prioritized for conservation actions to sustain them over the long-term.