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In Silico Gene-Level Evolution Explains Microbial Population Diversity through Differential Gene Mobility.
Bram van Dijk1, Paulien Hogeweg2
1Department of Theoretical Biology and Bioinformatics, Utrecht University, The Netherlands b.vandijk@uu.nl.
Genome Biology and Evolution
|December 30, 2015
Summary
Horizontal gene transfer (HGT) shapes microbial diversity. Mobile toxin genes and core resistance genes maintain ecosystem dynamics and phylogenetic structure, challenging clonal evolution models.
Area of Science:
- Microbial Ecology
- Evolutionary Biology
- Genomics
Background:
- Microbial communities exhibit remarkable ecological and phylogenetic diversity.
- The role of pervasive horizontal gene transfer (HGT) in shaping this diversity, especially in the context of clonal expansion and antagonistic interactions, remains incompletely understood.
- It is unclear whether HGT of antibiotic production and resistance genes erases phylogenetic structure.
Purpose of the Study:
- To investigate the role of HGT in shaping microbial diversity and phylogenetic structure within a spatial eco-evolutionary model.
- To determine how the mobility of toxin and resistance genes influences ecosystem dynamics.
- To explore the relationship between gene mobility, phylogeny, and the emergence of antagonistic interactions.
Main Methods:
- Development of a spatial eco-evolutionary model of prokaryotes, inspired by Vibrionaceae populations.
- Analysis of gene mobility patterns for toxin and resistance genes.
- Examination of the correlation between gene distribution and cellular phylogeny.
- Simulation of interstrain HGT and its impact on phylogenetic robustness.
- Observation of emergent antagonistic interactions within subpopulations.
Main Results:
- Toxin genes were found to be highly mobile, while resistance genes exhibited minimized mobility.
- Differential gene mobility was identified as crucial for maintaining a diverse and dynamic ecosystem.
- The resistance gene repertoire formed a core genome aligned with cellular phylogeny, whereas toxin genes showed a patchy distribution independent of phylogeny.
- Interstrain HGT enhanced the robustness of emergent phylogenetic structure against selective sweeps.
- Antagonistic interactions were observed between, rather than within, spatially structured subpopulations.
Conclusions:
- Multilevel evolution, driven by differential gene mobility via HGT, provides a robust explanation for microbial ecosystem diversity and phylogenetic structure.
- The findings challenge the notion that clonal dynamics alone drive microbial diversification.
- The study highlights the importance of HGT in maintaining complex microbial ecosystems and shaping inter- and intra-population interactions.
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