SNP calling
SNPs were called using kSNP (k=91, min frac = 1) (Gardner, Slezak, & Hall, 2015), from 81 genomes of P. subaeruginosa assembled in the present study, five from a past study (McTaggart et al., 2023), two genomes of P. azurescens (Dörner et al., 2022; K McKernan et al., 2021), and a genome of P. cyanescens (Reynolds et al., 2018) (Table S1). PLINK (Purcell et al., 2007) was used to remove SNP sites under linkage disequilibrium across the entire dataset (r2 cutoff = 0.99). Relationships among SNPs were visualised with a neighbour net in SplitsTree v.4.14.8 (Huson & Bryant, 2005).