2.6 Positive selection analyses
We indicated positive selection by the ratio of the rate of
nonsynonymous to synonymous substitutions (dN/dS or ω) per gene among
lineages. Using our phylogenetic tree topology as the guide tree, we ran
branch-site model (Yang, 2007)
(Parameters: null hypothesis: model=2, NSsites=2, fix_omega=1, omega=1;
alternative hypothesis: model=2, NSsites-2, fix_omega=0, omega=1) in
the codeml module of PAML4 to detect positive selection for the
one-to-one orthologous genes of five species within the macrotisgroup, respectively. For each analysis, we selected only one species as
foreground branch, and regarded all other species as the background
branches. A likelihood rate test (LRT) was performed to detect positive
selection on the foreground branch, and the Bayes Empirical Bayes (BEB)
analysis (Yang et al., 2005) was
implemented to calculate posterior probabilities and to deduce
positively selected sites. P -values of all positively selected
genes (PSGs) were also normalized by FDR using Benjamini-Hochberg
approach(Benjamini and Hochberg, 1995) andP value less than 0.05 was considered significant.