Phylogeny of pneumococcal population structure.

<p>Maximum likelihood phylogeny of 937 pneumococcal carriage isolates inferred from an alignment of 1,111 core COGs including 78,525 polymorphic sites using RAxML with GTR+Γ nucleotide substitution model and 100 bootstrap replicates. Clades are colored by sequence cluster (SC), which are labeled on the outside ring. Some SCs are further divided into monophyletic sub-clusters (A, B, C) based on ancestral recombination history. Pneumococcal serotypes and MLST are labeled on each clade and bootstrap values are labeled on internal branches.