Table 4.

Summary of the molecular diversity indices for different categorical variables based on Dataset-2 (235,019 SNPs) and Dataset-4 (944 SNPs that fell within 22 selective sweeps identified using SweeD). Dataset-4 was used to assess reduction in diversity indices within each group (but not among groups) as compared to the genome-wide SNPs in Dataset-2.

Groups	N*	Dataset-2 (235,019 genome-wide SNPs)**					Dataset-4 (944 SNPs with 22 selective sweeps)**
		S	Ps	Θ S	Θ π	D	S	Ps	Θ S	Θ π	D
Groups based on TRUCTURE at K = 3
Group-1	192	234,655	0.998	0.171	0.212	0.765	942	0.998	0.171	0.140	−0.595
Group-2	69	133,423	0.568	0.118	0.114	−0.119	283	0.300	0.062	0.052	−0.570
Group-3	35	172,317	0.733	0.178	0.143	−0.747	442	0.468	0.114	0.069	−1.492
Groups based on NJ cluster analysis
Group-1A	88	226,991	0.966	0.191	0.210	0.340	865	0.916	0.181	0.131	−0.965
Group-1B	69	221,508	0.943	0.196	0.185	−0.202	860	0.911	0.190	0.121	−1.269
Group-1C	32	204,603	0.871	0.216	0.215	−0.020	761	0.806	0.200	0.170	−0.590
Group-2	71	145,321	0.618	0.128	0.119	−0.258	305	0.323	0.067	0.054	−0.661
Group-3	36	173,390	0.738	0.178	0.142	−0.770	462	0.489	0.118	0.069	−1.573
Groups based on endosperm modification
QPM	187	233,320	0.993	0.171	0.211	0.754	937	0.993	0.171	0.113	−1.097
Non-QPM	111	229,277	0.976	0.185	0.213	0.514	878	0.930	0.176	0.131	−0.854
Groups based on genetic background of QPM donor parents
CML144	99	205,635	0.875	0.169	0.179	0.201	638	0.676	0.131	0.089	−1.097
CML159	15	170,423	0.725	0.223	0.170	−1.067	487	0.516	0.159	0.108	−1.425
CML176	46	218,615	0.930	0.212	0.207	−0.088	825	0.874	0.199	0.133	−1.217
Non-CML	27	184,241	0.784	0.203	0.156	−0.927	628	0.66525	0.1726	0.10821	−1.4805
Groups based on genetic background of recurrent parents
Ecuador-573	69	197,259	0.839	0.175	0.148	−0.532	653	0.692	0.144	0.074	−1.714
Kitale-SYN	30	206,194	0.877	0.221	0.226	0.084	739	0.783	0.198	0.158	−0.775
Pool-9A	44	191,329	0.814	0.187	0.167	−0.407	596	0.631	0.145	0.092	−1.365
Pool-9A-SR	80	223,315	0.950	0.192	0.209	0.309	850	0.900	0.182	0.122	−1.135
Pop-502-SR	17	153,519	0.653	0.193	0.162	−0.711	470	0.498	0.147	0.107	−1.172
SADVLA	10	140,062	0.596	0.211	0.160	−1.217	398	0.422	0.149	0.102	−1.575
SUSUMA	24	175,493	0.747	0.200	0.151	−0.998	594	0.629	0.169	0.106	−1.499
Tuxpeno	13	156,379	0.665	0.214	0.159	−1.201	426	0.451	0.145	0.096	−1.565
Groups based on heterotic grouping
Heterotic group A	123	226,605	0.964	0.179	0.199	0.369	848	0.898	0.167	0.103	−1.273
Heterotic group B	95	232,840	0.991	0.193	0.207	0.250	921	0.976	0.190	0.132	−1.045
Heterotic group AB	11	171,143	0.728	0.249	0.231	−0.339	489	0.518	0.177	0.158	−0.509
All inbred lines without groups
All samples	298	234,956	1.000	0.159	0.220	1.202	943	0.999	0.159	0.125	−0.682

^*In cases where the sample size (N) do not add up to 298, some lines were excluded from the selective sweep analyses, which included the following: (i) two lines assigned to a “mixed” group at K = 3 and those remained unassigned to any of the sub-groups in the NJ cluster analysis; (ii) 69 lines with yet unknown heterotic groups; (iii) 11 lines with uncertain recurrent parent genome and (iv) 26 lines with uncertain genetic background of QPM donor parents. See Supplementary Table S1 for details.

**Number of segregating sites (S); Proportion of polymorphic sites (Ps); Theta (θ_S); Nucleotide diversity (Θπ); Tajima’s D test statistic (D).