Speciation trajectories in recombining bacterial species

PLoS Comput Biol. 2017 Jul 3;13(7):e1005640. doi: 10.1371/journal.pcbi.1005640. eCollection 2017 Jul.


It is generally agreed that bacterial diversity can be classified into genetically and ecologically cohesive units, but what produces such variation is a topic of intensive research. Recombination may maintain coherent species of frequently recombining bacteria, but the emergence of distinct clusters within a recombining species, and the impact of habitat structure in this process are not well described, limiting our understanding of how new species are created. Here we present a model of bacterial evolution in overlapping habitat space. We show that the amount of habitat overlap determines the outcome for a pair of clusters, which may range from fast clonal divergence with little interaction between the clusters to a stationary population structure, where different clusters maintain an equilibrium distance between each other for an indefinite time. We fit our model to two data sets. In Streptococcus pneumoniae, we find a genomically and ecologically distinct subset, held at a relatively constant genetic distance from the majority of the population through frequent recombination with it, while in Campylobacter jejuni, we find a minority population we predict will continue to diverge at a higher rate. This approach may predict and define speciation trajectories in multiple bacterial species.

MeSH terms

  • Bacteria / genetics*
  • Cluster Analysis
  • Ecosystem
  • Evolution, Molecular*
  • Genetic Speciation*
  • Genetic Variation
  • Models, Genetic*
  • Recombination, Genetic

Grants and funding

This work was funded by the Academy of Finland (grant number 286607 to PM; grant number 251170 to the Finnish Centre of Excellence in Computational Inference Research COIN). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.