Dear community,

My question is rather simple though I can't find a clear answer. How important is that the phylogeny to be used in any selection analysis is "the best" phylogeny we can get? I've read the chapters in the phylo handbook and others and it seems it's not that important, meaning that the inference of selection is robust to the phylogeny. Is this correct? I ask, in particular, when you have a phylogeny with some nodes not as well supported as others.

Thanks in advance,

Eduardo

Hi Eduardo,

There are no rigorous results to claim that selection methods are relatively insensitive to small changes in topologies, but all empirical evidence points to good robustness.
You have to get the phylogeny really wrong to really influence selection inference a lot.

If it doubt, I would simply run your analysis using several alternative topologies (e.g. you could collapse all poorly resolved internal nodes into a polytomy, assuming branch lengths are sufficiently short),
and see if that makes a difference.

Sergei