Specific-gene studies of evolutionary mechanisms in an age of genome-wide surveying

Annals of the New York Academy of Sciences

Volumn 1289, Issue 1, 2013, Pages 1-17

  Watt, Ward B ^a  

^a STANFORD UNIVERSITY   (United States)

Author keywords

Adaptation; Evolutionary mechanisms; Exaptation; Genomics; Molecular evolution; Specific genes

Indexed keywords

GLOBIN; GLUCOSE 6 PHOSPHATE ISOMERASE; MELANIN; PHOSPHOENOLPYRUVATE CARBOXYKINASE (GTP); PHOSPHOGLUCOMUTASE;

ADAPTIVE BEHAVIOR; ALLELE; AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARTICLE; ARTIFICIAL SELECTION; BREEDING; DROSOPHILA MELANOGASTER; DROSOPHILA SIMULANS; ECOLOGICAL GENETICS; ENERGY METABOLISM; EPISTASIS; FEASIBILITY STUDY; FLOWER; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC SCREENING; GENETIC VARIABILITY; GENOMICS; GENOTYPE ENVIRONMENT INTERACTION; GENOTYPE PHENOTYPE CORRELATION; GLYCOLYSIS; HUMAN; LEPIDOPTERA; METABOLOMICS; MOLECULAR EVOLUTION; NATURAL POPULATION; NATURAL SELECTION; NONHUMAN; OXYGEN TRANSPORT; PHENOTYPE; PROTEIN EXPRESSION; PROTEOMICS; QUANTITATIVE GENETICS; QUANTITATIVE TRAIT LOCUS; REPRODUCIBILITY; SINGLE NUCLEOTIDE POLYMORPHISM; SPECIES COMPARISON;

EID: 84879317754     PISSN: 00778923     EISSN: 17496632     Source Type: Book Series    
DOI: 10.1111/nyas.12139     Document Type: Article

References (168)

1. Ward, L.D. & M. Kellis. 2012. Evidence of abundant purifying selection in humans for recently acquired regulatory functions. Science 337: 1675-1678.
2. Sella, G., D.A. Petrov, M. Przeworski & P. Andolfatto. 2009. Pervasive natural selection in the Drosophila genome? PLoS Genet. 5: e1000495.
3. Vera, J.C., C.W. Wheat, H. W. Fescemyer, et al. 2008. Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing. Mol. Ecol. 17: 1636-1647.
4. Dermitzakis, E.T. & A.G. Clark. 2009. Life after GWA studies. Science 326: 239-240.
5. Chakravarti, A. 2011. Genomics is not enough. Science 344: 15.
6. Suhre, K., S.-Y. Shin, A.-K. Petersen, et al. 2011. Human metabolic individuality in biomedical and pharmaceutical research. Nature 477: 54-60.
7. Anderson, J.T., J.H. Willis & T. Mitchell-Olds. 2011. Evolutionary genetics of plant adaptation. Trends Genet. 27: 258-266.
8. Fournier-Level, A., A. Korte, M.D. Cooper, et al. 2011. A map of local adaptation in Arabidopsis thaliana. Science 334: 86-89.
9. Hancock, A.M., B. Brachi, N. Faure, et al. 2011. Adaptation to climate across the Arabidopsis thaliana genome. Science 334: 83-86.
10. Endler, J.A. 1986. Natural Selection in the Wild. Princeton, NJ: Princeton University Press.
11. Feder, M.E. & W.B. Watt. 1992. "Functional biology of adaptation." In Genes in Ecology. R.J. Berry, T.J. Crawford & G.M. Hewitt, Eds.: 365-392. UK: British Ecological Society, Cambridge Press.
12. Watt, W.B. 2000. Avoiding paradigm-based limits to knowledge of evolution. Evol. Biol. 32: 73-96.
13. Watt, W.B. & A.M. Dean. 2000. Molecular-functional studies of adaptive genetic variation in prokaryotes and eukaryotes. Annu. Rev. Genet. 34: 593-622.
14. Laland, K.N., F. J. Odling-Smee, W. Hoppitt & T. Uller. 2013. More on how and why: cause and effect in biology revisited. Biol. Philos. In press.
15. Watt, W.B. 2013. Causal mechanisms of evolution and the capacity for niche construction. Biol. Philos.: In press.
16. Whitehead, A.N. 1929. The Aims of Education. New York, NY: Macmillan.
17. Ford, E.B. 1964. Ecological Genetics. London, UK: Methuen.
18. Majerus, M.E.N. 1998. Melanism: Evolution in Action. Oxford, UK: Oxford University Press.
19. Kettlewell, H.B.D. 1955. Selection experiments on industrial melanism in the Lepidoptera. Heredity 9: 323-342.
20. Kettlewell, H.B.D. 1956. Further selection experiments on industrial melanism in the Lepidoptera. Heredity 10: 287-301.
21. Cook, L.M., B.S. Grant, I.J. Saccheri, & J. Mallet. 2012. Selective bird predation on the peppered moth: the last experiment of Michael Majerus. Biol. Lett. 8: 609-612. doi: 10.1098/rsbl.2011.1136.
22. Gerould, J.H. 1921. Blue-green caterpillars: the origin and ecology of a mutation in hemolymph color in Colias (Eurymus) philodice. J. Exp. Zool. 34: 385-415.
23. Gerould, J.H. 1926. Inheritance of olive-green and blue-green variations appearing in the life cycle of a butterfly, Colias philodice. J. Exp. Zool. 43: 413-427.
24. Fisher, R.A. 1958. The Genetical Theory of Natural Selection. 2nd ed. NY: Dover.
25. Lerner, I.M. 1954. Genetic Homeostasis. Edinburgh, UK: Oliver & Boyd.
26. Mayr, E. 1961. Cause and effect in biology. Science 134: 1501-1506.
27. Mayr, E. 1980. "Some thoughts on the history of the evolutionary synthesis." In The Evolutionary Synthesis. E. Mayr & W.B. Provine, Eds.: 1-48. Cambridge, MA: Harvard University Press.
28. Hubby, J.L. & R.C. Lewontin. 1966. 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.
29. Lewontin, R.C. & J.L. Hubby. 1966. A molecular approach to the study of genic heterozygosity in natural populations. II: amount of variation and degree of heterozygosity in natural populations of Drosophila pseudoobscura. Genetics 54: 595-609.
30. Gillespie, J.H. & K.-I. Kojima. 1968. The degree of polymorphism in enzymes involved in energy production compared to that in non-specific enzymes in two Drosophila ananassae population. Proc. Natl. Acad. Sci. USA 61: 582-585.
31. Lewontin, R.C. 1974. The Genetic Basis of Evolutionary Change. NY: Columbia University Press.
32. Gillespie, J.H. 1991. The Causes of Molecular Evolution. NY: Oxford University Press.
33. Gillespie, J.H. 1994. Substitution processes in molecular evolution, II: exchangeable models from popu-lation genetics. Evolution 48: 1101-1113.
34. Watt, W.B. 1994. Allozymes in evolutionary genetics: self-imposed burden or extraordinary tool? Genetics 136: 11-16.
35. Watt, W.B. 1995. Allozymes in evolutionary genetics: beyond the twin pitfalls of "neutralism" and "selec-tionism." Revue Suisse de Zoologie 102: 869-882.
36. Falconer, D.S. 1981. Introduction to Quantitative Genetics, 2nd ed. London, UK: Longmans.
37. Kingsolver, J.G. & D.C. Wiernasz. 1991. Development, function, and the quantitative genetics of wing melanin pattern in Pieris butterflies. Evolution 45: 1480-1492.
38. Campbell, D.R., N.M. Waser & M.V. Price. 1991. Components of phenotypic selection-pollen export and flower corolla width in Ipomopsis aggregata. Evolution 45: 1458-1467.
39. Campbell, D.R., N.M. Waser & M.V. Price. 1996. Mechanisms of hummingbird-mediated selection for flower width in Ipomopsis aggregata. Ecology 77: 1463-1472.
40. Kingsolver, J.G., H.E. Hoekstra, J.M. Hoekstra, et al. 2001. The strength of phenotypic selection in natural populations. Am. Nat. 157: 245-261.
41. Hoekstra, H.E., J.M. Hoekstra, D. Berrigan, et al. 2001. Strength and tempo of directional selection in the wild. Proc. Natl. Acad. Sci. USA 98: 9157-9160.
42. Waddington, C.H. 1953. Genetic assimilation of an acquired character. Evolution 7: 118-126.
43. Milkman, R.D. 1970. The genetic basis of natural variation in Drosophila melanogaster. Adv. Genet. 15: 55-114.
44. Conley, C.A., R. Silburn, M.A. Singer, et al. 2000. Crossveinless2 contains cysteine-rich domains and is required for high levels of BMP-like activity during the formation of the crossveins in Drosophila. Development 127: 3947-3959.
45. Gibson, G. & D.S. Hogness. 1996. Effect of polymorphism in the Drosophila regulatory gene ultrabithorax on homeotic stability. Science 217: 200-203.
46. Dworkin, I. & G. Gibson. 2006. Epidermal growth factor receptor and transforming growth factor-β signaling contributes to variation for wing shape in Drosophila melanogaster. Genetics 173: 1417-1431.
47. Watt, W.B. 1968. Adaptive significance of pigment polymorphisms in Colias butterflies. I: variation of melanin pigment in relation to thermoregulation. Evolution 22: 437-458.
48. Watt, W.B. 1983. Adaptation at specific loci II. Demographic and biochemical elements in the maintenance of the Colias PGI polymorphism. Genetics 103: 691-724.
49. Watt, W.B. 1985. Bioenergetics and evolutionary genetics-opportunities for new synthesis. Amer. Nat. 125: 118-143.
50. Koehn, R.K. 1969. Esterase heterogeneity: dynamics of a polymorphism. Science 163: 943-944.
51. Clarke, B. 1975. The contribution of ecological genetics to evolutionary theory: detecting the direct effects of natural selection on particular polymorphic loci. Genetics 79: 101-113.
52. Place, A.R. & D.A. Powers. 1979. Genetic variation and relative catalytic efficiencies: lactate dehydrogenase B allozymes of Fundulus heteroclitus. Proc. Natl. Acad. Sci. USA 76: 2354-2358.
53. Powers, D.A. 1986. "A multidisciplinary approach to the study of genetic variation within species." In New Directions in Ecological Physiology. M.E. Feder, A.F. Bennett, W.W. Burggren & R.B. Huey, Eds.: 102-130. Cambridge, UK: Cambridge Univ. Press.
54. Bijlsma, R. & W. van Delden. 1977. Polymorphism at the G6PD and 6PGD loci in Drosophila melanogaster. I: evidence for selection in experimental populations. Genet. Res. Camb. 30: 221-236.
55. Bijlsma, R. & C. van der Meulen-Brijns. 1979. Polymorphism at the G6PD and 6PGD loci in Drosophila melanogaster. III: developmental and biochemical aspects. Biochem. Genet. 17: 1131-1144.
56. Cavener, D.R. & M.T. Clegg. 1981. Evidence for biochemical and physiological differences between enzyme genotypes in Drosophila melanogaster. Proc. Natl. Acad. Sci. USA 78: 4444-4447.
57. Dykhuizen, D.E. & D.L. Hartl. 1980. Selective neutrality of 6PGD allozymes in E. coli and the effects of genetic background. Genetics 96: 801-817.
58. Hartl, D.L. & D.E. Dykhuizen. 1981. Potential for selection among nearly neutral allozymes of 6-phosphogluconate dehydrogenase in Escherichia coli. Proc. Natl. Acad. Sci. USA 78: 6344-6348.
59. Dean, A.M. 1989. Selection and neutrality in lactose operons of Escherichia coli. Genetics 123: 441-454.
60. Crawford, D.L. & D.A. Powers. 1989. Molecular basis of evolutionary adaptation at the lactate dehydrogenase-B locus in the fish Fundulus heteroclitus. Proc. Natl. Acad. Sci. USA 86: 9365-9369.
61. Powers, D.A., T. Lauerman, D.L. Crawford & L. DiMichele. 1991. Genetic mechanisms for adapting to a changing environment. Annu. Rev. Genet. 25: 629-659.
62. Watt, W.B. 1992. Eggs, enzymes, and evolution-natural genetic variants change insect fecundity. Proc. Natl. Acad. Sci. USA 89: 10608-10612.
63. Gould, S.J. & R.C. Lewontin. 1979. The spandrels of San Marco and the Panglossian paradigm: a critique of the adaptationist programme. Proc. R. Soc. London B205: 581-598.
64. Rose, M.R. & G.V. Lauder Eds.: 1996. Adaptation. New York, NY: Academic Press.
65. West-Eberhard, M.J. 2003. Developmental Plasticity and Evolution. Oxford, UK: Oxford University Press.
66. Gibson, G. & S.V. Muse. 2009. A Primer of Genome Science, 3rd ed. Sunderland, MA: Sinauer Assoc.
67. International Human Genome Sequencing Consortium. 2001. Initial sequencing and analysis of the human genome. Nature 409: 860-921.
68. Venter, J.C., M. D. Adams, E.W. Myers, et al. 2001. The sequence of the human genome. Science 291: 1304-1351.
69. Thoday, J.M. 1961. Location of polygenes. Nature 191: 368-370.
70. Lander, E.S. & D. Botstein. 1989. Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121: 185-199. Erratum: 1994. Genetics 131: 705.
71. Mackay, T.F.C. 1009. Mutations and quantitative genetic variation: lessons from Drosophila. Phil. Trans. R. Soc. B365: 1229-1239.
72. International SNP map working group. 2001. A map of human genome sequence variation containing 1.42 million single-nucleotide polymorphisms. Nature 409: 928-933.
73. The Drosophila 12 Genomes Consortium. 2007. Evolution of genes and genones on the Drosophila phylogeny. Nature 450: 203-218.
74. Putnam, N.H., T. Butts, D.K.E. Ferrier, et al. 2008. The amphioxus genome and the evolution of the chordate karyotype. Nature 453: 10764-1072.
75. Duan, J., R. Li, D. Cheng, et al. 2010. SilkDB 2.0: a platform for silkworm (Bombyx mori) genome biology. Nucl. Acids Res. 38: D453-D456, silkworm.genomics.org.cn/silkdb/
76. Brenchley, R., M. Spannagi, M. Pfeifer, et al. 2012. Analysis of the bread wheat genome using whole-genome shotgun sequencing. Nature 491: 705-710.
77. Andolfatto, P. 2005. Adaptive evolution of non-coding DNA in Drosophila. Nature 437: 1149-1152.
78. Ellegren, H., L. Smeds, R. Burri, et al. 2012. The genomic landscape of species divergence in Ficedula flycatchers. Nature 491: 756-760.
79. Manolio, T.A., F.S. Collins, N.J. Cox, et al. 2009. Finding the missing heritability of complex diseases. Nature 461: 747-753.
80. Connolly, C.F. & J.M. Akey. 2012. On the prospects of whole-genome association mapping in Saccharomyces cerevisiae. Genetics 191: 1345-1353.
81. Bloom, J.S., I.M. Ehrenreich, W.T. Loo, et al. 2013. Finding the sources of missing heritability in a yeast cross. Nature 494: 234-237.
82. Barabasi, A.-L. & Z.N.Olivai. 2004. Network biology: understanding the cell's functional organization. Nature Rev. Genet. 5: 101-113.
83. Greenberg, A.J., S.R. Stockwell & A.G. Clark. 2008. Evolutionary constraint and adaptation in the metabolic network of Drosophila. Mol. Biol. Evol. 25: 2537-2546.
84. Hahn, M.W., G.C. Conant & A. Wagner. 2004. Molecular evolution in large genetic networks: does connectivity equal constraint? J. Mol. Evol. 58: 203-211.
85. Vitkup, D., P. Kharchenko & A. Wagner. 2006. Influence of metabolic network structure and function on enzyme evolution. Genome Biol. 7: R39.
86. Sawyer, S.A. & D.L. Hartl. 1992. Population genetics of polymorphism and divergence. Genetics 132: 1161-1176.
87. Hillenmeyer, M.E., E. Fung, J. Wildenhain, et al. 2008. The chemical genomic portrait of yeast: uncovering a phenotype for all genes. Science 320: 362-365.
88. Rockman, M. 2012. The QTN program and the alleles that matter for evolution: all that's gold does not glitter. Evolution 66: 1-13.
89. Travisano, M. & R.G. Shaw. 2012. Lost in the map. Evolution 67: 305-314.
90. Stern, D.L. & V. Orgogozo. 2008. The loci of evolution: how predictable is genetic evolution? Evolution 62: 2155-2177.
91. Feder, M.E. & T.Mitchell-Olds. 2003. Ecological and evolutionary functional genomics. Nat. Rev. Genet. 4: 649-655.
92. Barrett, R.D.H. & H.E. Hoekstra. 2011. Molecular spandrels: tests of adaptation at the genetic level. Nat. Rev. Genet. 12: 767-780.
93. Eanes, W.F. 1999. Analysis of selection on enzyme polymorphisms. Annu. Rev. Syst. Ecol. 30: 301-326.
94. Feder, M.E., N. Blair & H. Figueras. 1997. Natural thermal stress and heat-shock protein expression in Drosophila larvae and pupae. Funct. Ecol. 11: 90-100.
95. Krebs, R.A. & M.E. Feder. 1997. Natural variation in the expression of the heat-shock protein hsp70 in a population of Drosophila melanogaster and its correlation with tolerance of ecologically relevant thermal stress. Evolution 50: 173-179.
96. Hoffman, A.A. & P.A. Parsons. 1997. Extreme Environmental Change and Evolution. Cambridge, UK: Cambridge University Press.
97. Schmidt, P.S. & D.R. Conde. 2006. Environmental heterogeneity and the maintenance of genetic variation for reproductive diapause in Drosophila melanogaster. Evolution 60: 1602-1611.
98. Schmidt, P.S., C.T. Zhu, J. Das, et al. 2008. An amino acid polymorphism in the couch potato gene forms the basis for climatic adaptation in Drosophila melanogaster. Proc. Natl. Acad. Sci. USA 105: 16207-16211.
99. Paaby, A.B., M.J. Blackett, A.A. Hoffman, et al. 2010. Identification of a candidate adaptive polymorphism for Drosophila life history by parallel independent clines on two continents. Mol. Ecol. 9: 760-774.
100. Chaneton, B., P. Hillmann, L. Zheng, et al. 2012. Serine is a natural ligand and allosteric activator of pyruvate kinase M2. Nature 491: 458-462.
101. Riley, R.M., W. Jin & G. Gibson. 2003. Contrasting selection pressures on components of the Ras-mediated signal transduction pathway in Drosophila. Mol. Ecol. 12: 1315-1323.
102. Lehmann, F.-O. & M.H. Dickinson. 1997. The change in power requirements and muscle efficiency during elevated force production in the fruit fly Drosophila melanogaster. J. Exp. Biol. 200: 1133-1143.
103. Dickinson, M.H. 2006. Primer: insect flight. Curr. Biol. 16: R309-R314.
104. Montooth, K.L., J.H. Marden & A.G. Clark. 2003. Mapping determinants of variation in energy metabolism, respiration and flight in Drosophila. Genetics 165: 623-635.
105. Breen, M.S., C. Kemena, P.K. Vlasov, et al. 2012. Epistasis as the primary factor in molecular evolution. Nature 490: 535-538.
106. Watt, W.B. 2003. "Mechanistic studies of butterfly adaptations." In Butterflies: Ecology and Evolution Taking Flight. C.L. Boggs, W.B. Watt & P.R. Ehrlich, Eds.: 319-352. Chicago, IL: University of Chicago Press.
107. Wheat, C.W. & W.B. Watt. 2008. A mitochondrial-DNA-based phylogeny for some evolutionary-genetic model species of Colias butterflies (Lepidoptera, Pieridae). Mol. Phylog. Evol. 47: 893-902.
108. Watt, W.B., K. Donohue & P.A. Carter. 1996. Adaptation at specific loci. VI: divergence vs. parallelism of polymorphic allozymes in molecular function and fitness-component effects among Colias species (Lepidoptera, Pieridae). Mol. Biol. Evol. 13: 699-709.
109. Watt, W.B., C.W. Wheat, E.H. Meyer & J.-F. Martin. 2003. Adaptation at specific loci. VII: natural selection, dispersal, and the diversity of molecular-functional variation patterns among butterfly species complexes (Colias: Lepidoptera, Pieridae). Mol. Ecol. 12: 1265-1275.
110. Wheat, C.W., W.B. Watt, D.D. Pollock & P.M. Schulte. 2006. From DNA to fitness differences: sequences and structures of adaptive variants of Colias phosphoglucose isomerase (PGI). Mol. Biol. Evol. 23: 499-512.
111. Wang, B.-Q., W.B. Watt, C. Aakre & N. Hawthorne. 2009. Emergence of complex haplotypes from microevolutionary variation in sequence and structure of Colias phosphoglucose isomerase. J. Mol. Evol. 68: 433-447.
112. Hill, J.A. & W.B. Watt. Unpublished results.
113. Hanski, I. & I. Saccheri. 2006. Molecular-level variation affects population growth in a butterfly metapopulation. PLoS Biol. 4: 719-226.
114. Orsini, L., C.W. Wheat, C.R. Haig et al. 2009. Fitness differences associated with Pgi SNP genotypes in the Glanville fritillary butterfly (Melitaea cinxia). J. Evol. Biol. 22: 367-275.
115. Wheat, C.W., C.R. Haig, J.H. Marden, et al. 2010. Nucleotide polymorphism at a gene (Pgi) under balancing selection in a butterfly metapopulation. Mol. Biol. Evol. 27: 267-281.
116. Carter, P.A. & W.B. Watt. 1988. Adaptation at specific loci. V: metabolically adjacent enzyme loci may have very distinct experiences of selective pressures. Genetics 119: 913-924.
117. Watt, W.B., E. Wang, B. Wang, et al. Unpublished results.
118. Watt, W.B., R.R. Hudson, B.-Q. Wang & E. Wang. 2013. An enzyme, PEPCK, polymorphic in two cell compartments and in parallel in two clades. BMC Evol. Biol. 13: 9 (pp. 1-15).
119. Eanes, W.F. 1994. "Patterns of polymorphism and between species divergence in the enzymes of central metabolism." In Non-neutral Evolution: Theories and Molecular Data. B. Golding, Eds.: 18-28. New York: Chapman & Hall.
120. Labate, J. & W.F. Eanes. 1992. Direct measurement of in vivo flux differences between electrophoretic variants of G6PD from Drosophila melanogaster. Genetics 132: 783-787.
121. Verrelli, B.C. & W.F. Eanes. 2001a. Clinal variation for amino acid polymorphisms at the Pgm locus in Drosophila melanogaster. Genetics 157: 1649-1663.
122. Verrelli, B.C. & W.F. Eanes. 2001b. The functional impact of Pgm amino acid polymorphism on glycogen content in Drosophila melanogaster. Genetics 159: 201-210.
123. Leigh Brown, A.J. 1977. Physiological correlates of an enzyme polymorphism. Nature 269: 803-804.
124. Flowers, J.M., E. Sezgin, S. Kumagai, et al. 2007. Adaptive evolution of metabolic pathways in Drosophila. Mol. Biol. Evol. 24: 1347-1354.
125. Rawson, P.D. & R.S. Burton. 2002. Functional coadaptation between cytochrome c and cytochrome c oxidase within allopatric populations of a marine copepod. Proc. Natl. Acad. Sci. USA 99: 12955-12958.
126. Sackton, T.M., R.A. Haney & D.M. Rand. 2003. Cytonuclear coadaptation in Drosophila: disruption of cytochrome c oxidase activity in backcross genotypes. Evolution 57: 2315-2325.
127. Rand, D.M., R.A. Haney & A.J. Fry. 2004. Cytonuclear evolution: the genomics of cooperation. Trends Ecol. Evol. 19: 645-653.
128. Willett, C.S. & R.S. Burton. 2006. Evolution of interacting proteins in the mitochondrial electron transport system in a marine copepod. Mol. Biol. Evol. 21: 443-453.
129. Edmands, S., S.L. Northrup & A.S. Hwang. 2009. Maladapted gene complexes within populations of the intertidal copepod Tigriopus californicus? Evolution 61: 2184-2192.
130. Blair, W.F. 1950. Ecological factors in speciation of Peromyscus. Evolution 4: 253-275.
131. Snyder, L.R.G. 1978. Genetics of hemoglobin in the deer mouse, Peromyscus maniculatus. I. Multiple α- and β-globin structural loci. Genetics 89: 511-530.
132. Snyder, L.R.G. 1981. Deer mouse hemoglobins: is there genetic adaptation to high altitude? Bioscience 31: 299-304.
133. Chappell, M.A., J.P. Hayes & L.R.G. Snyder. 1988. Hemoglobin polymorphisms in deer mice (Peromyscus maniculatus): physiology of β-globin variants and α-globin recombinants. Evolution 42: 681-688.
134. Snyder, L.R.G., M. A. Chappell & J.P. Hayes. 1988. α-chain hemoglobin polymorphisms are correlated with altitude in the deer mouse, Peromyscus maniculatus. Evolution 42: 689-697.
135. Storz, J.F., A.M. Runck, S.J. Sabatino, et al. 2009. Evolutionary and functional insights into the mechanism underlying high-altitude adaptation of deer mouse hemoglobin. Proc. Natl. Acad. Sci. USA 106: 14450-14456.
136. Storz, J.F., A.M. Runck, H. Moriyama, et al. 2010. Genetic differences in hemoglobin function between highland and lowland deer mice. J. Exp. Biol 213: 2565-2574.
137. Chen, Y.P., S.A. Woodin, D.E. Lincoln & C.R. Lovell. 1996. An unusual dehalogenating peroxidase from the marine terebellid polychaete Amphitrite ornata. J. Biol.Chem. 271: 4609-4612.
138. Lebioda, L., M.W. LaCount, E. Zhang, et al. 1999. An enzymatic globin from a marine worm. Nature 401: 445.
139. Han, K., S.A. Woodin, D.E. Lincoln, et al. 2001. Amphitrite ornata, a marine worm, contains two haloperoxidase genes. Mar. Biotechnol. 3: 287-292.
140. 2. Biochemistry 49: 6064-6069.
141. Du, J., X. Huang, S. Sun, et al. 2011. Amphitritre ornata dehaloperoxidase (DHP): investigations of structural factors that influence the mechanism of halophenol dehalogenation using "peroxidase-like" myoglobin mutants and "myoglobin-like" DHP mutants. Biochemistry 50: 8172-8180.
142. Bridgham, J.T., S.M. Carroll & J.W. Thornton. 2006. Evolution of hormone-receptor complexity by molecular exploitation. Science 312: 97-101.
143. Gould, S.J. & E.S.Vrba. 1982. Exaptation-a missing term in the science of form. Paleobiology 8: 4-15.
144. Hoekstra, H.E. & M.W. Nachman. 2003. Different genes underlie adaptive melanism in different populations of rock pocket mice. Mol. Ecol. 12: 1185-1194.
145. Hoekstra, H.E., R.J. Hirschmann, R.A. Bundey, et al. 2006. A single amino acid mutation contributes to adaptive beach mouse color pattern. Science 313: 101-104.
146. Steiner, C.C., J.N. Weber & H.E. Hoekstra. 2007. Adaptive variation in beach mice produced by two interacting pigment genes. PLoS Biol. 5: e219.
147. Linnen, C.R., E.P. Kingsley, J.D. Jensen & H.E. Hoekstra. 2009. On the origin and spread of an adaptive allele in deer mice. Science 325: 1095-1098.
148. Vigneri, S.N., J.N. Larson & H.E. Hoekstra. 2010. The selective advantage of cryptic coloration in mice. Evolution 64: 2153-2158.
149. Linnen, C.R., Y.-P. Poli, B.K. Petersen, et al. 2013. Adaptive evolution of multiple traits through multiple mutations at a single gene. Science 339: 1312-1316.
150. van't Hof, A.E., N. Edmonds, M. Dalikova, et al. 2011. Industrial melanism in British peppered moths has a singular and recent mutational origin. Science 332: 958-960.
151. Bell, M.A. & S.A. Foster, Eds.: 1994. Evolutionary Biology of the Threespine Stickleback. Oxford, UK: Oxford University Press.
152. Shapiro, M.D., M.E. Marks, C.L. Peichel, et al. 2004. Genetic and developmental basis of evolutionary pelvic reduction in threespine sticklebacks. Nature 428: 717-723.
153. Cresko, W.A., A. Amores, C. Wilson, et al. 2001. Parallel genetic basis for repeated evolution of armor loss in Alaskan threespine stickleback populations. Proc. Natl. Acad. Sci. USA 101: 6050-6055.
154. Jones, F.C., M.G. Grabherr, Y.F. Chan, et al. 2012. The genomic basis of adaptive evolution in threespine sticklebacks. Nature 484: 55-61.
155. Grant, P.R. 1986. Ecology and Evolution of Darwin's Finches. Princeton, NJ: Princeton University Press.
156. Abzhanov, A.M., M. Protas, B.R. Grant, et al. 2004. Bmp4 and morphological variation of beaks in Darwin's finches. Science 305: 1462-1466.
157. Abzhanov, A.M., W.P. Kuo, C. Hartmann, et al. 2006. The calmodulin pathway and evolution of elongated beak morphology in Darwin's finches. Nature 442: 563-567.
158. Mallarino, R., P.R. Grant, B.R. Grant, et al. 2011. Two developmental modules establish 3D beak shape variation in Darwin's finches. Proc. Natl. Acad. Sci. USA 108: 4057-4062.
159. Tian, D., H. Araki, E. Stahl, et al. 2002. Signature of balancing selection in Arabidopsis. Proc. Natl. Acad. Sci. USA 99: 11525-11530.
160. Mitchell-Olds, T. & J.M. Schmitt. 2006. Genetic mechanisms and evolutionary significance of natural variation in Arabidopsis. Nature 441: 947-952.
161. Prasad, K.V.S.K., B.-H. Song, C. Olson-Manning, et al. 2012. A gain-of-function polymorphism controlling complex traits and fitness in nature. Science 337: 1081-1084.
162. Ohno, S. 1970. Evolution by Gene Duplication. New York, NY: Springer.
163. Näsvall, J., L. Sun, J.R. Roth & D.I. Anderson. 2012. Real-time evolution of new genes by innovation, amplification, and divergence. Science 338: 384-387.
164. Irschick, D.J., R.C. Anderson, P. Brennan, et al. 2013. Evo-devo beyond morphology: from genes to resource use. Trends Ecol. Evol. 8: 267-273.
165. Wade, M.J. The co-evolutionary genetics of ecological communities. Nat. Rev. Genet. 8: 185-195.
166. Whitham, T.G., S.P. DiFazio, J.A. Schweitzer, et al. 2008. Extending genomics to natural communities and ecosystems. Science 320: 492-495.
167. Bailey, J.K., J.A. Schweitzer, F. Ubeda, et al. 2009. From genes to ecosystems: a synthesis of the effects of plant genetic factors across levels of organization. Phil. Trans. R. Soc. B364: 1607-1616.
168. Wymore, A.S., A.T.H. Keeley, K.M. Yturralde, et al. 2011. Genes to ecosystems: exploring the frontiers of ecology with one of the smallest biological units. N. Phytol. 191: 19-36.