CODEML analysis of common gene family genes between highly diverged species (A & B)

[Syed Abbas Bukhari]

Hi PAML users and admin, 

I have a basic biological interpretation question to ask here before starting a PAML analysis on my dataset. I have a set of common gene family genes in specie A and B which are differentially expressed in response to common phenotype in both species. Where specie A and B are very distantly related let say one is insect and other is fish.  Now i am interested for a given gene family genes: if the paralogous genes of specie A and paralogous genes of B are evolving at a same rate or some sort of selection is going on in there. I am wondering if i am allowed to do this comparative CODEML analysis of these paralogous genes belonging to same gene family in these two highly diverged species or not?  IF so is there any recommendations while doing this analysis in PAML.

I really appreciate your time in this regard. 

Thank you!

Abbas

[Ziheng]

The question does not sound very exciting.
If you are sure that these are paralogous, you can analyse the family in the fish as one data set and the family in the insects as another dataset. Suppose you use M0, estimating one w ratio from each dataset. Suppose the fish w = 0.5, and the insect w = 0.1. That means purifying selection removing nonsynymous mutations is more effective in the insects than in the fish, which can be due to either stronger selection in the insects or longer population size in the insects. I don't think you can infer too much from data like that.
Ziheng