Table 1. Genetic diversity (Watterson's θ [37]) for seven neutral genes (N), 13 putative domestication genes (D), and 14 putative improvement genes (I) sampled from wild (Wild), landrace (Land) and improved (Imp) sunflower populations.

			Watterson's θ			ML-HKA P-values
Type	Locus		Wild	Land	Imp	Wild	Land	Imp
N	c0025	Aleurain-like protease	0.0239	0.0150	0.0138	0.1937	0.2979	0.1760
N	c1111	Protein kinase family protein	0.0094	0.0006	0.0019	0.2125	0.6362	0.9305
N	c1351	Chlorophyll binding protein	0.0138	0.0180	0.0111	0.7964	0.7016	0.3830
N	c2016	DNAJ heat shock N-terminal domain-containing	0.0301	0.0189	0.0162	0.7361	0.8933	0.3601
N	c2307	Glyceraldehyde-3-phosphate dehydrogenase	0.0050	0.0055	0.0062	0.8146	0.7105	0.7910
N	c5369	S-adenosylmethionine synthetase	0.0111	0.0097	0.0052	0.8648	0.8339	0.7842
N	c5456	Vacuolar H+-ATPase subunit A	0.0185	0.0101	0.0054	0.2398	0.3041	0.8800
	AVG		0.0160	0.0111	0.0086
D	c1357	Pentatricopeptide repeat-containing protein	0.0107	0.0056	0.0056	0.6688	0.3820	0.2101
D	c1533	Microtubule-associated protein	0.0216	0.0096	0.0004	0.5902	0.9072	0.0151**
D	c1649	Putative protein	0.0093	0.0087	0.0000	0.9578	0.9188	0.0029**
D	c1666¶	Putative Ser/Thr protein kinase	0.0134	0.0139	0.0000	0.1076	0.0823*	0.0452**
D	c2873	11S globulin precursor	0.0047	0.0025	0.0000	0.8921	0.5324	0.1425
D	c2963	BEL1-related homeotic protein	0.0127	0.0018	0.0000	0.8280	0.1798	0.0007**
D	c3115	Nicotinate phosphoribosyltransferase-like protein	0.0027	0.0000	0.0000	0.1256	0.9774	0.9065
D	c5898¶	Unknown protein	0.0162	0.0015	0.0008	0.7698	0.0744*	0.0269**
D	c4973¶	Chorismate synthase	0.0084	0.0000	0.0000	0.9106	0.0053**	0.0062**
D	G13K16	No significant similarity	0.0095	0.0033	0.0026	0.8837	0.2176	0.1488
D	H4B03	Kinesin-related protein (MKRP2)	0.0132	0.0030	0.0003	0.0570	0.2177	0.5660
D	M23M12	CONSTANS 3	0.0138	0.0052	0.0016	0.2596	0.2188	0.9425
D	N21O05	Thiol protease	0.0029	0.0000	0.0000	0.1685	0.0053**	0.0050**
	AVG		0.0107	0.0042	0.0009
I	c1144	Calmodulin-binding protein	0.0024	0.0023	0.0000	0.7282	0.5471	0.0093**
I	c1236	NSL1 (NECROTIC SPOTTED LESIONS1)	0.0119	0.0068	0.0000	0.5399	0.5683	0.0051**
I	c1258	11S globulin precursor	0.0107	0.0066	0.0000	0.9099	0.4632	0.0000**
I	c1406¶	Protein kinase-like protein	0.0219	0.0194	0.0000	0.2071	0.1630	0.0050**
I	c1700	Mitochondrial dicarboxylate carrier	0.0213	0.0136	0.0084	0.8200	0.9343	0.5555
I	c1774	No significant similarity	0.0106	0.0109	0.0033	0.9305	0.8681	0.3536
I	c0019	Unknown protein	0.0250	0.0183	0.0000	0.1993	0.1024	0.0036**
I	c1921¶	Dof27	0.0154	0.0088	0.0010	0.9483	0.6381	0.0104**
I	c2150	NADP-specific glutatamate dehydrogenase	0.0321	0.0076	0.0000	0.3002	0.5340	0.0450**
I	c2588	ATIDD11 (INDETERMINATE-DOMAIN11)	0.0053	0.0087	0.0000	0.3958	0.8769	0.0017**
I	c3070	Gly-rich RNA binding protein	0.0088	0.0067	0.0077	0.9702	0.7709	0.7452
I	c5666	Peroxidase	0.0237	0.0057	0.0000	0.3859	0.4254	0.0192**
I	J22O06	Unknown protein	0.0264	0.0031	0.0000	0.3104	0.3827	0.0010**
I	L2K11	SDL-1 protein	0.0038	0.0040	0.0024	0.0879	0.0457**	0.1359
	AVG		0.0157	0.0088	0.0016

Six previously analysed genes are indicated by ¶. P-values are given for the results of the ML-HKA test for each candidate gene in each of the three populations. * Significant at P≤0.1,**P≤0.05. Comparisons that remained significant after false discovery rate correction are indicated in bold (FDR <0.05) and underlined (0.05< FDR <0.1).