The nonsynonymous and synonymous mutations were counted based on the branches of the phylogeny and the mutations on a branch were only counted once.
The branch-site selection test implemented in codeml (part of the PAML package v.4.8a 63 was then used to test for positive selection on three branches of the phylogeny leading to the "wood", "blast" and "root" fungi (see above 9.
The EST-associated matrix is more complete (fewer missing loci) and has slightly lower homoplasy than non-EST subsampled matrices of the same size, but there is no difference in phylogenetic support or relative attribution of base substitutions to internal versus terminal branches of the phylogeny.
By letting the model evolve along the branches of the phylogeny, which here represent the time since cladogenesis (Fig. 4b), we can estimate the rates (probability) of occurrence of the biogeographic processes (DAB, DBA, EA, EB) and infer the most probable ancestral ranges at every cladogenetic event (Fig. 4c; Sanmartín 2010).
To calculate the statistical reliability of the branches of the phylogeny, we applied a jackknife resampling technique that randomly removed 50% of the initial orthologous gene sets.
The elevated substitution rates of clpP1 are associated with statistically significant whole-gene positive selection in three branches of the phylogeny.
We applied models of codon evolution which allow for variation in dN/dS among codons but assume the same distribution in all branches of the phylogeny.
The disadvantage of this approach is that it can produce biases of its own, for example, by reducing the apparent indel rates on terminal branches of the phylogeny.
Nine out of ten amino acid substitutions occurred on the branches of the phylogeny predating the split of the clades III and IV or leading to the clades III and IV (Fig. 1).
Model M0 assumes a single rate of evolution for all codons (sites); all other models implemented allow for variable ω values across sites; however they do not allow ω to vary among branches of the phylogeny.
Model 1 was used to estimate ω along the central branches of the tree (Figure 1) and to infer the number of substitutions along these branches of the phylogeny.
