Aubret F, Shine R (2009). Genetic assimilation and the postcolonization erosion of phenotypic plasticity in island tiger snakes. Curr Biol 19: 1932–1936.
Baldwin JM (1896). A new factor in evolution. Am Nat 30: 441–451. 536–553.
Baublys KK (1975). Comments on some recent analyses of functional statements in biology. Philos Sci 42: 469–486.
Beharka AA, Nagaraja TG, Morill JL, Kennedy GA, Klemm RD (1998). Effects of form of the diet on anatomical, microbial, and fermentive development of the rumen of neonatal calves. J Dairy Sci 81: 1946–1955.
Belyaev DK (1979). Destabilizing selection as a factor in domestication. J Hered 70: 301–308.
Blackburn TM, Lockwood JL, Cassey P (2009). Avian Invasions: The Ecology and Evolution of Exotic Birds. Oxford University Press: New York.
Carroll SB (2008). Evo-devo and an expanding evolutionary synthesis: a genetic theory of morphological evolution. Cell 134: 25–36.
Carroll SP, Hendry AP, Reznick DN, Fox CW (2007). Evolution on ecological time-scales. Functional Ecol 21: 387–393.
Causton HC, Ren B, Koh SS, Harbison CT, Kanin E, Jennings EG et al. (2001). Remodeling of yeast genome expression in response to environmental change. Mol Biol Cell 12: 323–337.
Chapman RW, Mancia A, Beal M, Veloso A, Rathburn C, Blair A et al. (2011). The transcriptomic responses of the eastern oyster, Crassostrea virginica, to environmental conditions. Mol Ecol 20: 1431–1449.
Chevin L-M, Lande R, Mace GM (2010). Adaptation, plasticity, and extinction in a changing environment: towards a predictive theory. PLoS Biol 8: e1000357.
Chong S, Whitelaw E (2004). Epigenetic germline inheritance. Curr Opin Genet Dev 14: 692–696.
Clutton-Brock TH (1988). Reproductive Success: Studies on Individual Variation in Contrasting Breeding Systems. University of Chicago Press: Chicago.
Collins S, Bell G (2006). Evolution of natural algal populations at elevated CO2. Ecol Lett 9: 129–135.
Crispo E (2007). The Baldwin effect and genetic assimilation: revisiting two mechanisms of evolutionary change mediated by phenotypic plasticity. Evolution 61: 2469–2479.
Darwin C (1859). The Origin of Species. John Murray: London.
Erwin DE (1998). The end and the beginning: recoveries from mass extinctions. Trends Ecol Evol 13: 344–349.
Erwin DH, Davidson EH (2009). The evolution of hierarchical gene regulatory networks. Nature Rev Genet 10: 141–148.
Feinberg AP (2007). Phenotypic plasticity and the epigenetics of human disease. Nature 447: 433–440.
Fisher RA (1930). The Genetical Theory of Natural Selection. Oxford University PressL: Oxford.
Gilbert SF, Epel D (2009). Ecological Developmental Biology. Sinauer Associates: Sunderland MA.
Gould SJ, Lewontin RC (1979). The spandrels of San Marco and the Panglossian paradigm: a critique of the adaptationist programme. Proc R Soc Lond B Biol Sci 205: 581–598.
Gould SJ, Vrba ES (1982). Exaptation–a missing term in the science of form. Paleobiology 8: 4–15.
Grant V (1963). The Origin of Adaptations. Columbia University Press: New York.
Hairston Jr NG, Ellner SP, Geber MA, Yoshita T, Fox JA (2005). Rapid evolution and the convergence of ecological and evolutionary time. Ecol Lett 8: 1114–1127.
Hawkins T (1950). Opening of milk bottles by birds. Nature 165: 435–436.
Hernandez RD, Kelley JL, Elyashiv E, Melton SC, Auton A, McVean G et al. (2011). Classic selective sweeps were rare in recent human evolution. Science 331: 920–924.
Hudson LG, Zeinelden R, Stack MS (2008). Phenotypic plasticity of neoplastic ovarian epithelium: unique cadherin profiles in tumor progression. Clin Exp Metastasis 25: 643–655.
Hudson RR, Kreitman M, Aguadé M (1987). A test of neutral molecular evolution based on nucleotide data. Genetics 116: 153–159.
Hughes AL (1985). Male size, mating success, and mating strategy in the mosquitofish Gambusia affinis (Poeciliidae). Behav Ecol Sociobiol 17: 271–278.
Hughes AL (1999). Adaptive Evolution of Genes and Genomes. Oxford University Press: New York.
Hughes AL (2005). Evidence for abundant slightly deleterious polymorphisms in bacterial populations. Genetics 169: 553–558.
Hughes AL (2007). Looking for Darwin in all the wrong places: the misguided quest for positive selection at the nucleotide sequence level. Heredity 99: 364–373.
Hughes AL (2008a). The origin of adaptive phenotypes. Proc Natl Acad Sci USA 105: 13193–19194.
Hughes AL (2008b). Near neutrality: leading edge of the neutral theory of molecular evolution. Ann NY Acad Sci 1133: 162–179.
Hughes AL, Friedman R (2005). Loss of ancestral genes in the genomic evolution of Ciona intestinalis. Evol Devel 7: 196–200.
Hughes AL, Friedman R, Rivailler P, French JO (2008). Synonymous and nonsynonymous polymorphisms and divergences in bacterial genomes. Mol Biol Evol 25: 2199–2209.
Hughes AL, Packer B, Welsch R, Bergen AW, Chanock SJ, Yeager M (2003). Widespread purifying selection at polymorphic sites in human protein-coding loci. Proc Natl Acad Sci USA 100: 15754–15757.
Iacovitti L, Lee J, Joh TH, Reis DJ (1987). Expression of tyrosine hydroxylase in neurons of cultured cerebral cortex: evidence for phenotypic plasticity in neurons of the CNS. J Neurosci 7: 1264–1270.
Jeffrey WR (2001). Cavefish as a model system in evolutionary developmental biology. Devel Biol 231: 1–12.
Jensen JD, Thornton KR, Bustamente CD, Aquadro CF (2007). On the utility of linkage disequilibrium as a statistic for identifying targets of positive selection in nonequilibrium populations. Genetics 176: 2371–2379.
Kimura M (1976). How genes evolve; a population geneticist's view. Ann Génét 19: 153–168.
Kimura M (1983). The Neutral Theory of Molecular Evolution. Cambridge University Press: Cambridge.
Kimura M, Ohta T (1974). On some principles governing molecular evolution. Proc Natl Acad Sci USA 71: 2848–2852.
Kolar CS, Lodge DM (2001). Progress in invasion biology: predicting invaders. Trends Ecol Evol 16: 199–204.
Lande R (2009). Adaptation to an extraordinary environment by evolution of phenotypic plasticity and genetic assimilation. J Evol Biol 22: 1435–1446.
Ledon-Rettig CC, Pfennig DW, Nascone-Yoder N (2008). Ancestral variation and the potential for genetic accommodation in larval amphibians: implications for the evolution of novel feeding strategies. Evol Devel 10: 316–325.
Lesk AM (2008). Introduction to Bioinformatics, 3rd edn. Oxford University Press: New York.
Lewontin RC (1957). The adaptations of populations to varying environments. Cold Spring Harb Symp Quant Biol 22: 395–408.
Liman ER, Innan H (2003). Relaxed selective pressure on an essential component of pheromone transduction in primate evolution. Proc Natl Acad Sci USA 100: 3328–3332.
Lindquist S (1986). The heat-shock response. Annu Rev Biochem 55: 1151–1191.
Lynch M (2007). The Origins of Genome Architecture. Sinauer: Sunderland MA.
McBride CS (2007). Rapid evolution of smell and taste receptor genes during host specialization in Drosophila sechellia. Proc Natl Acad Sci USA 104: 4996–5001.
McClean CY, Reno PL, Pollen AA, Bassan AI, Capellini TD, Guenther C et al. (2011). Human-specific loss of regulatory DNA and the evolution of human-specific traits. Nature 471: 216–219.
McDonald JH, Kreitman M (1991). Adaptive protein evolution at the Adh locus in Drosophila. Nature 351: 114–116.
McKechnie AE, Freckleton RP, Jetz W (2006). Phenotypic plasticity in the scaling of avian basal metabolic rate. Proc R Soc Lond B 273: 931–937.
McKinney ML, Lockwood JL (1999). Biotic homogenization: a few winners replacing many losers in the next mass extinction. Trends Ecol Evol 14: 450–453.
Mita T, Tanabe K, Kita K (2009). Spread and evolution of Plasmodium falciparum drug resistance. Parasitol Int 58: 201–209.
Mittelbach GG, Osenberg CW, Wainwright PC (1999). Variation in feeding morphology between pumpkinseed populations: phenotypic plasticity or evolution? Evol Ecol Research 1: 111–128.
Moczek AP (1998). Horn polyphenism in the beetle Onthophagus Taurus: larval diet quality and plasticity in parental investment determine adult body size and male horn morphology. Behav Ecol 9: 636–641.
Moczek AP, Sultan S, Foster S, Ledón-Rettig, Dworkin I, Nijhout HF et al. (2011). The role of developmental plasticity in evolutionary innovation. Proc R Soc Lond B 278: 2705–2713.
Moyle RG, Filardi CE, Smith CE, Diamond J (2009). Explosive Pleistocene diversification and hemispheric expansion of a ‘great speciator’. Proc Natl Acad Sci USA 106: 1863–1868.
Myers N, Knoll AH (2001). The biotic crisis and the future of evolution. Proc Natl Acad Sci USA 98: 5389–5392.
Nei M (1987). Molecular Evolutionary Genetics. Columbia University Press: New York.
Nei M (2005). Selectionism and neutralism in molecular evolution. Mol Biol Evol 22: 2318–2342.
Nei M (2007). The new mutation theory of phenotypic evolution. Proc Natl Acad Sci USA 104: 12235–12242.
Nei M, Suzuki Y, Nozawa M (2010). The neutral theory of molecular evolution in the genomic era. Annu Rev Genomics Hum Genet 11: 265–289.
Nijhout HF (2003). Development and evolution of adaptive polyphenisms. Evol Devel 5: 9–18.
Peyton SR, Kim PD, Ghajar CM, Seliktar D, Putnam AJ (2008). Effects of matrix stiffness and RhoA on the phenotypic plasticity of smooth muscle cells in a 3-D biosynthetic hydrogel system. Biomaterials 29: 2597–2607.
Pfennig DW, Wund MA, Snell-Rood EC, Cruickshank T, Schlichting CD, Moczek AP (2010). Phenotypic plasticity's impacts on diversification and speciation. Trends Ecol Evol 25: 459–467.
Pigliucci M, Murren CJ (2003). Genetic assimilation and a possible evolutionary paradox: can macroevolution sometimes be so fast as to pass us by? Evolution 57: 1455–1464.
Pigliucci M, Murren CJ, Schlichting CD (2006). Phenotypic plasticity and evolution by genetic assimilation. J Exp Biol 209: 2362–2367.
Price TD, Qvarnström A, Irwin DE (2003). The role of phenotypic plasticity in driving genetic evolution. Proc R Soc Lond B Biol Sci 270: 1433–1440.
Reeve HK, Sherman PW (1993). Adaptation and the goals of evolutionary research. Quart Rev Biol 68: 1–68.
Reznick DN, Ghalambor CK (2001). The population ecology of contemporary adaptations: what empirical studies reveal about the conditions that promote adaptive evolution. Genetica 112–113: 183–198.
Richards EJ (2006). Inherited epigenetic variation–revisiting soft inheritance. Nat Rev Genet 7: 395–401.
Rivero A, Vézilier J, Weill M, Read AF, Gandon S (2010). Insecticide control of vector-borne diseases: when is insecticide resistance a problem? PLoS Pathog 6: e1001000.
Sabeti PC, Schaffner SK, Fry B, Lohmueller J, Varilly P, Shamovsky O et al. (2006). Positive natural selection in the human lineage. Science 312: 1614–1620.
Sax DV, Brown JH (2000). The paradox of invasion. Global Ecol Biogeogr 9: 363–371.
Schlichting CD, Smith H (2002). Phenotypic plasticity: linking molecular mechanisms with evolutionary outcomes. Evol Ecol 16: 189–211.
Schluter D, Grant PR (1984). Ecological correlates or morphological evolution in a Darwin's finch, Geospiza diffilis. Evolution 38: 865–869.
Schoener TW (2011). The newest synthesis: understanding the interplay of evolutionary and ecological dynamics. Science 331: 426–429.
Slijper EJ (1942a). Biologic-anatomical investigations on the bipedal gait and upright posture in mammals, with special reference to a little goat, born without forelegs. I. Proc Koninklijke Nederlandse Akad Wetenschappen 45: 288–295.
Slijper EJ (1942b). Biologic-anatomical investigations on the bipedal gait and upright posture in mammals, with special reference to a little goat, born without forelegs. II. Proc Koninklijke Nederlandse Akad Wetenschappen 45: 407–415.
Sturmbauer C (1998). Explosive speciation in the African Great Lakes: a dynamic model of adaptive radiation. J Fish Biol 53: 18–36.
Van Bocxlaer I, Loader SP, Roelants K, Biju SD, Menegon M, Bossuyt F (2010). Gradual adaptation toward a range-expansion phenotype initiated the global radiation of toads. Science 327: 679–682.
Van Kleunen M, Fischer M (2005). Constraints on the evolution of adaptive phenotypic plasticity in plants. New Phytol 166: 49–60.
Via S, Gomulkiewicz R, de Jong G, Scheiner SM, Schlichting CD, Van Tienderen P (1995). Adaptive phenotypic plasticity: consensus and controversy. Trends Ecol Evol 10: 212–217.
Vissa VD, Brennan PJ (2001). The genome of Mycobacterium leprae: a minimal mycobacterial gene set. Genome Biol 2001 2: reviews1023.1–1023.8.
Waddington CH (1953). Genetic assimilation of an acquired character. Evolution 7: 118–126.
Wang X, Thomas SD, Zhang J (2004). Relaxation of selective constraint and loss of function in the evolution of human bitter taste receptor genes. Human Mol Genet 13: 2671–2678.
West-Eberhard MJ (1986). Alternative adaptations, speciation, and phylogeny (A Review). Proc Natl Acad Sci USA 83: 1388–1392.
West-Eberhard MJ (2003). Developmental Plasticity and Evolution. Oxford University Press: New York.
West-Eberhard MJ (2005). Developmental plasticity and the origin of species differences. Proc Natl Acad Sci USA 102: 6543–6549.
West-Eberhard MJ, Smith JA, Winter C (2011). Photosynthesis reorganized. Science 332: 311–312.
Willi Y, van Buskirk J, Hoffmann AA (2006). Limits to the adaptive potential of small populations. Annu Rev Ecol Evol Syst 37: 433–458.
Williamson MH, Fitter A (1996). The characters of successful invaders. Biol Conserv 78: 163–170.
Wund MA, Baker JA, Clancy B, Golub JL, Foster SA (2008). A test of the ‘flexible stem’ model of evolution: ancestral plasticity, genetic accommodation, and morphological divergence in the threespine stickleback radiation. Am Nat 172: 449–462.
Yacoby S (2005). The phenotypic plasticity of myeloma plasma cells as expressed by dedifferentiation into an immature, resilient, and apoptosis-resistant phenotype. Clin Cancer Res 11: 7599–7606.
Yang Z, Nielsen R, Goldman N, Pedersen AM (2000). Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155: 431–449.
Yeh PJ, Price TD (2004). Adaptive phenotypic plasticity and the successful colonization of a novel environment. Am Nat 164: 531–542.
Youngson NA, Chong S, Whitelaw E (2010). Gene silencing is an ancient means of producing multiple phenotypes from the same genotype. Bioessays 33: 95–99.
Zhang J, Wagh P, Guay D, Sanchez-Pulido L, Padhi BK, Korzh V et al. (2010). Loss of fish actinotrichia proteins and the fin-to-limb transition. Nature 466: 234–238.