Date Awarded


Document Type


Degree Name

Master of Science (M.Sc.)


Virginia Institute of Marine Science


Jan R McDowell

Committee Member

Eric J Hilton

Committee Member

Mark J Brush


Relative to many highly migratory fishes, Striped Marlin, Kajikia audax, exhibit considerable stock structure. At least four genetically distinct stocks of Striped Marlin have been delineated in the Pacific and Indian oceans, although stock composition in the central North Pacific (CNP) remains unclear and the presence of an additional stock in the North Pacific has been suggested in two recent studies. The goals of this research were to clarify the number of Striped Marlin stocks in the North Pacific and utilize temporal sampling to better understand the stock dynamics of Striped Marlin exploited by the Hawaii-based pelagic longline fishery (HBPLLF). Fishery observers collected 417 samples of Striped Marlin from the HBPLLF from 2019-2020. Of these, 85 samples underwent genotyping-by-sequencing using DArTSeqTM and the data were co-analyzed with an existing single nucleotide polymorphism (SNP) dataset for 256 individuals of Striped Marlin collected from throughout the species’ range and reported in a previous study. Three of 12 Striped Marlin previously reported to comprise a putative second stock in the North Pacific and all with high observed heterozygosities were also re-sequenced to test the hypothesis that sample contamination resulted in the identification of a spurious stock. After re-sequencing, the observed heterozygosity of each of the three individuals was reduced by approximately 50%, confirming contamination and the original sequences for the 12 individuals comprising the putative second stock were removed from the dataset. Clustering analyses of the resulting dataset strongly supported a single North Pacific stock; the three re-sequenced individuals clustered into previously described stocks. The 73 (post-quality filtering) Striped Marlin sampled from the HBPLLF clustered into either the North Pacific (NPO; Japan, Taiwan, Hawaii, and California sample locations) or Oceania (New Zealand, western Australia, and eastern Australia sample locations) stocks, indicating mixing of the two stocks in the CNP. A panel of 48 SNPs with the highest power to discriminate between the two stocks was developed and 32 of these loci were used to genotype and assign an additional 325 Striped Marlin collected from the HBPLLF to stock of origin. Overall, 305 of these fish were assigned to stock of origin with high (> 90%) confidence and combined with DarTSeq-based assignments of the original 73 fish. Both stocks were present throughout the sampling period (NPO: 41.3%; Oceania: 58.7%). 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. Although the HBPLLF is known to exploit mostly sub-adult Striped Marlin, 13 (3.1%) samples were found to be in an active spawning condition at the time of capture based on visual inspection. Of these, 10 assigned to NPO and two assigned to Oceania (the 13th fish assigned into Oceania but scores were below 90%). Factors that may influence the stock composition of Striped Marlin in the HBPLLF, including stock-specific movements to different spawning grounds and alternate feeding areas, as well as seasonally displaced recruitment to the HBPLLF, are discussed.


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