Genomic analysis reveals multiple mismatches between biological and management units in yellowfin tuna (Thunnus albacares)

The South African (SAF) yellowfin tuna (Thunnus albacares) fishery represents a potential example of misalignment between management
units and biological processes. The SAF fishery spans an operational stock with a boundary at 20E, either side of which fish are considered
part of Atlantic or Indian Ocean regional stocks. However, the actual recruitment of fish from Atlantic and Indian Ocean spawning populations
into SAF waters is unknown. To address this knowledge gap, genomic analysis (11 101 SNPs) was performed on samples from Atlantic
and Indian Ocean spawning sites, including SAF sites spanning the current stock boundary. Outlier loci conferred high discriminatory power
to assignment tests and revealed that all SAF fish were assigned to the Indian Ocean population and that no Atlantic Ocean fish appeared in
the SAF samples. Additionally, several Indian Ocean migrants were detected at the Atlantic spawning site demonstrating asymmetric dispersal
and the occurrence of a mixed-stock fishery in Atlantic waters. This study highlights both the spatial inaccuracy of current stock designations
and a misunderstanding of interactions between the underlying biological units, which must be addressed in light of local and global declines
of the species. Specifically, the entire SAF fishery must be managed as part of the Indian Ocean stock.