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Discovering Complete Quasispecies in Bacterial Genomes
Frederic Bertels1, Chaitanya S Gokhale2, Arne Traulsen2
1Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany bertels@evolbio.mpg.de.
Genetics
|June 21, 2017
Summary
Repetitive extragenic palindromic doublets forming hairpins (REPINs) evolve like populations. Their low duplication rates suggest a trade-off between REPIN survival and host genome health.
Area of Science:
- Microbiology
- Evolutionary Biology
- Genomics
Background:
- Mobile genetic elements are widespread in genomes.
- Repetitive extragenic palindromic doublets forming hairpins (REPINs) are common bacterial nonautonomous mobile elements.
- REPINs exist as populations within genomes, replicating and mutating.
Purpose of the Study:
- To model REPIN population evolution using the quasispecies model.
- To estimate effective duplication rates for REPIN populations.
- To investigate the evolutionary dynamics and ecological interactions of REPINs.
Main Methods:
- Applied the quasispecies model to 10 REPIN populations from different bacterial strains.
- Estimated effective duplication rates per REPIN per bacterial generation.
- Analyzed population dynamics, including extinction, growth, and competition.
Main Results:
- Estimated REPIN duplication rates range from approximately 5 × 10⁻⁹ to 15 × 10⁻⁹ duplications per generation.
- Low duplication rates suggest a balance between REPIN propagation and host genome integrity.
- Observed diverse population dynamics, including signs of extinction, growth, and inter-REPIN competition.
Conclusions:
- REPIN evolution can be effectively modeled as a quasispecies.
- A universal trade-off likely exists between REPIN population survival and minimizing mutational load on the host.
- REPIN populations exhibit ecological dynamics analogous to other natural populations.
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