Gene-specific selective sweeps in bacteria and archaea caused by negative frequency-dependent selection.

Area of Science:

• Evolutionary Biology
• Microbial Genetics
• Population Genetics

Background:

• Prokaryotic gene fixation was thought to erase genomic diversity via genome-wide selective sweeps.
• Recent evidence suggests beneficial genes spread via recombination without genome-wide sweeps, creating a paradox with low prokaryotic recombination rates.

Purpose of the Study:

• Investigate mathematical models to resolve the paradox between gene-specific sweeps and low recombination rates in prokaryotes.
• Analyze the impact of ecological interactions, specifically negative frequency-dependent selection (NFDS), on prokaryotic evolution.

Main Methods:

• Mathematical modeling of population genetics.
• Analysis of selective sweep models under NFDS in prokaryotes.
• Consideration of ecological factors like viral predation (kill-the-winner dynamics).

Main Results:

• NFDS maintains genetic diversity, enabling gene-specific selective sweeps.
• NFDS can cause gene-specific sweeps even with locally elevated recombination, provided NFDS affects multiple loci and the basal recombination rate is low.
• These conditions paradoxically facilitate gene-specific sweeps by reducing effective recombination at affected loci.

Conclusions:

• NFDS, driven by ubiquitous viral predation, is a major and general phenomenon in prokaryotic populations.
• Gene-specific selective sweeps are expected to be widespread due to NFDS in free-living prokaryotes.