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Table 2 Sequence Diversity and Evolutionary Analysis of 6 Selenoprotein Loci Stratified by Estimated Population

From: Polymorphism analysis of six selenoprotein genes: support for a selective sweep at the glutathione peroxidase 1 locus (3p21) in Asian populations

Gene Ethnic Group SNPs Singletons SYN NSYN π × 10-4 Θ × 10-4 DTTajima's DF F
GPX1           
202 Total 38 14 1 3 5.2 8.7 -1.16256 -2.49532* -2.31912*
48 AA 23 6 1 3 6.5 7.0 -0.25380 -0.23160 -0.28398
62 CA 15 3 0 2 5.3 4.3 0.69670 0.119874 0.38011
46 HI 20 10 0 2 5.1 6.2 -0.55642 -1.92897** -1.72989
46 PR 15 6 0 2 2.0 4.7 -1.75961** -1.12837 -1.58364
GPX2           
204 Total 47 11 0 0 8.2 8.7 -0.18534 -0.85302 -0.67535
48 AA 27 7    8.1 6.7 0.69919 -0.22648 0.11635
62 CA 33 7    6.7 7.7 -0.43521 0.03790 -0.16317
46 HI 32 8    8.7 8.0 0.31148 -0.13732 0.02421
48 PR 30 8    6.6 7.4 -0.36659 -0.28952 -0.37648
GPX3           
204 Total 52 6 1 0 11.0 10.4 0.18669 0.76044 0.60998
48 AA 42 4 1   13.9 11.1 0.84504 1.12623 1.22113
62 CA 30 2 0   8.6 7.5 0.47394 1.29418 1.18465
46 HI 38 8 1   10.1 10.2 -0.03486 0.17869 0.12254
48 PR 37 10 1   9.5 9.8 -0.11667 -0.32911 -0.30155
GPX4           
204 Total 31 7 1 0 10.4 7.7 0.99362 -0.65746 0.03750
48 AA 24 6 0   9.9 7.9 0.85392 -0.15103 0.23582
62 CA 21 3 0   10.2 6.5 1.77252** 0.57981 1.19930
46 HI 18 3 0   10.2 6.0 2.24912* 0.46442 1.26672
48 PR 19 3 1   10.0 6.3 1.88377** 0.53274 1.17584
TXNRD1           
204 Total 43 10 3 0 3.7 5.2 -0.84233 -0.81317 -0.99372
48 AA 28 5 2   4.4 4.5 -0.09852 0.40341 0.26989
62 CA 22 3 1   3.8 3.4 0.44241 0.64623 0.68209
46 HI 24 7 1   3.9 3.9 -0.02622 -0.44254 -0.35427
48 PR 20 7 2   2.3 3.2 -0.96694 -0.87634 -1.07578
SEPP1           
204 Total 24 5 0 2 4.8 3.3 1.25024 -0.41307 0.31238
48 AA 17 3   1 3.8 3.1 0.73630 0.37764 0.59147
62 CA 18 2   1 5.2 3.1 2.05607* 0.80818 1.48364**
46 HI 17 2   2 5.0 3.1 1.83966** 0.79897 1.36158
48 PR 16 0   1 4.5 2.9 1.66728 1.59572* 1.91681*
  1. Single nucleotide polymorphisms (SNPs) were identified by re-sequencing 6 selenoprotein gene regions in a 102 member control population. Nucleotide diversity (π) and the population mutation parameter (Θ) were calculated using the most probable PHASED haplotypes. To determine whether variation was consistent with the expectations of the neutral equilibrium model, neutrality was tested using Tajima's (DT) and Fu and Li's (DF and F) statistics. DT, DF and F were computed using S, the number of segregating sites, in DNASP.
  2. *Statistical significance: P < 0.05
  3. **Statistical significance: P < 0.10, P > 0.05