Abstract
Genetic mutation is an essential factor in the evolution of biological organisms and a driving force of phenotypical innovation. On rare occasions, nature takes a major evolutionary leap during which an organism’s gene repertoire suddenly doubled. Genetic mutation affects both the whole genome duplication as it happens, and also during all the subsequent evolutionary steps. We develop a Boolean model of gene regulatory networks that simulates the duplication event and subsequent Darwinian evolution using an evolutionary algorithm. We analyze the role of these two different types of mutations on synthetic systems. Our results show that high duplication mutation rate triggers the development of new phenotypes, advantageous in a changing environment, to the detriment of environmental robustness. Additionally, our research highlights the necessity of a low evolutionary mutation rate for the survival of duplicated individuals within a mixed population, ensuring the spreading novel phenotype. We conclude that both types of mutations play complementary roles in determining the successful propagation of organisms with duplicated genomes.
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References
Albert, R.: Scale-free networks in cell biology. Journal of Cell Science 118, 4947–4957 (2005)
Aldana, M., Balleza, E., Kauffman, S., Resendiz, O.: Robustness and evolvability in genetic regulatory networks. Journal of Theoretical Biology 245, 433–448 (2007)
Aldana, M., Cluzel, P.: A natural class of robust networks. Proceedings of the National Academy of Sciences 100, 8710–8714 (2003)
Brunet, F.G., Crollius, H.R., Paris, M., Aury, J.M., Gibert, P., Jaillon, O., Laudet, V., Robinson-Rechavi, M.: Gene loss and evolutionary rates following whole-genome duplication in teleost fishes. Molecular Biology and Evolution 23(9), 1808–1816 (2006)
Darabos, C., Tomassini, M., Giacobini, M.: Dynamics of unperturbed and noisy generalized Boolean networks. Journal of Theoretical Biology 260, 531–544 (2009)
De Bodt, S., Maere, S., Van de Peer, Y.: Genome duplication and the origin of the angiosperms. TRENDS in Ecology and Evolution 20, 591–597 (2005)
Ferrada, E., Wagner, A.: Protein robustness promotes evolutionary innovations on large evolutionary time-scales. Proceedings of the Royal Society London B 275, 1595–1602 (2008)
Isalan, M., Lemerle, C., Michalodimitrakis, K., Horn, C., Beltrao, P., Raineri, E., Garriga-Canut, M., Serrano, L.: Evolvability and hierarchy in rewired bacterial gene networks. Nature 452, 840–846 (2008)
Kafri, R., Bar-Even, A., Pilpel, Y.: Transcription control reprogramming in genetic backup circuits. Nature Genetics 37, 295–299 (2005)
Kauffman, S.A.: Metabolic stability and epigenesis in randomly constructed genetic nets. Journal of Theoretical Biology 22, 437–467 (1969)
Kellis, M., Birren, B.W., Lander, E.S.: Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature 428, 617–624 (2004)
Ohno, S.: Evolution by Gene Duplication. George Allen and Unwin, London (1970)
Oikonomou, P., Cluzel, P.: Effects of topology on network evolution. Nature Physics 2, 532–536 (2006)
Pan, Q., Darabos, C., Tyler, A.L., Moore, J.H., Payne, J.L.: The influence of whole genome duplication and subsequent diversification on environmental robustness and evolutionary innovation in gene regulatory networks. In: Proceedings of the European Conference on Artificial Life, pp. 614–621 (2011)
Piškur, J.: Origin of the duplicated regions in the yeast genomes. Trends in Genetics 17, 302–303 (2001)
Sémon, M., Wolfe, K.H.: Consequences of genome duplication. Current Opinion in Genetics and Development 17, 505–512 (2007)
Taylor, J.S., Braasch, I., Frickey, T., Meyer, A., Van de Peer, Y.: Genome duplication, a trait shared by 22,000 species of ray-finned fish. Genome Research 13, 382–390 (2003)
Thakar, J., Pilione, M., Kirimanjeswara, G., Harvill, E.T., Albert, R.: Modeling systems-level regulation of host immune responses. PLoS Comput. Biol. 3(6), e109 (2007)
van Hoek, M.J.A., Hogeweg, P.: Metabolic adaptation after whole genome duplication. Molecular Biology and Evolution 26, 2441–2453 (2009)
Wagner, A.: Robustness and evolvability: a paradox resolved. Proc. Biol. Sci. 275(1630), 91–100 (2008)
Wilke, C.O., Wang, J.L., Ofria, C., Lenski, R.E., Adami, C.: Evolution of digital organisms at high mutation rates leads to survival of the flattest. Nature 412, 331–333 (2001)
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Pan, Q., Darabos, C., Moore, J.H. (2012). The Role of Mutations in Whole Genome Duplication. In: Giacobini, M., Vanneschi, L., Bush, W.S. (eds) Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics. EvoBIO 2012. Lecture Notes in Computer Science, vol 7246. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-29066-4_11
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DOI: https://doi.org/10.1007/978-3-642-29066-4_11
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