Table 4 Summary statistics on silent sites for candidate genes and all loci obtained with target-capture
Oryza group
LocusSummary statisticsausindicaaus-like weedindica-like weedwild-like weedwild
Rcπ0.00250.00260.00210.00400.00290.0057
θw0.00290.00330.00180.00390.00270.0089
Tajima’s D−0.5243−0.96360.60200.20430.4154−1.5138
Bh4π0.00680.00920.00590.00960.00130.0141
θw0.00740.00770.00740.01150.00150.0130
Tajima’s D−0.29990.8084−0.7779−1.2185−0.97260.3387
sh4π0.0003500.000900.00900.0058
θw0.0002300.002100.00830.0083
Tajima’s D1.1224NA-2.124NA0.6457−1.2382
PROG1π00.00110.00100.00890.00890.0087
θw00.00240.00230.01060.00710.0107
Tajima’s DNA−1.1491−1.1594−1.04851.4588−0.6036
Sdr4π0.00180.00220.00180.00360.00360.0037
θw0.00110.00230.00330.00340.00350.0063
Tajima’s D1.3759−0.1269−1.31650.24310.2431−1.3434
All 128 genesπ0.00410.00400.00440.00480.00620.0090
θw0.00400.00430.00440.00490.00600.0105
Tajima’s D−0.0211−0.2047−0.0885−0.15910.2740−0.8180
  • Nucleotide diversity (π or θw) of individual gene <0.0005.

  • Tajima’s D >2 or < -2.