Table 1.
Natural selection tests on HPT genes
| Model | np | l = ln L | Estimates of parameters | Positively selected sites |
|---|---|---|---|---|
| One-ratio | ||||
| ωHPT2 = ωBR = ωTA = ωPC | 1 | −8204.98 | ωHPT2=ωBR=ωTA=ωPC = 0.29798 | Not allowed (NA) |
| Branch-specific models | ||||
| ωHPT2 ≠ ωBR = ωTA = ωPC (2 ratio) | 2 | −8199.87 | ωHPT2=0.81568; ωBR=ωTA=ωPC=0.28457 | NA |
| ωHPT2 ≠ ωBR = ωTA ≠ ωPC (3 ratio) | 3 | −8199.06 |
ωHPT2=0.75587; ωPC=0.28095 ωHPT2=ωTA= 0.48924 |
NA |
| ωHPT2 ≠ ωBR ≠ ωTA ≠ ωPC (4 ratios) | 4 | −8199.36 |
ωHPT2= 0.81975; ωBR= 0.24071; ωTA= 0.18172; ωPC= 0.28853 |
NA |
| Branch-site-specific models (selection test of HPT2 as the foreground lineage) | ||||
| Model A (4 site classes) | 4 | −8034.75 |
p0=0.65921, p1=0.25827 (p2+p3=0.08252); ω0=0.09024, (ω1=1.0), ω2=4.92076 |
Selected sites in HPT2: 9P, 79M, 89N, 100T, 103D, 149S, 164S, 167D, 204F, 212L, 217I, 246V, 270M, 271A, 356V (Probability > 0.6) |
| Model A Null (4 site classes) | 3 | −8036.70 | p0=0.55094, p1=0.21917 (p2+p3=0.22990), ω0=0.08916 (ω1=1.0, ω2=1.0) | NA |
In one-ratio and branch-specific models, ωHPT2, ωBR, ωTA, and ωPC stand for Ka/Ks values for HPT2, Brachipoideae HPT1, Triticeae-Aveninae HPT1, and Panicoideae HPT1 branches in Fig. 1B. In the site-specific model M1, two site classes were specified: highly conserved sites (ω0) and neutral sites (ω1=1). For the branch-site models, HPT2 was specified as the foreground group. In the branch-site model A, four site classes were specified. The first two classes have ω ratios of ω0 and ω1 respectively, corresponding to highly conserved sites and neutral sites across all lineages. In the other two site classes, the background lineages have ω0 or ω1 while the foreground lineages have ω2. p0, p1, and p2 represent the percentages of the corresponding site classes. Np: number of parameters. L: likelihood value. Amino acid sites were numbered according to HvHPT2 (HORVU.MOREX.r2.2HG0173050.1) in barley. (see Additional file 5 for detailed data)