Coyne J, Orr H. Speciation. Sunderland: MA p; 2004. p. 281.
Google Scholar
Kitano J, Mori S, Peichel CL. Phenotypic divergence and reproductive isolation between sympatric forms of Japanese threespine sticklebacks. Biol J Linnean Soc. 2007;91:671–85.
Article
Google Scholar
Barluenga M, Stölting KN, Salzburger W, Muschick M, Meyer A. Sympatric speciation in nicaraguan crater lake cichlid fish. Nature. 2006;439:719–23.
Article
CAS
PubMed
Google Scholar
Morris J, Navarro N, Rastas P, Rawlins LD, Sammy J, Mallet J, Dasmahapatra KK. The genetic architecture of adaptation: convergence and pleiotropy in heliconius wing pattern evolution. Heredity. 2019;123:138–52.
Article
PubMed
PubMed Central
Google Scholar
Supple MA, Hines HM, Dasmahapatra KK, Lewis JJ, Nielsen DM, Lavoie C, Ray DA, Salazar C, McMillan WO, Counterman BA. Genomic architecture of adaptive color pattern divergence and convergence in heliconius butterflies. Genome Res. 2013;23:1248–57.
Article
CAS
PubMed
PubMed Central
Google Scholar
Boyle EA, Li YI, Pritchard JK. An expanded view of complex traits: from polygenic to omnigenic. Cell. 2017;169:1177–86.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jacobs A, Hughes MR, Robinson PC, Adams CE, Elmer KR. The genetic architecture underlying the evolution of a rare piscivorous life history form in brown trout after secondary contact and strong introgression. Genes. 2018;9:280.
Article
PubMed Central
CAS
Google Scholar
Kirubakaran TG, Grove H, Kent MP, Sandve SR, Baranski M, Nome T, De Rosa MC, Righino B, Johansen T, Otterå H, et al. Two adjacent inversions maintain genomic differentiation between migratory and stationary ecotypes of Atlantic cod. Mol Ecol. 2016;25:2130–43.
Article
CAS
PubMed
Google Scholar
Prince DJ, O’Rourke SM, Thompson TQ, Ali OA, Lyman HS, Saglam IK, Hotaling TJ, Spidle AP, Miller MR. The evolutionary basis of premature migration in pacific salmon highlights the utility of genomics for informing conservation. Sci Adv. 2017;3:e1603198.
Article
PubMed
PubMed Central
Google Scholar
Mackay TF. The genetic architecture of quantitative traits. Ann Rev Genet. 2001;35:303–39.
Article
CAS
PubMed
Google Scholar
Robertson A. The nature of quantitative genetic variation. In: Heritage from Mendel, 1967. pp. 265–80.
Sinclair-Waters M, Ødegård J, Korsvoll SA, Moen T, Lien S, Primmer CR, Barson NJ. Beyond large-effect loci: large-scale GWAS reveals a mixed large-effect and polygenic architecture for age at maturity of Atlantic salmon. Genet Sel Evol. 2020;52:1–11.
Article
CAS
Google Scholar
Allen HL, Estrada K, Lettre G, Berndt SI, Weedon MN, Rivadeneira F, Willer CJ, Jackson AU, Vedantam S, Raychaudhuri S, et al. Hundreds of variants clustered in genomic loci and biological pathways affect human height. Nature. 2010;467:832–8.
Article
CAS
Google Scholar
Kardos M, Husby A, McFarlane SE, Qvarnström A, Ellegren H. Whole-genome resequencing of extreme phenotypes in collared flycatchers highlights the difficulty of detecting quantitative trait loci in natural populations. Mol Ecol Resour. 2016;16:727–41.
Article
CAS
PubMed
Google Scholar
Jonsson B, Jonsson N. Polymorphism and speciation in arctic charr. J Fish Biol. 2001;58:605–38.
Article
Google Scholar
Skúlason S. Sympatric morphs, populations and speciation in freshwater fish with emphasis on arctic charr. Evol Biol Divers. 1999:71–92.
Skúlason S, Snorrason SS, Ota D, Noakes DL. Genetically based differences in foraging behaviour among sympatric morphs of arctic charr (pisces: Salmonidae). Anim Behav. 1993;45:1179–92.
Article
Google Scholar
Hughes MR, Hooker OE, Van Leeuwen TE, Kettle-White A, Thorne A, Prodöhl P, Adams CE. Alternative routes to piscivory: contrasting growth trajectories in brown trout (Salmo trutta) ecotypes exhibiting contrasting life history strategies. Ecol Freshw Fish. 2019;28:4–10.
Article
Google Scholar
Thorne A, MacDonald AI, Thorley JL. The abundance of large, piscivorous ferox trout (Salmo trutta) in loch rannoch, scotland. PeerJ. 2016;4:e2646.
Article
PubMed
PubMed Central
Google Scholar
Keeley E, Parkinson E, Taylor E. The origins of ecotypic variation of rainbow trout: a test of environmental vs. genetically based differences in morphology. J Evol Biol. 2007;20:725–36.
Article
CAS
PubMed
Google Scholar
Hess JE, Zendt JS, Matala AR, Narum SR. Genetic basis of adult migration timing in anadromous steelhead discovered through multivariate association testing. Proc R Soc B Biol Sci. 2016;283:20153064.
Article
CAS
Google Scholar
Irvine JR. The Gerrard rainbow trout of Kootenay lake, British Columbia: a discussion of their life history with management, research and enhancement recommendations. BC Hydro Power Authority Fish Management Report. 1978;72:1–62.
Northcote T. Some impacts of man on kootenay lake and its salmonoids. Great Lakes Fish Comm. 1973;25:1–46.
Google Scholar
Monnet G, Rosenfeld JS, Richards JG. Adaptive differentiation of growth, energetics and behaviour between piscivore and insectivore juvenile rainbow trout along the pace-of-life continuum. J Anim Ecol. 2020;89:2717–32.
Article
PubMed
Google Scholar
Réale D, Garant D, Humphries MM, Bergeron P, Careau V, Montiglio P-O. Personality and the emergence of the pace-of-life syndrome concept at the population level. Philos Trans R Soc B Biol Sci. 2010;365:4051–63.
Article
Google Scholar
Ricklefs RE, Wikelski M. The physiology/life-history nexus. Trends Ecol Evol. 2002;17:462–8.
Article
Google Scholar
Wikelski ML, Spinney L, Schelsky W, Scheuerlein A, Gwinner E. Slow pace of life in tropical sedentary birds: a common-garden experiment on four stonechat populations from different latitudes. Proc R Soc Lond Ser B Biol Sci. 2003;270:2383–8.
Article
Google Scholar
Roff D. Evolution of life histories: theory and analysis. Berlin: Springer Science & Business Media; 1993.
Google Scholar
Skulason S, Smith TB. Resource polymorphisms in vertebrates. Trends Ecol Evol. 1995;10:366–70.
Article
CAS
PubMed
Google Scholar
Futschik A, Schlötterer C. The next generation of molecular markers from massively parallel sequencing of pooled DNA samples. Genetics. 2010;186:207–18.
Article
CAS
PubMed
PubMed Central
Google Scholar
McGirr JA, Martin CH. Novel candidate genes underlying extreme trophic specialization in caribbean pupfishes. Mol Biol Evol. 2017;34:873–88.
CAS
PubMed
Google Scholar
Roberts RB, Hu Y, Albertson RC, Kocher TD. Craniofacial divergence and ongoing adaptation via the hedgehog pathway. Proc Natl Acad Sci. 2011;108:13194–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Berthelot C, Brunet F, Chalopin D, Juanchich A, Bernard M, Noël B, Bento P, Da Silva C, Labadie K, Alberti A, et al. The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates. Nat Commun. 2014;5:1–10.
Article
Google Scholar
Campbell MA, Hale MC, McKinney GJ, Nichols KM, Pearse DE. Long-term conservation of ohnologs through partial tetrasomy following whole-genome duplication in salmonidae. G3: Genes Genomes Genet. 2019;9:2017–28.
Article
CAS
Google Scholar
Fariello MI, Boitard S, Mercier S, Robelin D, Faraut T, Arnould C, Recoquillay J, Bouchez O, Salin G, Dehais P, et al. Accounting for linkage disequilibrium in genome scans for selection without individual genotypes: the local score approach. Mol Ecol. 2017;26:3700–14.
Article
CAS
PubMed
Google Scholar
McKinnon JS, Mori S, Blackman BK, David L, Kingsley DM, Jamieson L, Chou J, Schluter D. Evidence for ecology’s role in speciation. Nature. 2004;429:294–8.
Article
CAS
PubMed
Google Scholar
Schluter D, McPhail JD. Ecological character displacement and speciation in sticklebacks. Am Nat. 1992;140:85–108.
Article
CAS
PubMed
Google Scholar
Skúlason S, Parsons KJ, Svanbäck R, Räsänen K, Ferguson MM, Adams CE, Amundsen P-A, Bartels P, Bean CW, Boughman JW, et al. A way forward with eco evo devo: an extended theory of resource polymorphism with postglacial fishes as model systems. Biol Rev. 2019;94:1786–808.
Article
PubMed
Google Scholar
Taylor EB, Foley C, Neufeld M. Genetic mixture analyses in support of restoration of a high value recreational fishery for rainbow trout (Oncorhynchus mykiss) from a large lake in interior British Columbia. Conserv Genet. 2019;20:891–902.
Article
CAS
Google Scholar
Fisheries F, Fishery and aquaculture statistics 2017/fao annuaire. statistiques des pêches et de l’aquaculture 2017/fao anuario. estadísticas de pesca y acuicultura 2017. Global aquaculture production statistics for the year. 2017.
Salem M, Vallejo RL, Leeds TD, Palti Y, Liu S, Sabbagh A, Rexroad CE III, Yao J. RNA-seq identifies SNP markers for growth traits in rainbow trout. PLoS ONE. 2012;7:e36264.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yoshida GM, Lhorente JP, Carvalheiro R, Yáñez J. Bayesian genome-wide association analysis for body weight in farmed Atlantic salmon (Salmo salar l.). Anim Genet. 2017;48:698–703.
Article
CAS
PubMed
Google Scholar
Gonzalez-Pena D, Gao G, Baranski M, Moen T, Cleveland BM, Kenney PB, Vallejo RL, Palti Y, Leeds TD. Genome-wide association study for identifying loci that affect fillet yield, carcass, and body weight traits in rainbow trout (oncorhynchus mykiss). Front Genet. 2016;7:203.
Article
PubMed
PubMed Central
Google Scholar
Neto RVR, Yoshida GM, Lhorente JP, Yáñez JM. Genome-wide association analysis for body weight identifies candidate genes related to development and metabolism in rainbow trout (oncorhynchus mykiss). Mol Genet Genom. 2019;294:563–71.
Article
CAS
Google Scholar
Chen X-Y, Gu X-T, Saiyin H, Wan B, Zhang Y-J, Li J, Wang Y-L, Gao R, Wang Y-F, Dong W-P, et al. Brain-selective kinase 2 (brsk2) phosphorylation on pctaire1 negatively regulates glucose-stimulated insulin secretion in pancreatic β-cells. J Biol Chem. 2012;287:30368–75.
Article
CAS
PubMed
PubMed Central
Google Scholar
Garcia de la Serrana D, Macqueen DJ. Insulin-like growth factor-binding proteins of teleost fishes. Front Endocrinol. 2018;9:80.
Article
Google Scholar
Wood AW, Duan G, Bern HA. Insulin-like growth factor signaling in fish. Int Rev Cytol. 2005;243:215–85.
Article
CAS
PubMed
Google Scholar
Mangelsdorf DJ. Vitamin a receptors. Nutr Rev. 1994;52:S32.
Article
CAS
PubMed
Google Scholar
Wolf G. Multiple functions of vitamin a. Physiol Rev. 1984;64:873–937.
Article
CAS
PubMed
Google Scholar
Morriss-Kay GM. Retinoids in mammalian embryonic development. In: Advances in organ biology, vol. 3. Elsevier. 1997. pp. 79–92.
Macqueen DJ, Johnston IA. A well-constrained estimate for the timing of the salmonid whole genome duplication reveals major decoupling from species diversification. Proc R Soc B Biol Sci. 2014;281:20132881.
Article
Google Scholar
Near TJ, Eytan RI, Dornburg A, Kuhn KL, Moore JA, Davis MP, Wainwright PC, Friedman M, Smith WL. Resolution of ray-finned fish phylogeny and timing of diversification. Proc Natl Acad Sci. 2012;109:13698–703.
Article
CAS
PubMed
PubMed Central
Google Scholar
Vandepoele K, De Vos W, Taylor JS, Meyer A, Van de Peer Y. Major events in the genome evolution of vertebrates: paranome age and size differ considerably between ray-finned fishes and land vertebrates. Proc Natl Acad Sci. 2004;101:1638–43.
Article
CAS
PubMed
PubMed Central
Google Scholar
Tamkee P, Parkinson E, Taylor E. The influence of wisconsinan glaciation and contemporary stream hydrology on microsatellite DNA variation in rainbow trout (Oncorhynchus mykiss). Can J Fish Aquat Sci. 2010;67:919–35.
Article
CAS
Google Scholar
Ltd RC. Kootenay lake action plan-2016. Nelson: Lands and Natural Resource Operations, The Ministry of Forests; 2016.
Google Scholar
Pearse DE, Barson NJ, Nome T, Gao G, Campbell MA, Abadía-Cardoso A, Anderson EC, Rundio DE, Williams TH, Naish KA, et al. Sex-dependent dominance maintains migration supergene in rainbow trout. Nat Ecol Evol. 2019;3:1731–42.
Article
PubMed
Google Scholar
Cruickshank TE, Hahn MW. Reanalysis suggests that genomic islands of speciation are due to reduced diversity, not reduced gene flow. Mol Ecol. 2014;23:3133–57.
Article
PubMed
Google Scholar
Booker TR, Yeaman S, Whitlock M. Variation in recombination rate affects detection of outliers in genome scans under neutrality. Mol Ecol. 2020;29:4274–9.
Article
CAS
PubMed
Google Scholar
Micheletti SJ, Narum SR. Utility of pooled sequencing for association mapping in nonmodel organisms. Mol Ecol Resour. 2018;18:825–37.
Article
CAS
PubMed
Google Scholar
Andrews S. Fastqc: a quality control tool for high throughput sequence data. 2010.
Kofler R, Orozco-terWengel P, De Maio N, Pandey RV, Nolte V, Futschik A, Kosiol C, Schlötterer C. Popoolation: a toolbox for population genetic analysis of next generation sequencing data from pooled individuals. PloS ONE. 2011a;6:e15925.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li H, Durbin R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics. 2009;25:1754–60.
Article
CAS
PubMed
PubMed Central
Google Scholar
Faust GG, Hall IM. Samblaster: fast duplicate marking and structural variant read extraction. Bioinformatics. 2014;30:2503–5. https://doi.org/10.1093/bioinformatics/btu314.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, et al. The sequence alignment/map format and samtools. Bioinformatics. 2009;25:2078–9.
Article
PubMed
PubMed Central
CAS
Google Scholar
Kofler R, Pandey RV, Schlötterer C. Popoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (pool-seq). Bioinformatics. 2011b;27:3435–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Weir BS, Cockerham CC. Estimating f-statistics for the analysis of population structure. Evolution. 1984:1358–70.
Turner S. qqman: Q-Q and Manhattan Plots for GWAS Data. R package version 0.1.4. 2017.https://CRAN.R-project.org/package=qqman.
Ferretti L, Ramos-Onsins SE, Pérez-Enciso M. Population genomics from pool sequencing. Mol Ecol. 2013;22:5561–76.
Article
PubMed
Google Scholar
Fracassetti M, Griffin PC, Willi Y. Validation of pooled whole-genome re-sequencing in Arabidopsis lyrata. PLoS ONE. 2015;10:e0140462.
Article
PubMed
PubMed Central
CAS
Google Scholar
Bonhomme M, Chevalet C, Servin B, Boitard S, Abdallah J, Blott S, SanCristobal M. Detecting selection in population trees: the Lewontin and Krakauer test extended. Genetics. 2010;186:241–62.
Article
PubMed
PubMed Central
Google Scholar
Haller BC, Galloway J, Kelleher J, Messer PW, Ralph PL. Tree-sequence recording in slim opens new horizons for forward-time simulation of whole genomes. Mol Ecol Resour. 2019;19:552–66.
Article
PubMed
PubMed Central
Google Scholar
Haller BC, Messer PW. Slim 3: Forward genetic simulations beyond the wright-fisher model. Mol Biol Evol. 2019;36:632–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Primmer C, Papakostas S, Leder E, Davis M, Ragan M. Annotated genes and nonannotated genomes: cross-species use of gene ontology in ecology and evolution research. Mol Ecol. 2013;22:3216–41.
Article
CAS
PubMed
Google Scholar
Quinlan AR, Hall IM. Bedtools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26:841–2.
Article
CAS
PubMed
PubMed Central
Google Scholar
Eden E, Lipson D, Yogev S, Yakhini Z. Discovering motifs in ranked lists of DNA sequences. PLoS Comput Biol. 2007;3:e39.
Article
PubMed
PubMed Central
CAS
Google Scholar
Eden E, Navon R, Steinfeld I, Lipson D, Yakhini Z. Gorilla: a tool for discovery and visualization of enriched go terms in ranked gene lists. BMC Bioinform. 2009;10:48.
Article
Google Scholar
Supek F, Bošnjak M, Škunca N, Šmuc T. Revigo summarizes and visualizes long lists of gene ontology terms. PloS ONE. 2011;6:e21800.
Article
CAS
PubMed
PubMed Central
Google Scholar