2.5 Calculation of evolution rates
We aligned nucleotide sequences using MUSCLE for each orthologous gene and formed a concatenated alignment for all orthologs. We used the constructed tree topology as the guide tree, and calculated pairwise rates of dS, dN, and dN/dS using the free-ratio model (Parameters: model=1, NSsites=0, fix_omega=0, omega=1) in PAML 4 (Yang, 2007) for each branch. The dN/dS value was used to measure the evolutionary rate along a lineage. The lineage-specific mean value was estimated by concatenated alignments from all orthologs.