Genome growth and the evolution of the genotype-phenotype map

  • Lee Altenberg
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Part of the Lecture Notes in Computer Science book series (LNCS, volume 899)

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References

  1. Aboitiz, F. 1991. Lineage selection and the capacity to evolve. Medical Hypotheses 36(2): 155–156.Google Scholar
  2. Alberch, P. 1981. From genes to phenotype: dynamical systems and evolvability. Genetica 84: 5–11.Google Scholar
  3. Altenberg, L. 1983. Letter to Nature. Unpublished.Google Scholar
  4. Altenberg, L. 1985. Knowledge representation in the genome: new genes, exons, and pleiotropy. Genetics 110, supplement: s41. Abstract of paper presented at the 1985 Meeting of the Genetics Society of America.Google Scholar
  5. Altenberg, L. 1994a. The evolution of evolvability in genetic programming. In K. E. Kinnear, editor, Advances in Genetic Programming, pages 47–74. MIT Press, Cambridge, MA.Google Scholar
  6. Altenberg, L. 1994b. Evolving better representations through selective genome growth. In J. D. Schaffer, H. P. Schwefel, and H. Kitano, editors, Proceedings of the IEEE World Congress on Computational Intelligence, pages 182–187, Piscataway N.J. IEEE.Google Scholar
  7. Altenberg, L. 1995. The Schema Theorem and Price's Theorem. In D. Whitley and M. D. Vose, editors, Foundations of Genetic Algorithms 3. Morgan Kaufmann, San Mateo, CA.Google Scholar
  8. Altenberg, L. and D. L. Brutlag. 1986. Selection for modularity in the genome. Unpublished manuscript. Cited in Doolittle (1987).Google Scholar
  9. Altenberg, L. and M. W. Feldman. 1987. Selection, generalized transmission, and the evolution of modifier genes. I. The reduction principle. Genetics 117: 559–572.Google Scholar
  10. Arnold, S. J., P. Alberch, V. Csanyi, R. C. Dawkins, S. B. Emerson, B. Fritzsch, T. J. Horder, J. Maynard Smith, M. J. Starck, E. S. Vrba, G. P. Wagner, and D. B. Wake. 1988. How do complex organisms evolve? In D. B. Wake and G. Roth, editors, Complex Organismal Functions: Integration and Evolution in Vertebrates, pages 403–433. John Wiley and Sons, New York.Google Scholar
  11. Baer, K. E. v. 1828. Entwichlungsgeschichte der Thiere: Beobachtung und Reflexion. Bornträger, Königsberg, pages 221–224.Google Scholar
  12. Barwise, J. and J. Perry. 1983. Situations and Attitudes. M.I.T. Press, Boston, pages 292–295.Google Scholar
  13. Blake, C. C. F. 1978. Nature 273: 267.Google Scholar
  14. Bonner, J. T. 1974. On Development: The Biology of Form. Harvard University, Cambridge, MA, page 61.Google Scholar
  15. Brakenhoff, R. H., H. J. M. Aarts, F. H. Reek, N. H. Lubsen, and J. G. G. Schoenmakers. 1990. Human.gamma.-crystallin genes: A gene family on its way to extinction. Journal of Molecular Biology 216(3): 519–532.Google Scholar
  16. Brandon, R. N. 1990. Adaptation and Environment. Princeton University Press, Princeton, pages 83–84.Google Scholar
  17. Burt, D. W. and I. R. Paton. 1992. Evolutionary origins of the transforming growth factor-β gene family. DNA and Cell Biology 11(7): 497–510.Google Scholar
  18. Cairns, J. and P. L. Foster. 1991. Adaptive reversion of a frameshift mutation in Escherichia coli. Genetics 128(4): 695–702.Google Scholar
  19. Cairns, J., J. Overbaugh, and S. Miller. 1988. The origin of mutants. Nature 335: 142–145.Google Scholar
  20. Casorati, G., A. Traunecker, and K. Karjalainen. 1993. The t cell receptor alpha-beta v-j shuffling shows lack of autonomy between the combining site and the constant domain of the receptor chains. European Journal of Immunology 23(2): 586–589.Google Scholar
  21. Cavalier-Smith, T. 1977. Visualising jumping genes. Nature 270: 10–12.Google Scholar
  22. Cheverud, J. 1984. Quantitative genetics and developmental constraints on evolution by selection. Journal of Theoretical Biology 110: 155–171.Google Scholar
  23. Cheverud, J. M., G. P. Wagner, and M. M. Dow. 1989. Methods for the comparative analysis of variation patterns. Systematic Zoology 38(3): 201–213.Google Scholar
  24. Conrad, M. 1979a. Bootstrapping on the adaptive landscape. BioSystems 11: 167–182.Google Scholar
  25. Conrad, M. 1982. Natural selection and the evolution of neutralism. BioSystems 15: 83–85.Google Scholar
  26. Craik, C., S. Buchman, and S. Beychok. 1980. Proceedings of the National Academy of Sciences U.S.A. 77: 1384–1388.Google Scholar
  27. Crick, F. 1979. Split genes and RNA splicing. Science 204: 264–271.PubMedGoogle Scholar
  28. Crow, J. F. and M. Kimura. 1970. An Introduction to Population Genetics Theory. Alpha Editions, Edina, MN, pages 418–430.Google Scholar
  29. Crow, J. F. and T. Nagylaki. 1976. The rate of change of a character correlated with fitness. American Naturalist 110(972): 207–213.Google Scholar
  30. Dawkins, R. 1989. The evolution of evolvability. In C. G. Langten, editor, Artificial life, the proceedings of an Interdisciplinary Workshop on the Synthesis and Simulation of Living Systems. Addison-Wesley, Redwood City, CA.Google Scholar
  31. De Vries, C., H. Veerman, F. Blasi, and H. Pannekoek. 1988. Artificial exon shuffling between tissue-type plasminogen activator (t-PA) and urokinase (u-PA): A comparative study on the fibrinolytic properties of T-PA/u-PA hybrid proteins. Biochemistry 27(7): 2565–2572.Google Scholar
  32. del Pino, E. M. and R. P. Elinson. 1983. A novel development pattern for frogs: gastrulation produces and embryonic disk. Nature 306: 589–591.Google Scholar
  33. Doolittle, R. F. 1985. The genealogy of some recently evolved vertebrate proteins. Trends in Biochemical Sciences 10: 233–237.Google Scholar
  34. Doolittle, W. F. 1987. The origin and function of intervening sequences in DNA: A review. American Naturalist 130: 915–928.Google Scholar
  35. Doolittle, W. F. and C. Sapienza. 1980. Selfish genes, the phenotype paradigm and genome evolution. Nature 284: 601–603.PubMedGoogle Scholar
  36. Dorit, R. L. and W. Gilbert. 1990. How big is the universe of exons? Science 250(4986): 1377–1382.Google Scholar
  37. Dorit, R. L., L. Schoenbach, and W. Gilbert. 1991. Exon shuffling and the underlying motifs of protein evolution. Journal of Cellular Biochemistry Supplement 15 PART D: 81.Google Scholar
  38. Eldredge, N. 1989. Macroevolutionary Dynamics: Species, Niches, and Adaptive Peaks. McGraw-Hill, New York, page 205.Google Scholar
  39. Eshel, I. 1973. Clone-selection and optimal rates of mutation. Journal of Applied Probability 10: 728–738.Google Scholar
  40. Feller, W. 1971. An Introduction to Probability Theory and Its Applications. John Wiley and Sons, New York, page 27.Google Scholar
  41. Fisher, R. A. 1930. The Genetical Theory of Natural Selection. Clarendon Press, Oxford, pages 30–37.Google Scholar
  42. Foster, P. L. and J. Cairns. 1992. Mechanisms of directed mutation. Genetics 131(4): 783–789.Google Scholar
  43. Frank, S. A. and M. Slatkin. 1990. The distribution of allelic effects under mutation and selection. Genetical Research, Cambridge 55: 111–117.Google Scholar
  44. Frazzetta, T. H. 1975. Complex Adaptations in Evolving Populations. Sinauer Associates, Sunderland, MA, pages 212–238.Google Scholar
  45. Gelfand, M. S. 1992. Statistical analysis and prediction of the exonic structure of human genes. Journal of Molecular Evolution 35: 239–252.Google Scholar
  46. Gilbert, W. 1978. Why genes in pieces? Nature 271: 501.PubMedGoogle Scholar
  47. Gilbert, W. and M. Glynias. 1993. On the ancient nature of introns. Gene 135(1–2): 137–144.Google Scholar
  48. Gillespie, J. H. 1984. Molecular evolution over the mutational landscape. Evolution 38(5): 1116–1129.Google Scholar
  49. Gimelfarb, A. 1986. Additive variation maintained under stabilizing selection: a two-locus model of pleiotropy for two quantitative characters. Genetics 112: 717–725.Google Scholar
  50. Gimelfarb, A. 1992. Pleiotropy and multilocus polymorphisms. Genetics 130: 223–227.Google Scholar
  51. Golub, G. H. and C. F. V. Loan. 1983. Matrix Computations. Johns Hopkins University Press, Baltimore, page 152.Google Scholar
  52. Goodwin, B. C. 1989. Evolution and the generative order. In B. C. Goodwin and P. T. Saunders, editors, Theoretical Biology: Epigenetic and Evolutionary Order, pages 89–100. Edinburgh University Press.Google Scholar
  53. Grafen, A. 1985. A geometric view of relatedness, Oxford Surveys in Evolutionary Biology 2: 28–89.Google Scholar
  54. Haefliger, D. N., J. E. Moskaitis, D. R. Schoenberg, and W. Wahli. 1989. Amphibian albumins as members of the albumin, alpha-fetoprotein, vitamin D-binding protein multigene family. Journal of Molecular Evolution 29(4): 344–354.Google Scholar
  55. Haldane, J. B. S. 1927. A mathematical theory of natural and artificial selection. part V. selection and mutation. Proceedings of the Cambridge Philosophical Society 23: 838–844.Google Scholar
  56. Hastings, A. and C. L. Hom. 1989. Pleiotropic stabilizing selection limits the number of polymorphic loci to be at most the number of characters. Genetics 122: 459–463.Google Scholar
  57. Hastings, A. and C. L. Hom. 1990. Multiple equilibria and maintenance of additive genetic variance in a model of pleiotropy. Evolution 44: 1153–1163.Google Scholar
  58. Kappen, C., K. Schughart, and F. H. Ruddle. 1989. Two steps in the evolution of antennapedia-class vertebrate homeobox genes. Proceedings of the National Academy of Sciences of the United States of America 86(14): 5459–5463.Google Scholar
  59. Kauffman, S. A. 1989a. Adaptation on rugged fitness landscapes. In D. Stein, editor, Lectures in the Sciences of Complexity, pages 527–618. Addison-Wesley, Redwood City. SFI Studies in the Sciences of Complexity, Lecture Volume I.Google Scholar
  60. Kauffman, S. A. 1989b. Principles of adaptation in complex systems. In D. Stein, editor, Lectures in the Sciences of Complexity, pages 619–712. Addison-Wesley, Redwood City. SFI Studies in the Sciences of Complexity, Lecture Volume I.Google Scholar
  61. Kauffman, S. A. and S. Levin. 1987. Towards a general theory of adaptive walks on rugged landscapes. Journal of Theoretical Biology 128: 11–45.Google Scholar
  62. Klenova, E. M., I. Botezato, V. Laudet, G. H. Goodwin, J. C. Wallace, and V. V. Lobanenkov. 1992. Isolation of a cDNA clone encoding the RNase-superfamily-related gene highly expressed in chicken bone marrow cells. Biochemical and Biophysical Research Communications 185(1): 231–239.Google Scholar
  63. Koehn, R. K., A. J. Zera, and J. G. Hall. 1983. Enzyme polymorphism and natural selection. In M. Nei and R. K. Koehn, editors, Evolution of Genes and Proteins, chapter 6, pages 115–136. Sinauer Associates, Sunderland, MA.Google Scholar
  64. Lande, R. and S. J. Arnold. 1983. The measurement of selection on correlated characters. Evolution 37(6): 1210–1226.Google Scholar
  65. Lerner, I. M. 1954. Developmental Homeostasis. Oliver and Boyd, Edinburgh.Google Scholar
  66. Levinton, J. 1988. Genetics, Paleontology, and Macroevolution. Cambridge University Press, Cambridge, pages 224–225, 494.Google Scholar
  67. Lewontin, R. C. 1978. Adaptation. Scientific American 239(3): 213–230.Google Scholar
  68. Li, W.-H. 1985. Accelerated evolution following gene duplication and its implication for the neutralist-selectionist controversy. In T. Ohta and K. Aoki, editors, Population Genetics and Molecular Evolution, pages 333–352. Springer-Verlag, Berlin.Google Scholar
  69. Liberman, U. and M. W. Feldman. 1986b. A general reduction principle for genetic modifiers of recombination. Theoretical Population Biology 30: 341–371.Google Scholar
  70. Luenberger, D. G. 1968. Optimization by Vector Space Methods. John Wiley and Sons, New York, pages 46–62.Google Scholar
  71. Macken, C. A. and A. S. Perelson. 1989. Protein evolution on rugged landscapes. Proceedings of the National Academy of Sciences of the United States of America 86: 6191–6195.Google Scholar
  72. Maynard Smith, J. 1970. Natural selection and the concept of a protein space. Nature 225: 563–564.Google Scholar
  73. Maynard Smith, J., R. Burian, S. Kauffman, P. Alberch, J. Campbell, B. Goodwin, R. Lande, D. Raup, and L. Wolpert. 1985. Developmental constraints and evolution. Quarterly Review of Biology 60(3): 265–571.Google Scholar
  74. Mencarelli, C., B. Magi, B. Marzocchi, M. Contorni, and V. Pallini. 1991. Evolutionary trends of neurofilament proteins in fish. Comparative Biochemistry and Physiology B Comparative Biochemistry 100(4): 733–740.Google Scholar
  75. Nemeschkal, H. L., R. Van Den Elzen, and H. Brieschke. 1992. The morphometric extraction of character complexes accomplishing common biological roles: Avian skeletons as a case study. Zeitschrift für Zoologische Systematik und Evolutionsforschung 30(3): 201–219.Google Scholar
  76. Nishikimi, M., T. Kawai, and K. Yagi. 1992. Guinea pigs possess a highly mutated gene for l-gulono-.gamma.-lactone oxidase, the key enzyme for l-ascorbic acid biosynthesis missing in this species. Journal of Biological Chemistry 267(30): 21967–21972.Google Scholar
  77. Ohta, T. 1988. Further simulation studies on evolution by gene duplication. Evolution 42: 375–386.Google Scholar
  78. Ohta, T. 1991. Role of diversifying selection and gene conversion in evolution of major histocompatibility complex loci. Proceedings of the National Academy of Sciences of the U.S.A. 88(15): 6716–6720.Google Scholar
  79. Olson, E. C. and R. L. Miller. 1958. Morphological Integration. University of Chicago Press, Chicago.Google Scholar
  80. Orgel, L. E. and F. H. C. Crick. 1980. Selfish DNA: The ultimate parasite. Nature 284: 604–607.PubMedGoogle Scholar
  81. Patthy, L. 1987. Intron-dependent evolution: preferred types of exons and introns. Febs (Federation Of European Biochemical Societies) Letters 214(1): 1–7.Google Scholar
  82. Press, W. H., S. A. Teukolsky, W. T. Vetterling, and B. P. Flannery. 1992. Numerical Recipes in C: The Art of Scientific Computing. Second Edition. Cambridge University Press, pages 278–280, 300–304.Google Scholar
  83. Price, G. R. 1970. Selection and covariance. Nature 227: 520–521.Google Scholar
  84. Price, G. R. 1972. Extension of covariance selection mathematics. Annals of Human Genetics 35: 485–489.Google Scholar
  85. Raff, R. A. 1992. Direct-developing sea urchins and the evolutionary reorganization of early development. Bioessays 14(4): 211–218.Google Scholar
  86. Raff, R. A., G. A. Wray, and J. J, Henry. 1990. Implications of radical evolutionary changes in early development for concepts of developmental constraint. In L. Warren and M. Meselson, editors, New Perspective on Evolution. A. R. Liss.Google Scholar
  87. Riedl, R. J. 1977. A systems-analytical approach to macroevolutionary phenomena. Quarterly Review of Biology 52: 351–370.Google Scholar
  88. Rieppel, O. 1991. Progress in evolution: Snakes as an example. Zeitschrift für Zoologische Systematik und Evolutionsforschung 29(3): 208–212.Google Scholar
  89. Robertson, A. 1966. A mathematica model of the culling process in dairy cattle. Animal Production 8: 95–108.Google Scholar
  90. Sanctis, G., G. Falcioni, B. Giardina, F. Ascoli, and M. Brunori. 1986. Journal of Molecular Biology 188: 73–76.Google Scholar
  91. Schank, J. C. and W. C. Wimsatt. 1987. Generative entrenchment and evolution. Philosophy of Science Association 1986 2: 33–60.Google Scholar
  92. Schmalhausen, I. I. 1949. Factors of Evolution: The Theory of Stabilizing Selection. University of Chicago Press, Chicago, page 273.Google Scholar
  93. Shi, Y. and B. M. Tyler. 1991. All internal promoter elements of neurospora crassa 5S ribosomal RNA and transfer RNA genes, including the A boxes, are functionally gene-specific. Journal of Biological Chemistry 266(13): 8015–8019.Google Scholar
  94. Sidow, A. 1992. Diversification of the wnt gene family on the ancestral lineage of vertebrates. Proceedings of the National Academy of Sciences of the United States of America 89(11): 5098–5102.Google Scholar
  95. Slatkin, M. 1970. Selection and polygenic characters. Proceedings of the National Academy of Sciences U.S.A. 66: 87–93.Google Scholar
  96. Smith, M. W. 1988. Structure of vertebrate genes: a statistical analysis implicating selection. Journal of Molecular Evolution 27: 45–55.Google Scholar
  97. Stanley, S. M. 1976. Clades versus clones in evolution: Why we have sex. Science 190: 282–283.Google Scholar
  98. Stoltzfus, A., D. F. Spencer, M. Zuker, J. M. J. Logsdon, and W. F. Doolittle. 1994. Testing the exon theory of genes: The evidence from protein structure. Science 265(5169): 202–207.Google Scholar
  99. Streydio, C., S. Swillens, M. Georges, C. Szpirer, and G. Vassart. 1992. Structure, evolution and chromosomal localization of the human pregnancy-specific β1 glycoprotein gene family. Genomics 6(4): 579–592.Google Scholar
  100. Strong, M. and G. A. Gutman. 1992. Evolutionary relationships within the potassium channel multigene family. Society For Neuroscience Abstracts 18: 78.Google Scholar
  101. Taylor, P. D. 1988. Inclusive fitness models with two sexes. Theoretical Population Biology 34: 145–168.Google Scholar
  102. Uyenoyama, M. K. 1988. On the evolution of genetic incompatibility systems: incompatibility as a mechanism for the regulation of outcrossing distance. In R. E. Michod and B. R. Levin, editors, The Evolution of Sex, pages 212–232. Sinauer Associates, Sunderland, MA.Google Scholar
  103. Via, S. and R. Lande. 1985. Genotype-environment interaction and the evolution of phenotypic plasticity. Evolution 39(3): 505–522.Google Scholar
  104. Waddington, C. H. 1957. The Strategy of the genes. Allen and Unwin, London.Google Scholar
  105. Wade, M. J. 1985. Soft selection, hard selection, kin selection, and group selection. American Naturalist 125: 61–73.Google Scholar
  106. Wagner, G. P. 1981. Feedback selection and the evolution of modifiers. Acta Biotheoretica 30: 79–102.Google Scholar
  107. Wagner, G. P. 1984. On the eigenvalue distribution of genetic and phenotypic dispersion matrices: Evidence for a nonrandom organization of quantitative character variation. Journal of Mathematical Biology 21: 77–95.Google Scholar
  108. Wagner, G. P. 1988. The systems approach: an interface between development and population genetic aspects of evolution. In D. M. Raup and D. Jablonski, editors, Patterns and Processes in the History of Life, pages 149–165. Springer-Verlag, Berlin.Google Scholar
  109. Wagner, G. P. 1989. Multivariate mutation-selection balance with constrained pleiotropic effects. Genetics 122: 223–234.Google Scholar
  110. Weinberger, E. D. 1991. Local properties of Kauffman's N-k model, a tuneably rugged energy landscape. Physical Review A 44(10): 6399–6413.Google Scholar
  111. Wimsatt, W. C. and J. C. Schank. 1988. Two constraints on the evolution of complex adaptations and the means for their avoidance. In M. H. Nitecki, editor, Evolutionary Progress, pages 231–274. University of Chicago.Google Scholar
  112. Wright, S. 1932. The roles of mutation, inbreeding, crossbreeding, and selection in evolution. Proceedings of the Sixth International Congress on Genetics 1: 356–366.Google Scholar
  113. Wu, X., D. M. Muzny, C. C. Lee, and C. T. Caskey. 1992. Two independent mutational events in the loss of urate oxidase during hominoid evolution. Journal of Molecular Evolution 34(1): 78–84.Google Scholar
  114. Zonneveld, A.-J. V., H. Veerman, and H. Pannekoek. 1986. Proceedings of the National Academy of Sciences U.S.A. 83: 4670–4674.Google Scholar

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© Springer-Verlag 1995

Authors and Affiliations

  • Lee Altenberg
    • 1
  1. 1.Institute of Statistics and Decision SciencesDuke UniversityDurhamUSA

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