Mimura, M. et al. Understanding and monitoring the consequences of human impacts on intraspecific variation. Evol. Appl. 10(2), 121–139 (2017).
Google Scholar
Leigh, D. M., Hendry, A. P., Vázquez-Domínguez, E. & Friesen, V. L. Estimated six per cent loss of genetic variation in wild populations since the industrial revolution. Evol. Appl. 12(8), 1505–1512 (2019).
Google Scholar
Habel, J. C., Husemann, M., Finger, A., Danley, P. D. & Zachos, F. E. The relevance of time series in molecular ecology and conservation biology. Biol. Rev. 89(2), 484–492 (2014).
Google Scholar
Klütsch, C. F. C. et al. Genetic changes caused by restocking and hydroelectric dams in demographically bottlenecked brown trout in a transnational subarctic riverine system. Ecol. Evol. 9(10), 6068–6081 (2019).
Google Scholar
Hansen, M. M., Fraser, D. J., Meier, K. & Mensberg, K.-L.D. Sixty years of anthropogenic pressure: A spatio-temporal genetic analysis of brown trout populations subject to stocking and population declines. Mol. Ecol. 18(12), 2549–2562 (2009).
Google Scholar
Savary, R. et al. Stocking activities for the Arctic char in Lake Geneva: Genetic effects in space and time. Ecol. Evol. 7(14), 5201–5211 (2017).
Google Scholar
Hughes, J. B., Daily, G. C. & Ehrlich, P. R. Population diversity: its extent and extinction. Science 278, 689–692 (1997).
Google Scholar
Perrier, C., Guyomard, R., Bagliniere, J.-L., Nikolic, N. & Evanno, G. Changes in the genetic structure of Atlantic salmon populations over four decades reveal substantial impacts of stocking and potential resiliency. Ecol. Evol. 3(7), 2334–2349 (2013).
Google Scholar
Vøllestad, L. A. & Hesthagen, T. Stocking of freshwater fish in Norway: management goals and effects. Nordic J. Freshwater Res. 75, 143–152 (2001).
Christie, M. R., Marine, M. L., French, R. A., Waples, R. S. & Blouin, M. S. Effective size of a wild salmonid population is greatly reduced by hatchery supplementation. Heredity 109, 254–260 (2012).
Google Scholar
Araki, H., Cooper, B. & Blouin, M. S. Carry-over effect of captive breeding reduces reproductive fitness of wild-born descendants in the wild. Biol. Lett. 5, 621–624 (2009).
Google Scholar
O’Sullivan, R. J. et al. Captive-bred Atlantic salmon released into the wild have fewer offspring than wild-bred fish and decrease population productivity. Proc. R. Soc. B 287, 20201671 (2020).
Google Scholar
Amundsen, P.-A. et al. Invasion of vendace Coregonus albula in a subarctic watercourse. Biol. Conserv. 88(3), 405–413 (1999).
Google Scholar
Jensen, H., Bøhn, T., Amundsen, P.-A. & Aspholm, P. E. Feeding ecology of piscivorous brown trout (Salmo trutta L.) in a subarctic watercourse. Ann. Zool. Fenn. 41(1), 319–328 (2004).
Jensen, H. et al. Predation by brown trout (Salmo trutta) along a diversifying prey community gradient. Can. J. Fish. Aquat. Sci. 65, 1831–1841 (2008).
Google Scholar
Jensen, H. et al. Food consumption rates of piscivorous brown trout (Salmo trutta) foraging on contrasting coregonid prey. Fish. Manag. Ecol. 22, 295–306 (2015).
Google Scholar
Haugland, Ø. Langtidsstudie av næringsøkologi og vekst hos storørret i Pasvikvassdraget. Mastergradsoppgave i biologi (Universitetet i Tromsø, Fakultet for Biovitenskap, fiskeri og økonomi, Institutt for arktisk og marin biologi, 2014).
Gossieaux, P., Bernatchez, L., Sirois, P. & Garant, D. Impacts of stocking and its intensity on effective population size in Brook Charr (Salvelinus fontinalis) populations. Conserv. Genet. 20(4), 729–742 (2019).
Google Scholar
Pinter, K., Epifanio, J. & Unfer, G. Release of hatchery-reared brown trout (Salmo trutta) as a threat to wild populations? A case study from Austria. Fish. Res. 219, 105296 (2019).
Google Scholar
Wringe, B. F., Purchase, C. F. & Fleming, I. A. In search of a “cultured fish phenotype”: A systematic review, meta-analysis and vote-counting analysis. Rev. Fish Biol. Fish. 26(3), 351–373 (2016).
Google Scholar
Gossieaux, P. et al. Effects of genetic origin on phenotypic divergence in Brook Trout populations stocked with domestic fish. Ecosphere 11(5), e03119 (2020).
Google Scholar
Fleming, I. A., Jonsson, B. & Gross, M. R. Phenotypic divergence of sea-ranched, farmed, and wild salmon. Can. J. Fish. Aquat. Sci. 51, 2808–2824 (1994).
Google Scholar
Heath, D. D., Heath, J. W., Bryden, C. A., Johnson, R. M. & Fox, C. W. Rapid evolution of egg size in captive salmon. Science 299, 1738–1740 (2003).
Google Scholar
Naish, K. A., Seamons, T. R., Dauer, M. B., Hauser, L. & Quinn, T. P. Relationship between effective population size, inbreeding and adult fitness-related traits in a steelhead (Oncorhynchus mykiss) population released in the wild. Mol. Ecol. 22, 1295–1309 (2013).
Google Scholar
Van Oosterhout, C., Weetman, D. & Hutchinson, W. F. Estimation and adjustment of microsatellite null alleles in nonequilibrium populations. Mol. Ecol. Notes 6(1), 255–256 (2006).
Google Scholar
Rousset, F. Genepop’007: a complete reimplementation of the Genepop software for Windows and Linux. Mol. Ecol. Resour. 8(6), 103–106 (2008).
Google Scholar
Peakall, R. & Smouse, P. E. GENALEX 6: Genetic analysis in Excel. Population genetic software for teaching and research. Mol. Ecol. Notes 6, 288–295 (2006).
Google Scholar
Peakall, R. & Smouse, P. E. GenAlEx 6.5: Genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinformatics 28(19), 2537–2539 (2012).
Google Scholar
Szpiech, Z. A., Jacobsson, M. & Rosenberg, N. A. ADZE: A rarefaction approach for counting alleles private to combinations of populations. Bioinformatics 24(21), 2498–2504 (2008).
Google Scholar
Waples, R. S. & Anderson, E. C. Purging putative siblings from population genetic data sets: A cautionary view. Mol. Ecol. 26(5), 1211–1224 (2017).
Google Scholar
Pritchard, J. K., Stephens, M. & Donnelly, P. Inference of population structure using multilocus genotype data. Genetics 155(2), 945–959 (2000).
Google Scholar
Jombart, T., Devillard, S. & Balloux, F. Discriminant analysis of principal components: A new method for the analysis of genetically structured populations. BMC Genet. 11, 94 (2010).
Google Scholar
Pew, J., Muir, P. H., Wang, J. & Frasier, T. R. Related: An R package for analysing pairwise relatedness from codominant molecular markers. Mol. Ecol. Resour. 15(3), 557–561 (2015).
Google Scholar
Piry, S., Luikart, G. & Cornuet, J.-M. Bottleneck: A computer program for detecting recent reductions in the effective population size using allele frequency data. J. Heredity 90(4), 502–503 (1999).
Google Scholar
Cornuet, J. M. & Luikart, G. Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics 144(4), 2001–2014 (1996).
Google Scholar
Peery, M. Z. et al. Reliability of genetic bottleneck tests for detecting recent population declines. Mol. Ecol. 21(14), 3403–3418 (2012).
Google Scholar
Luikart, G. Usefulness of molecular markers for detecting population bottlenecks and monitoring genetic change. Ph. D. Thesis. (University of Montana, 1997).
Do, C. et al. NEESTIMATOR v2: Re-implementation of software for the estimation of contemporary effective population size (Ne) from genetic data. Mol. Ecol. Resour. 14, 209–214 (2014).
Google Scholar
Waples, R. S. & Do, C. LDNE: A program for estimating effective population size from data on linkage disequilibrium. Mol. Ecol. Resour. 8, 753–756 (2008).
Google Scholar
Zhdanova, O. L. & Pudovkin, A. I. Nb_HetEx: A program to estimate the effective number of breeders. J. Hered. 99(6), 694–695 (2008).
Google Scholar
Nomura, T. Estimation of effective number of breeders from molecular coancestry of single cohort sample. Evol. Appl. 1, 462–474 (2008).
Google Scholar
Jones, O. R. & Wang, J. COLONY: A program for parentage and sibship inference from multilocus genotype data. Mol. Ecol. Resour. 10, 551–555 (2010).
Google Scholar
Wang, J. A. comparison of single-sample estimators of effective population sizes from genetic data. Mol. Ecol. 25, 4692–4711 (2016).
Google Scholar
Nei, M. & Chesser, R. K. Estimation of fixation indexes and gene diversities. Ann. Hum. Genet. 47(3), 253–259 (1983).
Google Scholar
Jost, L. Gst and its relatives do not measure differentiation. Mol. Ecol. 17(18), 4015–4026 (2008).
Google Scholar
Benjamini, Y. & Hochberg, Y. Controlling the false discovery rate: A practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B (Methodological) 57(1), 289–300 (1995).
Google Scholar
R Core Team. R: A Language and Environment for Statistical Computing. https://www.R-project.org/ (R Foundation for Statistical Computing, 2019).
White, T., van der Ende, J. & Nichols, T. E. Beyond Bonferroni revisited: Concerns over inflated false positive research findings in the fields of conservation genetics, biology, and medicine. Conserv. Genet. 20, 927–937 (2019).
Google Scholar
Falush, D., Stephens, M. & Pritchard, J. K. Inference of population structure using multilocus genotype data: Linked loci and correlated allele frequencies. Genetics 164(4), 1567–1587 (2003).
Google Scholar
Hubisz, M. J., Falush, D., Stephens, M. & Pritchard, J. K. Inferring weak population structure with the assistance of sample group information. Mol. Ecol. Resour. 9(5), 1322–1332 (2009).
Google Scholar
Miller, M. A., Pfeiffer, W. & Schwartz, T. Creating the CIPRES science gateway for inference of large phylogenetic trees. in 2010 Gateway Computing Environments Workshop (GCE) 1–8 (2010).
Besnier, F. & Glover, K. A. ParallelStructure: A R package to distribute parallel runs of the population genetics program STRUCTURE on multi-core computers. PLoS ONE 8(7), e70651 (2013).
Google Scholar
Li, Y.-L. & Liu, J.-X. StructureSelector: A web-based software to select and visualize the optimal number of clusters using multiple methods. Mol. Ecol. Resour. 18(1), 176–177 (2018).
Google Scholar
Puechmaille, S. J. The program structure does not reliably recover the correct population structure when sampling is uneven: Subsampling and new estimators alleviate the problem. Mol. Ecol. Resour. 16(3), 608–627 (2016).
Google Scholar
Kopelman, N. M., Mayzel, J., Jakobsson, M., Rosenberg, N. A. & Mayrose, I. CLUMPAK: A program for identifying clustering modes and packaging population structure inferences across K. Mol. Ecol. Resour. 15(5), 1179–1191 (2015).
Google Scholar
Anderson, E. C. & Dunham, K. K. The influence of family groups on inferences made with the program structure. Mol. Ecol. Resour. 8, 1219–1229 (2008).
Google Scholar
Dray, S. & Dufour, A. The ade4 package: Implementing the duality diagram for ecologists. J. Stat. Softw. 22(4), 1–20 (2007).
Google Scholar
Levene, H. Robust tests for equality of variances. in Contributions to Probability and Statistics: Essays in Honor of Harold Hotelling (Olkin, I., Hotelling, H. et al. eds.). 278–292 (Stanford University Press, 1960).
Kassambara, A. rstatix: Pipe-Friendly Framework for Basic Statistical Tests. R package version 0.4.0. https://CRAN.R-project.org/package=rstatix (2020).
Wang, J. An estimator for pairwise relatedness using molecular markers. Genetics 160, 1203–1215 (2002).
Google Scholar
White, S. L., Miller, W. L., Dowell, S. A., Bartron, M. L. & Wagner, T. Limited hatchery introgression into wild brook trout (Salvelinus fontinalis) populations despite reoccurring stocking. Evol. Appl. 11(9), 1567–1581 (2018).
Google Scholar
Lehnert, S. J. et al. Multiple decades of stocking has resulted in limited hatchery introgression in wild brook trout (Salvelinus fontinalis) populations of Nova Scotia. Evol. Appl. 13(5), 1069–1089 (2020).
Google Scholar
Knudsen, C. M. et al. Comparison of life history traits between first-generation hatchery and wild upper Yakima River spring Chinook salmon. Trans. Am. Fish. Soc. 135, 1130–1144 (2006).
Google Scholar
Hansen, M. M. & Mensberg, K.-L.D. Admixture analysis of stocked brown trout populations using mapped microsatellite DNA markers: Indigenous trout persist in introgressed populations. Biol. Lett. 5, 656–659 (2009).
Google Scholar
Christie, M. R., Ford, M. J. & Blouin, M. S. On the reproductive success of early-generation hatchery fish in the wild. Evol. Appl. 7, 883–896 (2014).
Google Scholar
Fraser, D. J. et al. Population correlates of rapid captive-induced maladaptation in a wild fish. Evol. Appl. 12, 1305–1317 (2019).
Google Scholar
Fischer, J. R. et al. Growth, condition, and trophic relations of stocked trout in southern Appalachian mountain streams. Trans. Am. Fish. Soc. 148, 771–784 (2019).
Google Scholar
Hendry, A. P. & Day, T. Population structure attributable to reproductive time: Isolation by time and adaptation by time. Mol. Ecol. 14, 901–916 (2005).
Google Scholar
Gauthey, Z. et al. Brown trout spawning habitat selection and its effects on egg survival. Ecol. Freshwater Fish 26, 133–140 (2017).
Google Scholar
Dupont, P.-P., Bourret, V. & Bernatchez, L. Interplay between ecological, behavioural and historical factors in shaping the genetic structure of sympatric walleye populations (Sander vitreus). Mol. Ecol. 16, 937–951 (2007).
Google Scholar
Sandoval-Castillo, J. et al. SWINGER: A user-friendly computer program to establish captive breeding groups that minimize relatedness without pedigree information. Mol. Ecol. Resour. 17, 278–287 (2017).
Google Scholar
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