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Sample cross-contamination remains a pervasive issue in genetics and genomics. With growing reliance on molecular methods for managing marine resources, the need to ensure the integrity of tissue samples that underpin these methods has never been more pressing. We conducted an experiment on wild-caught bigeye tuna (Thunnus obesus) to assess cross-contamination risk under seven at-sea and laboratory-based tissue sampling treatments. The six at-sea treatments (T1–T6) differ in sampling equipment, cleaning, and storage procedures. Combining observed heterozygosity (Ho) and relatedness coefficients (r) to flag cross-contamination, treatments T2–T6 proved effective at mitigating contamination risk. Each exhibited significantly smaller mean Ho and less Ho variability compared with intentionally contaminated samples in the T1 treatment. In T2-T6, no samples flagged as contaminated based on Ho outlier thresholds and elevated r were traced to the point of sampling at sea. Laboratory-based subsampling of T1 tissue (T7) also led to significantly smaller, less variable Ho values compared to T1, suggesting that recovery of samples contaminated onboard, or those of unknown provenance, is possible. We show that simple adjustments to current tissue sampling protocols dramatically reduce cross-contamination risk for downstream genetic analyses on tunas and potentially on other species and fisheries.

Archival (data-storage) and telemetry (acoustic and radio) tags are commonly used to provide data on the behavior and physiology of organisms, as well as data on their surrounding environment. For fishes, it is often advantageous to implant tags in the peritoneal cavity (i.e., intracoelomic implantation). The literature on best practices is limited for marine species, and near absent for tunas despite their regular application. We identify recommended practices using laparotomy in tropical tuna species following observations from thousands of tags implantations undertaken during implementation of several tagging programs across the Pacific. These recommended practices include descriptions of preferred tagging stations and equipment, fish selection, surgical procedures, and return of the fish to the wild. While these recommended practices were developed specifically for tropical tuna species, they are also likely applicable for other pelagic fishes. We present these guidelines to guide and promote the development of best practices for such procedures on pelagic species.