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In silico experimental evolution: a tool to test evolutionary scenarios.

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    Reduced selection strength in bacteria causes significant genome reduction, including a substantial decrease in noncoding DNA. This finding aids in understanding evolutionary trajectories of exceptional genomes.

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    Area of Science:

    • Evolutionary biology
    • Genomics
    • Computational biology

    Background:

    • Comparative genomics reveals species with exceptionally reduced genomes and gene repertoires compared to relatives.
    • Atypical genome evolution is influenced by intertwined factors like population size, environment, selection, and mutation rates.

    Purpose of the Study:

    • To develop a methodology using synthetic experiments to isolate and test the impact of evolutionary factors on genome size and organization.
    • To investigate the specific effects of reduced selection strength on bacterial genome evolution.

    Main Methods:

    • Developed an evolutionary model named 'aevol' to simulate populations under controlled evolutionary conditions.
    • Manipulated evolutionary parameters individually, focusing on a reduction in selection strength.
    • Analyzed changes in genome size, coding sequence repertoire, and noncoding DNA content.

    Main Results:

    • A strong reduction in selection strength led to an approximate 35% decrease in overall genome size.
    • Coding sequences were reduced by about 15%, primarily affecting genes with minimal fitness contribution.
    • The noncoding compartment experienced a significant reduction of approximately 55% under low selection strength.

    Conclusions:

    • Reduced selection strength is a key driver of genome reduction, particularly impacting noncoding DNA.
    • The findings provide insights into the evolution of reduced genomes, consistent with observations in Prochlorococcus strains.