While performing Phylogenetic and evolutionary analysis of a gene family what should be the sample ?
I am working on a gene family that has undergone various duplication & speciation events giving rise to orthologs as well as paralogs. I want to do selection pressure analysis. My question is :
Should I do selection pressure analysis using the different members of the gene family in my organism of interest ? (Kind of paralogs, however their Fxs have diverged during duplication events giving rise to different family members)
OR
Should I do selection pressure analysis using one family member across 10s of different species.
The two methods should answer rather different questions In the first case if the families are similar enough to align you might get differential selection coefficients across the families: some transitions from one family to another may have stronger selection coefficients across the families. This might give you insight into the order in which the families appear a particular species - I am thinking off the top of my head on this one and would welcome other answers.
The second seems more conventional: to find the relative strength of selection across the speciation events: which species show profound changes within each gene family.
I think I would do both and treat it as an exploratory analysis.
Thank you Patrice Showers Corneli for your answer, however, didn't get the explanation for the first one. How would it give insight into the order of appearance?
Vis-a-vis the second, Is it so that different species might have undergone different selection pressures? I mean in one species positive selection and negative selection in another.
One gene (member of gene family) in multiple species could worth doing because after gene duplication; mutation and subsequent selection in one species may drive a particular duplicated gene into functional gene, but not in other species. This will help to dig out these genes under selection.
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