Abstract
Identification of the population structure of harvested species is the first step in the management of wild fisheries. Although the marbled rockfish Sebastiscus marmoratus is a commercially important species in Japan, information on the population structure of this species is limited. We analyzed 646 individuals of S. marmoratus from 13 sampling locations in the coastal waters of western Japan using seven microsatellite markers with the aim to examine the genetic population structure and establish baseline data on the genetic diversity and effective population size (Ne) of this species. Our results indicate that western Japan populations are characterized by a large Ne and that genetic diversity is higher than has been previously reported. We performed several population genetics analyses but these failed to provide evidence of appreciable genetic population structure, although low but significant genetic differentiation was found in 2.6% of the population pairs. This study provides baseline information on the genetic diversity and population structure of S. marmoratus in the coastal waters of western Japan.
Similar content being viewed by others
References
Abdul-Muneer PM (2014) Application of microsatellite markers in conservation genetics and fisheries management: recent advances in population structure analysis and conservation strategies. Genet Res Int 2014:691759. https://doi.org/10.1155/2014/691759
Blacket MJ, Robin C, Good RT, Lee SF, Miller AD (2012) Universal primers for fluorescent labelling of PCR fragments—an efficient and cost-effective approach to genotyping by fluorescence. Mol Ecol Res 12:456–463
Bohonak AJ (2002) IBD (isolation by distance): a program for analyses of isolation by distance. J Hered 93:153–154
Buonaccorsi VP, Kimbrell CA, Lynn EA, Vetter RD (2002) Population structure of copper rockfish (Sebastes caurinus) reflects postglacial colonization and contemporary patterns of gene flow. Can J Fish Aquat Sci 59:1374–1384
Buonaccorsi VP, Westerman M, Stannard J, Kimbrell C, Vetter RD (2004) Molecular genetic structure suggests limited larval dispersal in grass rockfish, Sebastes rastrelliger. Mar Biol 145:779–788
Carlsson J (2008) Effects of microsatellite null alleles on assignment testing. J Hered 99:616–623
Cavalli-Sforza LL, Edwards AWF (1967) Phylogenetic analysis. Models and estimation procedures. Am J Hum Genet 19:233–257
Chapuis MP, Estoup A (2007) Microsatellite null alleles and estimation of population differentiation. Mol Biol Evol 24:621–631
Cope JM (2004) Population genetics and phylogeography of the blue rockfish (Sebastes mystinus) from Washington to California. Can J Fish Aquat Sci 61:332–342
Dupanloup I, Schneider S, Excoffier L (2002) A simulated annealing approach to define the genetic structure of populations. Mol Ecol 11:2571–2581
Eldridge WH, Naish KA (2007) Long-term effects of translocation and release numbers on fine-scale population structure among coho salmon (Oncorhynchus kisutch). Mol Ecol 16:2407–2421
Eldridge WH, Myers JM, Naish KA (2009) Long-term changes in the fine-scale population structure of coho salmon populations (Oncorhynchus kisutch) subject to extensive supportive breeding. Heredity 103:299–309
Excoffier L, Lischer HEL (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Res 10:564–567
Fisheries Agency and Japan Sea-Farming Association (1982–2017) Annual statistics of seed production and release in 1980–2015. Japan Sea-Farming Association, Tokyo (in Japanese)
Frankham R (1995) Effective population size/adult population size ratios in wildlife: a review. Genet Res Camb 66:95–107
Fujita H, Kohda M (1998) Timing and sites of parturition of the viviparous scorpionfish, Sebastiscus marmoratus. Environ Biol Fish 52:225–229
Gonzalez EB, Murakami T, Teshima Y, Yoshioka K, Jeong DS, Umino T (2009) Paternity testing of wild black rockfish Sebastes inermis (brownish type) from the Seto Inland Sea of Japan. Ichthyol Res 56:87–91
Jensen JL, Bohonak AJ, Kelley ST (2005) Isolation by distance, web service. BMC Genet 6:13. https://doi.org/10.1186/1471-2156-6-13
Johansson ML, Banks MA, Glunt KD, Hassel-Finnegan HM, Buonaccorsi VP (2008) Influence of habitat discontinuity, geographical distance, and oceanography on fine-scale population genetic structure of copper rockfish (Sebastes caurinus). Mol Ecol 17:3051–3061
Liu HB, Liu SF, Ye JB, Yuan YJ, Ding SX, Zhuang ZM (2014) Polymorphic microsatellite markers in the false kelpfish Sebastiscus marmoratus: isolation, characterization, and cross-species amplification. Genet Mol Res 13:134–138
Love MS, Yaklovich M, Thorsteinson L (2002) The rockfishes of the Northeast Pacific. University of California Press, Berkeley
Luikre L, Schwartz MK, Waples RS, Ryman N (2010) Compromising genetic diversity in the wild: unmonitored large-scale release of plants and animals. Trends Ecol Evol 25:520–529
Macbeth GM, Broderick D, Buckworth RC, Ovenden JR (2013) Linkage disequilibrium estimation of effective population size with immigrants from divergent populations: a case study on Spanish Mackerel (Scomberomorus commerson). G3: Genes | Genomes | Genetics 3:709–717
Marandel F, Lorance P, Berthelé O, Trenkel VM, Waples RS, Lamy J-B (2019) Estimating effective population size of large marine populations, is it feasible? Fish Fish 20:189–198
Morin PA, Dizon AE (2018) Genetics, management. In: Perrin WF, Würsig B, Thewissen JGM (eds) Encyclopedia of marine mammals. Elsevier, Amsterdam, pp 410–416
Murakami T, Aida S, Yoshioka K, Yoshida H, Blanco Gonzalez E, Nishibori M, Umino T (2006) Mitochondrial DNA and microsatellite DNA as genetic tags for stocked population of black rockfish Sebastes inermis of hatchery origin. Nippon Suisan Gakkaishi 72:710–716 (in Japanese with English abstract)
Nakabo T (2002) Fishes of Japan with pictorial keys to the species. Tokai University Press, Tokyo
Palumbi SR (1994) Genetic divergence, reproductive isolation, and marine speciation. Annu Rev Ecol Syst 25:547–557
Pritchard JK, Stephens M, Donnelly PJ (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959
Research Group for Technology (1975) Development of the marbled rockfish stock enhancement. Research and investigation reports for technology development of the marbled rockfish stock enhancement. Seto Inland Sea-Farming Association, Kobe, pp 1–144 (in Japanese)
Rice WR (1989) Analyzing tables of statistical tests. Evolution 43:223–225
Rocha-Olivares A, Vetter RD (1999) Effects of oceanographic circulation on the gene flow, genetic structure, and phylogeography of the rosethorn rockfish (Sebastes helvomaculatus). Can J Fish Aquat Sci 56:803–813
Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual, 2nd edn. Cold Spring Harbor Laboratory Press, New York
Shen SC (1993) Fishes of Taiwan. National Taiwan University Press, Taipei
Siegle MR, Taylor EB, Miller KM, Withler RE, Yamanaka KL (2013) Subtle population genetic structure in yelloweye rockfish (Sebastes ruberrimus) is consistent with a major oceanographic division in British Columbia Canada. PLoS ONE 8:e71083
Sun DQ, Shi G, Liu XZ, Wang RX, Xu TJ (2013) Genetic diversity and population structure of the marbled rockfish, Sebastiscus marmoratus, revealed by SSR markers. J Genet 90:e21–e24
Van Oosterhout C, William F, Hutchinson DP, Wills M, Shipley P (2004) Micro-Checker: software for identifying and correcting genotyping errors in microsatellite data. Mol Ecol Notes 4:535–538
Waples RS (1998) Separating the wheat from the chaff: patterns of genetic differentiation in high gene flow species. J Hered 89:438–450
Waples RS, Do C (2008) LDNe: a program for estimating effective population size from data on linkage disequilibrium. Mol Ecol Res 8:753–756
Ward RD (2006) The importance of identifying spatial population structure in restocking and stock enhancement programmes. Fish Res 80:9–18
Withler RE, Beacham TD, Schulze AD, Richards LJ, Miller KM (2001) Co-existing populations of Pacific Ocean perch, Sebastes alutus, in Queen Charlotte Sound, British Columbia. Mar Biol 139:1–12
Xu TJ, Quan XQ, Sun YN, Zhao KC, Wang RX (2010) A first set of polymorphic microsatellite loci from the marbled rockfish, Sebastiscus marmoratus. Biochem Genet 48:680–683
Yatomi H, Miyagawa T, Akiba M (2005) Ecological and genetic characteristics of common rockfish, Sebastiscus marmoratus in Shimizu harbor, Shizuoka. J School Mar Sci Technol Tokai Univ 3:21–38
Yin LN, Zhang H, Yanagimoto T, Gao TX (2012) Isolation and characterization of nine polymorphic microsatellite markers of the marbled rockfish Sebastiscus marmoratus (Scorpaeniformes, Scorpaenidae). Russ J Genet 48:1264–1266
Yokogawa K, Iguchi M (1992a) Food habitat and maturation of marbled rockfish, Sebastiscus marmoratus in southern coastal waters of the Harima Sea. Aquacult Sci 40:131–137 (in Japanese with English abstract)
Yokogawa K, Iguchi M (1992b) Age, growth and condition factor of marbled rockfish, Sebastiscus marmoratus in southern coastal waters of the Harima Sea. Aquacult Sci 40:227–234 (in Japanese with English abstract)
Acknowledgements
We are grateful to our colleagues who helped fish sampling, especially to Dr. Shingo Seki (Faculty of Agriculture and Marine Science, Kochi University) and Mr. Hiroyuki Hatanaka (Fukui Prefectural Fisheries Experimental Station), and the members of our laboratory. We also thank Dr. Eric Caldera (Smithsonian Institution, Washington D.C., USA) for reading the manuscript. We also thank the editor Dr. Masashi Sekino and two anonymous reviewers for reading the manuscript and providing critical comments.
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
Tomano, S., Yasuhara, S., Takagi, M. et al. The genetic variability and population structure of the marbled rockfish Sebastiscus marmoratus in western Japan, as inferred by microsatellite DNA markers. Fish Sci 85, 961–970 (2019). https://doi.org/10.1007/s12562-019-01359-3
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s12562-019-01359-3