Genome reduction occurred in early Prochlorococcus with an unusually low effective population size

Area of Science:

• Microbial evolution
• Genomics
• Oceanography

Background:

• Planktonic bacteria in oligotrophic oceans, like Prochlorococcus, exhibit genome reduction.
• The dominant theory, genome streamlining, suggests large effective population sizes (Ne) drive this reduction via selection for metabolic efficiency.
• Reconstructing ancestral Ne is challenging due to uncertainties in phylogenetic models.

Purpose of the Study:

• To investigate the role of effective population size (Ne) in the genome reduction of ancient Prochlorococcus.
• To test the prevailing genome streamlining theory by simulating evolutionary pressures.

Main Methods:

• Developed a novel agent-based modeling strategy.
• Simulated changes in the ratio of radical to conservative nonsynonymous nucleotide substitution rates (dR/dC) across a range of ancestral Ne.
• Utilized dR/dC as a proxy for Ne.

Main Results:

• Simulated dR/dC ratios increased with decreasing Ne, particularly when Ne fell below 10k-100k.
• These Ne magnitudes are characteristic of species where genetic drift, rather than selection, drives genome reduction.
• Findings contradict the assumption of large ancestral Ne for Prochlorococcus.

Conclusions:

• Simulations strongly support genetic drift as the primary driver of Prochlorococcus genome reduction.
• Challenges the established genome streamlining theory's reliance on strong selection in large populations.
• Suggests alternative evolutionary pathways for abundant marine bacteria.