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Evolution and Biocomputation pp 205–259Cite as

Genome growth and the evolution of the genotype-phenotype map

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References

  • Aboitiz, F. 1991. Lineage selection and the capacity to evolve. Medical Hypotheses 36(2): 155–156.

    Google Scholar 

  • Alberch, P. 1981. From genes to phenotype: dynamical systems and evolvability. Genetica 84: 5–11.

    Google Scholar 

  • Altenberg, L. 1983. Letter to Nature. Unpublished.

    Google Scholar 

  • 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 

  • 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 

  • 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 

  • 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 

  • Altenberg, L. and D. L. Brutlag. 1986. Selection for modularity in the genome. Unpublished manuscript. Cited in Doolittle (1987).

    Google Scholar 

  • 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 

  • 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 

  • Baer, K. E. v. 1828. Entwichlungsgeschichte der Thiere: Beobachtung und Reflexion. Bornträger, Königsberg, pages 221–224.

    Google Scholar 

  • Barwise, J. and J. Perry. 1983. Situations and Attitudes. M.I.T. Press, Boston, pages 292–295.

    Google Scholar 

  • Blake, C. C. F. 1978. Nature 273: 267.

    Google Scholar 

  • Bonner, J. T. 1974. On Development: The Biology of Form. Harvard University, Cambridge, MA, page 61.

    Google Scholar 

  • 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 

  • Brandon, R. N. 1990. Adaptation and Environment. Princeton University Press, Princeton, pages 83–84.

    Google Scholar 

  • 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 

  • Cairns, J. and P. L. Foster. 1991. Adaptive reversion of a frameshift mutation in Escherichia coli. Genetics 128(4): 695–702.

    Google Scholar 

  • Cairns, J., J. Overbaugh, and S. Miller. 1988. The origin of mutants. Nature 335: 142–145.

    Google Scholar 

  • 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 

  • Cavalier-Smith, T. 1977. Visualising jumping genes. Nature 270: 10–12.

    Google Scholar 

  • Cheverud, J. 1984. Quantitative genetics and developmental constraints on evolution by selection. Journal of Theoretical Biology 110: 155–171.

    Google Scholar 

  • 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 

  • Conrad, M. 1979a. Bootstrapping on the adaptive landscape. BioSystems 11: 167–182.

    Google Scholar 

  • Conrad, M. 1982. Natural selection and the evolution of neutralism. BioSystems 15: 83–85.

    Google Scholar 

  • Craik, C., S. Buchman, and S. Beychok. 1980. Proceedings of the National Academy of Sciences U.S.A. 77: 1384–1388.

    Google Scholar 

  • Crick, F. 1979. Split genes and RNA splicing. Science 204: 264–271.

    PubMed  Google Scholar 

  • Crow, J. F. and M. Kimura. 1970. An Introduction to Population Genetics Theory. Alpha Editions, Edina, MN, pages 418–430.

    Google Scholar 

  • 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 

  • 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 

  • 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 

  • 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 

  • Doolittle, R. F. 1985. The genealogy of some recently evolved vertebrate proteins. Trends in Biochemical Sciences 10: 233–237.

    Google Scholar 

  • Doolittle, W. F. 1987. The origin and function of intervening sequences in DNA: A review. American Naturalist 130: 915–928.

    Google Scholar 

  • Doolittle, W. F. and C. Sapienza. 1980. Selfish genes, the phenotype paradigm and genome evolution. Nature 284: 601–603.

    PubMed  Google Scholar 

  • Dorit, R. L. and W. Gilbert. 1990. How big is the universe of exons? Science 250(4986): 1377–1382.

    Google Scholar 

  • 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 

  • Eldredge, N. 1989. Macroevolutionary Dynamics: Species, Niches, and Adaptive Peaks. McGraw-Hill, New York, page 205.

    Google Scholar 

  • Eshel, I. 1973. Clone-selection and optimal rates of mutation. Journal of Applied Probability 10: 728–738.

    Google Scholar 

  • Feller, W. 1971. An Introduction to Probability Theory and Its Applications. John Wiley and Sons, New York, page 27.

    Google Scholar 

  • Fisher, R. A. 1930. The Genetical Theory of Natural Selection. Clarendon Press, Oxford, pages 30–37.

    Google Scholar 

  • Foster, P. L. and J. Cairns. 1992. Mechanisms of directed mutation. Genetics 131(4): 783–789.

    Google Scholar 

  • Frank, S. A. and M. Slatkin. 1990. The distribution of allelic effects under mutation and selection. Genetical Research, Cambridge 55: 111–117.

    Google Scholar 

  • Frazzetta, T. H. 1975. Complex Adaptations in Evolving Populations. Sinauer Associates, Sunderland, MA, pages 212–238.

    Google Scholar 

  • Gelfand, M. S. 1992. Statistical analysis and prediction of the exonic structure of human genes. Journal of Molecular Evolution 35: 239–252.

    Google Scholar 

  • Gilbert, W. 1978. Why genes in pieces? Nature 271: 501.

    PubMed  Google Scholar 

  • Gilbert, W. and M. Glynias. 1993. On the ancient nature of introns. Gene 135(1–2): 137–144.

    Google Scholar 

  • Gillespie, J. H. 1984. Molecular evolution over the mutational landscape. Evolution 38(5): 1116–1129.

    Google Scholar 

  • 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 

  • Gimelfarb, A. 1992. Pleiotropy and multilocus polymorphisms. Genetics 130: 223–227.

    Google Scholar 

  • Golub, G. H. and C. F. V. Loan. 1983. Matrix Computations. Johns Hopkins University Press, Baltimore, page 152.

    Google Scholar 

  • 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 

  • Grafen, A. 1985. A geometric view of relatedness, Oxford Surveys in Evolutionary Biology 2: 28–89.

    Google Scholar 

  • 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 

  • 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 

  • 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 

  • 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 

  • 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 

  • 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 

  • 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 

  • 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 

  • 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 

  • 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 

  • Lande, R. and S. J. Arnold. 1983. The measurement of selection on correlated characters. Evolution 37(6): 1210–1226.

    Google Scholar 

  • Lerner, I. M. 1954. Developmental Homeostasis. Oliver and Boyd, Edinburgh.

    Google Scholar 

  • Levinton, J. 1988. Genetics, Paleontology, and Macroevolution. Cambridge University Press, Cambridge, pages 224–225, 494.

    Google Scholar 

  • Lewontin, R. C. 1978. Adaptation. Scientific American 239(3): 213–230.

    Google Scholar 

  • 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 

  • Liberman, U. and M. W. Feldman. 1986b. A general reduction principle for genetic modifiers of recombination. Theoretical Population Biology 30: 341–371.

    Google Scholar 

  • Luenberger, D. G. 1968. Optimization by Vector Space Methods. John Wiley and Sons, New York, pages 46–62.

    Google Scholar 

  • 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 

  • Maynard Smith, J. 1970. Natural selection and the concept of a protein space. Nature 225: 563–564.

    Google Scholar 

  • 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 

  • 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 

  • 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 

  • 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 

  • Ohta, T. 1988. Further simulation studies on evolution by gene duplication. Evolution 42: 375–386.

    Google Scholar 

  • 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 

  • Olson, E. C. and R. L. Miller. 1958. Morphological Integration. University of Chicago Press, Chicago.

    Google Scholar 

  • Orgel, L. E. and F. H. C. Crick. 1980. Selfish DNA: The ultimate parasite. Nature 284: 604–607.

    PubMed  Google Scholar 

  • 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 

  • 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 

  • Price, G. R. 1970. Selection and covariance. Nature 227: 520–521.

    Google Scholar 

  • Price, G. R. 1972. Extension of covariance selection mathematics. Annals of Human Genetics 35: 485–489.

    Google Scholar 

  • Raff, R. A. 1992. Direct-developing sea urchins and the evolutionary reorganization of early development. Bioessays 14(4): 211–218.

    Google Scholar 

  • 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 

  • Riedl, R. J. 1977. A systems-analytical approach to macroevolutionary phenomena. Quarterly Review of Biology 52: 351–370.

    Google Scholar 

  • Rieppel, O. 1991. Progress in evolution: Snakes as an example. Zeitschrift für Zoologische Systematik und Evolutionsforschung 29(3): 208–212.

    Google Scholar 

  • Robertson, A. 1966. A mathematica model of the culling process in dairy cattle. Animal Production 8: 95–108.

    Google Scholar 

  • Sanctis, G., G. Falcioni, B. Giardina, F. Ascoli, and M. Brunori. 1986. Journal of Molecular Biology 188: 73–76.

    Google Scholar 

  • Schank, J. C. and W. C. Wimsatt. 1987. Generative entrenchment and evolution. Philosophy of Science Association 1986 2: 33–60.

    Google Scholar 

  • Schmalhausen, I. I. 1949. Factors of Evolution: The Theory of Stabilizing Selection. University of Chicago Press, Chicago, page 273.

    Google Scholar 

  • 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 

  • 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 

  • Slatkin, M. 1970. Selection and polygenic characters. Proceedings of the National Academy of Sciences U.S.A. 66: 87–93.

    Google Scholar 

  • Smith, M. W. 1988. Structure of vertebrate genes: a statistical analysis implicating selection. Journal of Molecular Evolution 27: 45–55.

    Google Scholar 

  • Stanley, S. M. 1976. Clades versus clones in evolution: Why we have sex. Science 190: 282–283.

    Google Scholar 

  • 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 

  • 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 

  • Strong, M. and G. A. Gutman. 1992. Evolutionary relationships within the potassium channel multigene family. Society For Neuroscience Abstracts 18: 78.

    Google Scholar 

  • Taylor, P. D. 1988. Inclusive fitness models with two sexes. Theoretical Population Biology 34: 145–168.

    Google Scholar 

  • 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 

  • Via, S. and R. Lande. 1985. Genotype-environment interaction and the evolution of phenotypic plasticity. Evolution 39(3): 505–522.

    Google Scholar 

  • Waddington, C. H. 1957. The Strategy of the genes. Allen and Unwin, London.

    Google Scholar 

  • Wade, M. J. 1985. Soft selection, hard selection, kin selection, and group selection. American Naturalist 125: 61–73.

    Google Scholar 

  • Wagner, G. P. 1981. Feedback selection and the evolution of modifiers. Acta Biotheoretica 30: 79–102.

    Google Scholar 

  • 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 

  • 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 

  • Wagner, G. P. 1989. Multivariate mutation-selection balance with constrained pleiotropic effects. Genetics 122: 223–234.

    Google Scholar 

  • 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 

  • 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 

  • 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 

  • 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 

  • 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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  1. Institute of Statistics and Decision Sciences, Duke University, 27708-0251, Durham, NC, USA

    Lee Altenberg

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Altenberg, L. (1995). Genome growth and the evolution of the genotype-phenotype map. In: Banzhaf, W., Eeckman, F.H. (eds) Evolution and Biocomputation. Lecture Notes in Computer Science, vol 899. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-59046-3_11

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