Speciation trajectories in recombining bacterial species.

Pekka Marttinen,William P Hanage,Mark M Tanaka

doi:10.1371/journal.pcbi.1005640

Abstract

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.

Highlights

Speciation in eukaryotes is well-studied [1], but the definition of bacterial species remains controversial due to recombination, which allows transfer of DNA between distant strains [2]
This does not apply to bacteria because, even if they reproduce clonally, DNA may be donated between distinct species
We present a mathematical model to describe bacterial speciation

Summary

Introduction

Speciation in eukaryotes is well-studied [1], but the definition of bacterial species remains controversial due to recombination, which allows transfer of DNA between distant strains [2]. In the Ecotype Model [10], niche -specific adaptive mutations cause genome-wide selective sweeps that remove variability between isolates in the same the niche, resulting in genetically differentiated clusters in different niches. A model of ecological differentiation among sympatric recombining bacteria has been developed [13, 14]. In this model the differentiation is triggered by an acquisition of a few habitat-specific alleles through horizontal gene transfer. If recombination between habitats is limited, the result is gradual diversification, eventually creating genomically and ecologically distinct clusters. The resulting pattern has a small number of short regions with strong habitat association, while the majority of the genome is relatively uncorrelated with habitat, a pattern observed between two clusters of closely related Vibrio bacteria [13]

Methods

Results

Discussion

Conclusion