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Gene frequency distributions reject a neutral model of genome evolution
Alexander E Lobkovsky1, Yuri I Wolf, Eugene V Koonin
1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA.
Genome Biology and Evolution
|January 15, 2013
Summary
Prokaryotic genome evolution shows a universal U-shaped gene frequency distribution. Mathematical modeling reveals that selection, not just neutral processes, significantly shapes these gene repertoires across species.
Area of Science:
- Microbial genomics
- Evolutionary biology
- Population genetics
Background:
- Prokaryotic evolution involves dynamic gene gain and loss, creating diverse gene repertoires even in related species.
- Prokaryotic pangenomes exhibit a consistent U-shaped gene frequency distribution: a core of universal genes, a shell of common genes, and a cloud of rare genes.
Purpose of the Study:
- To investigate the evolutionary processes driving the universal U-shaped gene frequency distribution in prokaryotic pangenomes.
- To differentiate between neutral evolution and selection as underlying mechanisms for this pattern.
Main Methods:
- Mathematical modeling and fitting of steady-state, infinite allele models to empirical gene frequency data.
- Analysis of gene frequency distributions across nearly 400 groups of bacterial and archaeal species at various phylogenetic depths.
- Utilizing the Akaike Information Criterion to compare model fits.
Main Results:
- The neutral model of genome evolution was confidently rejected as an explanation for the observed gene frequency distribution.
- Models incorporating purifying selection provided significantly better fits to the empirical data.
- Estimated selection strength decreased with evolutionary divergence but remained non-neutral.
Conclusions:
- The universal U-shaped gene frequency distribution in prokaryotes is substantially influenced by selection.
- Genome evolution in prokaryotes is not solely driven by neutral processes; selection plays a critical role in shaping gene repertoires.
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