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Table 2 Summary of the molecular diversity indices of three rice species based on six datasets of different marker density

From: Comparisons of molecular diversity indices, selective sweeps and population structure of African rice with its wild progenitor and Asian rice

Species and dataseta Results from Tajima’s neutrality testb
m S Ps θ S θπ D
All O. glaberrima
 Dataset-1 2358 6843 0.262 0.031 0.01620 − 1.381
 Dataset-2 2358 6057 0.262 0.031 0.01806 − 1.213
 Dataset-3 2358 158 0.203 0.024 0.00083 − 2.641
 Dataset-4 2358 320 0.272 0.033 0.01247 − 1.725
 Dataset-5 2358 416 0.292 0.035 0.02194 − 1.045
 Dataset-6 2358 374 0.263 0.032 0.01391 − 1.565
Group-1 O. glaberrima
 Dataset-1 983 4427 0.170 0.023 0.01425 − 1.101
 Dataset-2 983 4108 0.178 0.024 0.01592 − 0.979
 Dataset-3 983 76 0.097 0.013 0.00070 − 2.598
 Dataset-4 983 204 0.174 0.023 0.01378 − 1.169
 Dataset-5 983 261 0.183 0.025 0.01866 − 0.690
 Dataset-6 983 246 0.173 0.023 0.01423 − 1.115
Group-2 O. glaberrima
 Dataset-1 1375 5414 0.208 0.027 0.01499 − 1.270
 Dataset-2 1375 4834 0.209 0.027 0.01664 − 1.106
 Dataset-3 1375 106 0.136 0.017 0.00089 − 2.612
 Dataset-4 1375 244 0.208 0.027 0.00944 − 1.832
 Dataset-5 1375 354 0.248 0.032 0.02054 − 1.014
 Dataset-6 1375 285 0.201 0.026 0.01176 − 1.546
Minicore O. glaberrima
 Dataset-1 350 4664 0.179 0.028 0.01870 − 1.020
 Dataset-2 350 4061 0.176 0.027 0.02066 − 0.763
 Dataset-3 350 78 0.100 0.016 0.00106 − 2.733
 Dataset-4 350 198 0.169 0.026 0.01473 − 1.331
 Dataset-5 350 294 0.206 0.032 0.02453 − 0.719
 Dataset-6 350 265 0.186 0.029 0.01720 − 1.244
Subset of minicore O. glaberrima
 Dataset-1 163 4114 0.158 0.028 0.01948 − 0.986
 Dataset-2 163 3632 0.157 0.028 0.02147 − 0.744
 Dataset-3 163 54 0.069 0.012 0.00132 − 2.716
 Dataset-4 163 179 0.152 0.027 0.01655 − 1.232
 Dataset-5 163 265 0.186 0.033 0.02544 − 0.724
 Dataset-6 163 231 0.163 0.029 0.01809 − 1.190
Subset of minicore O. glaberrima
 Dataset-1 115 3904 0.150 0.028 0.02006 − 0.971
 Dataset-2 115 3491 0.151 0.028 0.02211 − 0.751
 Dataset-3 115 54 0.069 0.013 0.00162 − 2.756
 Dataset-4 115 174 0.148 0.028 0.01790 − 1.180
 Dataset-5 115 244 0.171 0.032 0.02622 − 0.615
 Dataset-6 115 218 0.153 0.029 0.01872 − 1.164
O. barthii
 Dataset-1 115 5685 0.218 0.041 0.04366 0.219
 Dataset-2 115 4919 0.213 0.040 0.04396 0.326
 Dataset-3 115 108 0.138 0.026 0.02020 − 0.731
 Dataset-4 115 254 0.216 0.041 0.02258 − 1.478
 Dataset-5 115 370 0.259 0.049 0.05148 0.184
 Dataset-6 115 317 0.223 0.042 0.04903 0.563
O. sativa spp. indica (lowland)
 Dataset-1 554 19,090 0.732 0.106 0.09722 − 0.257
 Dataset-2 554 17,327 0.751 0.109 0.10654 − 0.066
 Dataset-3 554 585 0.750 0.109 0.08782 − 0.581
 Dataset-4 554 819 0.697 0.101 0.09336 − 0.232
 Dataset-5 554 856 0.600 0.087 0.06371 − 0.810
 Dataset-6 554 1015 0.714 0.104 0.09803 − 0.163
O. sativa spp. japonica (upland)
 Dataset-1 218 12,734 0.488 0.082 0.04340 − 1.513
 Dataset-2 218 12,066 0.523 0.088 0.04751 − 1.474
 Dataset-3 218 398 0.510 0.086 0.04041 − 1.679
 Dataset-4 218 607 0.517 0.087 0.04355 − 1.588
 Dataset-5 218 604 0.424 0.071 0.04088 − 1.356
 Dataset-6 218 426 0.299 0.050 0.01159 − 2.447
Both lowland and upland O. sativa
 Dataset-1 772 20,642 0.792 0.110 0.17332 − 5.807
 Dataset-2 772 18,763 0.813 0.113 0.19298 − 6.165
 Dataset-3 772 654 0.838 0.116 0.18026 1.639
 Dataset-4 772 910 0.774 0.107 0.17936 1.999
 Dataset-5 772 961 0.674 0.093 0.13485 1.324
 Dataset-6 772 1067 0.751 0.104 0.15331 1.413
  1. aNumber of sequences or sample size (m); number of segregating sites (S); proportion of polymorphic sites (Ps) = S/n); θS = Ps/a1; nucleotide diversity (θπ); Tajima test (D)
  2. bDataset-1 = 26,073 SNPs; Dataset-2 = 23,079 SNPs; Dataset-2 = 780 SNPs; Dataset-4 = 1175 SNPs; Dataset-5 = 1426 SNPs; Dataset-6 = 1421 SNPs. See Table 1 for details