Duplications and functional divergence of ADP-glucose pyrophosphorylase genes in plants

Table 1 Temporary relaxation of purifying selection, positive selection, or both after duplications in the large and small subunit of AGPase from angiosperms.

Branches	Large subunit	p-value	Small subunit	p-value
Class 1 (Figure 1)	0.114	0.005	0.058	< 0.001
Class 2 (Figure 1)	0.086		0.029
All branches (Figure 1)	0.090		0.033
Class 1 (Additional file 3)	0.125	< 0.001	0.081	< 0.001
Class 2 (Additional file 3)	0.086		0.029
All branches (Additional file 3)	0.089		0.034

The branches of the trees shown in Figure 1B and Additional file 3A (large subunit) or Figure 1C and Additional file 3B (small subunit) were classified into two groups. One group includes the short branches (K_S < 0.1) following a duplication event (post-duplication; class 1) and the other group includes all the other branches (class 2). The overall ω value of each group and the overall ω value of all branches were estimated by CODEML. The LRT was used to compare the model with two different ω values (one for class1 branches and one for class 2 branches) to the null hypothesis model with a single ω value.