When the catch label hides the catch: a ddRAD-seq portrait of cryptic Auxis tunas in Indonesian Fisheries Management Area FMA-572

In Indonesia's neritic tuna fishery, the vernacular name "tongkol" lumps together morphologically similar species at the landing site, and national catch statistics aggregate them under a single category. This taxonomic ambiguity propagates into stock assessments and management decisions, yet the species composition of "tongkol" landings has rarely been verified at the genomic level. We applied double-digest restriction site-associated DNA sequencing (ddRAD-seq) to 217 individuals marketed as "tongkol" across six fishing grounds in Indonesia's Fisheries Management Area FMA-572 (western coast of Sumatra), complemented by mitochondrial COI barcoding to anchor species identity. Maximum-likelihood phylogenomics on thousands of genome-wide SNPs resolved two genomically distinct Auxis species co-occurring across most sampling sites, with COI barcodes corroborating the genome-wide assignment. The two species were indistinguishable by gross morphology at landing and were routinely sold under the same vernacular label, demonstrating that what is recorded in catch statistics as a single category is in fact a multi-species assemblage. Beyond confirming cryptic-species identity, the ddRAD-seq dataset provides the first genome-wide characterisation of Auxis tunas in Indonesian waters and a tractable framework for species-disaggregated catch reporting, molecular traceability at landing ports, and species-specific stock assessment within FMA-572 — with broader relevance for neritic tuna assessments coordinated under the Indian Ocean Tuna Comission framework.