Figure 1. Phylogenetic analysis of the clonal complex 180 isolates.

(A) A simplified representation of the 2,036,867 bp genome of S. pneumoniae OXC141 with tick marks every 0.5 Mb. The loci encoding the proteinaceous antigens PspA and PspC, as well as the capsule biosynthesis locus, are labelled, as are the prophage φOXC141, a putative ICE-related sequence, the ∼22 kb bacteriocin island and Pneumococcal Pathogenicity Island 1 (PPI-1). (B) A maximum likelihood phylogeny of the serotype 3 isolates based on the vertically inherited substitutions not introduced through recombination events. The tree and taxa are coloured according to their geographical location. (C) The panel surrounded by the dotted line contains one row for each isolate in the tree, with a column for each base in the reference genome. Red blocks indicate recombination events reconstructed as occurring on an internal branch, hence are shared by more than one isolate through common descent, while blue blocks indicate recombinations unique to one particular isolate.