Evaluating DNA cross-contamination risk using different tissue sampling procedures on board fishing and research vessels

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 (H-o) and relatedness coefficients (r) to flag cross-contamination, treatments T2-T6 proved effective at mitigating contamination risk. Each exhibited significantly smaller mean H-o and less H-o variability compared with intentionally contaminated samples in the T1 treatment. In T2-T6, no samples flagged as contaminated based on H-o 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 H-o 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.