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MBE Advance Access published online on March 18, 2009
Molecular Biology and Evolution, doi:10.1093/molbev/msp054
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© The Author 2009. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org

Research Article

Deletion rate evolution and its effect on genome size and coding density

Mats E. Pettersson, Charles G. Kurland and Otto G. Berg

Institution where the research was performed: Dept. of Molecular Evolution, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden

Corresponding author details: Otto G. Berg, Dept. of Molecular Evolution, Evolutionary Biology Centre, Norbyv. 18C, SE-75236 Uppsala, Sweden. Tel +4618-4714215, Fax +4618-4716404, otto.berg{at}ebc.uu.se

Received for publication September 11, 2008. Revision received March 12, 2009. Accepted for publication March 13, 2009.

Deletion rates are thought to be important factors in determining the genome size of organisms in nature. While it is indisputable that deletions, and thus deletion rates, affect genome size, it is unclear how, or indeed if, genome size is regulated via the deletion rate. Here, we employ a mathematical model to determine the evolutionary fate of deletion-rate mutants. Simulations are employed to explore the interactions between deletions, deletion-rate mutants and genome size. The results show that, in this model, the fate of deletion rate mutants will depend on the fraction of essential genomic material, on the frequency of sexual recombination as well as on the population size of the organism.

We find that there is no optimal deletion rate in any state. However, at one critical coding density all changes in deletion rate are neutral and the rate may drift either up or down. As a consequence, the coding density of the genome is expected to fluctuate around this critical density. Characteristic differences in the impact of deletion rate mutations on prokaryote and eukaryote genomes are described.

Key Words: Genome size • junk DNA • insertion-deletion dynamics • deletion bias • modifier evolution

Current affiliations: Dept. of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden (MEP); Dept. of Microbial Ecology, Lund University, Lund, Sweden (CGK); Dept. of Molecular Evolution, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden (OGB)


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