Population genetics of foxtail millet and its wild ancestor

Wang, Chunfang; Chen, Jinfeng; Zhi, Hui; Yang, Lu; Li, Wei; Wang, Yongfang; Li, Haiquan; Zhao, Baohua; Chen, Mingsheng; Diao, Xianmin

doi:10.1186/1471-2156-11-90

BMC Genomic Data

Table 3 Summary of nucleotide diversity and neutrality tests

From: Population genetics of foxtail millet and its wild ancestor

Loci	Length^a	Silent	Accessions^b	S	π	πsilent	Θ	θslient	D	D*	F*	ρ	Rm	Hap	Hdiv
Setaria italica ssp. viridis
DACP	1014	944.833	29	27	0.0062	0.0067	0.0068	0.0073	-0.3118	-0.4487	-0.4763	0.0002	0	13	0.877
SIGT	732	681.833	29	10	0.0014	0.0015	0.0035	0.0037	-1.9503*	-2.8589*	-3.0169*	0.0052	0	8	0.643
ADTY	997	892.011	31	41	0.01	0.0111	0.0105	0.0112	-0.1808	-0.5215	-0.5215	0.0076	0	17	0.931
PP2C	815	815	33	8	0.0021	0.0021	0.0024	0.0024	-0.3792	-0.6279	-0.6449	0.1034	1	8	0.799
SPS1	716	716	31	10	0.0018	0.0018	0.0035	0.0035	-1.5505	-1.3113	-1.6212	0	0	7	0.452
UPL	656	636.667	32	9	0.0024	0.0025	0.0034	0.0035	-0.8911	-1.0025	-1.1326	0.0027	0	6	0.609
TIFIIF	569	521	29	9	0.0025	0.0027	0.004	0.0044	-1.1863	-0.9376	-1.1834	0.0253	0	9	0.717
TRAN	440	195.187	32	14	0.0062	0.0063	0.0085	0.0085	-0.8844	-0.4649	-0.7027	1.1713	0	12	0.891
MDEH	525	525	31	19	0.0042	0.0042	0.0091	0.0091	-1.8459*	-2.6617*	-2.8235*	0.0315	0	14	0.819
Average	718	658.614	30.8	16.3	0.004	0.0043	0.0057	0.0059	-1.02	-1.2039	-1.347	0.1497	0.1	10.4	0.748
Setaria italica ssp. italica
DACP	964	896	46	19	0.0035	0.0038	0.0045	0.0048	-0.6808	0.9081	0.4346	0	0	7	0.633
SIGT	767	715.667	48	7	0.0012	0.0013	0.0021	0.0022	-1.0991	-0.3006	-0.6509	0	0	4	0.264
ADTY	1005	900	50	6	0.0002	0.0003	0.0013	0.0015	-2.0897*	-3.9817*	-3.9678*	0	0	3	0.079
PP2C	760	760	47	2	0.0007	0.0007	0.0006	0.0006	0.3793	-0.8753	-0.5879	Na	0	3	0.528
SPS1	695	695	46	4	0.0016	0.0016	0.0013	0.0013	0.476	1.0127	0.9907	0.0041	0	3	0.518
UPL	761	734.333	48	6	0.0012	0.0012	0.0018	0.0018	-0.8501	-0.5283	-0.7377	0.0077	0	7	0.54
TIFIIF	624	556.833	44	6	0.0019	0.002	0.0022	0.0017	-0.3342	-2.1726	-1.8723	0.0093	0	5	0.577
TRAN	435	188.543	49	10	0.0042	0.0056	0.0052	0.0036	-0.5283	-0.4341	-0.5478	0.0219	1	9	0.743
MDEH	549	549	43	15	0.0039	0.0039	0.0067	0.0067	-1.3336	0.7496	0.0648	0.2204	1	14	0.886
Average	729	666.153	46.8	8.3	0.0021	0.0023	0.0029	0.0027	-0.6734	-0.6247	-0.7638	0.0329	0.2	6.1	0.529

Note: Length, alignment length; Silent, alignment length on silent site; Aceessions, number of accessions sequenced for each locus; S, the number of segregating sites; π, average number of nucleatide difference per site between 2 sequence; π silent, π on silent sites; θ, the watterson estimator of population mutation rate θ; θ silent, θ on silent sites; D, Tajima's D; D* and F*, D* and F* of Fu and li; ρ, the population recombination rate; R_M, the minimum number of recombination events; Hap, number of haplotype; Hdiv, haplotype diversity.

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