Tracing the trails: Insights into the genetic connectivity and potential origin of Nile tilapia populations in Tanzanian Saline Rift Valley Lakes

Despite their elevated salinity levels, the East African Saline Rift Valley Lakes (SRVLs) are home to unique endemic fish species that support local communities. However, the non-native Nile tilapia (Oreochromis niloticus) has rapidly established itself in some of these lakes, threatening endemic fish populations. Yet, the genetic connectivity and potential origin of Nile tilapia populations in the SRVLs remain poorly understood. This study aimed to address this gap by analysing 203 mitochondrial cytochrome oxidase subunit I (COI) sequences (599 base pairs) from Nile tilapia collected across the SRVLs, fish farms, and three freshwater ecosystems in Tanzania. We identified five distinct haplotypes, three of which were shared among the SRVLs, local fish farms, and three freshwater ecosystems: Lake Victoria, the Pangani River, and Mindu Dam. Given the lack of apparent physical connectivity among most of these sites, these shared haplotypes suggest that human-mediated introductions and escape events from aquaculture are likely the main drivers of Nile tilapia's spread into the SRVLs, rather than natural gene flow. Furthermore, significant genetic differentiation was observed among some SRVL populations, suggesting multiple introductions from different source populations, or founder effects and genetic drift, particularly in smaller and newly established populations. Our findings highlight the need for stringent measures to prevent the further spread of Nile tilapia into other SRVLs. Additionally, effective management strategies are necessary in SRVLs where Nile tilapia has already been introduced to safeguard endemic fish stocks and mitigate unintended ecological impacts.