Brown JH, Gillooly JF, Allen AP, Savage VM, West GB. Toward a metabolic theory of ecology. Ecology. 2004;85:1771–89.
Article
Google Scholar
Kingsolver JG. The well-temperatured biologist. Am Nat. 2009;174:755–68.
Article
PubMed
Google Scholar
Deutsch CA, Tewksbury JJ, Huey RB, Sheldon KS, Ghalambor CK, Haak DC, et al. Impacts of climate warming on terrestrial ectotherms across latitude. Proc Natl Acad Sci. 2008;105:6668–72.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kingsolver JG, Diamond SE, Buckley LB. Heat stress and the fitness consequences of climate change for terrestrial ectotherms. Funct Ecol. 2013;27:1415–23.
Article
Google Scholar
Sunday JM, Bates AE, Kearney MR, Colwell RK, Dulvy NK, Longino JT, Huey RB. Thermal-safety margins and the necessity of thermoregulatory behavior across latitude and elevation. Proc Natl Acad Sci. 2014;111:5610–5615.
Article
CAS
PubMed
PubMed Central
Google Scholar
Huey RB, Kingsolver JG. Evolution of thermal sensitivity of ectotherm performance. Trends Ecol Evol. 1989;4:131–5.
Article
CAS
PubMed
Google Scholar
Richter K, Haslbeck M, Buchner J. The heat shock response: Life on the verge of death. Mol Cell. 2010;40:253–66.
Article
CAS
PubMed
Google Scholar
Angilletta MJ, Wilson RS, Navas CA, James RS. Tradeoffs and the evolution of thermal reaction norms. Trends Ecol Evol. 2003;18:234–40.
Article
Google Scholar
Cowles RB. Possible implications of reptilian thermal tolerance. Science. 1939;90:465–6.
Article
CAS
PubMed
Google Scholar
Hoffmann AA, Chown SL, Clusella-Trullas S. Upper thermal limits in terrestrial ectotherms: How constrained are they? Funct Ecol. 2013;27:934–49.
Article
Google Scholar
Krebs R, Loeschcke V. Estimating heritability in a threshold trait: Heat-shock tolerance in Drosophila buzzatii. Heredity. 1997;79:252–9.
Article
PubMed
Google Scholar
Kellermann V, Overgaard J, Hoffmann AA, Fløjgaard C, Svenning J-C, Loeschcke V. Upper thermal limits of Drosophila are linked to species distributions and strongly constrained phylogenetically. Proc Natl Acad Sci. 2012;109:16228–33.
Article
CAS
PubMed
PubMed Central
Google Scholar
Krebs RA, Feder ME, Lee J. Heritability of expression of the 70KD heat-shock protein in Drosophila melanogaster and its relevance to the evolution of thermotolerance. Evolution. 1998;52:841–7.
Article
CAS
Google Scholar
Williams BR, Van Heerwaarden B, Dowling DK, Sgrò CM. A multivariate test of evolutionary constraints for thermal tolerance in Drosophila melanogaster. J Evol Biol. 2012;25:1415–26.
Article
CAS
PubMed
Google Scholar
Morgan TJ, Mackay TFC. Quantitative trait loci for thermotolerance phenotypes in drosophila melanogaster. Heredity. 2006;96:232–42.
Article
CAS
PubMed
Google Scholar
Takahashi KH, Okada Y, Teramura K. Genome-wide deficiency screen for the genomic regions responsible for heat resistance in Drosophila melanogaster. BMC Genet. 2011;12:57.
Article
PubMed
PubMed Central
Google Scholar
Hoffmann AA, Willi Y. Detecting genetic responses to environmental change. Nat Rev Genet. 2008;9:421–32.
Article
CAS
PubMed
Google Scholar
Somero GN. Comparative physiology: A “crystal ball” for predicting consequences of global change. Am J Physiol Regul Integr Comp Physiol. 2011;301:R1–14.
Article
CAS
PubMed
Google Scholar
Meyer E, Aglyamova GV, Matz MV. Profiling gene expression responses of coral larvae (Acropora millepora) to elevated temperature and settlement inducers using a novel RNA-seq procedure. Mol Ecol. 2011;20:3599–616.
CAS
PubMed
Google Scholar
Teets NM, Peyton JT, Colinet H, Renault D, Kelley JL, Kawarasaki Y, et al. Gene expression changes governing extreme dehydration tolerance in an antarctic insect. Proc Natl Acad Sci. 2012;109:20744–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Barshis DJ, Ladner JT, Oliver TA, Seneca FO, Traylor-Knowles N, Palumbi SR. Genomic basis for coral resilience to climate change. Proc Natl Acad Sci. 2013;110:1387–92.
Article
CAS
PubMed
PubMed Central
Google Scholar
O’Neil ST, Dzurisin JDK, Williams CM, Lobo NF, Higgins JK, Deines JM, et al. Gene expression in closely related species mirrors local adaptation: Consequences for responses to a warming world. Mol Ecol. 2014;23:2686–98.
Article
PubMed
Google Scholar
Gomulkiewicz R, Kirkpatrick M. Quantitative genetics and the evolution of reaction norms. Evolution. 1992;46:390–411.
Article
Google Scholar
Murren CJ, Maclean HJ, Diamond SE, Steiner UK, Heskel MA, Handelsman CA, et al. Evolutionary change in continuous reaction norms. Am Nat. 2014;183:453–67.
Article
PubMed
Google Scholar
Sørensen JG, Nielsen MM, Kruhøffer M, Justesen J, Loeschcke V. Full genome gene expression analysis of the heat stress response in drosophila melanogaster. Cell Stress Chaperones. 2005;10:312–28.
Article
PubMed
PubMed Central
Google Scholar
Umphrey G. Morphometric discrimination among sibling species in the fulva - rudis - texana complex of the ant genus aphaenogaster. Can J Zool. 1996;74:528–59.
Article
Google Scholar
De Marco B, Cognato A. A multiple-gene phylogeny reveals polyphyly among eastern North American Aphaenogaster species. Zoologica. 2015. doi:10.1111/zsc.12168.
King JR, Warren RJ, Bradford MA. Social insects dominate eastern US temperate hardwood forest macroinvertebrate communities in warmer regions. PLoS ONE. 2013;8:e75843.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ness JH, Morin DF, Giladi I. Uncommon specialization in a mutualism between a temperate herbaceous plant guild and an ant: Are aphaenogaster ants keystone mutualists? Oikos. 2009;118:1793–804.
Article
Google Scholar
Zelikova TJ, Sanders NJ, Dunn RR. The mixed effects of experimental ant removal on seedling distribution, belowground invertebrates, and soil nutrients. Ecosphere. 2011;2:art63.
Article
Google Scholar
Rodriguez-Cabal MA, Stuble KL, Guénard B, Dunn RR, Sanders NJ. Disruption of ant-seed dispersal mutualisms by the invasive asian needle ant (pachycondyla chinensis). Biol Invasions. 2012;14:557–65.
Article
Google Scholar
Diamond SE, Nichols LM, McCoy N, Hirsch C, Pelini SL, Sanders NJ, Ellison AM, Gotelli NJ, Dunn RR. A physiological trait-based approach to predicting the responses of species to experimental climate warming. Ecology, 2012;93:2305–2312.
Article
PubMed
Google Scholar
Toro ID, Ribbons RR, Pelini SL. The little things that run the world revisited: A review of ant-mediated ecosystem services and disservices (Hymenoptera: Formicidae). Myrmecological News. 2012;17:133–146.
Google Scholar
Pelini SL, Diamond SE, Maclean HJ, Ellison AM, Gotelli NJ, Sanders NJ, Dunn RR. Common garden experiments reveal uncommon responses across temperatures, locations, and species of ants. Ecology and Evolution. 2012;2:3009–15.
Article
PubMed
PubMed Central
Google Scholar
Sharon B, Stuble KL, Lessard J-P, Dunn RR, Adler FR, Sanders NJ. Predicting future coexistence in a North American ant community. Ecology and Evolution. 2014;4:1804–1819.
Article
Google Scholar
Hijmans R, Cameron S, Parra J, Jones P, Jarvis A. Very high resolution interpolated climate surfaces of global land areas. Int J Climatol. 2005;25:1965–78.
Article
Google Scholar
Hofmann GE, Somero GN. Interspecific variation in thermal denaturation of proteins in the congeneric mussels mytilus trossulus and m. galloprovincialis: Evidence from the heat-shock response and protein ubiquitination. Mar Biol. 1996;126:65–75.
Article
CAS
Google Scholar
Feder ME, Hofmann GE. Heat-shock proteins, molecular chaperones, and the stress response: Evolutionary and ecological physiology. Annu Rev Physiol. 1999;61:243–82.
Article
CAS
PubMed
Google Scholar
Kültz D. Molecular and evolutionary basis of the cellular stress response. Annu Rev Physiol. 2005;67:225–57.
Article
PubMed
Google Scholar
Fields PA. Protein function at thermal extremes: Balancing stability and flexibility. Comp Biochem Physiol A Mol Integr Physiol. 2001;129:417–31.
Article
CAS
PubMed
Google Scholar
Lockwood BL, Somero GN. Functional determinants of temperature adaptation in enzymes of cold- versus warm-adapted mussels (genus mytilus). Mol Biol Evol. 2012;29:3061–70.
Article
CAS
PubMed
Google Scholar
Gordon DM. The rewards of restraint in the collective regulation of foraging by harvester ant colonies. Nature. 2013;498:91–3.
Article
CAS
PubMed
Google Scholar
Neelakanta G, Hudson AM, Sultana H, Cooley L, Fikrig E. Expression of ixodes scapularis antifreeze glycoprotein enhances cold tolerance in drosophila melanogaster. PLoS ONE. 2012;7:e33447.
Article
CAS
PubMed
PubMed Central
Google Scholar
Franssen SU, Bergmann N, Winters G, Klostermeier UC, Rosenstiel P, Bornberg-Bauer E, et al. Transcriptomic resilience to global warming in the seagrass zostera marina, a marine foundation species. Proc Natl Acad Sci. 2011;108:19276–81.
Article
CAS
PubMed
PubMed Central
Google Scholar
Waddington C. Genetic assimilation of an acquired character. Evolution. 1953;7:118–26.
Article
Google Scholar
Sikkink KL, Reynolds RM, Ituarte CM, Cresko WA, Phillips PC. Rapid evolution of phenotypic plasticity and shifting thresholds of genetic assimilation in the nematode Caenorhabditis remanei. G3 (Bethesda). 2014;4:1103–12.
Article
CAS
Google Scholar
Simao FA, Waterhouse RM, Ioannidis P, Kriventseva EV: BUSCO: Assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 2015, 10.1093/bioinformatics/btv351
Patro R, Mount SM, Kingsford C: Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms. Nature Biotechnology 2014, 32:462–464
Vijay N, Poelstra JW, Künstner A, Wolf JBW. Challenges and strategies in transcriptome assembly and differential gene expression quantification. a comprehensive in silico assessment of RNA-seq experiments. Mol Ecol. 2013;22:620–34.
Article
CAS
PubMed
Google Scholar
Ohtsu T, Kimura MT, Katagiri C. How drosophila species acquire cold tolerance. Eur J Biochem. 1998;252:608–11.
Article
CAS
PubMed
Google Scholar
Denlinger DL. Regulation of diapause. Annu Rev Entomol. 2002;47:93–122.
Article
CAS
PubMed
Google Scholar
Ghosh K, Dill K. Cellular proteomes have broad distributions of protein stability. Biophys J. 2010;99:3996–4002.
Article
CAS
PubMed
PubMed Central
Google Scholar
Teets NM, Peyton JT, Ragland GJ, Colinet H, Renault D, Hahn DA, et al. 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
Vesala L, Salminen T, Laiho A, Hoikkala A, Kankare M. Cold tolerance and cold-induced modulation of gene expression in two drosophila virilis group species with different distributions: Cold-induced changes in gene expression. Insect Mol Biol. 2012;21:107–18.
Article
CAS
PubMed
Google Scholar
Addo-Bediako A, Chown SL, Gaston KJ. Metabolic cold adaptation in insects: A large-scale perspective. Funct Ecol. 2002;16:332–8.
Article
Google Scholar
Kelly MW, Grosberg RK, Sanford E. Trade-offs, geography, and limits to thermal adaptation in a tide pool copepod. Am Nat. 2013;181:846–54.
Article
PubMed
Google Scholar
Warren RJ, Chick L. Upward ant distribution shift corresponds with minimum, not maximum, temperature tolerance. Glob Chang Biol. 2013;19:2082–8.
Article
PubMed
Google Scholar
Addo-Bediako A, Chown SL, Gaston KJ. Thermal tolerance, climatic variability and latitude. Proc R Soc B Biol Sci. 2000;267:739–45.
Article
CAS
Google Scholar
Hodgins-Davis A, Adomas AB, Warringer J, Townsend JP. Abundant gene-by-environment interactions in gene expression reaction norms to copper within saccharomyces cerevisiae. Genome Biol Evol. 2012;4:1061–79.
Article
PubMed
PubMed Central
Google Scholar
Aubin-Horth N, Renn SCP. Genomic reaction norms: Using integrative biology to understand molecular mechanisms of phenotypic plasticity. Molecular Ecology. 2009;18:3763–3780.
Article
CAS
PubMed
Google Scholar
González E, Joly S: Impact of RNA-seq attributes on false positive rates in differential expression analysis of de novo assembled transcriptomes. BMC Research Notes. 2013;6:503.
Article
PubMed
PubMed Central
Google Scholar
Sarup P, Sørensen JG, Kristensen TN, Hoffmann AA, Loeschcke V, Paige KN, et al. Candidate genes detected in transcriptome studies are strongly dependent on genetic background. PLoS ONE. 2011;6:e15644.
Article
CAS
PubMed
PubMed Central
Google Scholar
Pavlidis P, Jensen JD, Stephan W, Stamatakis A. A critical assessment of storytelling: Gene ontology categories and the importance of validating genomic scans. Mol Biol Evol. 2012;29:3237–48.
Article
CAS
PubMed
Google Scholar
Khaitovich P, Weiss G, Lachmann M, Hellmann I, Enard W, Muetzel B, et al. A neutral model of transcriptome evolution. PLoS Biol. 2004;2:E132.
Article
PubMed
PubMed Central
Google Scholar
Whitehead A, Crawford DL. Neutral and adaptive variation in gene expression. Proc Natl Acad Sci. 2006;103:5425–30.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ogasawara O, Okubo K. On theoretical models of gene expression evolution with random genetic drift and natural selection. PLoS ONE. 2009;4:e7943.
Article
PubMed
PubMed Central
Google Scholar
Gadau J, Helmkampf M, Nygaard S, Roux J, Simola DF, Smith CR, et al. The genomic impact of 100 million years of social evolution in seven ant species. Trends Genet. 2012;28:14–21.
Article
CAS
PubMed
PubMed Central
Google Scholar
Feder ME, Walser J-C. The biological limitations of transcriptomics in elucidating stress and stress responses. J Evol Biol. 2005;18:901–10.
Article
CAS
PubMed
Google Scholar
Hoekstra LA, Montooth KL. Inducing extra copies of the hsp70 gene in drosophila melanogaster increases energetic demand. BMC Evol Biol. 2013;13:1–11.
Article
Google Scholar
Arnold FH, Wintrode PL, Miyazaki K, Gershenson A. How enzymes adapt: Lessons from directed evolution. Trends Biochem Sci. 2001;26:100–6.
Article
CAS
PubMed
Google Scholar
Lubertazzi D. The biology and natural history of aphaenogaster rudis. Psyche (Camb Mass). 2012;2012:1–11.
Article
Google Scholar
Gotelli NJ, Ellison AM. A Primer of Ecological Statistics. 2nd ed. Sunderland: Sinauer Associates, Inc; 2012.
Google Scholar
Cottingham KL, Lennon JT, Brown BL. Knowing when to draw the line: Designing more informative ecological experiments. Front Ecol Environ. 2005;3:145–52.
Article
Google Scholar
Lohse M, Bolger AM, Nagel A, Fernie AR, Lunn JE, Stitt M, et al. RobiNA: A user-friendly, integrated software solution for RNA-seq-based transcriptomics. Nucleic Acids Res. 2012;40:W622–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, et al. Full-length transcriptome assembly from RNA-seq data without a reference genome. Nat Biotechnol. 2011;29:644–52.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yang Y, Smith SA. Optimizing de novo assembly of short-read RNA-seq data for phylogenomics. BMC Genomics. 2013;14:328.
Article
CAS
PubMed
PubMed Central
Google Scholar
Huang X, Madan A. CAP3: A DNA sequence assembly program. Genome Res. 1999;9:868–77.
Article
CAS
PubMed
PubMed Central
Google Scholar
Schmieder R, Edwards R. Fast identification and removal of sequence contamination from genomic and metagenomic datasets. PLoS ONE. 2011;6:e17288.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chen T-W, Gan R-CR WTH, Huang P-J, Lee C-Y, Chen Y-YM, Chen C-C, et al. FastAnnotator- an efficient transcript annotation web tool. BMC Genomics. 2012;13 Suppl 7:S9.
Article
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
Anders S, Huber W. Differential expression analysis for sequence count data. Genome Biol. 2010;11:R106.
Article
CAS
PubMed
PubMed Central
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 Methodol. 1995;57:289–300.
Google Scholar
Hothorn T, Hornik K, van de Wiel M, Zeileis A. Implementing a class of permutation tests: The coin package. J Stat Softw. 2008;28:1–23.
Article
Google Scholar
R Core Team. R: A language and environment for statistical computing. 2013.
Google Scholar
Grossmann S, Bauer S, Robinson PN, Vingron M. Improved detection of overrepresentation of gene-ontology annotations with parent–child analysis. Bioinformatics. 2007;23:3024–31.
Article
CAS
PubMed
Google Scholar
Alexa A, Rahnenführer J, Lengauer T. Improved scoring of functional groups from gene expression data by decorrelating GO graph structure. Bioinformatics. 2006;22:1600–7.
Article
CAS
PubMed
Google Scholar