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).