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).