TABLE 1

Summary of molecular evolution analysisa

Functional categoryNo. of genesSite model (M0/M1a/M2a)Beta site model (M7/M8)
No. of positively selected genesProportion of genes under positive selectionNo. of genes with dN/dS value of >1Median percentileNo. of positively selected genesProportion of genes under positive selectionNo. of genes with dN/dS value of >1Median percentile
Apoptosis60020.71520.33310.684
Capsid and envelope2040.230.53960.28620.644
DNA binding1120.1820.62420.1820.714
Host infection2330.1320.30440.1720.538
Hypothetical protein158210.13290.571170.107300.464
Replication1450.3540.52450.3540.670
Transcription1760.3550.63660.3540.689
All249410.1647420.16845
  • a The data are separated by the site-based test (testing for selection at specific amino acids, using the M1a and M2a models) and the beta site test (testing for selection at specific sites, using a different set of parameters in the M7 and M8 models), implemented by PAML codeML. We considered genes to be under positive selection if the best-fitting model was M2a for the site-based models and M8 for the beta site models. The median percentile given is the probability that the median of the functional group is an outlier of the empirical distribution by chance.