Dynamics of gene duplication and transposons in microbial genomes following a sudden environmental change

Nicholas D Chia, Nigel Goldenfeld

Research output: Contribution to journalArticle

5 Citations (Scopus)

Abstract

A variety of genome transformations can occur as a microbial population adapts to a large environmental change. In particular, genomic surveys indicate that, following the transition to an obligate, host-dependent symbiont, the density of transposons first rises, then subsequently declines over evolutionary time. Here we show that these observations can be accounted for by a class of generic stochastic models for the evolution of genomes in the presence of continuous selection and gene duplication. The models use a fitness function that allows for partial contributions from multiple gene copies, is an increasing but bounded function of copy number, and is optimal for one fully adapted gene copy. We use Monte Carlo simulation to show that the dynamics result in an initial rise in gene copy number followed by a subsequent falloff due to adaptation to the new environmental parameters. These results are robust for reasonable gene duplication and mutation parameters when adapting to a novel target sequence. Our model provides a generic explanation for the dynamics of microbial transposon density following a large environmental change such as host restriction.

Original languageEnglish (US)
Article number021906
JournalPhysical Review E - Statistical, Nonlinear, and Soft Matter Physics
Volume83
Issue number2
DOIs
StatePublished - Feb 16 2011
Externally publishedYes

Fingerprint

genome
Duplication
genes
Genome
Gene
Continuous Selection
fitness
mutations
Fitness Function
Genomics
Stochastic Model
constrictions
Mutation
Monte Carlo Simulation
Restriction
Partial
Target
Dependent
Model
simulation

ASJC Scopus subject areas

  • Condensed Matter Physics
  • Statistical and Nonlinear Physics
  • Statistics and Probability

Cite this

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