TABLE 3.

Sequence variation statistics and diversity parameters among the worldwide strains of Clavibacter michiganensis subsp. michiganensis calculated using DnaSP 5.10

Country	Gene	No. of:			Haplotype frequencya	Total no. of segregating sites	% of polymorphic sites	Nucleotide diversity (π)	No. of mutations (η)	Haplotype (gene) diversity	Value for indicated neutrality testb			Minimum no. of recombination events
		Strains	Nucleotides	Haplotypes							Tajima’s D	Fu and Li’s D*	Fu and Li’s F*
Worldwide	atpD	184	455	9	0.049	8	1.758	0.493 × 10−2	8	0.768	1.391 NS	1.215 NS	1.523 NS	1
	gyrB	184	468	7	0.038	6	1.282	0.131 × 10−2	6	0.462	−0.837 NS	0.043 NS	−0.307 NS	2
	ppk	184	495	15	0.081	28	5.656	0.190 × 10−2	28	0.789	0.617 NS	−2.069 NS	−1.166 NS	2
	recA	184	415	6	0.032	6	1.445	0.140 × 10−2	6	0.457	−0.901 NS	−2.012 NS	−1.940 NS	0
	rpoB	120	277	5	0.041	8	2.888	0.101 × 10−2	9	0.159	−2.027*	−2.553*	−2.815*	0
	Concatenated	184	1,833	43	0.233	48	2.618	0.509 × 10−2	48	0.936	0.374 NS	−1.553 NS	−0.862 NS	7
Iran	atpD	37	455	6	0.162	7	1.538	0.429 × 10−2	7	0.739	0.462 NS	−0.202 NS	0.003 NS	1
	gyrB	37	468	6	0.162	5	1.068	0.245 × 10−2	5	0.488	−0.109 NS	1.124 NS	0.875 NS	2
	ppk	37	495	6	0.162	18	3.363	0.914 × 10−2	18	0.450	0.164 NS	−0.207 NS	−0.100 NS	0
	recA	37	415	3	0.081	5	1.204	0.139 × 10−2	6	0.368	−1.628 NS	−2.856*	−2.898*	0
	rpoB	37	277	1	0.027	0	0.000	0.000 × 10−2	0	0.000	NA	NA	NA	NA
	Concatenated	37	1,833	15	0.405	35	1.909	0.447 × 10−2	36	0.869	−0.173 NS	−0.643 NS	−0.573 NS	4
Europec	atpD	32	455	6	0.187	7	1.538	0.456 × 10−2	7	0.734	0.563 NS	1.269 NS	1.231 NS	1
	gyrB	32	468	2	0.062	1	0.213	0.037 × 10−2	1	0.175	−0.448 NS	0.587 NS	0.344 NS	1
	ppk	32	495	9	0.281	16	3.232	0.104 × 10−2	16	0.847	1.258 NS	1.185 NS	1.420 NS	1
	recA	32	415	4	0.125	2	0.481	0.116 × 10−2	3	0.425	−0.816 NS	−0.282 NS	−0.506 NS	0
	rpoB	32	277	3	0.093	5	1.805	0.189 × 10−2	5	0.325	1.555 NS	−2.413 NS	−2.511 NS	0
	Concatenated	32	1,833	13	0.406	26	1.418	0.447 × 10−2	27	0.909	0.787 NS	1.221 NS	1.273 NS	3
Chile	atpD	25	455	3	0.120	3	0.659	0.127 × 10−2	3	0.290	−0.670 NS	−0.202 NS	−0.386 NS	0
	gyrB	25	468	2	0.080	1	0.213	0.047 × 10−2	1	0.220	−0.280 NS	0.617 NS	0.429 NS	0
	ppk	25	495	2	0.080	10	2.020	0.444 × 10−2	10	0.220	−0.559 NS	1.407*	0.955 NS	0
	recA	25	415	2	0.080	2	0.481	0.135 × 10−2	2	0.280	0.124 NS	0.831 NS	0.731 NS	0
	rpoB	NA	ND	ND	ND	ND	ND	ND	ND	ND	ND	ND	ND	ND
	Concatenated	25	1,833	3	0.120	16	0.872	0.194 × 10−2	16	0.290	−0.564 NS	1.198 NS	0.772 NS	0
Uruguay	atpD	39	455	5	0.128	8	1.758	0.622 × 10−2	8	0.781	1.423 NS	0.636 NS	1.035 NS	0
	gyrB	39	468	2	0.510	1	0.213	0.089 × 10−2	1	0.416	1.089 NS	0.566 NS	0.823 NS	0
	ppk	39	495	4	0.102	13	0.026	0.073 × 10−2	13	0.714	2.277*	1.505*	2.067**	0
	recA	39	415	4	0.102	4	0.963	0.315 × 10−2	4	0.538	0.914 NS	−0.030 NS	0.294 NS	1
	rpoB	NA	ND	ND	ND	ND	ND	ND	ND	ND	ND	ND	ND	ND
	Concatenated	39	1,833	10	0.256	26	1.418	0.538 × 10−2	26	0.860	2.060*	1.189 NS	1.756*	2
USA	atpD	20	455	5	0.250	8	1.758	0.636 × 10−2	8	0.784	0.956 NS	1.342 NS	1.425 NS	0
	gyrB	20	468	2	0.100	1	0.213	0.094 × 10−2	1	0.442	1.025 NS	0.649 NS	0.856 NS	0
	ppk	20	495	6	0.300	15	3.030	0.124 × 10−2	15	0.795	1.165 NS	1.177 NS	1.362 NS	1
	recA	20	415	3	0.150	2	0.481	0.127 × 10−2	2	0.484	−0.155 NS	0.866 NS	0.677 NS	0
	rpoB	20	277	3	0.150	6	2.166	0.249 × 10−2	6	0.279	−1.887*	−2.258 NS	−2.487 NS	0
	Concatenated	20	1,833	8	0.400	26	1.418	0.515 × 10−2	26	0.821	1.111 NS	1.420*	1.546 NS	3

^aNumber of haplotypes/number of strains.

^bND, not determined; NA, not applicable; NS, not significant. *, P ≤ 0.05; **, P ≤ 0.01.

^cIncludes strains isolated in Belgium, France, Spain, Portugal, and the Netherlands.