Abstract
Recent research suggests that rather than being random, gene order may be coupled with gene functionality. These findings may be explained by mechanisms that require physical proximity such as co-expression and co-regulation. Alternatively, they may be due to evolutionary-dynamics forces, as expressed in genetic drift or linkage disequilibrium.
This paper proposes a biologically plausible model for evolutionary development. Using the model, which includes natural selection and the development of gene networks and cellular organisms, the co-evolution of recombination rate and gene functionality is examined. The results presented here are compatible with previous biological findings showing that functionally related genes are clustered.
These results imply that evolutionary pressure in a complex environment is sufficient for the emergence of gene order that is coupled with functionality. They shed further light on the mechanisms that may cause such gene clusters.
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References
Bäck, T., Schwefel, H.P., 1993. An overview of evolutionary algorithms for parameter optimization. Evol. Comput. 1, 1–3.
Barton, N.H., 1995. A general model for the evolution of recombination. Genet. Res. 65, 123–45.
Blumenthal, T., Gleason, K.S., 2003. Caenorhabditis elegans operons: form and function. Nat. Rev. Genet. 4, 112–20.
Bodmer, W.F., Parsons, P.A., 1962. Linkage and recombination in evolution. Adv. Genet. 11, 1–00.
Charlesworth, B., 1976. Recombination modification in a fluctuating environment. Genetics 83, 181–95.
Charlesworth, D., Charlesworth, B., 1975. Theoretical genetics of Batesian mimicry II. Evolution of supergenes. J. Theor. Biol. 55, 305–24.
Cho, R.J., Campbell, M.J., Winzeler, E.A., Steinmetz, L., Conway, A., Wodicka, L., Wolfsberg, T.G., Gabrielian, A.E., Landsman, D., Lockhart, D.J., Davis, R.W., 1998. A genome-wide transcriptional analysis of the mitotic cell cycle. Mol. Cell 2, 65–3.
Cohen, B.A., Mitra, R.D., Hughes, J.D., Church, G.M., 2000. A computational analysis of whole-genome expression data reveals chromosomal domains of gene expression. Nat. Genet. 26, 183–86.
Cooper, D.N., 1999. Human Gene Evolution Oxford. Bios Scientific Publishers, San Diego.
de Laat, W., Grosveld, F., 2003. Spatial organization of gene expression: the active chromatin hub. Chromosom. Res. 11, 447–59.
Dellaert, F., Beer, R.D., 1994. Co-evolving body and brain in autonomous agents using a developmental model. Technical Report CES-94-16, Cleveland, OH 44106.
Eberharter, A., Becker, P.B., 2002. Histone acetylation: a switch between repressive and permissive chromatin. Second in review series on chromatin dynamics. EMBO Rep. 3, 224–29.
Eggenberger, P., 1997. Evolving morphologies of simulated 3d organisms based on differential gene expression. In: Husbands, P., Harvey, I. (Eds.), The 4th European Conference on Artificial Life (ECAL97). MIT Press, Cambridge.
Felsenstein, J., Yokoyama, S., 1976. The evolutionary advantage of recombination. II. Individual selection for recombination. Genet. 83, 845–59.
Fischer, G., Rocha, E.P.C., Brunet, F.G., Vergassola, M., Dujon, B., 2006. Highly variable rates of genome rearrangements between Hemiascomycetous yeast lineages. PLoS Genet. 2(3).
Fisher, R.A., 1930. The Genetical Theory of Natural Selection. Oxford University Press, London.
Florens, L., Washburn, M.P., Raine, J.D., Anthony, R.M., Grainger, M., Haynes, J.D., Moch, J.K., Muster, N., Sacci, J.B., Tabb, D.L., Witney, A.A., Wolters, D., Wu, Y., Gardner, M.J., Holder, A.A., Sinden, R.E., Yates, J.R., Carucci, D.J., 2002. A proteomic view of the Plasmodium falciparum life cycle. Nature 419, 520–26.
Fouss, F., Pirotte, A., Saerens, M., 2005. A novel way of computing similarities between nodes of a graph, with application to collaborative recommendation. The 2005 IEEE/WIC/ACM International Conference on Web Intelligence, pp. 550–56.
Goldberg, D.E., 1989. Genetic Algorithms in Search, Optimization, and Machine Learning. Addison–Wesley, Reading.
Gotoh, O., 1982. An improved algorithm for matching biological sequences. J. Mol. Biol. 162, 705–08.
Gruau, F., 1992. Genetic synthesis of Boolean neural networks with a cell rewriting developmental process. In: Schaffer, J.D. (Ed.), COGANN-92: International Workshop on Combinations of Genetic Algorithms and Neural Networks., IEEE Computer Society Press, Baltimore, MD, USA, pp. 55–4.
Haldane, J.B.S., 1919. The combination of linkage values and the calculation of distances between the loci of linked factors. J. Genet. 8, 299–09.
Hertz, J.A., Palmer, R.G., Krogh, A.S., 1991. Introduction to the Theory of Neural Computation. Addison–Wesley, Reading.
Hill, W.G., Robertson, A., 1966. The effect of linkage on limits to artificial selection. Genet. Res. 8, 269–94.
Holland, J.H., 1975. Adaptation in Natural and Artificial Systems: An Introductory Analysis with Applications to Biology, Control, and Artificial Intelligence. University of Michigan Press, Ann Arbor.
Hopfield, J.J., 1984. Neurons with graded response have collective computational properties like those of two-state neurons. Proc. Natl. Acad. Sci. USA 81, 3088–092.
Hughes, A.L., da Silva, J., Friedman, R., 2001. Ancient genome duplications did not structure the human hox-bearing chromosomes. Gen. Res. 11, 771–80.
Hurst, L.D., Williams, E.J., Pal, C., 2002. Natural selection promotes the conservation of linkage of co-expressed genes. Trends Genet. 18, 604–06.
Hurst, L.D., Pal, C., Lercher, M.J., 2004. The evolutionary dynamics of eukaryotic gene order. Nat. Rev. Genet. 5, 299–10.
Hurst, L.D., Lercher, M.J., 2005. Unusual linkage patterns of ligands and their cognate receptors indicate a novel reason for non-random gene order in the human genome. BMC Evol. Biol. 5, 62.
Kamath, R.S., Fraser, A.G., Dong, Y., Poulin, G., Durbin, R., Gotta, M., Kanapin, A., Le Bot, N., Moreno, S., Sohrmann, M., Welchman, D.P., Zipperlen, P., Ahringer, J., 2003. Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature 421, 231–37.
Keller, N.P., Hohn, T.M., 1997. Metabolic pathway gene clusters in filamentous fungi. Fungal. Genet. Biol. 21, 17–9.
Khavkin, E., Coe, E.H., 1997. Mapped genomic locations for developmental functions and QTLs reflect concerted groups in maize (<SMALL>Zea mays</SMALL> L.). TAG Theor. Appl. Gen. 95, 343–52.
Kitano, H., 1990. Designing neural networks using genetic algorithms with graph generation system. Complex Syst. 4, 461–76.
Kondrashov, A.S., 1988. Deleterious mutations and the evolution of sexual reproduction. Nature 336, 435–40.
Lawrence, J.G., Roth, J.R., 1996. Selfish operons: horizontal transfer may drive the evolution of gene clusters. Genetics 143, 1843–860.
Lee, J.M., Sonnhammer, E.L., 2003. Genomic gene clustering analysis of pathways in eukaryotes. Genom. Res. 13, 875–82.
Lercher, M.J., Urrutia, A.O., Hurst, L.D., 2002. Clustering of housekeeping genes provides a unified model of gene order in the human genome. Nat. Genet. 31, 180–83.
Lercher, M.J., Blumenthal, T., Hurst, L.D., 2003. Coexpression of neighboring genes in Caenorhabditis elegans is mostly due to operons and duplicate genes. Genome Res. 13, 238–43.
McAdams, H.H., Arkin, A., 1998. Simulation of prokaryotic genetic circuits. Annu. Rev. Biophys. Biomol. Struct. 27, 199–24.
Megy, K., Audic, S., Claverie, J.M., 2003. Positional clustering of differentially expressed genes on human chromosomes 20, 21 and 22. Genom. Biol. 4, 1.
Mjolsness, E., Sharp, D.H., Reinitz, J., 1991. A connectionist model of development. J. Theor. Biol. 152, 429–53.
Nei, M., 1967. Modification of linkage intensity by natural selection. Genetics 57, 625–41.
Nei, M., 1968. Evolutionary change of linkage intensity. Nature 218, 1160–161.
Nei, M., 1969. Linkage modifications and sex difference in recombination. Genetics 63, 681–99.
Otto, S.P., Lenormand, T., 2002. Resolving the paradox of sex and recombination. Nat. Rev. Genet. 3, 252–61.
Pal, C., Hurst, L.D., 2003. Evidence for co-evolution of gene order and recombination rate. Nat. Genet. 33, 392–95.
Pal, C., Hurst, L.D., 2004. Evidence against the selfish operon theory. Trends Genet. 20, 232–34.
Papp, B., Pal, C., Hurst, L.D., 2003. Evolution of cis-regulatory elements in duplicated genes of yeast. Trends Genet. 19, 417–22.
Qi, X., Bakht, S., Leggett, M., Maxwell, C., Melton, R., Osbourn, A., 2004. A gene cluster for secondary metabolism in oat: implications for the evolution of metabolic diversity in plants. Proc. Natl. Acad. Sci. USA 101, 8233–238.
Richard, K.B., 1993. Interposing an Ontogenetic Model Between Genetic Algorithms and Neural Networks. Advances in Neural Information Processing Systems, vol. 5. NIPS Conference. Kaufmann, Los Altos.
Roy, P.J., Stuart, J.M., Lund, J., Kim, S.K., 2002. Chromosomal clustering of muscle-expressed genes in Caenorhabditis elegans. Nature 418, 975–79.
Rust, A.G., 1998. Developmental self Organization in Artificial Neural Networks, Ph.D. University of Hertfordshire.
Rust, A.G., Adams, R., Bolouri, H., 2000. Evolutionary neural topiary: growing and sculpting artificial neurons to order. In: M.A., B., et al.. (Eds.), Artificial Life VII: The 7th International Conference. MIT Press, Cambridge.
Shopland, L.S., Johnson, C.V., Byron, M., McNeil, J., Lawrence, J.B., 2003. Clustering of multiple specific genes and gene-rich R-bands around SC-35 domains: evidence for local euchromatic neighborhoods. J. Cell. Biol. 162, 981–90.
Sims, K., 1994a. Evolving virtual creatures. Comput. Graph. 28, 15–2.
Sims, K., 1994b. Evolving 3D morphology and behavior by competition. Artif. Life 1, 535–72.
Singer, G.A., Lloyd, A.T., Huminiecki, L.B., Wolfe, K.H., 2005. Clusters of co-expressed genes in mammalian genomes are conserved by natural selection. Mol. Biol. Evol. 22, 767–75.
Stefano, N., Domenico, P., 1995. Evolving artificial neural networks that develop in time. In: Proceedings of the Third European Conference on Advances in Artificial Life. Springer, Berlin.
Strahl, B.D., Allis, C.D., 2000. The language of covalent histone modifications. Nature 403, 41–5.
Thomas, B., ck, Hans-Paul, S., 1993. An overview of evolutionary algorithms for parameter optimization. Evol. Comput. 1, 1–3.
Williams, E.J., Bowles, D.J., 2004. Coexpression of neighboring genes in the genome of Arabidopsis thaliana. Genom. Res. 14, 1060–067.
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Yerushalmi, U., Teicher, M. Examining Emergence of Functional Gene Clustering in a Simulated Evolution. Bull. Math. Biol. 69, 2261–2280 (2007). https://doi.org/10.1007/s11538-007-9219-8
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DOI: https://doi.org/10.1007/s11538-007-9219-8