I was wondering if it makes sense to keep characters that are parsimony-uninformative (autapomorphies) when making a phylogeny analysis using Bayesian inference. Since it is a probabilistic method, it may be informative to keep these characters. Does it make sense?
As far as I know, excluding autapomorphies can affect the results of probabilistic methods, mainly branch lengths and dating, it you are doing it also.
Have you already tried running the analysis by adding and removing them?
As Fabio said before, it may be useful in dating and to account differences between lineages. If your goal is just the topology, I'd guess it will not matter that much, apart from making your analysis run longer.
Ok. I will keep then. I think it is important to show if there is "morphological long branch". Even in parsimony it is interesting if there is a branch full of "autapomorphies", because it highlights that the taxon is very different from the others, and taxa such as these are usually "wildcards" too;