Table 4. Summary statistics on silent sites for candidate genes and all loci obtained with target-capture.

		Oryza group
Locus	Summary statistics	aus	indica	aus-like weed	indica-like weed	wild-like weed	wild
Rc	π	0.0025	0.0026	0.0021	0.0040	0.0029	0.0057
	θw	0.0029	0.0033	0.0018	0.0039	0.0027	0.0089
	Tajima’s D	−0.5243	−0.9636	0.6020	0.2043	0.4154	−1.5138
Bh4	π	0.0068	0.0092	0.0059	0.0096	0.0013	0.0141
	θw	0.0074	0.0077	0.0074	0.0115	0.0015	0.0130
	Tajima’s D	−0.2999	0.8084	−0.7779	−1.2185	−0.9726	0.3387
sh4	π	0.00035	0	0.0009	0	0.0090	0.0058
	θw	0.00023	0	0.0021	0	0.0083	0.0083
	Tajima’s D	1.1224	NA	-2.124	NA	0.6457	−1.2382
PROG1	π	0	0.0011	0.0010	0.0089	0.0089	0.0087
	θw	0	0.0024	0.0023	0.0106	0.0071	0.0107
	Tajima’s D	NA	−1.1491	−1.1594	−1.0485	1.4588	−0.6036
Sdr4	π	0.0018	0.0022	0.0018	0.0036	0.0036	0.0037
	θw	0.0011	0.0023	0.0033	0.0034	0.0035	0.0063
	Tajima’s D	1.3759	−0.1269	−1.3165	0.2431	0.2431	−1.3434
All 128 genes	π	0.0041	0.0040	0.0044	0.0048	0.0062	0.0090
	θw	0.0040	0.0043	0.0044	0.0049	0.0060	0.0105
	Tajima’s D	−0.0211	−0.2047	−0.0885	−0.1591	0.2740	−0.8180

Nucleotide diversity (π or θw) of individual gene <0.0005.

Tajima’s D >2 or < -2.