Forgive if the question is not in the realm of this site but I've received quite a lot of help here so I'm tempted to ask anyway.
When one wants to do evolutionary analyses involving certain hypothesis testing, as with the case with maximum likelihood analyses of selection forces acting on gene(s), it is usually advised to specify an evolutionary tree. Now when the analysis involves multiple gene families or cases when one is investigating genome wide cases of positive selection some genes will show evolutionary patterns that are not consistent to standard species evolutionary tree.
My question now is does it matter (will it affect the results?) in terms of evolutionary analysis whether the tree used for hypothesis testing is consistent to the species tree or not? I'm eagerly looking forward for an answer as I'm at a point where I don't have rational basis to choose between trees when a gene tree differs from species tree.