Álvarez D, Metcalfe NB. (2007). The tradeoff between catch-up growth and escape speed: variation between habitats in the cost of compensation. Oikos 116: 1144–1151.
Aykanat T, Heath JW, Dixon B, Heath DD. (2012a). Additive, non-additive and maternal effects of cytokine transcription in response to immunostimulation with Vibrio vaccine in Chinook salmon (Oncorhynchus tshawytscha. Immunogenetics 64: 691–703.
Aykanat T, Bryden CA, Heath DD. (2012b). Sex-biased genetic component distribution among populations: additive genetic and maternal contributions to phenotypic differences among populations of Chinook salmon. J Evol Biol 25: 682–690.
Bernardo J. (1996). Maternal effects in animal ecology. Am Zool 36: 83–105.
Bower NI, Taylor RG, Johnston IA. (2009). Phasing of muscle gene expression with fasting-induced recovery growth in Atlantic salmon. Front Zool 6: 18.
Carlson SM, Seamons TR. (2008). A review of quantitative genetic components of fitness in salmonids: implications for adaptation to future change. Evol Appl 1: 222–238.
Cheung VG, Spielman RS. (2002). The genetics of variation in gene expression. Nat Genet 32: 522–525.
Coghlan SM, Ringler NH. (2004). A comparison of Atlantic salmon embryo and fry stocking in the Salmon River, New York. North Am J Fish Manag 24: 1385–1397.
COSEWIC. (2006) COSEWIC assessment and Status Report on the Atlantic Salmon Salmo salar (Lake Ontario population) in Canada. Committee on the Status of Endangered Wildlife in Canada, Ottawa, pp vii+26.
Crawford SS. (2001). Salmonine introductions to the Laurentian Great Lakes: an historical review and evaluation of ecological effects. Canadian Special Publication of Fisheries and Aquatic Sciences 132. NRC Press: Ottawa, ON, Canada.
Crawford DL, Powers DA. (1989). Molecular basis of evolutionary adaptation at the lactate dehydrogenase-B locus in the fish Fundulus heteroclitus. Proc Natl Acad Sci USA 86: 9365–9369.
Crawford DL, Powers DA. (1992). Evolutionary adaptation to different thermal environments via transcriptional regulation. Mol Biol Evol 9: 806–813.
Crockett EL, Sidell BD. (1990). Some pathways of energy metabolism are cold adapted in Antarctic fishes. Physiol Zool 63: 472–488.
Desai BN, Myers BR, Schreiber SL. (2002). FKBP12-rapamycin-associated protein associates with mitochondria and senses osmotic stress via mitochondrial dysfunction. Proc Natl Acad Sci USA 99: 4319–4324.
Dimond P, Smitka J. (2005). Evaluation of selected strains of Atlantic salmon as potential candidates for the restoration of Lake Ontario. Trout Unlimited Canada Technical Report ON-012: Geulph, ON, Canada, pp 41.
Eliason EJ, Clark TD, Hague MJ, Hanson LM, Gallagher ZS, Jeffries KM et al(. (2011). Differences in thermal tolerance among sockeye salmon populations. Science 332: 109–112.
Evans ML, Neff BD. (2009). Non-additive genetic effects contribute to larval spinal deformity in two populations of Chinook salmon (Oncorhynchus tshawytscha. Aquaculture 296: 169–173.
Falconer DS, Mackay TFC. (1996). Introduction to Quantitative Genetics. Longmans Green: Harlow, Essex, UK.
Forsman A. (2014). Effects of genotypic and phenotypic variation on establishment are important for conservation, invasion, and infection biology. Proc Natl Acad Sci USA 111: 302–307.
Francetic T, Li Q. (2011). Skeletal myogenesis and Myf5 activation. Transcription 2: 109–114.
Fraser HB. (2013). Gene expression drives local adaptation in humans. Genome Res 23: 1089–1096.
Gallardo JA, Lhorente JP, Neira R. (2010). The consequences of including non-additive effects on the genetic evaluation of harvest body weight in Coho salmon (Oncorhynchus kisutch. Genet Sel Evol 42: 19.
Garcia de la serrana D, Devlin RH, Johnston IA. (2015). RNAseq analysis of fast skeletal muscle in restriction-fed transgenic coho salmon (Oncorhynchus kisutch: an experimental model uncoupling the growth hormone and nutritional signals regulating growth. BMC Genomics 16: 564.
Gleason LU, Burton RS. (2015). RNA-seq reveals regional differences in transcriptome response to heat stress in the marine snail Chlorostoma funebralis. Mol Ecol 24: 610–627.
Han R, Campbell KP. (2007). Dysferlin and muscle membrane repair. Curr Opin Cell Biol 19: 409–416.
Hansen MM, Olivieri I, Waller DM, Nielsen EE, GeM Working Group. (2012). Monitoring adaptive genetic responses to environmental change. Mol Ecol 21: 1311–1329.
He X, Johansson ML, Heath DD. (2016). Role of genomics and transcriptomics in selection of reintroduction source populations. Conserv Biol 30: 1010–1018.
Heath DD, Fox CW, Heath JW. (1999). Maternal effects on offspring size: variation through early development of Chinook salmon. Evolution 53: 1605–1611.
Hevrøy EM, Jordal A-EO, Hordvik I, Espe M, Hemre G-I, Olsvik PA. (2006). Myosin heavy chain mRNA expression correlates higher with muscle protein accretion than growth in Atlantic salmon, Salmo salar. Aquaculture 252: 453–461.
Hochachka PW, Somero GN. (1984) Biochemical Adaptation. Princeton University Press: Princeton, NJ, USA.
Hodgins-Davis A, Townsend JP. (2009). Evolving gene expression: from G to E to GxE. Trends Ecol Evol 24: 649–658.
Houde ALS, Garner SR, Neff BD. (2015xa). Restoring species through reintroductions: strategies for source population selection. Restor Ecol 23: 746–753.
Houde ALS, Black CA, Wilson CC, Pitcher TE, Neff BD. (2015b). Genetic and maternal effects on juvenile survival and fitness-related traits in three populations of Atlantic salmon. Can J Fish Aquat Sci 72: 751–758.
Houde ALS, Pitcher TE. (2016). Fullfact: an R package for the analysis of genetic and maternal variance components from full factorial mating designs. Ecol Evol 6: 1656–1665.
Houde AL, Wilson CC, Neff BD. (2013). Genetic architecture of survival and fitness-related traits in two populations of Atlantic salmon. Heredity 111: 513–519.
Hutter S, Saminadin-Peter SS, Stephan W, Parsch J. (2008). Gene expression variation in African and European populations of Drosophila melanogaster. Genome Biol 9: R12.
Jinks J, Perkins JM, Pooni H. (1973). The incidence of epistasis in normal and extreme environments. Heredity 31: 263–269.
Jobling M. (1993) Bioenergetics: feed intake and energy partitioning. In: Rankin JC, Jensen FB (eds). Fish Ecophysiology, Chapman & Hall Fish and Fisheries Series. Springer: Netherlands, pp 1–44.
King TL, Kalinowski ST, Schill WB, Spidle AP, Lubinski BA. (2001). Population structure of Atlantic salmon (Salmo salar L.): a range-wide perspective from microsatellite DNA variation. Mol Ecol 10: 807–821.
King MC, Wilson AC. (1975). Evolution at two levels in humans and chimpanzees. Science 188: 107–116.
Kuznetsova A, Brockhoff PB, Christensen RHB. (2016). lmerTest: tests in linear mixed effects models. R package version. 2, pp 0-32.
Larsson T, Mørkøre T, Kolstad K, Østbye T-K, Afanasyev S, Krasnov A. (2012). Gene expression profiling of soft and firm Atlantic salmon fillet. PLoS One 7: e39219.
Lecker SH. (2003). Ubiquitin-protein ligases in muscle wasting: multiple parallel pathways? Curr Opin Clin Nutr Metab Care 6: 271–275.
Løvoll M, Austbø L, Jørgensen JB, Rimstad E, Frost P. (2011). Transcription of reference genes used for quantitative RT-PCR in Atlantic salmon is affected by viral infection. Vet Res 42: 8.
Lynch M, Walsh B. (1998) Genetics and Analysis of Quantitative Traits. Sinauer Associates: Sunderland, MA, USA.
Mallona I, Weiss J, Egea-Cortines M. (2011). pcrEfficiency: a web tool for PCR amplification efficiency prediction. BMC Bioinformatics 12: 404.
Murakami M, Ichisaka T, Maeda M, Oshiro N, Hara K, Edenhofer F et al. (2004). mTOR is essential for growth and proliferation in early mouse embryos and embryonic stem cells. Mol Cell Biol 24: 6710–6718.
Oleksiak MF, Churchill GA, Crawford DL. (2002). Variation in gene expression within and among natural populations. Nat Genet 32: 261–266.
Olsvik PA, Lie KK, Jordal A-EO, Nilsen TO, Hordvik I. (2005). Evaluation of potential reference genes in real-time RT-PCR studies of Atlantic salmon. BMC Mol Biol 6: 21.
Palstra AP, Beltran S, Burgerhout E, Brittijn SA, Magnoni LJ, Henkel CV et al. (2013). Deep RNA sequencing of the skeletal muscle transcriptome in swimming fish. PLoS One 8: e53171.
Parrish DL, Behnke RJ, Gephard SR, McCormick SD, Reeves GH. (1998). Why aren’t there more Atlantic salmon (Salmo salar? Can J Fish Aquat Sci 55: 281–287.
Pfaffl MW. (2001). A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res 29: e45.
Price AL, Helgason A, Thorleifsson G, McCarroll SA, Kong A, Stefansson K. (2011). Single-tissue and cross-tissue heritability of gene expression via identity-by-descent in related or unrelated individuals. PLoS Genet 7: e1001317.
Ruijter JM, Ramakers C, Hoogaars WMH, Karlen Y, Bakker O, van den Hoff MJB et al. (2009). Amplification efficiency: linking baseline and bias in the analysis of quantitative PCR data. Nucleic Acids Res 37: e45.
Schlichting CD, Smith H. (2002). Phenotypic plasticity: linking molecular mechanisms with evolutionary outcomes. Evol Ecol 16: 189–211.
Schulte PM. (2004). Changes in gene expression as biochemical adaptations to environmental change: a tribute to Peter Hochachka. Comp Biochem Physiol B Biochem Mol Biol 139: 519–529.
Stewart TJ, Schaner T. (2002). Lake Ontario salmonid introductions 1970 to 1999: stocking, fishery and fish community influences. In: Lake Ontario Fish Communities and Fisheries: 2001 Annual Report of the Lake Ontario Management Unit. Queen’s Printer for Ontario: Picton, ON, Canada.
Storey JD, Madeoy J, Strout JL, Wurfel M, Ronald J, Akey JM. (2007). Gene-expression variation within and among human populations. Am J Hum Genet 80: 502–509.
Tedeschi JN, Kennington WJ, Tomkins JL, Berry O, Whiting S, Meekan MG et al. (2016). Heritable variation in heat shock gene expression: a potential mechanism for adaptation to thermal stress in embryos of sea turtles. Proc R Soc B 283: 20152320.
Torstensen Be, Nanton Da, Olsvik Pa, Sundvold H, Stubhaug I. (2009). Gene expression of fatty acid-binding proteins, fatty acid transport proteins (cd36 and FATP) and β-oxidation-related genes in Atlantic salmon (Salmo salar L.) fed fish oil or vegetable oil. Aquac Nutr 15: 440–451.
Videvall E, Sletvold N, Hagenblad J, Ågren J, Hansson B. (2016). Strong maternal effects on gene expression in Arabidopsis lyrata hybrids. Mol Biol Evol 33: 984–994.
Wheeler HE, Shah KP, Brenner J, Garcia T, Aquino-Michaels K et alConsortium Gte. (2016). Survey of the heritability and sparse architecture of gene expression traits across human tissues. PLoS Genet 12: e1006423.
Whitehead A, Crawford DL. (2005). Variation in tissue-specific gene expression among natural populations. Genome Biol 6: R13.
Whitehead A, Triant DA, Champlin D, Nacci D. (2010). Comparative transcriptomics implicates mechanisms of evolved pollution tolerance in a killifish population. Mol Ecol 19: 5186–5203.
Wolf JB, Wade MJ. (2009). What are maternal effects (and what are they not)? Philos Trans R Soc Lond B Biol Sci 364: 1107–1115.