Mechanistic approaches to the study of evolution: the functional synthesis (original) (raw)

• Dykhuizen, D. E. & Hartl, D. L. Selection in chemostats. Microbiol. Rev. 47, 150–168 (1983).
  CAS PubMed PubMed Central Google Scholar
• Elena, S. F. & Lenski, R. E. Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation. Nature Rev. Genet. 4, 457–469 (2003).
  Article CAS PubMed Google Scholar
• Losos, J. B., Jackman, T. R., Larson, A., Queiroz, K. & Rodriguez-Schettino, L. Contingency and determinism in replicated adaptive radiations of island lizards. Science 279, 2115–2118 (1998).
  Article CAS PubMed Google Scholar
• Powers, D. A., Lauerman, T., Crawford, D. & DiMichele, L. Genetic mechanisms for adapting to a changing environment. Annu. Rev. Genet. 25, 629–659 (1991).
  Article CAS PubMed Google Scholar
• Wourms, M. K. & Wasserman, F. E. Butterfly wing markings are more advantageous during handling than during the initial strike of an avian predator. Evolution 39, 845–851 (1985).
  Article PubMed Google Scholar
• Moller, A. P. Female choice selects for male sexual tail ornaments in the monogamous swallow. Nature 332, 640–642 (1988).
  Article Google Scholar
• Rainey, P. B. & Rainey, K. Evolution of cooperation and conflict in experimental bacterial populations. Nature 425, 72–74 (2003).
  Article CAS PubMed Google Scholar
• Denver, D. R. et al. The transcriptional consequences of mutation and natural selection in Caenorhabditis elegans. Nature Genet. 37, 544–548 (2005).
  Article CAS PubMed Google Scholar
• Endler, J. A. Natural selection on color patterns in Poecilia reticulata. Evolution 34, 76–91 (1980).
  Article PubMed Google Scholar
• Thornton, J. W. Resurrecting ancient genes: experimental analysis of extinct molecules. Nature Rev. Genet. 5, 366–375 (2004). An introduction to gene 'resurrection' — that is, phylogenetic reconstruction, biochemical synthesis and functional characterization of ancient sequences — as a strategy for testing evolutionary hypotheses.
  Article CAS PubMed Google Scholar
• Fitzpatrick, M. J., Feder, E., Rowe, L. & Sokolowski, M. B. Maintaining a behaviour polymorphism by frequency-dependent selection on a single gene. Nature 447, 210–212 (2007). Polymorphism in activity of a cGMP-dependent protein kinase that elicits different foraging behaviours in Drosophila melanogaster larva is maintained by negative frequency-dependent selection during starvation.
  Article CAS PubMed Google Scholar
• Douglas, S. J., Dawson-Scully, K. & Sokolowski, M. B. The neurogenetics and evolution of food-related behaviour. Trends Neurosci. 28, 644–652 (2005).
  Article CAS PubMed Google Scholar
• Toth, A. L. & Robinson, G. E. Evo–devo and the evolution of social behavior. Trends Genet. 23, 334–341 (2007).
  Article CAS PubMed Google Scholar
• Colosimo, P. F. et al. Widespread parallel evolution in sticklebacks by repeated fixation of Ectodysplasin alleles. Science 307, 1928–1933 (2005). Using transgenic, phylogenetic and quantitative genetic analysis, the authors identify an allele that is involved in the loss of external armour during the evolution of numerous freshwater stickleback populations.
  Article CAS PubMed Google Scholar
• Gompel, N., Prud'homme, B., Wittkopp, P. J., Kassner, V. A. & Carroll, S. B. Chance caught on the wing: _cis_-regulatory evolution and the origin of pigment patterns in Drosophila. Nature 433, 481–487 (2005). This pioneering study in the evolution of development (along with reference 16) used transgenic techniques to identify decisively specific regulatory elements that underlie evolutionary differences in the expression of genes that drive pigmentation patterns between fruitfly species.
  Article CAS PubMed Google Scholar
• Prud'homme, B. et al. Repeated morphological evolution through _cis_-regulatory changes in a pleiotropic gene. Nature 440, 1050–1053 (2006).
  Article CAS PubMed Google Scholar
• Konishi, S. et al. An SNP caused loss of seed shattering during rice domestication. Science 312, 1392–1396 (2006). A beautiful example of the functional synthesis to study the evolution of development: fine quantitative genetic mapping identified a single substitution associated with the loss of seed shattering that occurs during rice domestication; transgenic and functional analysis established the specific effects of the historical mutation on gene expression, seed development and the shattering phenotype.
  Article CAS PubMed Google Scholar
• Wang, H. et al. The origin of the naked grains of maize. Nature 436, 714–719 (2005).
  Article CAS PubMed PubMed Central Google Scholar
• Daborn, P. J. et al. A single p450 allele associated with insecticide resistance in Drosophila. Science 297, 2253–2256 (2002).
  Article CAS PubMed Google Scholar
• Chung, H. et al. _Cis_-regulatory elements in the accord retrotransposon result in tissue-specific expression of the Drosophila melanogaster insecticide resistance gene Cyp6g1. Genetics 175, 1071–1077 (2007). Using genetic manipulation in fruitflies, the authors show decisively that a transposon insertion in the regulatory region of a gene that metabolizes insecticides is sufficient to recapitulate the evolution of DDT (dichloro-diphenyl-trichloroethane) resistance.
  Article CAS PubMed PubMed Central Google Scholar
• Bantinaki, E. et al. Adaptive divergence in experimental populations of Pseudomonas fluorescens. III. Mutational origins of wrinkly spreader diversity. Genetics 176, 441–453 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Gilbert, S. F., Opitz, J. M. & Raff, R. A. Resynthesizing evolutionary and developmental biology. Dev. Biol. 173, 357–372 (1996).
  Article CAS PubMed Google Scholar
• Wilson, E. O. Sociobiology: The New Synthesis (Belknap, Cambridge, 1975).
  Google Scholar
• Hubby, J. L. & Lewontin, R. C. A molecular approach to the study of genic heterozygosity in natural populations. I. The number of alleles at different loci in Drosophila pseudoobscura. Genetics 54, 577–594 (1966).
  CAS PubMed PubMed Central Google Scholar
• Kreitman, M. Nucleotide polymorphism at the alcohol dehydrogenase locus of Drosophila melanogaster. Nature 304, 412–417 (1983).
  Article CAS PubMed Google Scholar
• Golding, G. B. & Dean, A. M. The structural basis of molecular adaptation. Mol. Biol. Evol. 15, 355–369 (1998). A review summarizing classic early work in the functional synthesis.
  Article CAS PubMed Google Scholar
• McDonald, J. H. & Kreitman, M. Adaptive protein evolution at the adh locus in Drosophila. Nature 351, 652–654 (1991).
  Article CAS PubMed Google Scholar
• Yang, Z. & Nielsen, R. Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol. Biol. Evol. 19, 908–917 (2002).
  Article CAS PubMed Google Scholar
• Tajima, F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123, 585–596 (1989).
  CAS PubMed PubMed Central Google Scholar
• Nielsen, R. Molecular signatures of natural selection. Annu. Rev. Genet. 39, 197–218 (2005).
  Article CAS PubMed Google Scholar
• Nielsen, R. Statistical tests of selective neutrality in the age of genomics. Heredity 86, 641–647 (2001).
  Article CAS PubMed Google Scholar
• Eyre-Walker, A. Changing effective population size and the McDonald–Kreitman test. Genetics 62, 2017–2024 (2002).
  Google Scholar
• Koehn, R. K. & Hilbish, T. J. The adaptive importance of genetic variation. Am. Sci. 75, 134–141 (1987).
  Google Scholar
• Watt, W. B. in The Evolution of Population Biology (eds Singh, R. S. & Uyenoyama, M. K.) (Cambridge Univ. Press, Cambridge, 2004).
  Google Scholar
• Wheat, C. W., Watt, W. B., Pollock, D. D. & Schulte, P. M. From DNA to fitness differences: sequences and structures of adaptive variants of Colias phosphoglucose isomerase (PGI). Mol. Biol. Evol. 23, 499–512 (2006).
  Article CAS PubMed Google Scholar
• Brideau, N. J. et al. Two Dobzhansky–Muller genes interact to cause hybrid lethality in Drosophila. Science 314, 1292–1295 (2006).
  Article CAS PubMed Google Scholar
• Geffeney, S. L., Fujimoto, E., Brodie, E. D. 3rd, Brodie, E. D. Jr & Ruben, P. C. Evolutionary diversification of TTX-resistant sodium channels in a predator–prey interaction. Nature 434, 759–763 (2005). An elegant mechanistic-structural explanation of the repeated evolution of resistance to the tetrodotoxin of toxic newt prey, caused by amino-acid replacements in the voltage-gated sodium channels of garter snake muscles.
  Article CAS PubMed Google Scholar
• Zhang, J. Parallel adaptive origins of digestive RNases in Asian and African leaf monkeys. Nature Genet. 38, 819–823 (2006). Evolution of foregut fermentation in Asian and African leaf-eating monkeys is characterized by parallel amino-acid replacements that produce similar functional shifts in digestive RNases.
  Article CAS PubMed Google Scholar
• Zhang, J. et al. The crystal structure of a high oxygen affinity species of haemoglobin (bar-headed goose haemoglobin in the oxy form). J. Mol. Biol. 255, 484–493 (1996).
  Article CAS PubMed Google Scholar
• Zhang, J. & Rosenberg, H. F. Complementary advantageous substitutions in the evolution of an antiviral RNase of higher primates. Proc. Natl Acad. Sci. USA 99, 5486–5491 (2002).
  Article CAS PubMed PubMed Central Google Scholar
• Jermann, T. M., Opitz, J. G., Stackhouse, J. & Benner, S. A. Reconstructing the evolutionary history of the artiodactyl ribonuclease superfamily. Nature 374, 57–59 (1995).
  Article CAS PubMed Google Scholar
• Jessen, T. H., Weber, R. E., Fermi, G., Tame, J. & Braunitzer, G. Adaptation of bird hemoglobins to high altitudes: demonstration of molecular mechanism by protein engineering. Proc. Natl Acad. Sci. USA 88, 6519–6522 (1991).
  Article CAS PubMed PubMed Central Google Scholar
• Gaucher, E. A., Thomson, J. M., Burgan, M. F. & Benner, S. A. Inferring the palaeoenvironment of ancient bacteria on the basis of resurrected proteins. Nature 425, 285–288 (2003).
  Article CAS PubMed Google Scholar
• Chang, B. S., Jonsson, K., Kazmi, M. A., Donoghue, M. J. & Sakmar, T. P. Recreating a functional ancestral archosaur visual pigment. Mol. Biol. Evol. 19, 1483–1489 (2002).
  Article CAS PubMed Google Scholar
• Thomson, J. M. et al. Resurrecting ancestral alcohol dehydrogenases from yeast. Nature Genet. 37, 630–635 (2005). Ancestral yeast alcohol dehydrogenase (ADH) was reconstructed, expressed and shown to have the functional characteristics that are typical of extant ADH1, which is involved in ethanol production, rather than ADH2, which is involved in ethanol consumption.
  Article CAS PubMed Google Scholar
• Ugalde, J. A., Chang, B. S. & Matz, M. V. Evolution of coral pigments recreated. Science 305, 1433 (2004).
  Article CAS PubMed Google Scholar
• Soong, T. W. & Venkatesh, B. Adaptive evolution of tetrodotoxin resistance in animals. Trends Genet. 22, 621–626 (2006).
  Article CAS PubMed Google Scholar
• Doebley, J., Stec, A. & Hubbard, L. The evolution of apical dominance in maize. Nature 386, 485–488 (1997).
  Article CAS PubMed Google Scholar
• Shapiro, M. D. et al. Genetic and developmental basis of evolutionary pelvic reduction in threespine sticklebacks. Nature 428, 717–723 (2004).
  Article CAS PubMed Google Scholar
• Stern, D. L. Evolutionary developmental biology and the problem of variation. Evolution 54, 1079–1091 (2000).
  Article CAS PubMed Google Scholar
• Sucena, E., Delon, I., Jones, I., Payre, F. & Stern, D. L. Regulatory evolution of shavenbaby/ovo underlies multiple cases of morphological parallelism. Nature 424, 935–938 (2003).
  Article CAS PubMed Google Scholar
• Shimizu, K. K. et al. Darwinian selection on a selfing locus. Science 306, 2081–2084 (2004).
  Article CAS PubMed Google Scholar
• de Meaux, J., Pop, A. & Mitchell-Olds, T. _cis_-regulatory evolution of chalcone-synthase expression in the genus Arabidopsis. Genetics 174, 2181–2202 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• Benderoth, M. et al. Positive selection driving diversification in plant secondary metabolism. Proc. Natl Acad. Sci. USA 103, 9118–9123 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• Protas, M. E. et al. Genetic analysis of cavefish reveals molecular convergence in the evolution of albinism. Nature Genet. 38, 107–111 (2006).
  Article CAS PubMed Google Scholar
• Osborne, K. A. et al. Natural behavior polymorphism due to a cGMP-dependent protein kinase of Drosophila. Science 277, 834–836 (1997).
  Article CAS PubMed Google Scholar
• Newcomb, R. D. et al. A single amino acid substitution converts a carboxylesterase to an organophosphorus hydrolase and confers insecticide resistance on a blowfly. Proc. Natl Acad. Sci. USA 94, 7464–7468 (1997).
  Article CAS PubMed PubMed Central Google Scholar
• Newcomb, R. D., East, P. D., Russell, R. J. & Oakeshott, J. G. Isolation of α cluster esterase genes associated with organophosphate resistance in Lucilia cuprina. Insect Mol. Biol. 5, 211–216 (1996).
  Article CAS PubMed Google Scholar
• Parker, A. G., Campbell, P. M., Spackman, M. E., Russell, R. J. & Oakeshott, J. G. Comparison of an esterase associated with organophosphate resistance in Lucilia cuprina with an orthologue not associated with resistance in Drosophila melanogaster. Pestic. Biochem. Physiol. 55, 85–99 (1996).
  Article CAS PubMed Google Scholar
• Newcomb, R. D., Campbell, P. M., Russell, R. J. & Oakeshott, J. G. cDNA cloning, baculovirus-expression and kinetic properties of the esterase, E3, involved in organophosphorus resistance in Lucilia cuprina. Insect Biochem. Mol. Biol. 27, 15–25 (1997).
  Article CAS PubMed Google Scholar
• Hartley, C. J. et al. Amplification of DNA from preserved specimens shows blowflies were preadapted for the rapid evolution of insecticide resistance. Proc. Natl Acad. Sci. USA 103, 8757–8762 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• Claudianos, C., Russell, R. J. & Oakeshott, J. G. The same amino acid substitution in orthologous esterases confers organophosphate resistance on the house fly and a blowfly. Insect Biochem. Mol. Biol. 29, 675–686 (1999).
  Article CAS PubMed Google Scholar
• Hoekstra, H. E., Hirschmann, R. J., Bundey, R. A., Insel, P. A. & Crossland, J. P. A single amino acid mutation contributes to adaptive beach mouse color pattern. Science 313, 101–104 (2006).
  Article CAS PubMed Google Scholar
• Steiner, C. C., Weber, J. N. & Hoekstra, H. E. Adaptive variation in beach mice produced by interacting pigmentation genes. PLoS Biol. 5, e219 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Yokoyama, S., Zhang, H., Radlwimmer, F. B. & Blow, N. S. Adaptive evolution of color vision of the Comoran coelacanth (Latimeria chalumnae). Proc. Natl Acad. Sci. USA 96, 6279–6284 (1999).
  Article CAS PubMed PubMed Central Google Scholar
• Yokoyama, S. & Tada, T. Adaptive evolution of the African and Indonesian coelacanths to deep-sea environments. Gene 261, 35–42 (2000).
  Article CAS PubMed Google Scholar
• Yokoyama, S. Color vision of the coelacanth (Latimeria chalumnae) and adaptive evolution of rhodopsin (RH1) and rhodopsin-like (RH2) pigments. J. Hered. 91, 215–220 (2000).
  Article CAS PubMed Google Scholar
• Shi, Y., Radlwimmer, F. B. & Yokoyama, S. Molecular genetics and the evolution of ultraviolet vision in vertebrates. Proc. Natl Acad. Sci. USA 98, 11731–11736 (2001).
  Article CAS PubMed PubMed Central Google Scholar
• Shi, Y. & Yokoyama, S. Molecular analysis of the evolutionary significance of ultraviolet vision in vertebrates. Proc. Natl Acad. Sci. USA 100, 8308–8313 (2003).
  Article CAS PubMed PubMed Central Google Scholar
• Yokoyama, S., Starmer, W. T., Takahashi, Y. & Tada, T. Tertiary structure and spectral tuning of UV and violet pigments in vertebrates. Gene 365, 95–103 (2006).
  Article CAS PubMed Google Scholar
• Yokoyama, S. & Radlwimmer, F. B. The molecular genetics and evolution of red and green color vision in vertebrates. Genetics 158, 1697–1710 (2001).
  CAS PubMed PubMed Central Google Scholar
• Yokoyama, S. & Radlwimmer, F. B. The molecular genetics of red and green color vision in mammals. Genetics 153, 919–932 (1999).
  CAS PubMed PubMed Central Google Scholar
• Yokoyama, S. & Radlwimmer, F. B. The 'five-sites' rule and the evolution of red and green color vision in mammals. Mol. Biol. Evol. 15, 560–567 (1998).
  Article CAS PubMed Google Scholar
• Wright, S. The roles of mutation, inbreeding, crossbreeding, and selection in evolution. Proc. 6th Int. Cong. Genet. 1, 356–366 (1932).
  Google Scholar
• Phillips, P. C. & Arnold, S. J. Visualizing multivariate selection. Evolution 43, 1209–1222 (1989).
  Article PubMed Google Scholar
• Gavrilets, S. A dynamical theory of speciation on holey adaptive landscapes. Am. Nat. 154, 1–22 (1999).
  Article PubMed Google Scholar
• Gillespie, J. H. Molecular evolution over the mutational landscape. Evolution 38, 1116–1129 (1984).
  Article CAS PubMed Google Scholar
• Kauffman, S. A. The Origins of Order: Self-organization and Selection in Evolution (Oxford Univ. Press, Oxford, 1993).
  Google Scholar
• Fisher, R. A. The Genetical Theory of Natural Selection (Oxford Univ. Press, Oxford, 1930).
  Book Google Scholar
• Maynard Smith, J. Natural selection and the concept of a protein space. Nature 225, 563–564 (1970).
  Article Google Scholar
• Weinreich, D. M., Delaney, N. F., Depristo, M. A. & Hartl, D. L. Darwinian evolution can follow only very few mutational paths to fitter proteins. Science 312, 111–114 (2006).
  Article CAS PubMed Google Scholar
• Gillespie, J. H. A simple stochastic gene substitution model. Theor. Popul. Biol. 23, 2020–2015 (1983).
  Article Google Scholar
• Weinreich, D. M., Watson, R. A. & Chao, L. Perspective: sign epistasis and genetic constraint on evolutionary trajectories. Evolution 59, 1165–1174 (2005).
  CAS PubMed Google Scholar
• Lunzer, M., Miller, S. P., Felsheim, R. & Dean, A. M. The biochemical architecture of an ancient adaptive landscape. Science 310, 499–501 (2005).
  Article CAS PubMed Google Scholar
• Zhu, G., Golding, G. B. & Dean, A. M. The selective cause of an ancient adaptation. Science 307, 1279–1282 (2005).
  Article CAS PubMed Google Scholar
• Hurley, J. H. & Dean, A. M. Structure of 3-isopropylmalate dehydrogenase in complex with NAD+: ligand-induced loop closing and mechanism for cofactor specificity. Structure 2, 1007–1016 (1994).
  Article CAS PubMed Google Scholar
• Hurley, J. H., Dean, A. M., Koshland, D. E. Jr & Stroud, R. M. Catalytic mechanism of NADP+-dependent isocitrate dehydrogenase: implications from the structures of magnesium-isocitrate and NADP+ complexes. Biochemistry 30, 8671–8678 (1991).
  Article CAS PubMed Google Scholar
• Miller, S. P., Lunzer, M. & Dean, A. M. Direct demonstration of an adaptive constraint. Science 314, 458–461 (2006).
  Article CAS PubMed Google Scholar
• Dean, A. M. & Golding, G. B. Protein engineering reveals ancient adaptive replacements in isocitrate dehydrogenase. Proc. Natl Acad. Sci. USA 94, 3104–3109 (1997).
  Article CAS PubMed PubMed Central Google Scholar
• Chen, R., Greer, A. & Dean, A. M. A highly active decarboxylating dehydrogenase with rationally inverted coenzyme specificity. Proc. Natl Acad. Sci. USA 92, 11666–11670 (1995).
  Article CAS PubMed PubMed Central Google Scholar
• Gould, S. J. & Lewontin, R. C. 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 (1979).
  Article CAS PubMed Google Scholar
• Bridgham, J. T., Carroll, S. M. & Thornton, J. W. Evolution of hormone-receptor complexity by molecular exploitation. Science 312, 97–101 (2006).
  Article CAS PubMed Google Scholar
• Ortlund, E. A., Bridgham, J. T., Redinbo, M. R. & Thornton, J. W. Crystal structure of an ancient protein: evolution of a new function by conformational epistasis. Science 16 August 2007 (doi:101126/science.1142819).
• Thornton, J. W., Need, E. & Crews, D. Resurrecting the ancestral steroid receptor: ancient origin of estrogen signaling. Science 301, 1714–1717 (2003).
  Article CAS PubMed Google Scholar
• Thornton, J. W. Evolution of vertebrate steroid receptors from an ancestral estrogen receptor by ligand exploitation and serial genome expansions. Proc. Natl Acad. Sci. USA 98, 5671–5676 (2001).
  Article CAS PubMed PubMed Central Google Scholar
• Paley, W. Natural Theology: or, Evidences of the Existence and Attributes of the Deity, Collected from the Appearances of Nature (E. Paulder, London, 1802).
  Google Scholar
• Force, A. et al. Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151, 1531–1545 (1999).
  CAS PubMed PubMed Central Google Scholar
• Ohno, S. Evolution by Gene Duplication (Springer, New York, 1970).
  Book Google Scholar
• Copley, S. D. Enzymes with extra talents: moonlighting functions and catalytic promiscuity. Curr. Opin. Chem. Biol. 7, 265–272 (2003).
  Article CAS PubMed Google Scholar
• O'Brien, P. J. & Herschlag, D. Catalytic promiscuity and the evolution of new enzymatic activities. Chem. Biol. (London) 6, R91–R105 (1999).
  CAS Google Scholar
• Khersonsky, O., Roodveldt, C. & Tawfik, D. S. Enzyme promiscuity: evolutionary and mechanistic aspects. Curr. Opin. Chem. Biol. 10, 498–508 (2006).
  Article CAS PubMed Google Scholar
• Gerlt, J. A. & Babbitt, P. C. Divergent evolution of enzymatic function: mechanistically diverse superfamilies and functionally distinct suprafamilies. Annu. Rev. Biochem. 70, 209–246 (2001).
  Article CAS PubMed Google Scholar
• Carroll, S. B. Endless forms: the evolution of gene regulation and morphological diversity. Cell 101, 577–580 (2000).
  Article CAS PubMed Google Scholar
• Hoekstra, H. E. & Coyne, J. A. The locus of evolution: evo devo and the genetics of adaptation. Evolution 61, 995–1016 (2007).
  Article PubMed Google Scholar
• Leu, J. Y. & Murray, A. W. Experimental evolution of mating discrimination in budding yeast. Curr. Biol. 16, 280–286 (2006).
  Article CAS PubMed Google Scholar
• Velicer, G. J. et al. Comprehensive mutation identification in an evolved bacterial cooperator and its cheating ancestor. Proc. Natl Acad. Sci. USA 103, 8107–8112 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• Woods, R., Schneider, D., Winkworth, C. L., Riley, M. A. & Lenski, R. E. Tests of parallel molecular evolution in a long-term experiment with Escherichia coli. Proc. Natl Acad. Sci. USA 103, 9107–9112 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• Zhong, S., Khodursky, A., Dykhuizen, D. E. & Dean, A. M. Evolutionary genomics of ecological specialization. Proc. Natl Acad. Sci. USA 101, 11719–11724 (2004).
  Article CAS PubMed PubMed Central Google Scholar
• Davidson, E. H. The Regulatory Genome: Gene Regulatory Networks in Development and Evolution (Academic, Burlington, 2006).
  Google Scholar
• Kuhn, T. The Structure of Scientific Revolutions (Univ. Chicago Press, Chicago, 1996).
  Book Google Scholar
• Kornegay, J. R., Schilling, J. W. & Wilson, A. C. Molecular adaptation of a leaf-eating bird: stomach lysozyme of the hoatzin. Mol. Biol. Evol. 11, 921–928 (1994).
  CAS PubMed Google Scholar
• Nachman, M. W., Hoekstra, H. E. & D'Agostino, S. L. The genetic basis of adaptive melanism in pocket mice. Proc. Natl Acad. Sci. USA 100, 5268–5273 (2003).
  Article CAS PubMed PubMed Central Google Scholar
• Hiebl, I., Braunitzer, G. & Schneeganss, D. The primary structures of the major and minor hemoglobin-components of adult Andean goose (Chloephaga melanoptera, Anatidae): the mutation Leu>Ser in position 55 of the β-chains. Biol. Chem. Hoppe-Seyler 368, 1559–1569 (1987).
  Article CAS PubMed Google Scholar
• Bateson, W. Preface from Mendel's Principles of Heredity: A Defense (Cambridge Univ. Press, Cambridge, 1902).
  Book Google Scholar
• Goldschmidt, R. The material basis of evolution (Yale, New Haven, 1940).
  Google Scholar
• Bateson, W. Materials for the Study of Variation Treated with Especial Regard to Discontinuity in the Origin of Species (Macmillan, London, 1894).
  Google Scholar
• Wilks, H. M. et al. A specific, highly active malate dehydrogenase by redesign of a lactate dehydrogenase framework. Science 242, 1541–1544 (1988).
  Article CAS PubMed Google Scholar
• Cresko, W. A. et al. Parallel genetic basis for repeated evolution of armor loss in Alaskan threespine stickleback populations. Proc. Natl Acad. Sci. USA 101, 6050–6055 (2004).
  Article CAS PubMed PubMed Central Google Scholar
• Spiller, B., Gershenson, A., Arnold, F. H. & Stevens, R. C. A structural view of evolutionary divergence. Proc. Natl Acad. Sci. USA 96, 12305–12310 (1999).
  Article CAS PubMed PubMed Central Google Scholar
• Rothman, S. C., Voorhies, M. & Kirsch, J. F. Directed evolution relieves product inhibition and confers in vivo function to a rationally designed tyrosine aminotransferase. Protein Sci. 13, 763–772 (2004).
  Article CAS PubMed PubMed Central Google Scholar
• Oue, S., Okamoto, A., Yano, T. & Kagamiyama, H. Redesigning the substrate specificity of an enzyme by cumulative effects of the mutations of non-active site residues. J. Biol. Chem. 274, 2344–2349 (1999).
  Article CAS PubMed Google Scholar
• Hsu, C. C., Hong, Z., Wada, M., Franke, D. & Wong, C. H. Directed evolution of D-sialic acid aldolase to L-3-deoxy-manno-2-octulosonic acid (L-KDO) aldolase. Proc. Natl Acad. Sci. USA 102, 9122–9126 (2005).
  Article CAS PubMed PubMed Central Google Scholar
• Whitlock, M. C., Phillips, P. C., Moore, F. B. G. & Tonsor, S. J. Multiple fitness peaks and epistasis. Annu. Rev. Ecol. Syst. 26, 601–629 (1995).
  Article Google Scholar
• Provine, W. B. The origins of theoretical population genetics (Univ. Chicago Press, Chicago, 1971).
  Google Scholar
• Gavrilets, S. Evolution and speciation on holey adaptive landscapes. Trends Ecol. Evol. 12, 307–312 (1997).
  Article CAS PubMed Google Scholar
• Yokoyama, S. Molecular evolution of color vision in vertebrates. Gene 300, 69–78 (2002).
  Article CAS PubMed Google Scholar