Nucleotide substitutions in protein-coding genes can be divided into synonymous (S) and non-synonymous (N) ones that alter amino acids (including nonsense mutations causing stop codons). The S substit
Each column is labelled to indicate the steps leading to the mutation rate numbers (see Methods for more details). We first calculate the number of SNPs per sub-clone detected in each clone tree gener
we estimated the non-synonymous/synonymous rate ratio (dN/dS) at each codon site using the Bayesian approach implemented in the CodeML program of the PAML4 package (Yang 2007) .
1The dN/dS ratio of the class of codons under positive selection is given with the percentage of codon sites predicted to be in that class. 2The P-value rejecting the model of neutral evolution (M8A)
1SELECTON results for the putatively asexual fungus V. dahliae were calculated by analyzing a MAT1-1-1 codon sequence alignment including sequences from all other fungi listed except P. fulva. Results
