SNP genotyping reveals a mixed-stock fishery for striped marlin, <i>Kajikia audax</i>, in the central North Pacific Ocean

Abstract At least four genetically distinctive stocks of Striped Marlin have been delineated in the Pacific and Indian oceans; however, the number of stocks in the central North Pacific (CNP) and their distributions remain unclear. To better understand the stock dynamics of Striped Marlin exploited by the Hawaii-based pelagic longline fishery (HBPLLF) in the CNP, fishery observers collected tissue samples of Striped Marlin monthly from September 2019 to October 2020 (n = 417). We generated DArTseq data from 85 of these samples and re-sequenced samples previously assigned to a second putative NPO stock. These data were co-analyzed with an existing single nucleotide polymorphism (SNP) dataset for 256 Striped Marlin collected from throughout the species’ range to reassess evidence of a second NPO stock and to identify SNPs capable of discriminating stocks. This analysis confirmed that the second putative NPO stock was an artifact of sample cross-contamination and supported the hypothesis of a single North Pacific stock. Striped Marlin from the HBPLLF were assigned into either the North Pacific (NPO; Japan, Taiwan, Hawaii, and California) or OCEANIA (New Zealand, western Australia, and eastern Australia) stocks, indicating a mixed stock fishery in the CNP. A panel of 32 SNPs to discriminate between the two stocks was identified and used to genotype the remaining 325 HBPLLF fish. Overall, 305 of these fish were assigned to the stock of origin with high (&amp;gt; 90%) confidence. Both NPO and OCEANIA stocks were present throughout the sampling period (NPO: 41%; OCEANIA: 59%). Temporal changes in stock composition were identified, with NPO fish dominant during the winter and spring and OCEANIA fish dominant during the summer and fall. Factors that may influence the stock composition of Striped Marlin in the HBPLLF include stock-specific movements to different spawning grounds and alternate feeding areas and seasonally displaced recruitment to the HBPLLF. The current management boundaries for Pacific Striped Marlin do not align with the best available biological data. The mixed-stock fishery identified here could inform the replacement of static management boundaries with flexible management and assessment approaches that consider stock mixing.