Application of microsatellite genotyping by amplicon sequencing for delimitation of African tilapiine species relevant for aquaculture

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.

Automated summary

The introduction of Nile tilapia may negatively impact native fish stocks, emphasizing the importance of delineating species boundaries. Microsatellite genotyping by amplicon sequencing is an effective tool for species delimitation and studying genetic diversity.