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

TL;DR

This paper presents a stochastic model explaining the observed rise and fall of transposon density in microbial genomes after environmental shifts, highlighting the role of gene duplication and adaptation dynamics.

Contribution

The study introduces a generic stochastic model that captures the dynamics of gene duplication and transposon density changes during microbial adaptation to environmental changes.

Findings

Initial increase in gene copy number and transposon density post-environmental change.

Subsequent decline in transposon density as adaptation progresses.

Model robustness across various gene duplication and mutation parameters.

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 fall 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 changes such as host restriction.