title: In Silico Gene-Level Evolution Explains Microbial Population Diversity through Differential Gene Mobility.
abstract: Microbial communities can show astonishing ecological and phylogenetic diversity. What is the role of pervasive horizontal gene transfer (HGT) in shaping this diversity in the presence of clonally expanding "killer strains"? Does HGT of antibiotic production and resistance genes erase phylogenetic structure? To answer these questions, we study a spatial eco-evolutionary model of prokaryotes, inspired by recent findings on antagonistic interactions in Vibrionaceae populations. We find toxin genes evolve to be highly mobile, whereas resistance genes minimize mobility. This differential gene mobility is a requirement to maintain a diverse and dynamic ecosystem. The resistance gene repertoire acts as a core genome that corresponds to the phylogeny of cells, whereas toxin genes do not follow this phylogeny and have a patchy distribution. We also show that interstrain HGT makes the emergent phylogenetic structure robust to selective sweeps. Finally, in this evolved ecosystem we observe antagonistic interactions between, rather than within, spatially structure subpopulations, as has been previously observed for prokaryotes in soils and oceans. In contrast to ascribing the diversification and evolution of microbial communities to clonal dynamics, we show that multilevel evolution can elegantly explain the observed phylogenetic structure and ecosystem diversity.
authors.affiliation: Department of Theoretical Biology and Bioinformatics, Utrecht University, The Netherlands b.vandijk@uu.nl.
authors.forename: Bram
authors.initials: B
authors.lastname: van Dijk
authors.affiliation: Department of Theoretical Biology and Bioinformatics, Utrecht University, The Netherlands.
authors.forename: Paulien
authors.initials: P
authors.lastname: Hogeweg
mesh_terms: D000898:Antibiosis / Q000235:genetics; D001427:Bacterial Toxins / Q000235:genetics; D003198:Computer Simulation; D019143:Evolution, Molecular; D022761:Gene Transfer, Horizontal; D005798:Genes, Bacterial; D011110:Polymorphism, Genetic; D014737:Vibrionaceae / Q000235:genetics
chemical_list: D001427:Bacterial Toxins
keywords: HGT; accessory genome; antagonistic interactions; core genome; diversity; eco-evolutionary dynamics; flexible genomes; gene mobility; gene-level selection; horizontal gene transfer; microbial evolution; multilevel evolution; resistance; toxin