The natural genetic resource in Oreochromis mossambicus and threats from invasive introgression

Abstract

Oreochromis is a broad genus of cichlid fishes endemic to Africa and the Middle East. They are widely utilised for aquaculture with frequent cross-breeding among congeneric species. Hybridization is a common natural phenomenon among Oreochromis but becomes a problem when translocated to a non-native environment. Escape of aquaculture hybrids and non-native Oreochromis into the wild can create invasive genotypes that threaten native species through introgressive hybridization. Mozambique tilapia (Oreochromis mossambicus) is a laterally compressed deep-bodied cichlid species, native to inland and coastal waters in southeastern Africa. It is one of three major Oreochromis species commonly used for aquaculture globally, because of important life history traits such as tolerance to salinity, temperature, and severe drought. Molecular studies on Oreochromis are mostly from naturalised Asian and American populations while the genetic structure of wild native populations is virtually unknown. Hence, most studies to date investigated hybridization in introduced Oreochromis populations. However, in South Africa, O. mossambicus is vulnerable to extinction due to genetic invasion, through hybridization with O. niloticus. Some existing molecular studies of this phenomenon are available, mainly restricted to the Limpopo river system, but these do not use a whole-genome approach. Therefore, there is a need to update the extent of O. niloticus invasion within the natural distribution range of O. mossambicus by including populations of O. mossambicus in other river systems, using genome associated markers. This PhD study focused on verifying the utility of DNA barcoding in the genus Oreochromis (Chapter 2), 2) a better understanding of the biodiversity of native wild species in the genus using DNA barcodes (Chapter 3), 3) Development of gene-linked microsatellites from O. niloticus genome and preliminary results on introgressive hybridization in O. mossambicus from South Africa (Chapter 4) and 4) the development of a robust SNPs-based tool using genomic resource for the detection of potential introgressive hybridization between O. mossambicus and O. niloticus (Chapter 5). I improved the knowledge of Oreochromis biodiversity by highlighting the importance of knowing the wild origin of native stocks through a combination of appropriate taxonomy and DNA barcoding. The results from analyses of the wild-collected fraction of available COI sequences in BOLD and NCBI databases showed the presence of cryptic lineages, misidentification, potential introgressive hybridization, and ancestral polymorphism. I further expanded our search to include mtDNA of other species from the Oreochromini tribe and assessed diversity in O. mossambicus, O. niloticus, and other Oreochromis from southern Africa by adding sampled 81 specimens from 43 native locations and 13 specimens from a hatchery. The result indicated strong genetic subdivision in O. mossambicus and O. niloticus, and polyphyly of species in the tribe Oreochromini. I also observed that feral and aquaculture populations are substantially admixed, which could be a source of errors in identification, and selection within improved farm stocks I successfully mined perfect microsatellites (tetramers and pentamers) from the O. niloticus genome. Then, link the microsatellites (closest 5000bp) to the CDSs of 247 exons and designed 55 primers. Eight of these primers were tested and found to be polymorphic. Applying Bayesian approaches identified four admixed individuals of O. mossambicus×O. niloticus and five admixture between the two lineages of O. mossambicus within South Africa. Hybrids of the two species were identified at the lower Limpopo river systems that were not sampled before. This indicates that hybridization has progressed to this system but some areas still retain pure samples of O. mossambicus. These results illustrate the power of the new set of markers to detect introgression between O. mossambicus and O. niloticus, Nonetheless, this study will serve as an important baseline for future research addressing the problem of introgression in O. mossambicus. I developed a gene-capture panel for Pseudocrenilabrinae (O. mossambicus ) based on 247 exon loci verified on the genome of O. niloticus. This molecular tool will be useful for detecting admixture levels of O. niloticus in other cichlid fish. It can be used to genotype hundreds of Oreochromis from both farms and wild specimens. This is a valuable resource for future research in cichlids that could assist in the reliable evaluation of introgressive hybridization of O. niloticus with other cichlids outside of southern Africa.. My overall perspective is that the complexities observed in cichlid species particularly Oreochromis genus were due to lack of adequate knowledge on the origin of native wild stocks used for aquaculture globally. The consequences (e.g misidentification, taxonomic challenges and introgressive hybridization) can only be addressed with the use of modern genomic tools such as developed in this study for proper conservation and ecological assessment.