Pherotype polymorphism in Streptococcus pneumoniae and its effects on population structure and recombination

Natural transformation in the Gram-positive pathogen Streptococcus pneumoniae occurs when cells become \"competent\", a state that is induced in response to high extracellular concentrations of a secreted peptide signal called CSP (Competence Stimulating Peptide) encoded by the comC locus. Two main CSP signal types (pherotypes) are known to dominate the pherotype diversity across strains. Using thousands of fully sequenced pneumococcal genomes, we confirm that pneumococcal populations are highly genetically structured and that there is significant variation among diverged populations in pherotype frequencies; most carry only a single pherotype. Moreover, we find that the relative frequencies