High fitness costs and instability of gene duplications reduce rates of evolution of new genes by duplication-divergence mechanisms

Mol Biol Evol. 2014 Jun;31(6):1526-35. doi: 10.1093/molbev/msu111. Epub 2014 Mar 22.


An important mechanism for generation of new genes is by duplication-divergence of existing genes. Duplication-divergence includes several different submodels, such as subfunctionalization where after accumulation of neutral mutations the original function is distributed between two partially functional and complementary genes, and neofunctionalization where a new function evolves in one of the duplicated copies while the old function is maintained in another copy. The likelihood of these mechanisms depends on the longevity of the duplicated state, which in turn depends on the fitness cost and genetic stability of the duplications. Here, we determined the fitness cost and stability of defined gene duplications/amplifications on a low copy number plasmid. Our experimental results show that the costs of carrying extra gene copies are substantial and that each additional kilo base pairs of DNA reduces fitness by approximately 0.15%. Furthermore, gene amplifications are highly unstable and rapidly segregate to lower copy numbers in absence of selection. Mathematical modeling shows that the fitness costs and instability strongly reduces the likelihood of both sub- and neofunctionalization, but that these effects can be offset by positive selection for novel beneficial functions.

Keywords: Escherichia coli; evolution of new genes; fitness cost; gene amplification.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Anti-Bacterial Agents / pharmacology*
  • Bacteria / drug effects*
  • DNA Copy Number Variations
  • Evolution, Molecular
  • Gene Amplification
  • Gene Duplication
  • Gene Frequency
  • Genes, Bacterial*
  • Genetic Fitness*
  • Models, Genetic
  • Plasmids / genetics*
  • Selection, Genetic
  • beta-Lactamases / genetics*


  • Anti-Bacterial Agents
  • beta-Lactamases