Fig 5. Maximum likelihood tree of 81 ST1 (or ST1-derived) isolates constructed using only vertically-inherited SNPs.

Predicted homologous recombination events are mapped onto the phylogeny (shown by squares on the branches) and coloured according to the BAPS cluster from which they are predicted to have been derived. Squares representing events with the same predicted donor at the isolate level and that have occurred on the same branches are joined together, and possibly represent multi-fragment recombination. ST1_28 and ST72_1, which are referred to in the text and in S8 Fig, are labelled. The scale bar indicates the number of SNPs.