The MLSA reference tree. A. The neighbour-joining tree of Figure 1 was relabelled so that all strains within a sequence cluster were assigned to the species inferred from the positions on the tree of the type strain and other well-characterized strains. The limits of the S. mitis and S. pseudopneumoniae clusters are somewhat unclear and the strains on the flanks of this cluster are shown as white circles (uncertain species) to indicate this. Strains that were re-checked as they were outliers of species clusters, or were distinct from all other strains, are indicated by a red asterisk. B. The tree constructed from the same set of concatenated sequences using minimum evolution. C. The neighbour-joining tree with the Mitis group clusters collapsed, to show more clearly the sequence clusters within the Anginosus and Salivarius groups. The positions of the type strains and bootstrap values for the nodes are shown.