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

Curr Opin Genet Dev. 2015 Dec;35:110-8. doi: 10.1016/j.gde.2015.11.002. Epub 2015 Dec 4.

Abstract

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.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.
  • Review

MeSH terms

  • Animals
  • Evolution, Molecular*
  • Gene Duplication / genetics*
  • Genome / genetics*
  • Humans
  • Models, Genetic
  • Plants