Genomic approach to distinguish between legal captive breeding and illegal wild fishing of threatened totoaba (Totoaba macdonaldi)

Understanding genetic diversity is essential for conservation strategies and sustainable aquaculture practices, and the legal origin of production, particularly for threatened species such as totoaba ( Totoaba macdonaldi ), an endemic large fish of the Gulf of California. A total of 170 individuals were sequenced using double-digest restriction-site associated DNA, of which 92 were wild individuals, and 78 were captive broodstock from two Units for Conservation and Management of Wildlife (UMAs: CREMES and UABC), yielding 4992 neutral SNPs. No significant genetic divergence was detected among wild locations, indicating no detectable population structure at the spatial scale analyzed. In contrast, significant differences were found between the wild population and the UMA captive broodstocks, as well as between the two UMAs. No relatedness was detected within the wild population, and significant levels of kinship were detected within the UMAs F1 and F2 broodstock. Population genetic methods classified all individuals into their respective source origins. The assignment accuracy test to source considering wild population vs pooled UMAs, the overall mean accuracy was high > 88% (WILD: 94–100% across locus subsets; UMAs: 84–88%), and > 91% for wild population vs. individual UMAs broodstock (CREMES ∼74–80%, UABC ∼90%, and WILD 100%). When controlling kinship, the overall mean accuracies decreased slightly to > 86% and > 90%, respectively. This study highlights the effectiveness of SNPs in monitoring genetic diversity in Totoaba, complementing the information needed to accurately assign individuals to their source origin, which is required for legal traceability and law enforcement.