Hi,
I am trying to test if one copy of a duplicated gene is under positive selection in 1 particular fish species. The other copy of the duplicated gene has been observed to be under positive selection in other fish lineages. There are about 25-30 fish species that have DNA sequences published of the two copies of the gene. My question is do I include as many species as possible or do I select certain species? My original plan for running paml is to create two seperate tree and DNA alignment files one for each copy of the gene. Is this a logical way to run my samples?
Most protein coding genes are under a lot of negative selection pressure to maintain the function of the protein. What is often reported as positive selection pressure is more often just a bit of relaxation of the negative pressure, allowing a little more change in the protein sequence but still maintaining many invariant sites over time.
I would build a tree including both copies of the gene to see if the branch lengths are longer (more diversity, less negative selection) for one gene copy vs the other. But you should also look at the dN:dS ratio of nonsynonymous to synonymous mutations observed for each gene. I would recommend the datamonkey adaptive evolution tools. http://www.datamonkey.org/
If the x-ray crystalographic 3D structure of the protein is in the PDB protein databank, you can see which sites on the structure are evolving faster or slower using the ConSurf evolutionary conservation of protein structure server: http://consurf.tau.ac.il/
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