title: Genetic variation in wild and farmed tilapia and catfish in Nigeria
Creators: name: Sanda, Mark Kauna
Publisher: name: University of Glasgow
Year: 2024

description: Aquacultural production is increasing rapidly in sub-Saharan Africa, often through the use of imported strains of fish species that are either native to the area or are so closely related to native species that they can successfully hybridise. This leads to a significant risk that escaped farmed fish will have significant deleterious genetic impacts on wild fish populations (as has been seen elsewhere in the world, notably in the context of salmon farming). The extent of this threat is evaluated in the first main chapter of this thesis, which reviews the state of freshwater aquaculture in sub-Saharan Africa, with a special emphasis on the legal and regulatory frameworks present in each of the main countries involved in aquaculture. It concludes that most lack the necessary means to monitor and control the impact of farming practices on wild fish populations. The remainder of the thesis concentrates on the situation prevailing in Nigeria, one of the main fish producing nations in sub-Saharan Africa.

Species of Tilapia and the African catfish Clarias gariepinus are important native freshwater fish species in Nigeria that have contributed immensely to both capture fisheries and aquaculture. They are widely distributed across the country in rivers, lakes, and reservoirs. The tilapia species used for aquaculture are selectively bred, mostly being genetically improved farmed strains that have been introduced from Thailand and Egypt. Escapes of these farmed fish can potentially interbreed with wild populations, leading to genetic introgression and a loss of genetic diversity in native species, as well as posing significant challenges for both conservation efforts and aquaculture management. However, studies on the genetic diversity and differentiation between introduced strains of tilapia (such as the Genetically Improved Farmed Tilapia, GIFT) and native tilapia species in Nigeria are scarce. Furthermore, recent attempts to investigate the population structure and genetic diversity of C. gariepinus have been based only on mitochondrial DNA and microsatellite markers. While these studies might have laid the foundation for the investigation of species diversity, a genomic perspective has been lacking.

This study therefore investigated the genetic diversity and population structure of farmed and wild tilapia and C. gariepinus populations in Nigeria. It utilised analysis of haplotypes of mitochondrial DNA cytochrome c oxidase subunit I (COI) and double-digest restriction site-associated nuclear DNA sequencing (ddRADseq) to study the tilapia group. Meanwhile a triple restriction site-associated DNA sequencing (3RAD) approach, in parallel with analysis of COI mtDNA haplotypes, was used to assess the genetic diversity and differentiation in C. gariepinus populations.

The phylogenetic tree of tilapia species based on analysis of COI haplotypes was unresolved, but differentiated the mouthbrooders and the substrate spawners. Although there were discrepancies between morphological identification keys and genetic species identification based on the mtDNA analyses, tilapia were found to be highly admixed based on the ddRADseq data, with evidence of hybridisation between named species in the wild. Extensive ongoing hybridisation was also observed among the farmed populations and between farmed and wild samples, highlighting the indiscriminate breeding practices among Nigerian farmers. Population structure analysis was unable to differentiate between farmed and wild Oreochromis spp. including O. niloticus, O. aureus, O. urolepis, and O. mossambicus.

In the C. gariepinus mtDNA analysis, samples of farmed and wild fish appeared to be genetically distinct, with low genetic diversity within the wild population compared to previous studies but higher than in the farmed populations. The analysis of the COI gene identified two distinct haplotypes specific to the farmed populations of C. gariepinus. Notably, samples of an albino population captured from the wild was found to be associated with these unique farmed haplotypes. This finding was supported by the results of the 3RAD analysis, which showed that the albino population exhibited clustering with farmed rather than wild populations, further confirming their origin as escaped individuals from aquaculture facilities. The 3RAD analyses suggested higher genetic diversity in wild compared to farmed populations but also higher levels of inbreeding in the former, which could be a warning sign that wild populations have suffered from bottlenecks that could compromise their long-term resilience. The 3RAD analyses also suggested high admixture among farmed populations, suggesting that hybridisation has been used extensively in the production of broodstocks.

This study has therefore revealed insights into the genetic interactions between farmed and wild fish populations in Nigeria, highlighting genetic mixing of farmed and wild tilapia and providing genetic evidence of escaped farmed catfish strains living in the wild. It highlights the need for conservation management strategies such as aquaculture zoning and genetic monitoring in order to mitigate the genetic impacts of aquaculture on wild fish populations.