Table 1 Estimates of polymorphism within S. lycopersicum and divergence between S. lycopersicum and S. peruvianum of 50 loci; all indel regions were ignored

From: Multilocus sequence data reveal extensive departures from equilibrium in domesticated tomato (Solanum lycopersicum L.)

Chr	Marker	n	nt ^a (nt coding)	S^b	θ^c	π^d	Tajima's D^e	Mean pairwise no. of SNPs between species	Div ^f
10	437_2	33	655 (298)	8	3.22	0.79	−2.241^***	3	0.52
4	3300_2	35	536 (426)	1	0.45	0.39	−0.211	NA^g	NA
4	4301_3	32	445 (445)	1	0.56	0.14	−1.142	5	1.14
5	3155_3	33	862 (209)	5	1.43	1.03	−0.747	9	1.08
6	1260_2	33	377 (377)	1	0.65	0.16	−1.140	5	1.37
7	3332_3	32	151 (4)	1	1.69	2.40	0.643	2	1.59
9	2534_1b	33	656 (17)	9	3.47	1.67	−1.577^*	10	1.51
	2325_3	32	419 (419)	5	2.96	1.44	−1.376	7	1.74
	1287_1	36	145 (111)	1	1.66	3.55	1.668^*	3	1.76
1	1523_4	32	248 (88)	0	0.00	0.00	ND^h	NA	NA
	1589_1	32	142 (37)	0	0.00	0.00	ND^h	2	1.64
	1675_1	31	149 (149)	0	0.00	0.00	ND^h	3	2.17
10	1724_1	35	232 (149)	3	3.14	2.42	−0.518	12	5.34
6	175_1	36	123 (123)	2	3.92	6.75	1.401	NA	NA
6	1863_3	32	727 (102)	5	1.71	1.59	−0.195	NA	NA
	1909_2	33	163 (61)	1	1.51	1.88	0.371	3	2.77
12	2189_1	34	249 (159)	3	2.95	5.11	1.670^*	2	1.00
	220_1	32	150 (150)	2	3.31	0.83	−1.504	NA	NA
	2280_1	32	141 (141)	0	0.00	0.00	ND^h	5	5.00
	241_2b	33	272 (0)	2	1.81	1.49	−0.354	NA	NA
	2486_1	34	198 (141)	5	6.37	2.57	−1.576^*	2	1.10
	2582_1	32	127 (127)	0	0.00	0.00	ND^h	1	0.79
	2719_1	33	153 (0)	1	1.62	3.31	1.580	3	2.33
1	2819_5	32	656 (125)	16	6.07	1.53	−2.509^***	4	0.70
	2875_4b	34	582 (0)	7	3.25	2.47	−0.692	17	3.22
	296_1b	32	659 (0)	3	1.13	1.37	0.485	4	0.87
6	U146140	33	570 (59)	0	0.00	0.00	ND^h	13	2.33
5	C2_At1g13380	33	684 (155)	1	0.36	0.09	−1.140	15	2.42
5	C2_At1g14000	34	716 (202)	3	1.03	0.90	−0.285	7	0.97
6	C2_At1g20050	34	899 (151)	5	1.44	1.26	−0.332	12	1.49
	C2_At1g32130	34	430 (225)	1	0.57	0.39	−0.483	4	0.95
6	C2_At1g44575	34	739 (182)	5	1.74	1.08	−1.002	48	7.31
1	C2_At1g50020	35	1218 (119)	0	0.00	0.00	ND^h	6	1.22
	C2_At1g73180	34	266 (180)	9	8.43	8.74	0.111	NA	NA
1	C2_At2g15890	34	769 (163)	2	0.64	0.23	−1.277	11	1.52
11	C2_At2g22570	35	1082 (199)	4	0.90	0.46	−1.212	7	2.48
9	C2_At2g36930	33	274 (182)	0	0.00	0.00	ND^h	3	1.14
5	U221402	33	601 (75)	2	0.83	0.20	−1.502^*	9	1.51
	U318882	33	582 (109)	0	0.00	0.00	ND^h	6	1.07
7	U146437	33	352 (235)	5	3.54	2.05	−1.124	6	1.84
1	hp2 exon 2	32	347 (347)	1	0.72	0.35	−0.783	5	1.42
3	Pds	30	584 (36)	1	0.43	0.11	−1.147	6	1.05
3	Psy1	31	592 (57)	3	1.27	0.33	−1.731^**	2	0.39
6	Cyc-B 5′ region	31	436 (5)	0	0.00	0.00	ND^h	14	3.24
1	hp2 3′region	31	490 (215)	1	0.51	0.13	−1.145	15	3.06
2	fw 2.2	34	482 (23)	7	3.57	1.88	−1.364	16	3.34
10	TG11	32	559 (0)	4	1.78	1.82	0.063	12	2.06
10	CRTISO	34	449 (0)	1	0.60	0.64	0.085	9	2.18
5	rin	36	415 (0)	3	1.75	2.14	0.502	17	5.89
11	PTOX	33	456 (273)	5	2.71	1.49	−1.198	6	1.32
Total or mean		33	23 209 (7050)	145	1.71	1.34	−0.573	351	2.04

Abbreviations: NA, not available; ND, not defined; SNP, single nucleotide polymorphism.
^aLength based on NCBI aligned PopSet, may include indels.
^bNumber of segregating sites.
^cDiversity based on S per kb (Watterson, 1975).
^dMean pairwise diversity per kb (Nei and Li, 1979).
^e^*P⩽0.05, ^**P⩽0.01, ^***P⩽0.001.
^fNet nucleotide divergence (Nei, 1987) × 100.
^gNot available, S. arcanum homologous sequence was not isolated.
^hUndefined because there was no polymorphism.

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Table 1 Estimates of polymorphism within S. lycopersicum and divergence between S. lycopersicum and S. peruvianum of 50 loci; all indel regions were ignored

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