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.