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Subfunctionalization
Subfunctionalization was proposed by Stoltzfus (1999)〔Stoltzfus, Arlin. "On the possibility of constructive neutral evolution." Journal of Molecular Evolution 49.2 (1999): 169-181.〕 and Force et al. (1999)〔Force, Allan, et al. "Preservation of duplicate genes by complementary, degenerative mutations." Genetics 151.4 (1999): 1531-1545.〕 as one of the possible outcomes of functional divergence that occurs after a gene duplication event, in which pairs of genes that originate from duplication, or paralogs, take on separate functions.〔“ScienceDirect Ad,” Chaos, Solitons & Fractals, vol. 15, no. 5. p. II, Mar-2003〕〔S. Rastogi and D. A. Liberles, “Subfunctionalization of duplicated genes as a transition state to neofunctionalization,” BMC Evolutionary Biology, vol. 5, no. 1, p. 28, 2005〕〔B. Conrad and S. E. Antonarakis, “Gene duplication: a drive for phenotypic diversity and cause of human disease.,” Annual review of genomics and human genetics, vol. 8, pp. 17-35, Jan. 2007.〕 Subfunctionalization is a neutral mutation process; meaning that no new adaptations are formed.〔S. Ohno, Evolution by Gene Duplication. New York, Heidelberg, Berlin: Springer-Verlag, 1970, pp. 59-87〕〔B. Conrad and S. E. Antonarakis, “Gene duplication: a drive for phenotypic diversity and cause of human disease.,” Annual review of genomics and human genetics, vol. 8, pp. 17-35, Jan. 2007〕 During the process of gene duplication paralogs simply undergo a division of labor by retaining different parts (subfunctions) of their original ancestral function.〔M. Sémon and K. H. Wolfe, “Preferential subfunctionalization of slow-evolving genes after allopolyploidization in Xenopus laevis.,” Proceedings of the National Academy of Sciences of the United States of America, vol. 105, no. 24, pp. 8333-8, Jun. 2008〕 This partitioning event occurs because of segmental gene silencing leading to the formation of paralogs that are no longer duplicates, because each gene only retains a single function.〔B. Conrad and S. E. Antonarakis, “Gene duplication: a drive for phenotypic diversity and cause of human disease.,” Annual review of genomics and human genetics, vol. 8, pp. 17-35, Jan. 2007〕 It is important to note that the ancestral gene was capable of performing both functions and the descendant duplicate genes can now only perform one of the original ancestral functions.〔B. Conrad and S. E. Antonarakis, “Gene duplication: a drive for phenotypic diversity and cause of human disease.,” Annual review of genomics and human genetics, vol. 8, pp. 17-35, Jan. 2007〕
==Alternative Hypothesis==
Subfunctionalization after gene duplication is thought to be the newer model of functional divergence.〔R. De Smet and Y. Van de Peer, “Redundancy and rewiring of genetic networks following genome-wide duplication events.,” Current opinion in plant biology, pp. 1-9, Feb. 2012〕 Before 1910, scientists were unaware that genes were capable of multifunctionalization.〔B. Conrad and S. E. Antonarakis, “Gene duplication: a drive for phenotypic diversity and cause of human disease.,” Annual review of genomics and human genetics, vol. 8, pp. 17-35, Jan. 2007〕 The original thought was that each gene possessed one function, but in fact genes have independently mutable regions and possessed the ability to subfunctionalize.〔J. G. Ruby, A. Stark, W. K. Johnston, M. Kellis, D. P. Bartel, and E. C. Lai, “Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs.,” Genome research, vol. 17, no. 12, pp. 1850-64, Dec. 2007〕〔B. Conrad and S. E. Antonarakis, “Gene duplication: a drive for phenotypic diversity and cause of human disease.,” Annual review of genomics and human genetics, vol. 8, pp. 17-35, Jan. 2007〕 Neofunctionalization, where one paralogous copy derives a new function after gene duplication, is thought to be the classical model of functional divergence.〔J. G. Ruby, A. Stark, W. K. Johnston, M. Kellis, D. P. Bartel, and E. C. Lai, “Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs.,” Genome research, vol. 17, no. 12, pp. 1850-64, Dec. 2007〕 Nevertheless, because of its neutral mutation process subfunctionalization seem to present a more parsimonious explanation for the retention of duplicates in a genome.〔S. Rastogi and D. A. Liberles, “Subfunctionalization of duplicated genes as a transition state to neofunctionalization,” BMC Evolutionary Biology, vol. 5, no. 1, p. 28, 2005〕〔D. (University of H. Graur and W.-H. (University of C. Li, Fundamentals of Molecular Evolution, Second. Sinauer Associates, Inc.,, 2000〕〔G. D. Amoutzias, Y. He, J. Gordon, D. Mossialos, S. G. Oliver, and Y. Van de Peer, “Posttranslational regulation impacts the fate of duplicated genes.,” Proceedings of the National Academy of Sciences of the United States of America, vol. 107, no. 7, pp. 2967-71, Feb. 2010〕
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