Increased Mutation Rate Is Linked to Genome Reduction in Prokaryotes

Area of Science:

• Microbial evolution
• Genomics
• Molecular biology

Background:

• Genome size variation is a key evolutionary question.
• Effective population size (Ne) is a proposed driver of genome reduction, especially in endosymbionts.
• However, genome reduction in free-living prokaryotes suggests multiple contributing factors beyond Ne.

Purpose of the Study:

• To investigate the evolutionary forces driving prokaryotic genome reduction.
• To differentiate the roles of mutation rate and effective population size in genome size evolution.
• To explore proximate causes for increased mutation rates in reduced genomes.

Main Methods:

• Molecular evolutionary analyses
• Phylogenomic analyses of nine prokaryotic lineages
• Correlation analysis between gene loss rate and substitution rates (dS, dN/dS)

Main Results:

• Gene loss rate strongly correlated with synonymous substitution rate (dS) in most lineages studied.
• Correlation between gene loss and dN/dS was weak or absent, suggesting Ne is not the primary driver.
• Lineages with smaller genomes and higher substitution rates often lacked DNA repair genes.

Conclusions:

• Increased mutation rate, rather than effective population size, is a primary driver of prokaryotic genome reduction.
• Loss of DNA repair genes may explain elevated mutation rates in certain lineages.
• Convergent mechanisms likely underlie genome reduction in diverse prokaryotic groups.