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Despite their high abundance and species richness, tilapiines have been compromised by various factors especially overfishing, climate change, and uncontrolled fish transfers and introductions. Fish introductions have negatively impacted native tilapiine populations through competition, predation, hybridization, and introgression compromising their genetic integrity. The hybridization levels of different tilapiines in the Lake Victoria basin remain relatively understudied. The study utilized nuclear microsatellite and mitochondrial DNA (mtDNA) genetic markers to investigate hybridization signals and compare the genetic diversity of different tilapiines in Lake Victoria, Kenya, using next-generation sequencing. Low levels of hybridization from Oreochromis niloticus into other Oreochromis species were detected by Bayesian clustering analysis and principal coordinate analysis (PCoA). The results contribute to the need for conservation measures for these fish species. [ABSTRACT FROM AUTHOR]

Background: Nile tilapia, Oreochromis niloticus (Linnaeus, 1758) is among the economically most important freshwater fish species in East Africa, and a major source of protein for local consumption. Human induced translocations of non-native stocks for aquaculture and fisheries have been found as a potential threat to the genetic diversity and integrity of local populations. In the present study, we investigate the genetic structure of O. niloticus from 16 waterbodies across Ethiopia using 37 microsatellite loci with SSR-GBAS techniques. Results: The samples are structured into three main clusters shaped either by biogeographic factors or stocking activities. High FST values (Global FST = 0.438) between populations indicate a high level of genetic differentiation and may suggest long term isolation even within the same drainage systems. Natural populations of the Omo-Turkana system and the lakes in the Southern Main Ethiopian Rift showed the highest genetic variability while low variability was found in stocked populations of lakes Hora, Hashenge and Hayq. Conclusions: The results presented herein, may provide an essential basis for the management and conservation of the unique genetic resources in northern East Africa, and advance our understanding of biodiversity, phylogeny, evolution and development towards phylogenetically more accurate taxonomic classifications. [ABSTRACT FROM AUTHOR]

Microsatellites play an important role when investigating population and ecological genetics, although high effort in development and genotyping constitute a technical constraint and remains a major bottleneck. Here we use a microsatellite genotyping approach utilizing sequences of amplicons for allele calling (SSR-GBS) based on Illumina that requires less effort and time. The approach consist of development of highly polymorphic loci, sequencing of multiplexed PCR amplified microsatellites on an Illumina Miseq PE 300 platform and bioinformatic treatment of the sequenced data using custom scripts. The procedure allows automation in allele calling, which can be more reliably replicated and thereby removes biases that might prevent concatenation of datasets from different analyses. Additionally, the methodology enhances information content in the sequenced data beyond the traditional amplicon length (AL) approaches. Using 26 newly developed microsatellite markers and SSR-GBS we investigate the population genetic assessment of anthropogenically altered populations of East African Nile tilapia to show the potential of this genotyping approach. More precisely, we compare genotypic data generated considering AL and whole amplicon information (WAI). We found that genotypes based on WAI are not only able to recover a higher number of alleles but also a more detailed genetic structure pattern. We discuss the capability and importance of WAI allele calling and show perspectives for implementation in the future conservation genetic studies. More specifically, we demonstrate how the current markers and techniques might contribute useful information for studies concerning resources sustainable exploitation and conservation using the East African Nile tilapia. [ABSTRACT FROM AUTHOR]

The introduction of new genetic lineages into a population promotes interbreeding or hybridization and can be associated with the loss of genetic adaptation. This may contribute to financial losses for fish farmers following investments into fish strains that do not perform to their expectations. Oreochromis niloticus is one of the tilapiine species that has been widely distributed in areas far from its native range mainly for aquaculture purposes. This is principally due to its fast growth rates, adaptability to new habitats in addition to attractive market prices. Oreochromis niloticus has also been previously associated with the loss of native tilapiine species such as O. variabilis and O. esculentus in Lake Victoria and other lakes in Africa. To understand the impacts of O. niloticus translocation on native fish stocks, its species borders need to be delimited. Here we use microsatellite genotyping by amplicon sequencing (SSR-GBAS) for species delimitation of O. niloticus and seven related species from different regions in East and West Africa obtained from natural and farm environments. In total, 47 markers previously developed for O. niloticus were tested for cross-species amplification resulting in thirty-eight working markers. Most species were represented by different genetic units with little admixture between them even if ocuring in the same waterbodies. Exceptions involved the farmed populations from O. niloticus and O. mossambicus , which may be indicative of hybrid introgression. Our approach did also detect lower genetic diversity on the critically endangered species O. variabilis and O. esculentus. The possibility of introgressive hybridisation between O. niloticus and some of its congenerics may affect the sustainability of its exploitation. Moreover, long-term projects to monitor the response of genetic diversity and species boundaries to anthropogenic activities are required. In this context, SSR-GBAS can be a powerful tool given its high sample throughput and higher reproducibility compared to other methods. • 38 from the 47 markers SSR-GBAS tested worked on all East African tilapine species. • Almost all species were clearly differentiated. • Lack of differentiation between two species and admixture was found. • Aquaculture activities may be contributing to some of the admixture found. [ABSTRACT FROM AUTHOR]