(a) Phylogenetic relationships between species sequenced in this study. Throughout, green indicates mutualists and orange indicates generalists. Acacia–ant mutualist Pseudomyrmex spinicola and generalist P. gracilis are pictured. Photographs ©Alex Wild/alexanderwild.com and used with permission. (b) Mean±s.d. of genetic distances of each species from P. gracilis in 38,862 25 kb windows across the genome and limited to 4,082 coding regions (CDS). Estimates of dN, dS and dN/dS are also shown. Significance (P<0.01) was determined between species with paired t-tests across all windows and Wilcoxon signed-rank tests across all genes. We indicate significance only between the pairs of species: P. concolor versus P. pallidus, P. flavicornis versus P. sp. PSW-54 and P. dendroicus versus P. elongatus. All other significance values are shown in Supplementary Table 3.