Fig. 4.

Population structure of X. fastidiosa. Maximum likelihood phylogeny of core genome alignment of 1.79 Mb of 55 X. fastidiosa strains analyzed in this study, before (a) and after (b) filtering for the recombinant regions. The phylogenetic tree was mid-point rooted, representing an increasing order of nodes. For (a), a total of 33,824 backbone entries were concatenated to obtain core genome alignments of 1.79 MB. Population structure was inferred using nested clustering implemented in hierBAPS. For (b), recombinant regions detected by fastGEAR in all subspecies of X. fastidiosa were excluded to build a recombination-free phylogenetic tree. Bootstrap support was >98% for all nodes, except where otherwise indicated