I've been scouring the literature for objective means to select "good" outgroups in phylogenetic studies, but without success. I've never seen an explanation why a given outgroup was selected. It seems as though it's a realm that deserves study, unless I'm overlooking something.
The basic idea is to select an outgroup that is related, but at an ancestral/basal level, relative to the taxa of interest. Typically it appears as though researchers use an outgroup because another also used it. There should be rigor applied to objectively determine the outgroup choice.
Outgroups often don't get the attention they merit. To my students I recommend two things. Use multiple outgroups, to test the monophyly of the ingroup (you assume it with the use of a single outgroup), and include among the outgroups all taxa thought to be related to the ingroup, i.e. exemplars from its sister group, or taxa thought to represent putative sister groups. Dense sampling of relevant outgroups will avoid assumptions of ingroup monophyly and improve the likelihood of your ingroup network being rooted at an appropriate branch
Outgroups often don't get the attention they merit. To my students I recommend two things. Use multiple outgroups, to test the monophyly of the ingroup (you assume it with the use of a single outgroup), and include among the outgroups all taxa thought to be related to the ingroup, i.e. exemplars from its sister group, or taxa thought to represent putative sister groups. Dense sampling of relevant outgroups will avoid assumptions of ingroup monophyly and improve the likelihood of your ingroup network being rooted at an appropriate branch
I agree with you on the gist of the approach, but like you said, it is based on certain assumptions which I have yet to see a rigorous test. What I envision is a model that examines aspects of the tree to determine whether the data "fits" the monophyletic assumption; It does not yet exist.
Outgroups are used to identify the position of the root on a phylogenetic tree. So in my view, the best available outgroup is the one that has diverged less from the root. A simple way of assessing this is by looking at the genetic distance separating each possible outgroup from your ingroup. Often, when assessing a set of outgroups, I find that the outgroup closest to the ingroup varies among loci. Note that I also definitely suggest the inclusion of multiple outgroups in a phylogenetic study, but looking at genetic distances can help, especially if different outgroups give conflicting results.
I've swapped various outgroups using the distance as a guide, however, the topology does not always remain fixed. What is bothersome is that it boils down to a subjective process of what may either "look good" and confirm pre-existing bias of how the tree should look. It is entirely typical that researchers fail to disclose how the outgroup was chosen, and what others may have been tested and rejected, and why. Looks like a doctoral thesis to make this happen.
I always state in papers why I have used a certain outgroup(s).
I usually use multiple outgroups to test the monophyly of the ingroup and include exemplars from its sister group, or taxa thought to represent putative sister groups.
You can also root the tree using the most basal of the sister group, assuming there has been a phylogenetic analysis to determine this.
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