Waddington CH. Canalization of development and the inheritance of acquired characters. Nature. 1942;150:563–5.
Article
Google Scholar
Flatt T. The evolutionary genetics of canalization. Q Rev Biol. 2005;80:287–316.
Article
PubMed
Google Scholar
Siegal ML, Bergman A. Waddington’s canalization revisited: developmental stability and evolution. Proc Natl Acad Sci U S A. 2002;6:10528–32.
Article
Google Scholar
Hatle JD, Borst DW, Juliano SA. Plasticity and canalization in the control of reproduction in the lubber grasshopper. Integr Comp Biol. 2003;43:635–45. doi:10.1093/icb/43.5.635..
Article
CAS
PubMed
Google Scholar
Manu, Surkova S, Spirov AV, Gursky VV, Janssens H, Kim AR, Radulescu O, Vanario-Alonso CE, Sharp DH, Samsonova M, Reinitz J. Canalization of gene expression in the Drosophila blastoderm by gap gene cross regulation. PLoS Biol. 2009;7:e1000049.
Article
CAS
PubMed
PubMed Central
Google Scholar
Shaw JR, Hampton TH, King BL, Whitehead A, Galvez F, Gross RH, Keith N, Notch E, Jung D, Glaholt SP, Chen CY, Colbourne JK, Stanton BA. Natural selection canalizes expression variation of environmentally induced plasticity-enabling genes. Mol Biol Evol. 2014;31:3002–15.
Article
PubMed
PubMed Central
Google Scholar
Chanderbali AS, Yoo MJ, Zahn LM, Brockington SF, Wall PK, Gitzendanner MA, Albert VA, Leebens-Mack J, Altman NS, Ma H, dePamphilis CW, Soltis DE, Soltis PS. Conservation and canalization of gene expression during angiosperm diversification accompany the origin and evolution of the flower. Proc Natl Acad Sci U S A. 2010;107:22570–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lachaise D, Silvain JF. How two Afrotropical endemics made two cosmopolitan human commensals: the Drosophila melanogaster–D. simulans palaeogeographic riddle. Genetica. 2004;120:17–39.
Article
PubMed
Google Scholar
Stephan W, Li H. The recent demographic and adaptive history of Drosophila melanogaster. Heredity. 2007;98:65–8.
Article
CAS
PubMed
Google Scholar
Clarke A. The influence of climate change on the distribution and evolution of organisms. In: Johnston IA, Bennett AF, editors. Animals and Temperature: Phenotypic and Evolutionary Adaptation. Cambridge: Cambridge University Press; 1996. p. 377–407.
Chapter
Google Scholar
David JR, Gibert P, Pla E, Petavy G, Karan D, Moreteau B. Cold stress tolerance in Drosophila: analysis of chill coma recovery in D. Melanogaster. J Therm Biol. 1998;23:291–9.
Article
Google Scholar
Ayrinhac A, Debat V, Gibert P, Kister AG, Legout H, Moreteau B, Vergilino R, David JR. Cold adaptation in geographical populations of Drosophila melanogaster : phenotypic plasticity is more important than genetic variability. Funct Ecol. 2004;18:700–6.
Article
Google Scholar
King MC, Wilson AC. Evolution at two levels in humans and chimpanzees. Science. 1975;188:107–16.
Article
CAS
PubMed
Google Scholar
Wray GA, Hahn MW, Abouheif E, Balhoff JP, Pizer M, Rockman MV, Romano LA. The evolution of transcriptional regulation in eukaryotes. Mol Biol Evol. 2003;20:1377–419.
Article
CAS
PubMed
Google Scholar
Whitehead A, Crawford DL. Variation within and among species in gene expression: raw material for evolution. Mol Ecol. 2006;15:1197–211.
Article
CAS
PubMed
Google Scholar
Wray GA. The evolutionary significance of cis-regulatory mutations. Nat Rev Genet. 2007;8:206–16.
Article
CAS
PubMed
Google Scholar
Hutter S, Saminadin-Peter SS, Stephan W, Parsch J. Gene expression variation in African and European populations of Drosophila melanogaster. Genome Biol. 2008;9:R12.
Article
PubMed
PubMed Central
Google Scholar
Müller L, Hutter S, Stamboliyska R, Saminadin-Peter SS, Stephan W, Parsch J. Population transcriptomics of Drosophila melanogaster females. BMC Genomics. 2011;12:81.
Article
PubMed
PubMed Central
Google Scholar
Qin W, Neal SJ, Robertson RM, Westwood JT, Walker VK. Cold hardening and transcriptional change in Drosophila melanogaster. Insect Mol Biol. 2005;14:607–13.
Article
CAS
PubMed
Google Scholar
Zhang J, Marshall KE, Westwood JT, Clark MS, Sinclair BJ. Divergent transcriptomic responses to repeated and single cold exposures in Drosophila melanogaster. J Exp Biol. 2011;214:4021–9.
Article
PubMed
Google Scholar
Vermeulen CJ, Sørensen P, Kirilova Gagalova K, Loeschcke V. Transcriptomic analysis of inbreeding depression in cold-sensitive Drosophila melanogaster shows upregulation of the immune response. J Evol Biol. 2013;26:1890–902.
Article
CAS
PubMed
Google Scholar
Telonis-Scott M, Hallas R, McKechnie SW, Wee CW, Hoffmann AA. Selection for cold resistance alters gene transcript levels in Drosophila melanogaster. J Insect Physiol. 2009;55:549–55.
Article
CAS
PubMed
Google Scholar
Pool JE, Corbett-Detig RB, Sugino RP, Stevens KA, Cardeno CM, Crepeau MW, Duchen P, Emerson JJ, Saelao P, Begun DJ, Langley CH. Population Genomics of sub-saharan Drosophila melanogaster: African diversity and non-African admixture. PLoS Genet. 2012;8, e1003080.
Article
PubMed
PubMed Central
Google Scholar
Svetec N, Werzner A, Wilches R, Pavlidis P, Alvarez-Castro JM, Broman KW, Metzler D, Stephan W. Identification of X-linked quantitative trait loci affecting cold tolerance in Drosophila melanogaster and fine mapping by selective sweep analysis. Mol Ecol. 2010;20:530–44.
Article
PubMed
PubMed Central
Google Scholar
Colinet H, Lee SF, Hoffmann A. Functional characterization of the Frost gene in Drosophila melanogaster: importance for recovery from chill coma. PLoS One. 2010;5, e10925.
Article
PubMed
PubMed Central
Google Scholar
Colinet H, Lee SF, Hoffmann A. Knocking down expression of Hsp22 and Hsp23 by RNA interference affects recovery from chill coma in Drosophila melanogaster. J Exp Biol. 2010;213:4146–50.
Article
CAS
PubMed
Google Scholar
Colinet H, Lee SF, Hoffmann A. Temporal expression of heat shock genes during cold stress and recovery from chill coma in adult Drosophila melanogaster. FEBS Journal. 2010;277:174–85.
Article
CAS
PubMed
Google Scholar
Wilches R, Voigt S, Duchen P, Laurent S, Stephan W. Fine-mapping and selective sweep analysis of QTL for cold tolerance in Drosophila melanogaster. G3 (Bethesda). 2014;4:1635–45.
Article
Google Scholar
Dietzl G, Chen D, Schnorrer F, Su KC, Barinova Y, Fellner M, Gasser B, Kinsey K, Oppel S, Scheiblauer S, Couto A, Marra V, Keleman K, Dickson BJ. A genome-wide transgenic RNAi library for conditional gene inactivation in Drosophila. Nature. 2007;448:151–6.
Article
CAS
PubMed
Google Scholar
Udaka H, Percival-Smith A, Sinclair BJ. Increased abundance of Frost mRNA during recovery from cold stress is not essential for cold tolerance in Drosophila melanogaster. Insect Mol Biol. 2013;22:541–50.
Article
CAS
PubMed
Google Scholar
St Pierre SE, Ponting L, Stefancsik R, McQuilton P, FlyBase Consortium. FlyBase 102--advanced approaches to interrogating FlyBase. Nucleic Acids Res. 2014;42:D780–8.
Article
CAS
PubMed
Google Scholar
Pearson K. On Lines and Planes of Closest Fit to Systems of Points in Space. Philos Mag. 1901;2:559–72.
Article
Google Scholar
Costa M, Calleja M, Alonso CR, Simpson P. The bristle patterning genes hairy and extramacrochaetae regulate the development of structures required for flight in Diptera. Dev Biol. 2014;388:205–15.
Article
CAS
PubMed
PubMed Central
Google Scholar
Fan CY, Lee S, Cyr DM. Mechanisms for regulation of Hsp70 function by Hsp40. Cell Stress Chaperones. 2003;8:309–16.
Article
CAS
PubMed
PubMed Central
Google Scholar
Takayama S, Xie Z, Reed JC. An evolutionary conserved family of Hsp70/Hsc70 molecular chaperone regulators. J Biol Chem. 1999;274:781–6.
Article
CAS
PubMed
Google Scholar
Goto SG. A novel gene that is up-regulated during recovery from cold shock in Drosophila melanogaster. Gene. 2001;270:259–64.
Article
CAS
PubMed
Google Scholar
Kim LK, Choi UY, Cho HS, Lee JS, Lee WB, Kim J, Jeong K, Shim J, Kim-Ha J, Kim YJ. Down-regulation of NF-kappa B target genes by the AP-1 and STAT complex during the innate immune response in Drosophila. PLoS Biol. 2007;5, e238.
Article
PubMed
PubMed Central
Google Scholar
Tian C, Gao B, Rodriguez Mdel C, Lanz-Mendoza H, Ma B, Zhu S. Gene expression, antiparasitic activity, and functional evolution of the drosomycin family. Mol Immunol. 2008;45:3909–16.
Article
CAS
PubMed
Google Scholar
Hoffmann JA, Hetru C, Reichhart JM. The humoral antibacterial response of Drosophila. FEBS Lett. 1993;325:63–6.
Article
CAS
PubMed
Google Scholar
Daborn PJ, Yen JL, Bogwitz MR, Le Goff G, Feil E, Jeffers S, Tijet N, Perry T, Heckel D, Batterham P, Feyereisen R, Wilson TG, Ffrench-Constant RH. A single p450 allele associated with insecticide resistance in Drosophila. Science. 2002;297:2253–6.
Article
CAS
PubMed
Google Scholar
Daborn PJ, Lumb C, Boey A, Wong W, Ffrench-Constant RH, Batterham P. Evaluating the insecticide resistance potential of eight Drosophila melanogaster cytochrome P450 genes by transgenic over-expression. Insect Biochem Mol Biol. 2007;37:512–9.
Article
CAS
PubMed
Google Scholar
Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:550.
Article
PubMed
PubMed Central
Google Scholar
Li B, Dewey CN. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics. 2011;12:323.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wagner GP, Kin K, Lynch VJ. Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples. Theory Biosci. 2012;131:281–5.
Article
CAS
PubMed
Google Scholar
Levine MT, Eckert ML, Begun DJ. Whole-genome expression plasticity across tropical and temperate Drosophila melanogaster populations from Eastern Australia. Mol Biol Evol. 2011;28:249–56.
Article
CAS
PubMed
Google Scholar
Voigt S, Laurent S, Litovchenko M, Stephan W. Positive Selection at the Polyhomeotic Locus Led to Decreased Thermosensitivity of Gene Expression in Temperate Drosophila melanogaster. Genetics. 2015;200:591–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhao L, Wit J, Svetec N, Begun DJ. Parallel gene expression differences between low and high latitude populations of Drosophila melanogaster and Drosophila simulans. PLoS Genet. 2015;11, e1005184.
Article
PubMed
PubMed Central
Google Scholar
Sinclair BJ, Gibbs AG, Roberts SP. Gene transcription during exposure to, and recovery from, cold and desiccation stress in Drosophila melanogaster. Insect Mol Biol. 2007;16:435–43.
Article
CAS
PubMed
Google Scholar
Ma S, Huang Y, van Huystee RB. Improved plant RNA stability in storage. Anal Biochem. 2004;326:122–4.
Article
CAS
PubMed
Google Scholar
Kriegenburg F, Ellgaard L, Hartmann-Petersen R. Molecular chaperones in targeting misfolded proteins for ubiquitin-dependent degradation. FEBS J. 2012;279:532–42.
Article
CAS
PubMed
Google Scholar
Teets NM, Peyton JT, Ragland GJ, Colinet H, Renault D, Hahn DA, Denlinger DL. Combined transcriptomic and metabolomic approach uncovers molecular mechanisms of cold tolerance in a temperate flesh fly. Physiol Genomics. 2012;44:764–77.
Article
CAS
PubMed
Google Scholar
Dennis AB, Dunning LT, Sinclair BJ, Buckley TR. Parallel molecular routes to cold adaptation in eight genera of New Zealand stick insects. Sci Rep. 2015;5:13965.
Article
PubMed
PubMed Central
Google Scholar
Sternlicht H, Farr GW, Sternlicht ML, Driscoll JK, Willison K, Yaffe MB. The t-complex polypeptide 1 complex is a chaperonin for tubulin and actin in vivo. Proc Natl Acad Sci U S A. 1993;90:9422–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Orvar BL, Sangwan V, Omann F, Dhindsa RS. Early steps in cold sensing by plant cells: the role of actin cytoskeleton and membrane fluidity. Plant J. 2000;23:785–94.
Article
CAS
PubMed
Google Scholar
Kim M, Robich RM, Rinehart JP, Denlinger DL. Upregulation of two actin genes and redistribution of actin during diapause and cold stress in the northern house mosquito, Culex pipiens. J Insect Physiol. 2006;52:1226–33.
Article
CAS
PubMed
PubMed Central
Google Scholar
Colinet H, Nguyen TT, Cloutier C, Michaud D, Hance T. Proteomic profiling of a parasitic wasp exposed to constant and fluctuating cold exposure. Insect Biochem Mol Biol. 2007;37:1177–88.
Article
CAS
PubMed
Google Scholar
Kayukawa T, Ishikawa Y. Chaperonin contributes to cold hardiness of the onion maggot Delia antiqua through repression of depolymerization of actin at low temperatures. PLoS One. 2009;4, e8277.
Article
PubMed
PubMed Central
Google Scholar
Stamnes M. Regulating the actin cytoskeleton during vesicular transport. Curr Opin Cell Biol. 2002;14:428–33.
Article
CAS
PubMed
Google Scholar
Vaccari T, Rusten TE, Menut L, Nezis IP, Brech A, Stenmark H, Bilder D. Comparative analysis of ESCRT-I, ESCRT-II and ESCRT-III function in Drosophila by efficient isolation of ESCRT mutants. J Cell Sci. 2009;122:2413–23.
Article
CAS
PubMed
PubMed Central
Google Scholar
Marshall KE, Sinclair BJ. The impacts of repeated cold exposure on insects. J Exp Biol. 2012;215:1607–13.
Article
PubMed
Google Scholar
Paparazzo F, Tellier A, Stephan W, Hutter S. Survival Rate and Transcriptional Response upon Infection with the Generalist Parasite Beauveria bassiana in a World-Wide Sample of Drosophila melanogaster. PLoS One. 2015;10, e0132129.
Article
PubMed
PubMed Central
Google Scholar
Wurmser F, Mary-Huard T, Daudin JJ, Joly D, Montchamp-Moreau C. Variation of gene expression associated with colonisation of an anthropized environment: comparison between African and European populations of Drosophila simulans. PLoS One. 2013;8, e79750.
Article
PubMed
PubMed Central
Google Scholar
Kim E, Choi Y, Lee S, Seo Y, Yoon J, Baek K. Characterization of the Drosophila melanogaster retinin gene encoding a cornea-specific protein. Insect Mol Biol. 2008;17:537–43.
Article
CAS
PubMed
Google Scholar
Ellegren H, Parsch J. The evolution of sex-biased genes and sex-biased gene expression. Nat Rev Genet. 2007;8:689–98.
Article
CAS
PubMed
Google Scholar
Saunders DS, Henrich VC, Gilbert LI. Induction of diapause in Drosophila melanogaster: photoperiodic regulation and the impact of arrhythmic clock mutations on time measurement. Proc Natl Acad Sci U S A. 1989;86:3748–52.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kelty JD, Lee Jr RE. Induction of rapid cold hardening by cooling at ecologically relevant rates in Drosophila melanogaster. J Insect Physiol. 1999;45:719–26.
Article
CAS
PubMed
Google Scholar
Chen J, Nolte V, Schlötterer C. Temperature-Related Reaction Norms of Gene Expression: Regulatory Architecture and Functional Implications. Mol Biol Evol. 2015;32:2393–402.
Article
PubMed
PubMed Central
Google Scholar
Ghalambor CK, Hoke KL, Ruell EW, Fischer EK, Reznick DN, Hughes KA. Non-adaptive plasticity potentiates rapid adaptive evolution of gene expression in nature. Nature. 2015;525:372–5.
Article
CAS
PubMed
Google Scholar
Bubliy OA, Loeschcke V. Effect of low stressful temperature on genetic variation of five quantitative traits in Drosophila melanogaster. Heredity (Edinb). 2002;89:70–5.
Article
CAS
Google Scholar
Glinka S, Ometto L, Mousset S, Stephan W, De Lorenzo D. Demography and natural selection have shaped genetic variation in Drosophila melanogaster: a multi-locus approach. Genetics. 2003;165:1269–78.
PubMed
PubMed Central
Google Scholar
Sedlazeck FJ, Rescheneder P, von Haeseler A. NextGenMap: fast and accurate read mapping in highly polymorphic genomes. Bioinformatics. 2013;29:2790–1.
Article
CAS
PubMed
Google Scholar
R Core Team. R: a language and environment for statistical computing. Vienna: R Foundation for Statistical Computing; 2015. https://www.R-project.org/.
Google Scholar
Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J Royal Stat Soc B. 1995;57:289–300.
Google Scholar
Bourgon R, Gentleman R, Huber W. Independent filtering increases detection power for high-throughput experiments. Proc Natl Acad Sci U S A. 2010;107:9546–51.
Article
CAS
PubMed
PubMed Central
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 Bioinformatics. 2009;10:48.
Article
PubMed
PubMed Central
Google Scholar
Arvidsson S, Kwasniewski M, Riaño-Pachón DM, Mueller-Roeber B. QuantPrime--a flexible tool for reliable high-throughput primer design for quantitative PCR. BMC Bioinformatics. 2008;9:465.
Article
PubMed
PubMed Central
Google Scholar
Hellemans J, Mortier G, De Paepe A, Speleman F, Vandesompele J. qBase relative quantification framework and software for management and automated analysis of real-time quantitative PCR data. Genome Biol. 2007;8:R19.
Article
PubMed
PubMed Central
Google Scholar