Examples of individual gene trees produced from the sequences of all 420 strains. A-C shows the ppaC, pyk and tuf gene trees, which each fail to resolve some of the species clusters. Strain SK264 (assigned as S. parasanguinis; labelled in Figure 2A) was used as the query strain in Figures 7 and 8. The ppaC allele of this strain is assigned as resident compatible as it falls within an unresolved cluster that includes the other S. parasanguinis sequences. For both pyk and tuf, the sequences from SK264 fall within clusters that are well resolved (bootstrap values of ≥ 80%) from the cluster that includes all (or the great majority) of the other S. parasanguinis sequences and are assigned as foreign alleles. For pyk the source of the foreign allele is unclear as its sequence falls within a cluster that includes those from several species. For tuf, the sequence appears to have been introduced from an S. australis strain. The major unresolved clusters in the trees are indicated.