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Fractionation and subfunctionalization following genome duplications : mechanisms that drive gene content and their consequences

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  • A gene's duplication relaxes selection. Loss of duplicate, low-function DNA (fractionation) sometimes follows, mostly by deletion in plants, but mostly via the pseudogene pathway in fish and other clades with smaller population sizes. Subfunctionalization — the founding term of the Xfunctionalization lexicon — while not the general cause of differences in duplicate gene retention, becomes primary as the number of a gene's cis — regulatory sites increases. Balanced gene drive explains retention for the average gene. Both maintenance-of-balance and subfunctionalization drive gene content nonrandomly, and currently fall outside of our accepted Theory of Evolution. The ‘typical’ mutation encountered by a gene duplicate is not a neutral loss-of-function; dominant mutations (Muller's lexicon; these are not neutral) abound, and confound X functionalization terms like ‘neofunctionalization’. Confusion of words may cause confusion of thought. As with many plants, fish tetraploidies provide a higher throughput surrogate-genetic method to infer function from human and other vertebrate ENCODE-like regulatory sites. ‘Not only have studies on polyploid fractionation led to reconsiderations of fundamental evolutionary theory, but fractionation in polyploids permits higher-throughput comparative genomic experiments using ENCODE-like data yielding the logical precision expected of genetic analyses.’
  • Keywords: The Theory of Evolution, fractionation, Gene Balance Hypothesis, genome dominance, Whole genome duplication, subfunctionalization, dominant mutation
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  • Freeling, M., Scanlon, M. J., & Fowler, J. F. (2015). Fractionation and subfunctionalization following genome duplications: mechanisms that drive gene content and their consequences. Current Opinion in Genetics & Development, 35, 110-118. doi:10.1016/j.gde.2015.11.002
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  • 35
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  • Funded by a USDA NIFA grant #2013-02581 to the authors.
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