So I have a project student (undergraduate) who has been assigned a project to study the evolution of a gene (and possibly related genes) through species. I am not an evolutionary biologist, and hence am not too experienced in the workflow usually followed in studying the evolution of a gene in molecular phylogenetics. I have a brief idea, but may be wrong, and hence please do correct me.
The first aim is obviously sequence data collection for the requisite gene (and a few for a good outgroup), plot them in a phylogenetic tree, and analyse the distances, Ka and Ks ratio.
The next logical thing in my mind was a simple data collection for SNP analysis, and see if the SNP's are conserved, across species, and possibly if they impact protein structure.
But that's where i draw a blank. Any other ideas?