Abstract
Three different techniques for stock identification, namely scale patterns, otolith thermal marks, and single-nucleotide polymorphism (SNP) markers, were applied to the same mixture samples of chum salmon collected in a setnet fishery in the Sea of Okhotsk, off Hokkaido, Japan, to evaluate consistency and accuracy among the techniques. The scale pattern and SNP analyses provided similar estimates for two regional origins (Hokkaido and Honshu) with data for 2011–2013; for each year, the Hokkaido-origin stock was dominant in September and early October, but the Honshu-origin stock was dominant by late October. The SNP analysis specified five geographical origins of chum salmon (the Okhotsk coast, Hokkaido and Honshu coasts of the Sea of Japan, and Hokkaido and Honshu coasts of the Pacific), whereas the other techniques did not identify multi-regional origins. Recaptures of otolith-marked chum salmon were used for estimating the proportions of fish originating from the Hokkaido Sea of Japan region; these estimates differed from those based on the SNP analysis. This study demonstrated that scale pattern and SNP analyses have the potential to provide nearly consistent estimates for the two regional origins, and can possibly help us to understand the interception of migrating chum salmon in Japan.
Similar content being viewed by others
References
Abaunza P, Murta AG, Campbell N, Cimmaruta R, Comesaña AS, Dahle G, García Santamaría MT, Gordo LS, Iversen SA, MacKenzie K, Magoulas A, Mattiucci S, Molloy J, Nascetti G, Pinto AL, Quinta R, Ramos P, Sanjuan A, Santos AT, Stransky C, Zimmermann C (2008) Stock identity of horse mackerel (Trachurus trachurus) in the Northeast Atlantic and Mediterranean Sea: integrating the results from different stock identification approaches. Fish Res 89:196–209
Anderson EC, Waples RS, Kalinowski T (2008) An improved method for predicting the accuracy of genetic stock identification. Can J Fish Aquat Sci 65:1475–1486
Beacham TD, Candy JR, Supernault KJ, Ming T, Deagle B, Schulze A, Tuck D, Kaukinen KH, Irvine JR, Miller KM, Withler RE (2001) Evaluation and application of microsatellite and major histocompatibility complex variation for stock identification of coho salmon in British Columbia. Trans Am Fish Soc 130:1116–1149
Beacham TD, Candy JR, McIntosh B, MacConnachie C, Tabata A, Kaukinen K, Deng L, Miller KM, Withler RE (2005) Estimation of stock composition and individual identification of sockeye salmon on a Pacific Rim basis using microsatellite and major histocompatibility complex variation. Trans Am Fish Soc 134:1124–1146
Beacham TD, Sato S, Urawa S, Le KD, Wetklo M (2008) Population structure and stock identification of chum salmon Oncorhynchus keta from Japan determined by microsatellite DNA variation. Fish Sci 74:983–994
Begg GA, Waldman JR (1999) An holistic approach to fish stock identification. Fish Res 43:35–44
Bernard DR, Clark JE (1996) Estimating salmon harvest with coded wire tags. Can J Fish Aquat Sci 53:2323–2332
Bradbury IR, Hamilton LC, Chaput G, Robertson MJ, Goraguer H, Walsh A, Morris V, Reddin D, Dempson JB, Sheehan TF, King T, Bernatchez L (2016) Genetic mixed stock analysis of an interceptory Atlantic salmon fishery in the Northwest Atlantic. Fish Res 174:234–244
Cadrin SX, Friedland KD, Waldman JR (2005) Stock identification methods—applications in fishery science. Elsevier Academic Press, Burlington
Clark JE, Bernard DR (1987) A compound multivariate binomial-hypergeometric distribution describing coded microwire tag recovery from commercial salmon catches in southeastern Alaska. Informational leaflet no. 261. Alaska Department of Fish and Game, Juneau, AK
Clemento AJ, Crandall ED, Garza JC, Anderson EC (2014) Evaluation of a single nucleotide polymorphism baseline for genetic stock identification of Chinook salmon (Oncorhynchus tshawytscha) in the California current large marine ecosystem. Fish Bull 112:112–130
Debevec EM, Gates RB, Masuda M, Pella J, Reynolds J, Seeb LW (2000) SPAM (version 3.2): statistics program for analyzing mixtures. J Hered 91:509–510
Devries DR, Frie RV (1996) Determination of age and growth. In: Murphy BR, Willis DW (eds) Fisheries techniques, 2nd edn. American Fisheries Society, Bethesda, pp 483–512
Elfstrom CM, Smith CT, Seeb LW (2007) Thirty-eight single nucleotide polymorphism markers for high-throughput genotyping of chum salmon. Mol Ecol Notes 7:1211–1215
Freidland KD, Cadrin SX (2005) Analyses of calcified structures-texture and spacing patterns. In: Cadrin SX, et al. (eds) Stock identification methods—applications in fishery science. Elsevier Academic Press, Burlington, MA, pp 185–195
Fukuzawa H, Hirabayashi Y (2018) Preliminary 2017 salmon enhancement production in Japan. NPAFC document 1762, 3 pp. Hokkaido National Fisheries Research Institute, Japan Fisheries Research and Education Agency. Available at https://www.npafc.org. Accessed 15 May 2018
Geiger HJ (1990) Parametric bootstrap confidence intervals for estimating contributions to fisheries from marked salmon populations. In: Parker NC, et al. (eds) Fish-marking techniques. American Fisheries Society Symposium 7, Bethesda, MD, pp 667–676
Gomez-Uchida D, Seeb JE, Habicht C, Seeb LW (2012) Allele frequency stability in large, wild exploited populations over multiple generations: insights from Alaska sockeye salmon (Oncorhynchus nerka). Can J Fish Aquat Sci 69:916–929
Hagen P, Munk K, Van Alen B, White B (1995) Thermal mark technology for inseason fisheries management: a case study. Alaska Fish Res Bull 2:143–155
Hasegawa E, Nara K, Hiroi O (2004) A consideration about estimating method for the effect of restricted set netting on migration of chum salmon by using mark-recapture results. Natl Salmon Resour Center Tech Rep 170:17–49 (in Japanese)
Kalinowski ST, Manlove KR, Taper M (2007) ONCOR: software for genetic stock identification. Montana State University, Bozeman
Kobayashi T (2009) History of propagation for salmon in Japan. Hokkaido University Press, Sapporo (in Japanese)
Koljonen ML, Gross R, Koskiniemi J (2014) Wild Estonian and Russian sea trout (Salmo trutta) in Finnish coastal sea trout catches: results of genetic mixed-stock analysis. Hereditas 151:117–195
Meek MH, Baerwald MR, Stephens MR, Goodbla A, Miller MR, Tomalty KMH, May B (2016) Sequencing improves our ability to study threatened migratory species: genetic population assignment in California’s central valley chinook salmon. Ecol Evol 6:7706–7716
Millar RB (1990) A versatile computer program for mixed stock fishery composition estimation. Canadian technical report of fisheries and aquatic sciences 1753. Science Branch, Department of Fisheries and Oceans, Newfoundland, Canada
Miyauchi Y, Gohda Y, Hirama Y, Okamoto Y, Ohnuki T (2015) Shortening of marking time to increase otolith thermal marking pattern of chum salmon (Oncorhynchus keta) released from hatcheries. J Fish Tech 7:89–95 (in Japanese with English abstract)
Nandor GF, Longwill JR, Webb DL (2010) Overview of the coded wire tag program in the Greater Pacific Region of North America. PNAMP special publication: tagging, telemetry and marking measures for monitoring fish populations—a compendium of new and recent science for use in informing technique and decision modalities. Pacific Northwest Aquatic Monitoring Partnership Spec Publ 2:5–46
Prager MH, Shertzer KW (2005) An introduction to statistical algorithms useful in stock composition analysis. In: Cadrin SX, et al. (eds) Stock identification methods—applications in fishery science. Elsevier Academic Press, Burlington, pp 499–516
Rannala B, Mountain JL (1997) Detecting immigration by using multilocus genotypes. Proc Natl Acad Sci USA 94:9197–9201
Saito T (2017) Estimating the origins of adult chum salmon Oncorhynchus keta in the Okhotsk and Sea of Japan regions using discriminant analysis of scale characteristics. Fish Sci 83:383–400
Saito T, Okamoto Y, Sasaki K (2015) Biological characteristics of chum salmon in Japan. Bull Fish Res Agen 39:85–120 (in Japanese with English abstract)
Sato S, Templin WD, Seeb LW, Seeb JE, Urawa S (2014) Genetic structure and diversity of Japanese chum salmon populations inferred by single nucleotide polymorphism markers. Trans Am Fish Soc 143:1231–1246
Satterthwaite WH, Mohr MS, O’Farrell MR, Anderson EC, Banks MA, Bates SJ, Bellinger MR, Borgerson LA, Crandall ED, Garza JC, Kormos BJ, Lawson PW, Palmer-Zwahlen ML (2014) Use of genetic stock identification data for comparison of the ocean spatial distribution, size at age, and fishery exposure of an untagged stock and its indicator: California coastal versus Klamath River chinook salmon. Trans Am Fish Soc 143:117–133
Seeb LW, Templin WD, Sato S, Abe S, Warheit K, Park JY, Seeb JE (2011) Single nucleotide polymorphisms across a species’ range: implications for conservation studies of Pacific salmon. Mol Ecol Resour 11:195–217
Shaklee JB, Beacham TD, Seeb L, White BA (1999) Managing fisheries using genetic data: case studies from four species of Pacific salmon. Fish Res 43:45–78
Small MP, Rogers Olive SD, Seeb LW, Seeb JE, Pascal CE, Warheit KI, Templin W (2015) Chum salmon genetic diversity in the northeastern Pacific ocean assessed with single nucleotide polymorphisms (SNPs): applications to fishery management. N Am J Fish Manage 35:974–987
Smith CT, Baker J, Park L, Seeb LW, Elfstrom C, Abe S, Seeb JE (2005a) Characterization of 13 single nucleotide polymorphism markers for chum salmon. Mol Ecol Notes 5:259–262
Smith CT, Elfstrom CM, Seeb LW, Seeb JE (2005b) Use of sequence data from rainbow trout and Atlantic salmon for SNP detection in Pacific salmon. Mol Ecol 14:4193–4203
Sokal RR, Rohlf FJ (1995) Biometry, 3rd edn. Freeman, New York
Takahashi F (2009) Knowledge at present, obtained from recaptures of otolith thermal-marked chum salmon. FRA Salmonid Res Rep 3:6–7 (in Japanese)
Urawa S (2001) Otolith marking of Pacific salmon: techniques and applications. Natl Salmon Resour Center Newslett 7:3–11 (in Japanese)
Volk EC, Schroder SL, Fresh KL (1990) Inducement of unique otolith banding patterns as a practical means to mass-mark juvenile Pacific salmon. In: Parker NC, et al. (eds) Fish-marking techniques. American Fisheries Society Symposium 7, Bethesda, MD, pp 203–215
Volk EC, Schroder SL, Grimm JJ (2005) Otolith thermal marking. In: Cadrin SX, et al. (eds) Stock identification methods—applications in fishery science. Elsevier Academic Press, Burlington, pp 447–463
Waldman JR (1999) The importance of comparative studies in stock analysis. Fish Res 43:237–246
Warren-Myers FW, Dempster T, Swearer SE (2018) Otolith mass marking techniques for aquaculture and restocking: benefits and limitations. Rev Fish Biol Fish 28:485–501
Williamson DH, Jones GP, Thorrold SR, Frisch AJ (2009) Transgenerational marking of marine fish larvae: stable-isotope retention, physiological effects and health issues. J Fish Biol 74:891–905
Wirgin I, Waldman JR (2005) Use of nuclear DNA in stock identification: single-copy and repetitive sequence markers. In: Cadrin SX, et al. (eds) Stock identification methods—applications in fishery science. Elsevier Academic Press, Burlington, pp 331–370
Zemeckis DR, Martins D, Kerr LA, Cadrin SX (2014) Stock identification of Atlantic cod (Gadus morhua) in US waters: an interdisciplinary approach. ICES J Mar Sci 71:1490–1506
Acknowledgments
We thank Yutaka Ishimura, Yuichi Kitaguchi, Tsukasa Hamaya, Mitsunori Ratsu, and Satoru Takahashi for help with the fish measurements and tissue sampling. Salmon-monitoring data collected by the Japan Fisheries Research and Education Agency were used as the baseline datasets in the scale pattern analysis. Kaoru Kaneko assisted with scale measurements. Otolith thermal marks were confirmed by staff of the otolith-analysis laboratory at the Hokkaido National Fisheries Research Institute (Sapporo). Yukiko Fuzisaki assisted with the SNP analysis. Cynthia Kulongowski, with the Edanz Group (www.edanzediting.com/ac), edited a draft of this manuscript. We also thank the journal editor and two anonymous reviewers for their constructive comments for revising the manuscript.
Author information
Authors and Affiliations
Corresponding author
Additional information
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Rights and permissions
About this article
Cite this article
Saito, T., Honda, K., Sasaki, K. et al. Stock composition of adult chum salmon Oncorhynchus keta caught in a setnet fishery estimated using genetic identification, scale patterns, and otolith thermal marking. Fish Sci 86, 271–286 (2020). https://doi.org/10.1007/s12562-020-01401-9
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s12562-020-01401-9