Abstract
A central problem in understanding bacterial speciation is how clusters of closely related strains emerge and persist in the face of recombination. We use a neutral Fisher–Wright model in which genotypes, defined by the alleles at 140 house-keeping loci, change in each generation by mutation or recombination, and examine conditions in which an initially uniform population gives rise to resolved clusters. Where recombination occurs at equal frequency between all members of the population, we observe a transition between clonal structure and sexual structure as the rate of recombination increases. In the clonal situation, clearly resolved clusters are regularly formed, break up or go extinct. In the sexual situation, the formation of distinct clusters is prevented by the cohesive force of recombination. Where the rate of recombination is a declining log-linear function of the genetic distance between the donor and recipient strain, distinct clusters emerge even with high rates of recombination. These clusters arise in the absence of selection, and have many of the properties of species, with high recombination rates and thus sexual cohesion within clusters and low rates between clusters. Distance-scaled recombination can thus lead to a population splitting into distinct genotypic clusters, a process that mimics sympatric speciation. However, empirical estimates of the relationship between sequence divergence and recombination rate indicate that the decline in recombination is an insufficiently steep function of genetic distance to generate species in nature under neutral drift, and thus that other mechanisms should be invoked to explain speciation in the presence of recombination.
Highlights
Despite the well-documented extent of lateral gene transfer among the prokaryotes (Gogarten et al 2002), which has led some researchers to doubt whether the term ‘species’ has any meaning for these organisms (Lawrence 2002; Gevers et al 2005), we can define clusters of similar phenotype or genotype which often correspond to named species
Few studies have addressed the necessary conditions for the formation of genotypic clusters, their dynamics or properties, which could shed light on the reasons why, even in the face of promiscuous recombination, we can define entities among the bacteria which we recognize as species (Hanage et al 2005a,b)
Large multilocus sequence typing (MLST) datasets are available for several bacterial species, and we have described a population genetic model that can be applied to this rich source of data (Fraser et al 2005; Hanage et al 2006a)
Summary
Despite the well-documented extent of lateral gene transfer among the prokaryotes (Gogarten et al 2002), which has led some researchers to doubt whether the term ‘species’ has any meaning for these organisms (Lawrence 2002; Gevers et al 2005), we can define clusters of similar phenotype or genotype which often correspond to named species. These clusters show a variety of forms, levels of within-cluster diversity and degree of resolution from neighbouring clusters. The effect of more persistent selection or population substructure in affecting basic neutral speciation models can subsequently be explored
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