My current research focuses on the family of polyketide synthase (PKS) genes in filamentous fungi, particularly on entomopathogenic fungi. Our previous work identified a group of reducing clade III PKSs that are highly specific and highly conserved for these insect-pathogenic fungi. Interestingly unlike other groups of PKSs, a reducing clade III PKS is present as a single copy gene in a fungal genome, verified by the data from two available genome sequences of two fungi, Beauveria bassiana and Cordyceps militaris.

In the evolutionary viewpoint, the fact that this reducing clade III PKS gene is very conserved and single-copied in the genome might lead to a hypothesis (my hypothesis) that this PKS could be an ancestor of this PKS gene family.

I would like to ask an expert in the field how to determine which clade is an ancestor and which clades are descendants and/or the ratio of nonsynonymous to synonymous substitution using a software. I understand that PAML can do that. However, the program seems difficult to use and we are not evolution people. I have tried the graphical user interface version of this software, PAMLX, still I could not complete the analysis, likely due to the incorrect settings or options selected. I was wondering if anyone can give me a clue in this analysis. Any input or comment is highly appreciated.