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An intensive parasite survey was conducted in 2008 to better understand the parasite fauna occurrence, distribution and diversity in the commercial aquaculture fish species in Uganda. A total of 265 fish collected from hatcheries and grow-out systems were examined for parasites using routine parasitological techniques. The survey yielded 17 parasite species: 11 from Oreochromis niloticus and ten from Clarias gariepinus. Four parasites-Amirthalingamia macracantha, Monobothrioides sp., Zoogonoides sp. and a member of the family Amphilinidae-were recorded for the first time in the country. The parasite diversity was similar between hosts; however, O. niloticus was dominated by free-living stage-transmitted parasites in lower numbers, whereas both trophically and free-living stage-transmitted parasites were equally represented in C. gariepinus in relatively high intensities. The patterns in parasite numbers and composition in the two hosts reflect differences in fish habitat use and diet. A shift in parasite composition from monoxenous species-dominated communities in small-sized fish to heteroxenous in large fishes was recorded in both hosts. This was linked to ontogenetic feeding changes and prolonged exposure to parasites. Polyculture systems showed no effect on parasite intensity and composition. The gills were highly parasitized, mainly by protozoans and monogeneans. Generally, the occurrence and diversity of parasites in these fish species highlight the likelihood of disease outbreak in the proposed intensive aquaculture systems. This calls for raising awareness in fish health management among potential farmers, service providers and researchers.

This chapter focuses on ways to assess the likelihood of gene flow before approved use and actual entry of transgenic fish into the environment. A step-by-step approach for assessing gene flow based on a fault tree of the chain of events necessary for introgression of transgenes into a wild population is presented. Partition entry and introgression into subcomponents are discussed. The importance of assessing how both the transgene and overall genetic background of the escaping transgenic fish may affect the likelihood and consequences of gene flow to wild relatives is addressed. The main data needed for assessing gene flow are identified. Moreover, possible modelling, field and laboratory studies to obtain the data needed are described.

The Lake Victoria Region (LVR) can rightly be regarded as one of the sites of the world's worst vertebrate species extinction of the twentieth century. The LVR, which includes Lakes Victoria, Kyoga, Edward and George, and numerous small satellite lakes around each of the main lakes, originally contained over 500 species of fish. As a result of human influence, including the establishment of a commercial fishery and the introduction of several exotic species, hundreds of endemic species have gone extinct in this evolutionarily young system. Recently, it was discovered that part of the apparently extinct fish biodiversity from the main lakes continues to exist in several of the minor satellite lakes around the main lakes. The findings of the ecological survey of the fish species of the satellite lakes are summarized and results of some preliminary genetic analysis are discussed. Major genetic and ecological changes in the fish fauna that have taken place in the LVR fishery are highlighted. Emphasis is put on the importance of the minor lakes in conserving the endangered fish species of the entire region, and their role as preserves of the history of the LVR. The findings allude to the historical importance of minor satellite lakes as ‘life boats’ and natural refugia for the fishes of the LVR, a region historically characterized by geological and climatic volatility.

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