8.3 years ago by
John, I think that your new outgroup choice will be fine, possibly even better. The general approach is to choose something close to the ingroup, but with no possibility of being actually within the (in)group you are studying. It would be better if you had support values to show that the new outgroup is confidently excluded from the ingroup.
More generally it is good to treat this as an experiment. Your hypothesis could be "outgroup choice does not significantly influence ingroup phylogenetic relationships". Try including a range of outgroups and also midpoint rooting. On the tree you show a number of additional credible looking outgroups at the top of the tree. If your ingroup phylogenetic hypothesis is correct and strongly supported changing OG shouldn't make much difference.
You can minimise long branch attraction perhaps by having the outgroup as a group rather than a single OTU, as this will break up the long branch. You must of course know that group to be a real grouping, else the whole tree could be skewed by artificially forcing it to exist.
Best of luck
EDIT, I didn't really answer your question. Yes it is fine to pick OG based on a tree rather than fossil or other evidence.