Responsible genetic approach to stock restoration, sea ranching and stock enhancement of marine fishes and invertebrates

• Addison JT, Bannister RCA (1994) Re-stocking and enhancement of clawed lobster stocks: a review. Crustaceana 67:131–155

  Article  Google Scholar 

• Agashe D (2009) The stabilizing effect of intraspecific genetic variation on population dynamics and in novel and ancestral habitats. Am Nat 174:255–267

  Article  PubMed  Google Scholar 

• Agnalt A-L, Jøstad KE, Kristiansen T, Nøstvold E, Farestveit E, Næss H, Paulsen OI, Svåsand T (2004) Enhancing the European lobster (Homarus gammarus) stock at Kvitsøy Islands: perspectives of rebuilding Norwegian stocks. Ch 30. In: Leber KM, Kitada S, Svåsand T, Blankenship HL (eds) Stock enhancement and sea ranching, 2nd edn. Blackwell, Oxford, pp 415–426

  Google Scholar 

• Aiken DE, Waddy SL (1986) Environmental influence on recruitment of American lobster, Homarus americanus: a perspective. Can J Fish Aquat Sci 43:2258–2270

  Article  Google Scholar 

• Alheit J, Hagen E (1997) Long-term climate forcing of European herring and sardine populations. Fish Oceanogr 6:130–139

  Article  Google Scholar 

• Allendorf FW (1986) Genetic drift and the loss of alleles versus heterozygosity. Zoo Biol 5:181–190

  Article  Google Scholar 

• Allendorf FW, Luikart G, Aitken SN (2013) Conservation and the genetics of populations, 2nd edn. Wiley, Oxford

  Google Scholar 

• Anderson EC, Garza JC (2006) The power of single-nucleotide polymorphisms for large-scale parentage inference. Genetics 172:2567–2582

  Article  CAS  PubMed  PubMed Central  Google Scholar 

• Anderson D, Hedgecock D (2010) Inbreeding depression and growth heterosis in larvae of the purple sea urchin Strongylocentrotus purpuratus (Stimpson). J Exp Mar Biol Ecol 384:68–75

  Article  Google Scholar 

• Anderson PJ, Piatt JF (1999) Community reorganization in the Gulf of Alaska following ocean climate regime shift. Mar Ecol Prog Ser 189:117–123

  Article  Google Scholar 

• Araki H, Cooper B, Blouin MS (2007) Genetic effects of captive breeding cause a rapid, cumulative fitness decline in the wild. Science 318:100–103

  Article  CAS  PubMed  Google Scholar 

• Araki H, Berejikian BA, Ford MJ, Blouin MS (2008) Fitness of hatchery-reared salmonids in the wild. Evol Appl 1:342–355

  Article  PubMed  PubMed Central  Google Scholar 

• Arkush KD, Giese AR, Mendonca HL, McBride AM, Marty GD, Hedrick PW (2002) Resistance to three pathogens in the endangered winter-run Chinook salmon (Oncorhynchus tshawytscha): effects of inbreeding and major histocompatibility complex genotypes. Can J Fish Aquat Sci 59:966–975

  Article  Google Scholar 

• Arnaud-Haond S, Vonau V, Bonhomme F, Boudry P, Blanc F, Prou J, Seaman T, Goyard E (2004) Spatio-temporal variation in the genetic composition of wild populations of pearl oyster (Pinctada margaritifera comingii) in French Polynesia following 10 years of juvenile translocation. Mol Ecol 13:2001–2007

  Article  CAS  PubMed  Google Scholar 

• Arnaud-Haond S, Teixeira S, Massa SI, Billot C, Saenger P, Coupland G, Duarte CM, Serrao EA (2006) Genetic structure at range edge: low diversity and high inbreeding in Southeast Asian mangrove (Avicennia marina) populations. Mol Ecol 15(12):3515–3525

  Article  CAS  PubMed  Google Scholar 

• Arnold WS (2006) Application of larval release for restocking and stock enhancement of coastal marine bivalve populations. Rev Fish Sci 16:65–71

  Article  Google Scholar 

• Ashley MV, Willson MF, Pergams ORW et al (2003) Evolutionarily enlightened management. Biol Conserv 111:115–123

  Article  Google Scholar 

• Audzijonyte A, Kuparinen A, Gorton R, Fulton EA (2013) Ecological consequences of body size decline in harvested fish species: positive feedback loops in trophic interactions amplify human impact. Biol Lett 9:20121103

  Article  PubMed  PubMed Central  Google Scholar 

• Bailey KM, Brown ES, Duffy-Anderson JT (2003) Aspects of distribution, transport and recruitment of Alaska plaice (Pleuronectes quadrituberculatus) in the Gulf of Alaska and eastern Bering Sea: comparison of marginal and central populations. J Sea Res 50:87–95

  Article  Google Scholar 

• Bailey JK, Schweitzer JA, Úbeda F et al (2009) From genes to ecosystems: a synthesis of the effects of plant genetic factors across levels of organization. Philos Trans R Soc B 364:1607–1616

  Article  Google Scholar 

• Bailey JK, Genung MA, Ware I, Gorman C, van Nuland ME et al (2014) Indirect genetic effects: an evolutionary mechanism linking feedbacks, genotypic diversity and coadaptation in a climate change context. Funct Ecol 28:87–95

  Article  Google Scholar 

• Bannister RCA, Addison JT (1998) Enhancing lobster stocks: a review of recent European methods, results and future prospects. Bull Mar Sci 62:369–387

  Google Scholar 

• Barrett RD, Schluter D (2008) Adaptation from standing genetic variation. Trends Ecol Evol 23:38–44

  Article  PubMed  Google Scholar 

• Bechtol WR, Kruse GH (2009a) Analysis of a stock-recruit relationship for red king crab off Kodiak Island, Alaska. Mar Coast Fish 1:29–44

  Article  Google Scholar 

• Bechtol WR, Kruse GH (2009b) Reconstruction of historical abundance and recuitment of red king crab during 1960–2004 around Kodiak, Alaska. Fish Res 100:86–98

  Article  Google Scholar 

• Bekkevold D, Hansen MM, Nielsen EE (2006) Genetic impact of gadoid culture on wild fish populations: predictions, lessons from salmonids, and possibilities for minimizing adverse effects. ICES J Mar Sci 63:198–208

  Article  Google Scholar 

• Bekkevold D, Gross R, Arula T, Helyar SJ, Ojaveer H (2016) Outlier loci detect intraspecific biodiversity amongst Spring and Autumn spawning herring across local scales. PLoS ONE 11:e0148499

  Article  PubMed  PubMed Central  CAS  Google Scholar 

• Berec L, Angulo E, Courchamp F (2006) Multiple Allee effects and population management. Trends Ecol Evol 22:185–191

  Article  PubMed  Google Scholar 

• Beverton RJH (1995) Spatial limitation of population size: the concentration hypothesis. Neth J Sea Res 34:1–6

  Article  Google Scholar 

• Beyer JE, Kirchner CH, Holtzhausen JA (1999) A method to determine size-specific natural mortality applied to west coast steenbras (Lithognathus aureti) in Namibia. Fish Res 41:133–153

  Article  Google Scholar 

• Blake SG, Black NJ, Oesterling MJ, Graves JE (1997) Genetic divergence and loss of diversity in two cultured populations of the bay scallop, Argopecten irradians (Lamarck, 1819). J Shellfish Res 16:55–58

  Google Scholar 

• Blanco Gonzalez E, Umino T (2009) Fine-scale genetic structure derived from stocking black sea bream Acanthopagrus schlegelii (Bleeker, 1854), in Heroshima Bay, Japan. Jpn J Appl Ichthyol 25:407–410

  Article  Google Scholar 

• Blanco Gonzalez E, Aritaki M, Knutsen H, Taniguchi N (2015) Effects of large-scale releases on the genetic structure of red sea bream (Pagrus major, Temminck et Schlegel) populations in Japan. PLoS ONE 10:e0125743

  Article  PubMed  PubMed Central  CAS  Google Scholar 

• Blankenship HL, Leber KM (1995) A responsible approach to marine stock enhancement. Am Fish Soc Symp 15:167–175

  Google Scholar 

• Blaxter JHS (2000) The enhancement of marine fish stocks. Adv Mar Biol 38:2–54

  Google Scholar 

• Bohnsack JA, Johnson DL, Ambrose RF (1991) Ecology of artificial reef habitats and fishes. In: Seaman WR Jr, Sprague LM (eds) Artificial habitats for marine and freshwater fisheries. Academic Press, London, pp 61–107

  Chapter  Google Scholar 

• Botsford LW, Castilla JC, Peterson CH (1997) The management of fisheries and marine ecosystems. Science 277:509–515

  Article  CAS  Google Scholar 

• Botsford LW, Nicheli F, Hastings A (2003) Principles for the design of marine reserves. Ecol Appl 13:25–31

  Article  Google Scholar 

• Brown C, Day RL (2002) The future of stock enhancements: lessons for hatchery practice from conservation biology. Fish Fish 3:79–94

  Article  Google Scholar 

• Bruford MW, Davies N, Dulloo ME, Faith DP, Walters M (2017) Monitoring changes in genetic diversity. In: Walters M, Scholes RJ (eds) The GEO handbook on biodiversity observation networks. Springer International Publishing, pp 107–128

• Brumbaugh RD, Coen LD (2009) Contemporary approaches for small-scale oyster reef restoration to address substrate versus recruitment limitation: a review and comments relevant for the Olympia oyster, Ostrea lurida Carpenter 1864. J Shellfish Res 28:47–161

  Article  Google Scholar 

• Brush SB (1995) In situ conservation of landraces in centers of crop diversity. Crop Sci 35:346–354

  Article  Google Scholar 

• Buckley RM (1989) Habitat alterations as a basis for enhancing marine fisheries. CalCOFI Rep 30:40–45

  Google Scholar 

• Bürger R, Lynch M (1995) Evolution and extinction in a changing environment: a quantitative genetic analysis. Evolution 49:151–163

  Article  PubMed  Google Scholar 

• Busack CA, Currens KP (1995) Genetic risks and hazards in hatchery operations: fundamental concepts and issues. Am Fish Soc Symp 15:71–80

  Google Scholar 

• Butcher A, Mayer D, Willet D, Johnston M, Smallwood D (2003) Scale pattern analysis is preferable to OTC marking of otoliths for differentiating between stocked and wild dusky flathead, Platycephalus fuscus, and sand whiting, Sillago ciliata. Fish Manag Ecol 10:163–172

  Article  Google Scholar 

• Butler MJ IV, Herrnkind WF (1997) A test of recruitment limitation and the potential for artificial enhancement of spiny lobster (Panulirus argus) populations in Florida. Can J Fish Aquat Sci 54:452–463

  Article  Google Scholar 

• Caballero A, Garcia-Dorado A (2013) Allelic diversity and its implications for the rate of adaptation. Genetics 195:1373–1384

  Article  PubMed  PubMed Central  Google Scholar 

• Caley MJ, Carr MH, Hixon MA, Hughes TP, Jones GP, Menge BA (1996) Recruitment and the local dynamics of open marine populations. Ann Rev Ecol Syst 27:477–500

  Article  Google Scholar 

• Carson EW, Karlsson S, Saillant E, Gold JR (2009) Genetic studies of hatchery-supplemented populations of red drum in four Texas bays. N Am J Fish Manag 29:1502–1510

  Article  Google Scholar 

• Chaoui L, Gagnaire PA, Guinand B, Quignard JP, Tsigenopoulos C, Kara MH, Bonhomme F (2012) Microsatellite length variation in candidate genes correlates with habitat in the gilthead sea bream Sparus aurata. Mol Ecol 21:5497–5511

  Article  CAS  PubMed  Google Scholar 

• Charlesworth D, Charlesworth B (1987) Inbreeding depression and its evolutionary consequences. Ann Rev Ecol Syst 18:237–268

  Article  Google Scholar 

• Charlesworth D, Morgan MT, Charlesworth B (1993) Mutation accumulation in finite outbreeding and inbreeding populations. Genet Res 55:39–56

  Article  Google Scholar 

• Chen K, Ciannelli L, Decker MB et al (2014) Reconstructing sour-sink dynamics in a population with a pelagic dispersal phase. PLoS ONE 9:e95316

  Article  PubMed  PubMed Central  CAS  Google Scholar 

• Chesson P (1998) Recruitment limitation: a theoretical perspective. Austral J Ecol 23:234–240

  Article  Google Scholar 

• Christensen V, Guenette S, Heymans JJ et al (2003) Hundred-year decline of North Atlantic predatory fishes. Fish Fish 4:1–24

  Article  Google Scholar 

• Coleman F, Travis J, Thistle AB (1998) Marine stock enhancement: a new perspective. Bull Mar Sci 62:303

  Google Scholar 

• Conover DO (1998) Local adaptation in marine fishes: evidence and implications for stock enhancement. Bull Mar Sci 62:477–493

  Google Scholar 

• Conover DO, Munch SB (2002) Sustaining fisheries yields over evolutionary time scales. Science 297:94–96

  Article  CAS  PubMed  Google Scholar 

• Conover DO, Clarke LM, Munch SB, Wagner GN (2006) Spatial and temporal scales of adaptive divergence in marine fishes and the implications for conservation. J Fish Biol 69:21–47

  Article  Google Scholar 

• Cowx IG (1994) Stocking strategies. Fish Manag Ecol 1:15–30

  Article  Google Scholar 

• Crnokrak P, Roff DA (1999) Inbreeding depression in the wild. Heredity 83:260–270

  Article  PubMed  Google Scholar 

• Crow JF, Kimura M (1970) An introduction to population genetics theory. Harper and Row, New York

  Google Scholar 

• Crowder LB, Lyman SJ, Figueira WF, Priddy J (2000) Source-sink population dynamics and the problem of siting marine reserves. Bull Mar Sci 66:799–820

  Google Scholar 

• Cury P, Roy C (1989) Optimal environmental window and pelagic fish recruitment success in upwelling areas. Can J Fish Aquat Sci 46:670–680

  Article  Google Scholar 

• David P (1998) Heterozygosity-fitness correlations: new perspectives on old problems. Heredity 80:531–537

  Article  PubMed  Google Scholar 

• Davis JLD, Young AC, Aguilar R (2004) Differences between hatchery-raised and wild blue crabs (Callinectes sapidus): implications for stock enhancement potential. Trans Am Fish Soc 133:1–14

  Article  Google Scholar 

• Davis JLD, Young-Williams AC, Hines AH, Zohar Y (2005) Assessing the potential for stock enhancement in the case of the Chesapeake Bay blue crab (Callinectes sapidus). Can J Fish Aquat Sci 62:109–122

  Article  Google Scholar 

• Doherty PJ (1999) Recruitment limitation is the theoretical basis for stock enhancement in marine populations. In: Howell BR, Moksness E, Svåsand T (eds) Stock enhancement and sea ranching. Fishing News Books, Oxford, pp 9–21

  Google Scholar 

• Eggleston D, Armstrong DA (1995) Pre- and post-settlement determinants of estuarine Dungeness crab recruitment. Ecol Monogr 65:193–216

  Article  Google Scholar 

• Eggleston DB, Johnson EG, Kellison GT, Plaia GR, Huggett CL (2008) Pilot evaluation of early juvenile blue crab stock enhancement using a replicated BACI design. Rev Fish Sci 16:91–100

  Article  Google Scholar 

• Evans D, Bartlett J, Sweijd N, Cook P, Elliott NG (2004) Loss of genetic variation at microsatellite loci in hatchery produced abalone in Australia (Haliotis rubra) and South Africa (Haliotis midae). Aquaculture 233:109–127

  Article  Google Scholar 

• Exadactylos A, Geffen AJ, Thorpe JP (1999) Growth and genetic variation in hatchery-reared larval and juvenile Dover sole, Solea solea (L.). Aquaculture 176:209–226

  Article  Google Scholar 

• Falconer DF, Mackay TFC (1996) Introduction to quantitative genetics. Prentice Hall, New York

  Google Scholar 

• FAO (UN Food and Agriculture Organization) (2013) In vivo conservation of animal genetic resources. FAO Animal Production and Health Guidelines. No. 14, Rome

• FAO (UN Food and Agriculture Organization) (2014) The state of world fisheries and aquaculture. No. 3, Rome

• Fogarty MJ, Botsford LW (2007) Population connectivity and spatial management of marine fisheries. Oceanography 20:112–123

  Article  Google Scholar 

• Fogarty MJ, Idoine JS (1986) Recruitment dynamics in an American lobster (Homarus americanus) population. Can J Fish Aquat Sci 43:2368–2376

  Article  Google Scholar 

• Ford MJ, Fuss H, Boelts B, LaHood E, Hard J, Miller J (2006) Changes in run timing and natural smolt production in a naturally spawning coho salmon (Oncorhynchus kisutch) population after 60 years of intensive hatchery supplementation. Can J Fish Aquat Sci 63:2343–2355

  Article  Google Scholar 

• Fox CJ, Planque BP, Darby CD (2000) Synchrony in the recruitment time-series of plaice (Pleuronectes platessa L.) around the United Kingdom and the influence of sea temperature. J Sea Res 44:159–168

  Article  Google Scholar 

• Francis RC, Hixon MA, Clarke ME, Murawski SA, Ralston S (2007) Ten commandments for ecosystem-based fisheries scientists. Fisheries 32:217–233

  Article  Google Scholar 

• Frankham R (1995) Effective population size/adult population size ratios in wildlife: a review. Genet Res 66:95–107

  Article  Google Scholar 

• Frankham R (2005) Genetics and extinction. Biol Conserv 126:131–140

  Article  Google Scholar 

• Frankham R, Bradshaw C, Brook RW (2014) Genetics in conservation management: revised recommendations for the 50/500 rule, Red List criteria and population viability analyses. Biol Conserv 170:56–63

  Article  Google Scholar 

• Fujio Y, von Brand E (1991) Differences in degree of homozygosity between seed and sown populations of the Japan Scallop Patinopecten yessoensis. Nipp Suis Gakk 57:45–50

  Article  Google Scholar 

• Gaffney PM, Rubin VP, Hedgecock D, Powers DA, Morris G, Hereford L (1996) Genetic effects of artificial propagation: signals from wild and hatchery populations of red abalone in California. Aquaculture 143:257–266

  Article  Google Scholar 

• Gagnaire P-A, Broquet T, Aurelle D, Viard F, Souissi A, Bonhomme F, Arnaud-Haond S et al (2015) Using neutral, selected, and hitchhiker loci to assess connectivity of marine populations in the genomic era. Evol Appl 8:769–786

  Article  PubMed  PubMed Central  Google Scholar 

• Gagnaire P-A, Gaggiotti OE (2016) Detecting polygenic selection in marine populations by combining population genomics and quantitative genetics approaches. Curr Zool 62(6):603–616

  Article  Google Scholar 

• Gamble RJ, Link JS (2012) Using an aggregate production simulation model with ecological interactions to explore effects of fishing and climate on a fish community. Mar Ecol Prog Ser 459:259–274

  Article  Google Scholar 

• Gamfeldt L, Källström B (2007) Increasing intraspecific diversity increased predictability in population survival in the face of perturbations. Oikos 116:700–705

  Article  Google Scholar 

• Gamfeldt L, Wallén J, Jonsson PR, Bentsson KM, Havenhand JN (2005) Increasing intraspecific diversity enhances settling success in a marine invertebrate. Ecology 86:3219–3224

  Article  Google Scholar 

• Garibaldi L (2012) The FAO global capture production database: a six-decade effort to catch the trend. Mar Policy 36:760–768

  Article  Google Scholar 

• Gascoigne J, Lipcius RH (2004) Allee effects in marine systems. Mar Ecol Prog Ser 269:49–59

  Article  Google Scholar 

• Geldenhuys G, Glanzmann B, Lombard D, Moolay S, Carr J, Bardien S (2014) Identification of a common found couple for 40 South African Afrikaner families with Parkinson’s disease. S Afr Med J 104:413–419

  Article  PubMed  Google Scholar 

• Ghalambor CJ, McKay JK, Carroll SP, Reznick DN (2007) Adaptive versus non-adaptive phenotypic plasticity and the potential for contemporary adaptation in new environments. Funct Ecol 21:394–407

  Article  Google Scholar 

• Gharrett AJ, Joyce J, Smoker WW (2013) Fine-scale temporal adaptation within a salmonid population: mechanism and consequences. Mol Ecol 22:4457–4469

  Article  PubMed  Google Scholar 

• Gilk SE, Wang IA, Hoover CL, Smoker WW, Taylor SG, Gray AK, Gharrett AJ (2004) Outbreeding depression in hybrids between spatially separated pink salmon, Oncorhynchus gorbuscha, populations: marine survival, homing ability, and variability in family size. Environ Biol Fish 69:287–297

  Article  Google Scholar 

• Griffies SM, Bryan K (1997) Predictability of North Atlantic multidecadal climate variability. Science 275:181–184

  Article  CAS  PubMed  Google Scholar 

• Gutierrez-Gonzalez JL, Perez-Enriquez R (2005) A genetic evaluation of stock enhancement of blue abalone Haliotis fulgens in Baja California, Mexico. Aquaculture 247:233–242

  Article  Google Scholar 

• Haddaway NR, Woodcock P, Macura B, Collins A (2015) Making literature review more reliable through application of lessons from systematic reviews. Conserv Biol 29:1596–1605

  Article  CAS  PubMed  Google Scholar 

• Halpern BS, Gaines SD, Warner RR (2005) Habitat size recruitment, and longevity as factors limiting population size in stage-structured species. Am Nat 165:82–94

  PubMed  Google Scholar 

• Hamasaki K, Kitada S (2008a) Potential of stock enhancement for decapod crustaceans. Rev Fish Sci 16:164–174

  Article  Google Scholar 

• Hamasaki K, Kitada S (2008b) The enhancement of abalone stocks: lessons from Japanese case studies. Fish Fish 9:243–260

  Article  Google Scholar 

• Hansson B, Westerberg L (2002) On the correlation between heterozygosity and fitness in natural populations. Mol Ecol 11:2467–2474

  Article  PubMed  Google Scholar 

• Hare MP, Allen SK Jr, Bloomer P, Camara MD, Carnegie RB, Murfree J, Luckenbach M et al (2006) A genetic test for recruitment enhancement in Chesapeake Bay oysters, Cassostrea virginica, after population supplementation with a disease tolerant strain. Conserv Genet 7:717–734

  Article  Google Scholar 

• Harvell CD, Kim K, Burkholder JM et al (1999) Emerging marine diseases: climate Links and anthropogenic factors. Science 285:1505–1510

  Article  CAS  PubMed  Google Scholar 

• Hauser L, Adcock GH, Smith PJ, Bernal Ramirez JH, Carvalho GR (2002) Loss of microsatellite diversity and low effective population size in an overexploited population of New Zealand snapper (Pagrus auratus). Proc Natl Acad Sci USA 99:1742–11747

  Article  CAS  Google Scholar 

• Hedgecock D (1994) Does variance in reproductive success limit effective population sizes of marine organisms? In: Beaumont AR (ed) Genetics and evolution of aquatic organisms. Chapman and Hall, London, pp 122–134

  Google Scholar 

• Hedgecock D (2004) Quantifying and minimizing risk that hatchery-enhancement will reduce genetic diversity of white seabass. Final report, California Sea Grant College Program, University of California, San Diego. http://repositories.cdlib.org/csgc/rcr/Fisheries04_03

• Hedgecock D, Coykendall K (2007) Genetic risks of marine hatchery enhancement: the good, the bad, and the unknown. In: Bert TM (ed) Ecological and genetic implications of aquaculture activities. Springer, Dordrecht, pp 85–101

  Chapter  Google Scholar 

• Hedgecock D, Pudovkin AI (2011) Sweepstakes reproductive success in highly fecund marine fish and shellfish: a review and commentary. Bull Mar Sci 87:971–1002

  Article  Google Scholar 

• Heithaus MR, Frid A, Wirsing AJ, Worm B (2008) Predicting ecological consequences of marine top predator declines. Trends Ecol Evol 23:202–210

  Article  PubMed  Google Scholar 

• Helson JG, Gardner JPA (2004) Contrasting patterns of mussel abundance at neighbouring sites: does recruitment limitation explain the absence of mussels on Cook Strait (New Zealand) shores? J Exp Mar Biol Ecol 312:285–298

  Article  Google Scholar 

• Hendry AP, Kinnison MT, Heino M et al (2011) Evolutionary principles and their practical application. Evol Appl 4:159–183

  Article  PubMed  PubMed Central  Google Scholar 

• Heppell SS, Crowder LB (1998) Prognostic evaluation of enhancement programs using population models and life history analysis. Bull Mar Sci 62:495–507

  Google Scholar 

• Herrnkind WF, Cobb JS (2007) Artificial shelters for clawed and spiny lobsters: a critical review of enhancement efforts. Am Fish Soc Symp 49:587–594

  Google Scholar 

• Heslinga GA, Orak O, Ngiramengior M (1984) Coral reef sanctuaries for Trochus shells. Mar Fish Rev 46:73–80

  Google Scholar 

• Hilborn R (1998) The economic performance of marine stock enhancement projects. Bull Mar Sci 62:661–674

  Google Scholar 

• Hilborn R, Quinn T, Schindler D, Rogers D (2003) Biocomplexity and fisheries sustainability. Proc Natl Acad Sci USA 100:6564–6568

  Article  CAS  PubMed  PubMed Central  Google Scholar 

• Hill WG, Goddard ME, Visscher PM (2008) Data and theory point to mainly additive genetic variance for complex traits. PLoS Genet 4:e1000008

  Article  PubMed  PubMed Central  CAS  Google Scholar 

• Hines AH, Johnson EG, Young AC, Aguilar R, Kramer MA, Goodison M, Zmora O, Zohar Y (2008) Release strategies for estuarine species with complex migratory life cycles: stock enhancement of Chesapeake blue crabs (Callinectes sapidus). Rev Fish Sci 16:175–185

  Article  Google Scholar 

• Hoban S, Hauffe HC, Pérez-Espona S, Arntzen JW, Bertorelle JW, Bryja J, Frith K et al (2013) Bringing genetic diversity to the forefront of conservation policy and management. Conserv Genet Resour 5:593–598

  Article  Google Scholar 

• Hoban S, Arntzen JA, Bruford MW et al (2014) Comparative evaluation of potential indicators and temporal sampling protocols for monitoring genetic erosion. Evol Appl 7:984–998

  Article  CAS  PubMed  PubMed Central  Google Scholar 

• Hoffman AA, Merilä J (1999) Heritable variation and evolution under favourable and unfavourable conditions. Trends Ecol Evol 14:96–101

  Article  Google Scholar 

• Hold N, Murray LG, Kaiser MJ, Hinz H, Beaumont AR, Taylor MI (2013) Potential effects of stock enhancement with hatchery-reared seed on genetic diversity and effective population size. Can J Fish Aquat Sci 70:330–338

  Article  Google Scholar 

• Hopper DU, Chapin FS, Ewel JJ, Hector A, Inchausti P, Lavorel S, Lawton JH et al (2005) Effects of biodiversity on ecosystem functioning: a consensus of current knowledge. Ecol Monogr 75:3–35

  Article  Google Scholar 

• Howell BR (1994) Fitness of hatchery-reared fish for survival in the sea. Aquac Fish Manag 25(supplement):3–17

  Google Scholar 

• Hughes TP (1990) Recruitment limitation, mortality, and population regulation in open systems: a case study. Ecology 71:12–20

  Article  Google Scholar 

• Hughes AR, Stachowicz JJ (2004) Genetic diversity enhances the resistance of a sea grass ecosystem to disturbance. Proc Natl Acad Sci USA 101:8998–9002

  Article  CAS  PubMed  PubMed Central  Google Scholar 

• Hughes AR, Inouye BD, Johnson MTJ, Underwood N, Vellend M (2008) Ecological consequences of genetic diversity. Ecol Lett 11:609–623

  Article  PubMed  Google Scholar 

• Hunt HL, Scheibling RE (1997) Role of early post-settlement mortality in recruiting of benthic marine invertebrates. Mar Ecol Prog Ser 155:269–301

  Article  Google Scholar 

• Hutchings JA (2005) Life history consequences of overexploitation to population recovery in Northwest Atlantic cod (Gadus morhua). Can J Fish Aquat Sci 62:824–832

  Article  Google Scholar 

• Hutchings JA (2014) Renaissance of a caveat: Allee effects in marine fish. ICES J Mar Sci 71:2152–2157

  Article  Google Scholar 

• Hutchings JA, Swain DP, Rowe S, Eddington JD, Puvanendran V, Brown JA (2007) Genetic variation in life-history reaction norms in marine fish. Proc R Soc B 274:1693–1699

  Article  PubMed  PubMed Central  Google Scholar 

• Hutchings JA, Butchart SHM, Collen B, Schwartz MK, Waples RS (2012) Red flags: correlates of impaired species recovery. Trends Ecol Evol 27:542–546

  Article  PubMed  Google Scholar 

• Iles TC, Beverton RJH (2000) The concentration hypothesis: the statistical evidence. ICES J Mar Sci 57:216–227

  Article  Google Scholar 

• Jackson JBC, Kirby MX, Berger WH et al (2001) Historical overfishing and the recent collapse of coastal ecosystems. Science 293:629–638

  Article  CAS  PubMed  Google Scholar 

• Jasper JR, Habicht C, Moffitt S, Brenner R, Marsh J, Lewis B, Creelman Fox E et al (2013) Source-sink estimates of genetic introgression show influence of hatchery strays on wild chum salmon populations in Prince William Sound, Alaska. PLoS ONE 8(12):e81916

  Article  PubMed  PubMed Central  Google Scholar 

• Jennings S, Greenstreet SPR, Reynolds JD (1999) Structural change in an exploited fish community: a consequence of differential fishing effects on species with contrasting life histories. J Anim Ecol 68:617–627

  Article  Google Scholar 

• Jensen JD, Foll M, Bernatchez L (2016) The past, present and future of genomic scans for selection. Mol Ecol 25:1–4

  Article  PubMed  Google Scholar 

• Johnson EG, Hines AH, Kramer MA, Young AC (2008) Importance of season and size of release to stocking success for the blue crab in Chesapeake Bay. Rev Fish Sci 16:243–253

  Article  Google Scholar 

• Jorde PE, Søvik G, Westgaard J-I, Albretsen J, André C, Hvingel C, Johansen T et al (2015) Genetically distinct populations of northern shrimp Pandalis borealis, in the North Atlantic: adaptation to different temperatures as an isolation factor. Mol Ecol 24:1742–1757

  Article  PubMed  Google Scholar 

• Jøstad KE, Prodöhl PA, Kristiansen TS, Hughes M, Farestveit E, Taggart JB, Agnalt A-L et al (2005) Communal larval rearing of European lobster (Homarus gammarus): family identification by microsatellite DNA profiling and offspring fitness comparisons. Aquaculture 247:275–285

  Article  CAS  Google Scholar 

• Kahilainen A, Puurtinen M, Kotiaho JS (2014) Conservation implications of species-genetic diversity correlations. Glob Ecol Conserv 2:315–323

  Article  Google Scholar 

• Kalinowski ST (2005) HP-RARE 1.0: a computer program for performing rarefaction on measures of allelic richness. Mol Ecol Notes 5:187–189

  Article  CAS  Google Scholar 

• Karlson RH, Levitan DR (1990) Recruitment-limitation in open populations of Diadema antillarum: an evaluation. Oecologia 82:40–44

  Article  PubMed  Google Scholar 

• Karlsson S, Saillant E, Bumguardner BW, Vega RR, Gold JR (2008) Genetic identification of hatchery-released red drum in Texas bays and estuaries. N Am J Fish Manag 28:1294–1304

  Article  Google Scholar 

• Karlsson S, Diserud OH, Fiske P, Hindar K (2016) Widespread genetic introgression of escaped farmed Atlantic salmon in wild salmon populations. ICES J Mar Sci 73:2488–2498

  Article  Google Scholar 

• Keller L, Reeve HK (1994) Partitioning of reproduction in animal societies. Trends Ecol Evol 9:98–103

  Article  CAS  PubMed  Google Scholar 

• Keller LF, Waller DM (2002) Inbreeding effects in wild populations. Trends Ecol Evol 17:230–241

  Article  Google Scholar 

• Kirk RA (1987) A history of marine fish culture in Europe and North America. Fishing News Books, Oxford

  Google Scholar 

• Kitada S, Kishino H (2006) Lessons learned from Japanese marine finfish stock enhancement programmes. Fish Res 80:101–112

  Article  Google Scholar 

• Kitada S, Taga Y, Kishino H (1992) Effectiveness of stock enhancement program evaluated by a two-stage sampling survey of commercial landings. Can J Fish Aquat Sci 49:1573–1582

  Article  Google Scholar 

• Kitada S, Shishidou H, Sugaya T, Kitakado T, Hamasaki K, Kishino H (2009) Genetic effects of long-term stock enhancement programs. Aquaculture 290:69–79

  Article  Google Scholar 

• Kostow KE (2004) Differences in juvenile phenotypes and survival between hatchery stocks and a natural population provide evidence for modified selection due to captive breeding. Can J Fish Aquat Sci 61:577–589

  Article  Google Scholar 

• Kuparinen A, Kieth DM, Hutchings JA (2014) Allee effect and the uncertainty of population recovery. Conserv Biol 28:790–798

  Article  PubMed  Google Scholar 

• Lamichhaney S, Martinez Barrio A, Rafati N et al (2012) Population-scale sequencing reveals genetic differentiation due to local adaptation in Atlantic herring. Proc Natl Acad Sci USA 109:19345–19350

  Article  CAS  PubMed  PubMed Central  Google Scholar 

• Lande R (1981) The minimum number of genes contributing to quantitative variation between and within populations. Genetics 99:541–553

  CAS  PubMed  PubMed Central  Google Scholar 

• Lankau RA, Strauss SY (2007) Mutual feedbacks maintain both genetic and species diversity in a plant community. Science 317:1561–1563

  Article  CAS  PubMed  Google Scholar 

• Law R (2000) Fishing, selection, and phenotypic evolution. ICES J Mar Sci 57:659–668

  Article  Google Scholar 

• Le Moan A, Gagnaire PA, Bonhomme F (2016) Parallel genetic divergence among coastal–marine ecotype pairs of European anchovy explained by differential introgression after secondary contact. Mol Ecol 25:3187–3202

  Article  PubMed  CAS  Google Scholar 

• Le Vay L, Carvalho GR, Quinitio ET, Lebata JH, Ut VN, Fushimi H (2007) Quality of hatchery-reared juveniles for marine fisheries enhancement. Aquaculture 268:168–180

  Google Scholar 

• Leber KM (2004) Summary of case studies of the effectiveness of stocking aquacultured fishes and invertebrates to replenish and enhance coastal fisheries. In: Bartley DM, Leber KM (eds) Marine Ranching, FAO Fish Technical Papers 429, pp 203–213

• Leber KM, Brennan NP, Arce SM (1995) Marine enhancement with striped mullet: are hatchery releases replenishing or displacing wild stocks? Am Fish Soc Symp 15:376–387

  Google Scholar 

• Leber KM, Brennan NP, Arc SM (1998) Recruitment patterns of cultured juvenile Pacific threadfin, Polydactylus sexfilis (Polynemidae), released along sandy marine shores in Hawaii. Bull Mar Sci 62:389–408

  Google Scholar 

• Leggett WC, Frank KT (1997) A comparative analysis of recruitment variability in North Atlantic flatfishes—testing the species range hypothesis. J Sea Res 37:281–299

  Article  Google Scholar 

• Leverone JR, Geiger SP, Stephenson SP, Arnold WS (2010) Increase in bay scallop (Argopecten irradians) populations following releases of competent larvae in two west Florida estuaries. J Shellfish Res 29:395–406

  Article  Google Scholar 

• Liao IC (2000) The state of finfish diversification in Asian aquaculture. Cah Opt Méd 47:109–125

  Google Scholar 

• Liermann M, Hilborn R (1997) Depensation in fish stocks: a hierarchic Bayesian meta-analysis. Can J Fish Aquat Sci 54:1976–1984

  Article  Google Scholar 

• Lind CE, Evans BS, Knauer J, Taylor JJU, Jerry DR (2009) Decreased genetic diversity and a reduced effective population size in cultured silver-lipped pearl oysters (Pinctada maxima). Aquaculture 286:12–19

  Article  Google Scholar 

• Link JS (2002) What does ecosystem-based fisheries management mean? Fisheries 27:18–21

  Article  Google Scholar 

• Linnane A, Mercer JP (1998) A comparison of methods for tagging juvenile lobsters (Homarus gammarus L.) reared for stock enhancement. Aquaculture 163:195–202

  Article  Google Scholar 

• Lipicius RN, Schreiber S, Wang H, Shen J, Sisson M (2008) Metapopulation source-sink dynamics and stock enhancement of marine species. Rev Fish Sci 16:101–110

  Article  Google Scholar 

• Longhurst A (2010) Mismanagement of marine fisheries. Cambridge University Press, Cambridge

  Book  Google Scholar 

• Lorenzen K (2000) Allometry of natural mortality as a basis for assessing optimal release size in fish-stocking programmes. Can J Fish Aquat Sci 57:2374–2381

  Article  Google Scholar 

• Lorenzen K (2005) Population dynamics and potential of fisheries stock enhancement: practical theory for assessment and policy analysis. Philos Trans R Soc B 360:171–189

  Article  Google Scholar 

• Lorenzen K (2006) Population management in fisheries enhancement: gaining key information from release experiments through use of a size-dependent mortality model. Fish Res 80:19–27

  Article  Google Scholar 

• Lorenzen K (2008) Understanding and managing enhancement fisheries systems. Rev Fish Sci 16:10–23

  Article  Google Scholar 

• Lorenzen K, Leber KM, Blankenship HL (2010) Responsible approach to marine stock enhancement: an update. Rev Fish Sci 18:189–210

  Article  Google Scholar 

• Luttikhuizen PC, Drent J, van Delden W, Piersma T (2003) Spatially structure genetic variation in a broadcast spawning bivalve: quantitative vs. molecular traits. J Evol Biol 16:260–272

  Article  CAS  PubMed  Google Scholar 

• Lynch M, O’Hely M (2001) Captive breeding and the genetic fitness of natural populations. Conserv Genet 2:363–378

  Article  Google Scholar 

• Lynch M, Conery J, Bürger R (1995) Mutation accumulation and the extinction of small populations. Am Nat 146:489–518

  Article  Google Scholar 

• Macaranas J, Fujio Y (1990) Strain differences in cultured fish–isozymes and performance traits as indicators. Aquaculture 85:69–82

  Article  CAS  Google Scholar 

• MacCall AD (1990) Dynamic geography of marine fish populations. University of Washington Press, Seattle

  Google Scholar 

• Mannion AM (1999) Domestication and the origins of agriculture: an appraisal. Prog Phys Geogr 23:37–56

  Article  Google Scholar 

• Mantua NJ, Hare SR (2002) The Pacific decadal oscillation. J Oceanogr 58:35–44

  Article  Google Scholar 

• Martin-Robichaud DJ, Haché R, Pernet F, Ritchie R (2007) Genomic evaluation of haddock (Melanogrammus aeglefinus L.) broodstock. Can Tech Rep Fisher Aquat Sci 2704:iv+10

• Masuda R, Tsukamoto K (1998) Stock enhancement in Japan: review and perspective. Bull Mar Sci 62:337–358

  Google Scholar 

• Matthews B, Narwani A, Hausch S et al (2011) Toward an integration of evolutionary biology and ecosystem science. Ecol Lett 14:690–701

  Article  PubMed  Google Scholar 

• McCay BJ (1988) Muddling through the clam beds: cooperative management of New Jersey’s hard clam spawner sanctuaries. J Shellfish Res 7:327–340

  Google Scholar 

• McCusker MR, Bentzen P (2010) Positive relationships between genetic diversity and abundance in fishes. Mol Ecol 19:4852–4862

  Article  PubMed  Google Scholar 

• McEachron LW, Colura RL, Bumguardner BW, Ward R (1998) Survival of stocked red drum in Texas. Bull Mar Sci 62:359–368

  Google Scholar 

• Mgaya YD, Gosling EM, Mercer JP, Donlon J (1995) Genetic variation at three polymorphic loci in wild and hatchery stocks of the abalone, Haliotis tuberculata Linnaeus. Aquaculture 136:71–80

  Article  Google Scholar 

• Milbury CA, Meritt DW, Newell RIE, Gaffney PM (2004) Mitochondrial DNA markers allow monitoring of oyster stock enhancement in the Chesapeake Bay. Mar Biol 145:351–359

  Article  CAS  Google Scholar 

• Mimura M, Yahara T, Faith DP, Vázquez-Dominguez E, Colautti RI et al (2017) Understanding and monitoring the consequences of human impacts of intraspecific variation. Evol Appl 10:121–139

  Article  PubMed  Google Scholar 

• Miyazaki T, Masuda R, Furutra S, Tsukamoto K (2000) Feeding behaviour of hatchery-eared juveniles of the Japanese flounder following a period of starvation. Aquaculture 190:129–138

  Article  Google Scholar 

• Mobrand LE, Barr J, Blankenship L, Campton DE, Evelyn TT, Flagg TA, Mahnken CV, Seeb LW, Seidel PR, Smoker WW (2005) Hatchery reform in Washington State: principles and emerging issues. Fisheries 30:11–23

  Article  Google Scholar 

• Moksness E, Stole R, van der Meeren G (1998) Profitability analysis of sea ranching with Atlantic salmon (Salmo salar), Arctic charr (Salvelinus alpinus) and European lobster (Homarus gammarus) in Norway. Bull Mar Sci 62:689–699

  Google Scholar 

• Molony BW, Lenanton R, Jackson G, Norriss J (2004) Stock enhancement as a fisheries management tool. Rev Fish Biol Fish 13:409–432

  Article  Google Scholar 

• Montes I, Iriondo M, Manzano C, Santis M, Conklin D, Carvalho G, Irigoien X et al (2016) No loss of genetic diversity in the exploited and recently collapsed population of Bay of Biscay anchovy (Engaulis encrasicholus, L.). Mar Biol 163:1–10

  Article  CAS  Google Scholar 

• Morgan LE, Botsford LW (2001) Managing with reserves: modeling uncertainty in larval dispersal for a sea urchin fishery. In: Spatial processes and management of marine populations. Alaska Sea Grant College Program, Fairbanks, Alaska

• Morgan SG, Fisher JL, Mace AJ (2009) Larval recruitment in a region of strong, persistent upwelling and recruitment limitation. Mar Ecol Prog Ser 394:79–99

  Article  Google Scholar 

• Moya-Laraño J (2011) Genetic variation, predator-prey interactions and food web structure. Philos Trans R Soc B 366:1425–1437

  Article  Google Scholar 

• Munro JL, Bell JD (1997) Enhancement of marine fisheries resources. Rev Fish Sci 5:185–222

  Article  Google Scholar 

• Mustafa S, Saad S, Rahman RA (2003) Species studies in sea ranching: an overview and economic perspectives. Rev Fish Biol Fish 13:165–175

  Article  Google Scholar 

• Naish KA, Taylor JE, Levin PS, Quinn TP, Winton JP, Huppert D, Hilborn R (2008) An evaluation of the effects of conservation and fishery enhancement hatcheries on wild populations of salmon. Adv Mar Biol 53:61–194

  Article  Google Scholar 

• Nakajima K, Kitada S, Habara Y, Sano S, Yokoyama E, Sugaya T, Iwamoto A et al (2014) Genetic effects of marine stock enhancement: a case study based on the highly piscivorous Japanese Spanish mackerel. Can J Fish Aquat Sci 71:301–314

  Article  CAS  Google Scholar 

• Nash CE (2011) The history of aquaculture. Wiley, Ames

  Book  Google Scholar 

• Navarrete SA, Weiters EA, Broitman BR, Castilla JC (2005) Scales of benthic-pelagic coupling and the intensity of species interactions: from recruitment limitation to top-down control. Proc Natl Acad Sci USA 102:18046–18051

  Article  CAS  PubMed  PubMed Central  Google Scholar 

• Neill WH, Miller JM, van der Veer HW, Weinmiller KO (1994) Ecophysiology of marine fish recruitment: a conceptual framework for understanding interannual variability. Neth J Sea Res 32:135–152

  Article  Google Scholar 

• Nicosia F, Lavalli K (1999) Homarid lobster hatcheries: their history and role in research, management, and aquaculture. Mar Fish Rev 61:1–57

  Google Scholar 

• Nielsen EE, Bach LA, Kotlicki P (2006) Hybidlab (version 1.0): a program for generating simulated hybrids from population samples. Mol Ecol Notes 6:971–973

  Article  Google Scholar 

• Nielsen EE, Hemmer-Hansen J, Poulsen NA, Loeschcke V, Moen T, Johansen T, Mittelholzer C et al (2009) Genomic signatures of local directional selection in a high gene flow marine organism; the Atlantic cod (Gadus morhua). BMC Evol Biol 9:276

  Article  PubMed  PubMed Central  CAS  Google Scholar 

• Novel P, Porta J, Fernández J, Méndez T, Gallardo-Gálvez JB (2013) Critical points for the maintenance of genetic variability over a production cycle in the European sea bass, Dicentrarchus labrax. Aquaculture 416–417:8–14

  Article  Google Scholar 

• Ochwada-Doyle F, Loneragan NR, Gray CA, Southers IM, Taylor MD (2012a) Competition between wild and captive-bred Penaeus plebejus and implications for stock enhancement. Mar Ecol Prog Ser 450:115–129

  Article  Google Scholar 

• Ochwada-Doyle F, Loneragan N, Gray C, Southers I, Taylor M (2012b) Complexity affects habitat preference and predation mortality in postlarval Penaeus plebejus: implications for stock enhancement. Mar Ecol Prog Ser 380:161–171

  Article  Google Scholar 

• Okouchi H, Kitada S, Iwamoto A, Fukunaga T (2004) Flounder stock enhancement in Miyako Bay, Japan. FAO Fisheries Technical Paper 429, p 179

• Olla BL, Davis MW, Ryer CH (1998) Understanding how the hatchery environment represses or promotes the development of behavioral survival skills. Bull Mar Sci 62:531–550

  Google Scholar 

• Olsen EM, Heino M, Lilly GR, Morgan MJ, Brattey J, Ernande B, Dieckman U (2004) Maturation trends indicative of rapid evolution preceded the collapse of northern cod. Nature 428:932–935

  Article  CAS  PubMed  Google Scholar 

• Olsen EM, Knutsen H, Gjøsæter J, Jorde PE, Knutsen JA, Stenseth NC (2008) Small-scale biocomplexity in coastal Atlantic cod supporting a Darwinian perspective on fisheries management. Evol Appl 1:524–533

  Article  PubMed  PubMed Central  Google Scholar 

• Olson RR, Olson MH (1989) Food limitation of planktotrophic marine invertebrate larvae: does it control recruitment success? Ann Rev Ecol Syst 20:225–247

  Article  Google Scholar 

• Oosthuizen E, Daan N (1974) Egg fecundity and maturity of North Sea cod, Gadus morhua. Neth J Sea Res 8:378–397

  Article  Google Scholar 

• Ovenden JR, Peel D, Street R et al (2007) The genetic effective and adult census size of an Australian population of tiger prawns (Penaeus esculentus). Mol Ecol 16:127–138

  Article  CAS  PubMed  Google Scholar 

• Pauly D, Christensen V, Guénette S et al (2002) Towards sustainability in world fisheries. Nature 418:689–695

  Article  CAS  PubMed  Google Scholar 

• Pauly D, Alder J, Bennett E, Christensen V, Tyedmers P, Watson R (2003) The future for fisheries. Science 302:1359–1361

  Article  CAS  PubMed  Google Scholar 

• Pearse DE (2016) Saving the spandrels? Adaptive genomic variation in conservation and fisheries management. J Fish Biol 89:2697–2716

  Article  CAS  PubMed  Google Scholar 

• Perez-Enriquez R, Takagi M, Taniguchi N (1999) Genetic variability and pedigree tracing of a hatchery-reared stock of red sea bream (Pagrus major) used for stock enhancement, based on microsatellite DNA markers. Aquaculture 173:413–423

  Article  Google Scholar 

• Perez-Enriquez R, Takaemura M, Tabata K, Taniguchi N (2001) Genetic diversity of red sea bream Pagrus major in western Japan in relation to stock enhancement. Fish Sci 67:71–78

  Article  CAS  Google Scholar 

• Pikitch EK, Santora C, Babcock EA et al (2004) Ecosystem-based fishery management. Science 305:346–347

  Article  CAS  PubMed  Google Scholar 

• Polacheck T (1990) Year around closed areas as a management tool. Nat Res Modell 4:327–354

  Article  Google Scholar 

• Porta J, Porta JM, Cañavate P, Martínez-Rodríguez G, Alvarez MC (2007) Substantial loss of genetic variation in a single generation of Senegalese sole (Solea senegalensis) culture: implications in the domestication process. J Fish Biol 71(Supplement B):223–234

  Article  CAS  Google Scholar 

• Pritchard J, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959

  CAS  PubMed  PubMed Central  Google Scholar 

• Purcell JE, Grover JJ (1990) Predation and food limitation as causes of mortality in larval herring at a spawning ground in British Columbia. Mar Ecol Prog Ser 59:55–61

  Article  Google Scholar 

• Purcell SW, Simutoga M (2008) Spatio-temporal and size-dependent variation in the success of releasing cultured sea cucumbers in the wild. Rev Fish Sci 16:204–214

  Article  Google Scholar 

• Ramachandran S, Deshpande O, Roseman CC, Rosenberg NA, Feldman MW, Cavalli-Sforza LL (2005) Support from the relationship of genetic and geographic distance in human populations for a serial founder effect originating in Africa. Proc Nat Acad Sci USA 102:15942–15947

  Article  CAS  PubMed  PubMed Central  Google Scholar 

• Reed DH, Frankham R (2001) How closely correlated are molecular and quantitative measures of genetic variation? A meta-analysis. Evolution 55:1095–1103

  Article  CAS  PubMed  Google Scholar 

• Reed DH, Frankham R (2003) Correlation between fitness and genetic diversity. Conserv Biol 17:230–237

  Article  Google Scholar 

• Reusch TBH, Ehlers A, Hämmerli A, Worm B (2005) Ecosystem recovery after climatic extremes enhanced by genotypic diversity. Proc Natl Acad Sci USA 102:2826–2831

  Article  CAS  PubMed  PubMed Central  Google Scholar 

• Reynolds LA, McGlathery KJ, Waycott M (2012) Genetic diversity enhances restoration success by augmenting ecosystem services. PLoS ONE 7:e38397

  Article  CAS  PubMed  PubMed Central  Google Scholar 

• Rhode C, Hepple J-A, Jansen S, Davis T, Vervalle J, Bester-van der Merwe AE, Roodt-Wildig R (2012) A population genetic analysis of abalone domestication events in South Africa: implications for the management of abalone resource. Aquaculture 356–357:235–242

  Article  Google Scholar 

• Roberts CM, Hawkins JP, Gell FR (2005) The role of marine reserves in achieving sustainable fisheries. Philos Trans R Soc B 360:123–132

  Article  Google Scholar 

• Rose KA, Cowan JH, Winemiller KO, Myers RA, Hilborn R (2001) Compensatory density dependence in fish populations: importance, controversy, understanding and prognosis. Fish Fish 2:293–327

  Article  Google Scholar 

• Rugger P, Spendani A, Occhipinti G, Fioravanti T, Santojanni A, Leonori I, DeFelice A, Arneri E, Procaccini G, Catanese G, Tičina V, Bonanno A, Cerioni PN, Giovannotti M, Grant WS, Barucchin VC (2016) Biocomplexity in populations of European anchovy in the Adriatic Sea. PLoS ONE 11(4):e0153061

  Article  CAS  Google Scholar 

• Ryman N, Laikre L (1991) Effects of supportive breeding on the genetically effective population size. Conserv Biol 5:325–329

  Article  Google Scholar 

• Ryman N, Utter F, Lairkre L (1995) Protection of intraspecific biodiversity of exploited fishes. Rev Fish Biol Fish 5:417–446

  Article  Google Scholar 

• Saillant E, Renshaw MA, Gatlin Lii DM, Neill WH, Vega RR, Gold JR (2009) An experimental assessment of genetic tagging and founder representation in hatchery-reared red drum (Sciaenops ocellatus) used in stock enhancement. J Appl Ichthyol 25:108–113

  Article  Google Scholar 

• Sanford E, Kelly MW (2011) Local adaptation in marine invertebrates. Annu Rev Mar Sci 3:509–535

  Article  Google Scholar 

• Schindler D, Hilborn R, Chasco B, Boatright C, Quinn T, Rogers L, Webster M (2010) Population diversity and the portfolio effect in an exploited species. Nature 465:609–613

  Article  CAS  PubMed  Google Scholar 

• Schlichting CD, Pigliucci M (1998) Phenotypic evolutions: a reaction norm perspective. Sinauer Associates, Sunderland

  Google Scholar 

• Schmalenbach I, Mehrtens F, Janke M, Buchholz F (2011) A mark-recapture study of hatchery-reared juvenile European lobsters, Homarus gammarus, released at the rocky island of Hegoland (German Bight, North Sea) from 2000 to 2009. Fish Res 108:22–30

  Article  Google Scholar 

• Secor DH, Houde ED (1998) Use of larval stocking in restoration of Chesapeake Bay striped bass. ICES J Mar Sci 55:228–239

  Article  Google Scholar 

• Secor DH, Hines AH, Place AR (2002) Japanese hatchery-based stock enhancement: lessons for the Chesapeake Bay blue crab. Publication Number UM-SG-TS-2002-02, Maryland Sea Grant Program, College Park, MD, p 46

• Segovia-Viadero M, Serrão EA, Canteras-Jordana JC, Gonzalez-Wangüemert M (2016) Do hatchery-reared sea urchins pose a threat to genetic diversity in wild populations? Heredity 116:378–383

  Article  CAS  PubMed  PubMed Central  Google Scholar 

• Seitz RD, Lipcius RN, Knick K, Seebo M, Long WC (2008) Stock enhancement and carrying capacity of blue crab nursery habitats in Chesapeake Bay. Rev Fish Sci 16:329–337

  Article  Google Scholar 

• Sekino M, Hara M, Taniguchi N (2002) Loss of microsatellite and mitochondrial DNA variation in hatchery strains of Japanese flounder Paralichthys olivaceus. Aquaculture 213:101–122

  Article  CAS  Google Scholar 

• Sekino M, Saitoh K, Yamada T, Kumagai A, Hara M, Yamashita Y (2003) Microsatellite-based pedigree tracing in a Japanese flounder Paralichthys olivaceus hatchery strain: implications for hatchery management related to stock enhancement program. Aquaculture 221:255–263

  Article  Google Scholar 

• Sekino M, Saido T, Fujita T, Kobayashi T, Takami H (2005) Microsatellite DNA markers of ezo abalone (Haliotis discus hannai): a preliminary assessment of natural populations samples from heavily stocked areas. Aquaculture 243:33–47

  Article  CAS  Google Scholar 

• Serafy JE, Ault JS, Capo TR, Schultz DR (1999) Red drum, Sciaenops ocellatus L., stock enhancement in Biscayne Bay, FL, USA: assessment of releasing unmarked early juveniles. Aquac Res 30:737–750

  Article  Google Scholar 

• Shanks AL, Roegner GC (2007) Recruitment limitation in Dungeness crab populations is driven by variation in atmospheric forcing. Ecology 88:1726–1737

  Article  PubMed  Google Scholar 

• Sharpe DMT, Hendry AP (2009) Life history change in commercially exploited fish stocks: an analysis of trends across studies. Evol Appl 2:260–275

  Article  PubMed  PubMed Central  Google Scholar 

• Shelbourne JE (1964) The artificial propagation of marine fish. Adv Mar Biol 2:1–83

  Article  Google Scholar 

• Simpson MR, Walsh SJ (2004) Changes in the spatial structure of Grand Bank yellowtail flounder: testing MacCall’s basin hypothesis. J Sea Res 51:199–210

  Article  Google Scholar 

• Smedstad OM, Salvanes AGV, Fosså JH, Nordeide JT (1994) Enhancement of cod, Gadus morhua L. in Masfjorden: an overview. Aquac Fish Manag 25:117–128

  Google Scholar 

• Smith PJ, Francis R, McVeagh M (1991) Loss of genetic diversity due to fishing pressure. Fish Res 10:309–316

  Article  Google Scholar 

• Solemdal P, Dahl E, Danielssen DS, Moksness E (1984) The cod hatchery in Flødevigen – background and realities. In: Dahl E, Danielssen DS, Moksness E, Solemdal P (eds) The propagation of cod, Flødevigen rapportser, Arendal, Norway, pp 17–45

• Sproul JT, Tominaga O (1992) An economic review of the Japanese flounder stock enhancement project in Ishikari Bay, Hokkaido. Bull Mar Sci 5:75–88

  Google Scholar 

• Stoner AW, Davis M (1994) Experimental outplanting of juvenile queen conch, Strombus gigas: comparison of wild and hatchery reared stocks. Fish Bull US 92:390–411

  Google Scholar 

• Stoner AW, Ray-Culp M (2000) Evidence for Allee effects in an over-harvested marine gastropod: density-dependent mating and egg production. Mar Ecol Prog Ser 202:297–302

  Article  Google Scholar 

• Støttrup JG, Sparrevohn CR (2007) Can stock enhancement enhance stocks? J Sea Res 57:104–113

  Article  Google Scholar 

• Straus KM, Vadopalas B, Davis JP, Friedman CS (2015) Reduced genetic variation and decreased effective number of breeders in five year-classes of cultured geoducks (Panopea generosa). J Shellfish Res 34:163–169

  Article  Google Scholar 

• Stunz GW, Levin PS, Minello TJ (2001) Selection of estuarine nursery habitats by wild-caught and hatchery-reared juvenile red drum in laboratory mesocosms. Environ Biol Fish 61:305–313

  Article  Google Scholar 

• Sugaya T, Sato M, Yokoyama E, Nemoto Y, Fujita T, Okouchi H, Hamasaki K et al (2008) Population genetic structure and variability of Pacific herring Clupea pallasii in the stocking area along the Pacific coast of northern Japan. Fish Sci 74:579–588

  Article  CAS  Google Scholar 

• Sun X, Hedgecock D (2017) Temporal genetic change in North American Pacific oyster populations suggests caution in seascape genetics analyses of high gene-flow species. Mar Ecol Prog Ser 565:79–93

  Article  Google Scholar 

• Suquet A, Malo F, Quere C, Ledu C, LeGrand J et al (2016) Gamete quality in triploid Pacific oyster (Crasostrea gigas). Aquaculture 451:11–15

  Article  Google Scholar 

• Sussarellu R, Huvet A, Lepègue S, Quillen V, Lelong C, Cornette F, Jensen LF et al (2015) Additive transcriptomic variation associated with reproductive traits suggest local adaptation in a recently settled population of Pacific oyster, Crassostrea gigas. BMC Genom 16:808

  Article  CAS  Google Scholar 

• Suttle CA (2007) Marine viruses—major players in the global ecosystem. Nat Rev Microbiol 5:801–812

  Article  CAS  PubMed  Google Scholar 

• Svåsand T, Skilbrei OT, van der Meeren GI, Holm M (1989) Review of morphological and behavioural differences between reared and wild individuals: implications for sea-ranching of Atlantic salmon, Salmo salar L., Atlantic cod, Gadus morhua L. and European lobster, Homarus gammarus L. Fish Manag Ecol 5:1–18

  Google Scholar 

• Svåsand T, Kristiansen TS, Pedersen T, Salvanes AGV, Engelsen R, Nævdal G, Nødtvedt M (2000) The enhancement of cod stocks. Fish Fish 1:173–205

  Article  Google Scholar 

• Svåsand T, Agnalt A-L, Skilbrei OT, Bothen J, Heggberget T (2004) An integrated development programme for marine stocking: The Norwegian example. In: Bartley DM, Leber KM (eds) Marine Ranching, FAO Fisheries Technical Paper, No. 429, FAO, Rome, pp 19–72

• Svåsand T, Crosetti D, García-Vázquez E, Verspoor E (eds) (2007) Genetic impact of aquaculture activities on native populations. Genimpact final scientific report. EU contract RICA-CT-2005-022802. http://www.imr.no/genimpact/filarkiv/2007/07/genetic_impact_of_aquaculture.pdf/en. Accessed 30 Sept 2014

• Swain DP, Hutchings JA, Foote CJ (2004) Environmental and genetic influences on stock identification characters. In: Cadrin SX, Friedland KD, Waldman J (eds) Stock identification methods. Academic Press, New York, pp 43–83

  Google Scholar 

• Tallmon DA, Koyuk A, Luikart G, Beaumont MA (2008) ONeSAMP: a program to estimate effective population size using approximate Bayesian computation. Mol Ecol Res 8:299–301

  Article  Google Scholar 

• Taniguchi N (2003) Genetic factors in broodstock management for seed production. Rev Fish Biol Fish 13:177–185

  Article  Google Scholar 

• Taniguchi N, Sumantadinata K, Iyama S (1983) Genetic change in the first and second generations of hatchery stock of black seabream. Aquaculture 35:309–320

  Article  Google Scholar 

• Tave D (1993) Genetics for fish hatchery managers. Van Nostrand Reinhold, New York

  Google Scholar 

• Taylor MD, Piola RF (2008) Scale stocking checks to differentiate between wild and hatchery-reared mulloway (Argyosomus japonicus). Fish Manag Ecol 15:211–216

  Article  Google Scholar 

• Taylor MD, Palmer PJ, Fielder DS, Southers IM (2005) Responsible estuarine finfish stock enhancement: an Australian perspective. J Fish Biol 67:329–331

  Article  Google Scholar 

• Tegner MJ, Butler RA (1989) Abalone seeding. In: Hahn K (ed) Handbook of culture of abalone and other marine gastropods. CRC Press, Boca Raton, pp 157–182

  Google Scholar 

• Teletchea F, Fontaine P (2014) Levels of domestication in fish: implications for the sustainable future of aquaculture. Fish Fish 15:181–195

  Article  Google Scholar 

• Tilman D (1999) Global environmental impacts of agricultural expansion: the need for sustainable and efficient practices. Proc Natl Acad Sci USA 96:5995–6000

  Article  CAS  PubMed  PubMed Central  Google Scholar 

• Trimble AC, Ruesink JL, Dumbauld BR (2009) Factors preventing the recovery of historically overexploited shellfish species, Ostrea lurida Carpenter 1864. J Shellfish Res 28:97–106

  Article  Google Scholar 

• Tringali MD (2006) A Bayesian approach for the genetic tracking of cultured and released individuals. Fish Res 77:159–172

  Article  Google Scholar 

• Tringali MD, Bert TM (1998) Risk to genetic effective population size should be an important consideration in fish stock-enhancement programs. Bull Mar Sci 62:641–659

  Google Scholar 

• Tringali MD, Seyoum S, Wallace EM et al (2008) Limits to the use of contemporary genetic analyses in delineating biological populations for restocking and stock enhancement. Rev Fish Sci 16:111–116

  Article  Google Scholar 

• Turner TF, Richardson LR, Gold JR (1999) Temporal genetic variation of mitochondrial DNA and the female effective population size of red drum (Sciaenops ocellatus) in northern Gulf of Mexico. Mol Ecol 8:1223–1229

  Article  Google Scholar 

• Turner TF, Wares JP, Gold JR (2002) Genetic effective size is three orders of magnitude smaller than adult census size in an abundant, estuarine-dependent marine fish (Sciaenops ocellatus). Genetics 162:1329–1339

  PubMed  PubMed Central  Google Scholar 

• Uthicke S, Purcell S (2004) Preservation of genetic diversity in restocking of the sea cucumber Holothuria scabra investigated by allozyme electrophoresis. Can J Fish Aquat Sci 61:519–528

  Article  CAS  Google Scholar 

• van der Meeren G (2000) Predation on hatchery-reared lobsters released into the wild. Can J Fish Aquat Sci 57:1794–1803

  Article  Google Scholar 

• Vellend M (2006) The consequences of genetic diversity in competitive communities. Ecology 87:304–311

  Article  PubMed  Google Scholar 

• Vellend M, Geber MA (2005) Connections between species diversity and genetic diversity. Ecol Lett 8:767–781

  Article  Google Scholar 

• Vigne J-D (2011) The origins of animal domestication and husbandry: a major change in the history of humanity and the biosphere. Compt Rend Biol 334:171–181

  Article  Google Scholar 

• Wahle RA (2003) Revealing stock–recruitment relationships in lobsters and crabs: is experimental ecology the key? Fish Res 65:3–32

  Article  Google Scholar 

• Wahle RA, Incze LS (1997) Pre- and post-settlement processes in recruitment of the American lobster. J Exp Mar Biol Ecol 217:179–207

  Article  Google Scholar 

• Walters CJ, Juanes F (1993) Recruitment limitation as a consequence of natural selection for use of restricted feeding habitats and predation risk taking by juvenile fishes. Can J Fish Aquat Sci 50:2058–2070

  Article  Google Scholar 

• Wang L, Liu S, Zhuang Z, Guo L, Meng Z, Lin H (2013) Population genetic studies revealed local adaptation in a high gene-flow marine fish, the small yellow croaker (Larimichthys polyactis). PLoS ONE 8:e83493

  Article  PubMed  PubMed Central  CAS  Google Scholar 

• Wang J, Santiago E, Caballero A (2016) Prediction and estimation of effective population size. Heredity 117:193–206

  Article  CAS  PubMed  Google Scholar 

• Waples RS, Do C (2008) ldne: a program for estimating effective population size from data on linkage disequilibrium. Mol Ecol Resour 8:753–756

  Article  PubMed  Google Scholar 

• Waples RS, Drake J (2004) Risk-benefit considerationfor marine stock enhancement: a Pacific salmon perspective. In: Leber KM, Kitada S, Blankenship HL, Svåsand T (eds) Stock enhancement and sea ranching, 2nd edn. Blackwell, Oxford, pp 160–306

  Google Scholar 

• Waples RS, Hindar K, Hard JJ (2012) Genetic risks associated with marine aquaculture. NOAA Technical Memorandum NMFS-NWFSC-119, Seattle, WA

• Waples RS, Hindar K, Karlsson S, Hard JJ (2016) Evaluating the Ryman–Laikre effect for marine stock enhancement and aquaculture. Curr Zool 62:617–627

  Article  Google Scholar 

• Welcomme RL, Bartley DM (1998) An evaluation of present techniques for the enhancement of fisheries. FAO Fisheries Technical Paper 374, Rome

• Whitham TG, Bailey JK, Schweitzer JA, Shuster SM, Bangert RK, LeRoy CJ, Lonsdorf EV (2006) A framework for community and ecosystem genetics: from genes to ecosystems. Nat Rev Genet 7:510–523

  Article  CAS  PubMed  Google Scholar 

• Whitham TG, DeFazio SP, Schweitzer JA, Shuster SM, Allan GJ, Bailey JK, Woolbright SA (2008) Extending genomics to natural communities and ecosystems. Science 320:492–495

  Article  CAS  PubMed  Google Scholar 

• Wilson JA, Langton RW, Van Orsdel C (1998) A model for the preliminary analysis of the economic feasibility of Atlantic cod enhancement in the Gulf of Maine (USA). Bull Mar Sci 62:675–687

  Google Scholar 

• Wolf JB (2003) Genetic architecture and evolutionary constraint when the environment contains genes. Proc Natl Acad Sci USA 100:4655–4660

  Article  CAS  PubMed  PubMed Central  Google Scholar 

• Wolf JB, Brodie ED III, Cheverud JM, Moore AJ, Wade MJ (1998) Evolutionary consequences of indirect genetic effects. Trends Ecol Evol 13:64–69

  Article  CAS  PubMed  Google Scholar 

• Worm B, Barbier EB, Beaumont N et al (2006) Impacts of biodiversity loss on ocean ecosystem services. Science 314:787–790

  Article  CAS  PubMed  Google Scholar 

• Xiao J, Cordes JF, Moss JA, Reece KS (2011) Genetic diversity in U.S. hatchery stocks of Crassostrea ariakensis (Fujita, 1913) and comparison with natural populations in Asia. J Shellfish Res 30:751–760

  Article  Google Scholar 

• Ye Y, Loneragan N, Die D, Watson R, Harch B (2005) Bioeconomic modelling and risk assessment of tiger prawn (Penaeus esculentus) stock enhancement in Exmouth Gulf, Australia. Fish Res 73:231–249

  Article  Google Scholar 

• Young AC, Johnson EG, Hines AH, Davis J, Zmora O, Zohar Y (2008) Do hatchery reared blue crabs differ from wild crabs, and does it matter? Rev Fish Sci 16:254–261

  Article  Google Scholar 

• Yu DH, Chu KH (2006) Genetic variation in wild and cultured populations of the pearl oyster Pinctada fucata from southern China. Aquaculture 258:220–227

  Article  CAS  Google Scholar 

• Zeder MA (2006) Documenting domestication: new genetic and archaeological paradigms. University of California Press, Berkeley

  Google Scholar 

• Zohar Y, Hines AH, Zmora O, Johnson EG, Lipcius RN, Seitz RD, Eggleston DB (2008) The Chesapeake Bay blue crab (Callinectes sapidus): a multidisciplinary approach to responsible sock replenishment. Rev Fish Sci 16:24–34

  Article  Google Scholar 

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