Table 3.

Polymorphisms at nine genes in the L. innocua-L. monocytogenes clade

Gene	No. strains	Size (bp)	No. alleles	No. (%) polymorphic sites	D.I.	Ks	Ka	Ka/Ks	π
gyrB	64	657	23	74 (11.26%)	0.91	0.1991	0.0010	0.0050	0.0384
dapE	64	669	39	146 (21.82%)	0.98	0.2337	0.0152	0.0650	0.0564
hisJ	64	714	32	187 (26.19%)	0.95	0.3999	0.0380	0.0951	0.1000
sigB	64	642	24	83 (12.93%)	0.92	0.2588	0.0054	0.0207	0.0518
ribC	64	633	34	163 (25.75%)	0.93	0.6002	0.0209	0.0348	0.1093
purM	64	693	31	170 (24.53%)	0.94	0.3955	0.0194	0.0490	0.0853
betL	64	534	32	171 (32.02%)	0.94	0.7918	0.0312	0.0394	0.1325
gap	64	621	18	28 (4.51%)	0.76	0.0240	0.0013	0.0547	0.0067
tuf	64	681	11	14 (2.06%)	0.80	0.0182	0.0021	0.1160	0.0058
Concatenated	64	5,844	61	1036 (17.73%)	0.99	0.2621	0.0147	0.0559	0.0623
Concatenated, L. innocua	34	5,844	31	391 (6.69%)	0.99	0.0365	0.0032	0.0865	0.0106
Concatenated, subgroupA	19	5,844	18	90 (1.54%)	0.99	0.0142	0.0018	0.1241	0.0046
Concatenated, subgroup B	13	5,844	11	135 (2.31%)	0.97	0.0280	0.0018	0.0628	0.0077
Concatenated, subgroup C	1	5,844	1	--	--	0.4659	0.0241	0.0517	--
Concatenated, subgroup D	1	5,844	1	--	--	0.4867	0.0225	0.0461	--
Concatenated, L. monocytogenes	30	5,844	30	820 (14.03%)	1.00	0.1781	0.0089	0.0500	0.0438
Concatenated, lineage I	10	5,844	4	84 (1.44%)	1.00	0.0174	0.0019	0.1112	0.0055
Concatenated, lineage II	10	5,844	6	250 (4.28%)	1.00	0.0493	0.0027	0.0537	0.0131
Concatenated, lineage III	10	5,844	10	522 (8.93%)	1.00	0.1459	0.0084	0.0575	0.0374

D.I.: discrimination index; Ks: number of synonymous changes per synonymous site; Ka: number of non-synonymous changes per non-synonymous site; π: nucleotide diversity.