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Competence in<jats:italic>S. pneumoniae<\/jats:italic>is triggered by a quorum-sensing mechanism controlled by the competence-stimulating peptide pheromone.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We studied the distribution of the two major pherotypes in the pneumococcal population and their association with serotype, antimicrobial resistance and genetic lineage. Using multilocus sequence data we evaluated pherotype influence on the dynamics of horizontal gene transfer. We show that pherotype is a clonal property of pneumococci. Standard population genetic analysis and multilocus infinite allele model simulations support the hypothesis that two genetically differentiated populations are defined by the major pherotypes.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>Severe limitations to gene flow can therefore occur in bacterial species in the absence of geographical barriers and within highly recombinogenic populations. This departure from panmixia can have important consequences for our understanding of the response of pneumococci to human imposed selective pressures such as vaccination and antibiotic use.<\/jats:p><\/jats:sec>","DOI":"10.1186\/1471-2180-9-191","type":"journal-article","created":{"date-parts":[[2009,9,8]],"date-time":"2009-09-08T06:14:53Z","timestamp":1252390493000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":30,"title":["Pherotypes are driving genetic differentiation within Streptococcus pneumoniae"],"prefix":"10.1186","volume":"9","author":[{"given":"Margarida","family":"Carrolo","sequence":"first","affiliation":[]},{"given":"Francisco R","family":"Pinto","sequence":"additional","affiliation":[]},{"given":"Jose","family":"Melo-Cristino","sequence":"additional","affiliation":[]},{"given":"Mario","family":"Ramirez","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2009,9,7]]},"reference":[{"key":"862_CR1","doi-asserted-by":"publisher","first-page":"29","DOI":"10.1038\/349029a0","volume":"349","author":"J Maynard Smith","year":"1991","unstructured":"Maynard Smith J, Dowson CG, Spratt BG: Localized sex in bacteria. 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