Calculating Tajima’s D
The CORFS for each SGB were aligned with MAFFT (Katoh et al., 2002) using default settings. Tajima’s D (Tajima, 1989) for each aligned set of CORFs was calculated with the ‘tajimasD’ function in the R package ‘strataG’ (Archer et al., 2017). P-values output by the ‘tajimasD’ function were corrected for multiple comparisons with the ‘p.adjust’ function in stats package in R based on the total number of ORFs per genome using the Benjamini and Hochberg method with the ‘method = “fdr”’ option (Benjamin and Hochberg, 1995).