Environmental DNA‐Based Quantification of an Invasive Tilapia Species in Tanzanian Inland Aquaculture

ABSTRACT It can be challenging to determine the identity of tilapia species in aquaculture using morphological characteristics alone. In central Tanzania, there is ongoing expansion of small‐scale inland aquaculture, mainly focused on the large‐bodied non‐native Nile tilapia ( Oreochromis niloticus ) and the native Wami tilapia ( Oreochromis urolepis ). The spread of Nile tilapia has been accompanied by blue‐spotted tilapia ( Oreochromis leucostictus ), a small‐bodied non‐native species that has the potential to compromise fisheries production. Given the phenotypic similarity of the three species, particularly at the juvenile stage, we developed an environmental DNA (eDNA)‐based assay to determine the distribution and relative abundance of the three Oreochromis species within aquaculture and natural settings in Tanzania. In a field test of the assay in 15 water bodies—comparing eDNA results with genotyping of sampled fish—we found that the confirmed presence of a species, as inferred from their mitochondrial DNA (mtDNA) ND1 haplotypes, led to an on average one‐thousand‐fold increase in eDNA copies relative to water bodies where the species was not confirmed. In a more expansive eDNA field survey across 52 water bodies from 32 locations, we found that the vast majority of water bodies were dominated by O. niloticus or O. urolepis , with O. leucostictus widespread but typically present in low relative abundance. Collectively, our results indicate that O. leucostictus is currently unlikely to compromise the productive capacity of aquaculture of the region. However, caution should be exercised to reduce the influence of the species on yield. We conclude that eDNA‐based methods can be a valuable source of information for the identification of fish in mixed cultured stocks and may, in the future, have a role in optimising regional aquaculture.