SEARCH

SEARCH BY CITATION

Literature cited

  • Aljanabi, S. M., and I. Martinez. 1997. Universal and rapid salt-extraction of high quality genomic DNA for PCR-based techniques. Nucleic Acids Research 25:46924693.
  • Allendorf, F. W., R. F. Leary, P. Spruell, and J. K. Wenburg. 2001. The problems with hybrids: setting conservation guidelines. Trends in Ecology & Evolution 16:613622.
  • Amos, W., J. I. Hoffman, A. Frodsham, L. Zhang, S. Best, and A. V. S. Hill. 2007. Automated binning of microsatellite alleles: problems and solutions. Molecular Ecology Notes 7:1014.
  • Angers, B., L. Bernatchez, A. Angers, and L. Desgroseillers. 1995. Specific microsatellite loci for brook charr reveal strong population subdivision on a microgeographic scale. Journal of Fish Biology 47:177185.
  • Araki, H., B. Cooper, and M. S. Blouin. 2009. Carry-over effect of captive breeding reduces reproductive fitness of wild-born descendants in the wild. Biology Letters 5:621624.
  • Beckman, B. R. 2011. Perspectives on concordant and discordant relations between insulin-like growth factor 1 (IGF1) and growth in fishes. General and Comparative Endocrinology 170:233252.
  • Bougas, B., S. Granier, C. Audet, and L. Bernatchez. 2010. The transcriptional landscape of cross-specific hybrids and its possible link with growth in brook charr (Salvelinus fontinalis Mitchill). Genetics 186:97107.
  • Bourret, V., P. T. O'Reilly, J. W. Carr, P. R. Berg, and L. Bernatchez. 2011. Temporal change in genetic integrity suggests loss of local adaptation in a wild Atlantic salmon (Salmo salar) population following introgression by farmed escapees. Heredity 106:500510.
  • Bower, N. I., and I. A. Johnston. 2010. Discovery and characterization of nutritionally regulated genes associated with muscle growth in Atlantic salmon. Physiological Genomics 42A:114130.
  • Bower, N. I., X. Li, R. Taylor, and I. A. Johnston. 2008. Switching to fast growth: the insulin-like growth factor (IGF) system in skeletal muscle of Atlantic salmon. Journal of Experimental Biology 211:38593870.
  • Burger, J. C., M. A. Chapman, and J. M. Burke. 2008. Molecular insights into the evolution of crop plants. American Journal of Botany 95:113122.
  • Carroll, S. P. 2011. Conciliation biology: the eco-evolutionary management of permanently invaded biotic systems. Evolutionary Applications, 4:184199.
  • Chauvigné, F., J. C. Gabillard, C. Weil, and P. Y. Rescan. 2003. Effect of refeeding on IGFI, IGFII, IGF receptors, FGF2, FGF6, and myostatin mRNA expression in rainbow trout myotomal muscle. General and Comparative Endocrinology 132:209215.
  • Côté, G., G. Perry, P. Blier, and L. Bernatchez. 2007. The influence of gene-environment interactions on GHR and IGF-I expression and their association with growth in brook charr, Salvelinus fontinalis (Mitchill). Bmc Genetics 8:87.
  • Crespel, A., C. Audet, L. Bernatchez, and D. Garant. 2012. Effects of rearing environment and strain combination on heterosis in brook trout. North American Journal of Aquaculture 74:188198.
  • Croisetière, S., L. Bernatchez, and P. Belhumeur. 2010. Temperature and length-dependent modulation of the MH class IIβ gene expression in brook charr (Salvelinus fontinalis) by a cis-acting minisatellite. Molecular Immunology 47:18171829.
  • Dehaan, P. W., and W. R. Ardren. 2005. Characterization of 20 highly variable tetranucleotide microsatellite loci for bull trout (Salvelinus confluentus) and cross-amplification in other Salvelinus species. Molecular Ecology Notes 5:582585.
  • Derome, N., P. Duchesne, and L. Bernatchez. 2006. Parallelism in gene transcription among sympatric lake whitefish (Coregonus clupeaformis Mitchill) ecotypes. Molecular Ecology 15:12391249.
  • Devlin, R. H., D. Sakhrani, W. E. Tymchuk, M. L. Rise, and B. Goh. 2009. Domestication and growth hormone transgenesis cause similar changes in gene expression in coho salmon (Oncorhynchus kisutch). Proceedings of the National Academy of Sciences 106:30473052.
  • Diamond, J. 2002. Evolution, consequences and future of plant and animal domestication. Nature 418:700707.
  • Drew, R. E., K. J. Rodnick, M. Settles, J. Wacyk, E. Churchill, M. S. Powell, R. W. Hardy et al. 2008. Effect of starvation on transcriptomes of brain and liver in adult female zebrafish (Danio rerio). Physiological Genomics 35:283295.
  • Edmands, S. 2007. Between a rock and a hard place: evaluating the relative risks of inbreeding and outbreeding for conservation and management. Molecular Ecology 16:463475.
  • Evanno, G., S. Regnaut, and J. Goudet. 2005. Detecting the number of clusters of individuals using the software structure: a simulation study. Molecular Ecology 14:26112620.
  • Evans, M. L., and L. Bernatchez. 2012. Oxidative phosphorylation gene transcription in whitefish species pairs reveals patterns of parallel and non-parallel physiological divergence. Journal of Evolutionary Biology 25:18231834.
  • Evans, T. G., E. Hammill, K. Kaukinen, A. D. Schulze, D. A. Patterson, K. K. English, J. M. R. Curtis et al. 2011. Transcriptomics of environmental acclimatization and survival in wild adult Pacific sockeye salmon (Oncorhynchus nerka) during spawning migration. Molecular Ecology 20:44724489.
  • Eya, J. C., M. F. Ashame, C. F. Pomeroy, B. B. Manning, and B. C. Peterson. 2012. Genetic variation in feed consumption, growth, nutrient utilization efficiency and mitochondrial function within a farmed population of channel catfish (Ictalurus punctatus). Comparative Biochemistry and Physiology, Part B 163:211220.
  • Fay, J. C., and P. J. Wittkopp. 2008. Evaluating the role of natural selection in the evolution of gene regulation. Heredity 100:191199.
  • Feder, M. E., and G. E. Hofmann. 1999. Heat-shock proteins, molecular chaperones, and the stress response: evolutionary and ecological physiology. Annual Review of Physiology 61:243282.
  • Fleming, I. A., and S. Einum. 1997. Experimental tests of genetic divergence of farmed from wild Atlantic salmon due to domestication. Ices Journal of Marine Science 54:10511063.
  • Fleming, I. A., T. Agustsson, B. Finstad, J. I. Johnsson, and B. T. Bjornsson. 2002. Effects of domestication on growth physiology and endocrinology of Atlantic salmon (Salmo salar). Canadian Journal of Fisheries and Aquatic Sciences 59:13231330.
  • Gabillard, J. C., B. B. Kamangar, and N. Montserrat. 2006a. Coordinated regulation of the GH/IGF system genes during refeeding in rainbow trout (Oncorhynchus mykiss). Journal of Endocrinology 191:1524.
  • Gabillard, J. C., K. Yao, M. Vandeputte, J. Gutierrez, and P. Y. Le Bail. 2006b. Differential expression of two GH receptor mRNAs following temperature change in rainbow trout (Oncorhynchus mykiss). Journal of Endocrinology 190:2937.
  • Gahr, S. A., R. L. Vallejo, G. M. Weber, B. S. Shepherd, J. T. Silverstein, and C. E. Rexroad. 2008. Effects of short-term growth hormone treatment on liver and muscle transcriptomes in rainbow trout (Oncorhynchus mykiss). Physiological Genomics 32:380392.
  • Gibson, G. 2008. The environmental contribution to gene expression profiles. Nature Reviews Genetics 9:575582.
  • Gjedrem, T. 2000. Genetic improvement of cold-water fish species. Aquaculture Research 31:2533.
  • Gjoen, H. M., and H. B. Bentsen. 1997. Past, present, and future of genetic improvement in salmon aquaculture. Ices Journal of Marine Science 54:10091014.
  • Goudet, J. 1995. FSTAT Version 1.2: a computer program to calculate F-statistics. The Journal of Heredity 86:485486.
  • Hansen, M. M., K. Meier, and K. L. Mensberg. 2010. Identifying footprints of selection in stocked brown trout populations: a spatio-temporal approach. Molecular Ecology 19:17871800.
  • Ingerslev, H. C., C. Cunningham, and H. I. Wergeland. 2006. Cloning and expression of TNF-α, IL-1β and COX-2 in an anadromous and landlocked strain of Atlantic salmon (Salmo salar L.) during the smolting period. Fish & Shellfish Immunology 20:450461.
  • Jensen, P. 2006. Domestication-From behaviour to genes and back again. Applied Animal Behaviour Science 97:315.
  • Jeukens, J., D. Bittner, R. Knudsen, and L. Bernatchez. 2009. Candidate genes and adaptive radiation: insights from transcriptional adaptation to the limnetic niche among coregonine fishes (Coregonus spp., Salmonidae). Molecular Biology and Evolution 26:155166.
  • Laikre, L., M. K. Schwartz, R. S. Waples, and N. Ryman. 2010. Compromising genetic diversity in the wild: unmonitored large-scale release of plants and animals. Trends in Ecology & Evolution 25:520529.
  • Lamaze, F. C., C. Sauvage, A. Marie, D. Garant, and L. Bernatchez. 2012. Dynamics of introgressive hybridization assessed by SNP population genomics of coding genes in stocked brook charr (Salvelinus fontinalis). Molecular Ecology 21:28772895.
  • Lê, S., J. Josse, and F. Husson. 2008. FactoMineR: An r package for multivariate analysis. Journal of Statistical Software. 25:118.
  • Marie, A. D., L. Bernatchez, and D. Garant. 2010. Loss of genetic integrity correlates with stocking intensity in brook charr (Salvelinus fontinalis). Molecular Ecology 19:20252037.
  • McGinnity, P., P. Prodohl, K. Ferguson, R. Hynes, N. O'Maoileidigh, N. Baker, D. Cotter et al. 2003. Fitness reduction and potential extinction of wild populations of Atlantic salmon, Salmo salar, as a result of interactions with escaped farm salmon. Proceedings of the Royal Society of London Series B-Biological Sciences 270:24432450.
  • Mignon-Grasteau, S., A. Boissy, J. Bouix, J. M. Faure, A. D. Fisher, G. N. Hinch, P. Jensen et al. 2005. Genetics of adaptation and domestication in livestock. Livestock Production Science 93:314.
  • Ministère des Ressources Naturelles et de la Faune du Québec. 2008. Lignes directrices sur les ensemencements de poissons. Secteur Faune Québec, Direction de l'expertise sur la faune et ses habitats. Québec. p.41.
  • Nolte, A., S. Renaut, and L. Bernatchez. 2009. Divergence in gene regulation at young life history stages of whitefish (Coregonus sp.) and the emergence of genomic isolation. BMC Evolutionary Biology 9:59.
  • Normandeau, E., J. A. Hutchings, D. J. Fraser, and L. Bernatchez. 2009. Population-specific gene expression responses to hybridization between farm and wild Atlantic salmon. Evolutionary Applications 2:489503.
  • Oleksiak, M. F., G. A. Churchill, and D. L. Crawford. 2002. Variation in gene expression within and among natural populations. Nature Genetics 32:261266.
  • Olsvik, P., K. Lie, A. E. Jordal, T. Nilsen, and I. Hordvik. 2005. Evaluation of potential reference genes in real-time RT-PCR studies of Atlantic salmon. BMC Molecular Biology 6:21.
  • van Oosterhout, C., W. F. Hutchinson, D. P. M. Wills, and P. Shipley. 2004. Micro-Checker: software for identifying and correcting genotyping errors in microsatellite data. Molecular Ecology Notes 4:535538.
  • O'Reilly, P. T., L. Hamilton, S. K. J. McConnell, and J. M. Wright. 1996. Rapid analysis of genetic variation in Atlantic salmon (Salmo salar) by PCR multiplexing of dinucleotide and tetranucleotide microsatellites. Canadian Journal of Fisheries and Aquatic Sciences 53:22922298.
  • Page, L. M., and B. M. Burr. 1991. A Field Guide to Freshwater Fishes of North America North of Mexico. Houghton Mifflin Harcourt, Boston, MA.
  • Pavey, S. A., H. Collin, P. Nosil, and S. M. Rogers. 2010. The role of gene expression in ecological spéciation. Annals of the New York Academy of Sciences 1206:110129.
  • Perry, G. M. L., T. L. King, J. St-Cyr, and M. Valcourt. 2005. Isolation and cross-familial amplification of 41 microsatellites for the brook charr (Salvelinus fontinalis). Molecular Ecology Notes 5:346351.
  • Pfaffl, M. W., A. Tichopad, C. Prgomet, and T. P. Neuvians. 2004. Determination of stable housekeeping genes, differentially regulated target genes and sample integrity: BestKeeper – Excel-based tool using pair-wise correlations. Biotechnology Letters 26:509515.
  • Pierron, F., V. Bourret, J. St-Cyr, P. Campbell, L. Bernatchez, and P. Couture. 2009. Transcriptional responses to environmental metal exposure in wild yellow perch (Perca flavescens) collected in lakes with differing environmental metal concentrations (Cd, Cu, Ni). Ecotoxicology 18:620631.
  • Pritchard, J. K., M. Stephens, and P. Donnelly. 2000. Inference of population structure using multilocus genotype data. Genetics 155:945959.
  • Quinn, N. L., C. R. McGowan, G. A. Cooper, B. F. Koop, and W. S. Davidson. 2011. Identification of genes associated with heat tolerance in Arctic charr exposed to acute thermal stress. Physiological Genomics 43:685696.
  • Randi, E. 2008. Detecting hybridization between wild species and their domesticated relatives. Molecular Ecology 17:285293.
  • Rescan, P. Y., J. Montfort, C. Ralliere, A. Le Cam, D. Esquerre, and K. Hugot. 2007. Dynamic gene expression in fish muscle during recovery growth induced by a fasting-refeeding schedule. BMC Genomics 8:438.
  • Rhymer, J. M., and D. Simberloff. 1996. Extinction by hybridization and introgression. Annual Review of Ecology and Systematics 27:83109.
  • Ricker, W. E. 1975. Computation and interpretation of biological statistics of fish populations. Bulletin of the Fisheries Research Board of Canada 191:1382.
  • Roberge, C., S. Einum, H. Guderley, and L. Bernatchez. 2006. Rapid parallel evolutionary changes of gene transcription profiles in farmed Atlantic salmon. Molecular Ecology 15:920.
  • Roberge, C., E. Normandeau, S. Einum, H. Guderley, and L. Bernatchez. 2008. Genetic consequences of interbreeding between farmed and wild Atlantic salmon: insights from the transcriptome. Molecular Ecology 17:314324.
  • Saera-Vila, A., J. A. Calduch-Giner, and J. Perez-Sanchez. 2005. Duplication of growth hormone receptor (GHR) in fish genome: gene organization and transcriptional regulation of GHR type I and II in gilthead sea bream (Sparus aurata). General and Comparative Endocrinology 142:193203.
  • Saera-Vila, A., J. A. Calduch-Giner, P. Prunet, and J. Perez-Sanchez. 2009. Dynamics of liver GH/IGF axis and selected stress markers in juvenile gilthead sea bream (Sparus aurata) exposed to acute confinement differential stress response of growth hormone receptors. Comparative Biochemistry and Physiology, Part A, Molecular and Integrative Physiology 154:197203.
  • Sánchez, C. C., G. M. Weber, G. Gao, B. M. Cleveland, J. Yao, and C. E. Rexroad III. 2011. Generation of a reference transcriptome for evaluating rainbow trout responses to various stressors. BMC Genomics 12:626.
  • Sauvage, C., N. Derome, E. Normandeau, J. St. -Cyr, C. Audet, and L. Bernatchez. 2010. Fast transcriptional responses to domestication in the brook charr Salvelinus fontinalis. Genetics 185:105112.
  • Sauvage, C., M. Vagner, N. Derôme, C. Audet, and L. Bernatchez. 2012a. Coding gene single nucleotide polymorphism mapping and quantitative trait loci detection for physiological reproductive traits in brook charr, Salvelinus fontinalis. G3 (Bethesda, MD) 2:379392.
  • Sauvage, C., M. Vagner, N. Derôme, C. Audet, and L. Bernatchez. 2012b. Coding gene SNP mapping reveals QTL linked to growth and stress response in brook charr (Salvelinus fontinalis). G3 (Bethesda, MD) 2:707720.
  • Scribner, K. T., J. R. Gust, and R. L. Fields. 1996. Isolation and characterization of novel salmon microsatellite loci: cross-species amplification and population genetic applications. Canadian Journal of Fisheries and Aquatic Sciences 53:833841.
  • Stevenson, R. D., and W. A. Woods. 2006. Condition indices for conservation: new uses for evolving tools. Integrative and Comparative Biology 46:11691190.
  • Suarez, A. V., and N. D. Tsutsui. 2008. The evolutionary consequences of biological invasions. Molecular Ecology 17:351360.
  • Taberlet, P., A. Valentini, H. R. Rezaei, S. Naderi, F. Pompanon, R. Negrini, and P. Ajmone-Marsan. 2008. Are cattle, sheep, and goats endangered species? Molecular Ecology 17:275284.
  • Tymchuk, W. E., L. F. Sundstrom, and R. H. Devlin. 2007. Growth and survival trade-offs and outbreeding depression in rainbow trout (Oncorhynchus mykiss). Evolution 61:12251237.
  • Tymchuk, W. E., B. Beckman, and R. H. Devlin. 2009. Altered expression of growth hormone/insulin-like growth factor I axis hormones in domesticated fish. Endocrinology 150:18091816.
  • Tymchuk, W. E., P. O'Reilly, J. Bittman, D. Macdonald, and P. Schulte. 2010. Conservation genomics of Atlantic salmon: variation in gene expression between and within regions of the Bay of Fundy. Molecular Ecology 19:18421859.
  • Wargelius, A., P. G. Fjelldal, S. Benedet, T. Hansen, B. Thrandur Björnsson, and U. Nordgarden. 2005. A peak in gh-receptor expression is associated with growth activation in Atlantic salmon vertebrae, while upregulation of igf-I receptor expression is related to increased bone density. General and Comparative Endocrinology 142:163168.
  • Weir, B. S., and C. C. Cockerham. 1984. Estimating F-statistics for the analysis of population structure. Evolution 38:13581370.
  • Whitehead, A., and D. L. Crawford. 2006. Neutral and adaptive variation in gene expression. Proceedings of the National Academy of Sciences 103:54255430.
  • Wiseman, S., H. Osachoff, E. Bassett, J. Malhotra, J. Bruno, G. VanAggelen, T. P. Mommsen et al. 2007. Gene expression pattern in the liver during recovery from an acute stressor in rainbow trout. Comparative Biochemistry and Physiology, Part D, Genomics and Proteomics 2:234244.