Table 2. Total number of SNPs, nucleotide diversity (mean θ_π) and mean D_T for all data and for gene regions separated by species and replicon.

	Global			Genes
	SNPs	θπ	Dt	SNPs	θπ	θπ syn	Dt
S. medicae
Chromosome	19,547	0.0019	0.014	13,865	0.0016	0.0042	0.04
pSMED02	16,178	0.0056	−0.56	16,178	0.0045	0.0105	−0.14
pSMED01	17,853	0.0031	−1.07	17,853	0.0027	0.0070	−1.04
S. meliloti
Chromosome	74,037	0.0048	−0.43	59,390	0.0045	0.0135	−0.38
pSymA	50,553	0.0126	−0.91	32,619	0.0116	0.0308	−0.86
pSymB	56,398	0.0078	−0.57	41,590	0.0072	0.0193	−0.89
S. meliloti 24
Chromosome	39,618	0.0022	−1.20	32,185	0.0020	0.0059	−1.11
First half	26,953	0.004	−0.66	22,042	0.0034	0.010	−0.63
Second half	12,665	0.0008	−2.23	10,143	0.0008	0.002	−1.68
pSymA	46,192	0.0134	−0.73	29,617	0.0123	0.0380	−0.74
pSymB	51,829	0.0079	−0.49	39,221	0.0075	0.0200	−0.51

Data are only from genes for which >90% of the sites have unambiguous base calls from ≥80% of the strains and were not identified as recently transferred between S. meliloti and S. medicae.