I have built the trees in starbeast with the same dataset (three nuclear markers). In one tree it is classified as 14 species and in another 16 species. I would like to know which one of these classification is better. One tree is classified based on GMYC and another based bPTP species delimitation method.
I would do a bayes factor test to test it. You run the analyses with the only differences are the number of species and d stepping stone sampling to estimate the marginal likelihood used for the Bayes factor test
Here is a tutorial which may be useful: http://beast.bio.ed.ac.uk/Model-selection
I am not sure if marginal likelihoods from competing models are directly comparable, or if you have to apply some correction as in: https://sysbio.oxfordjournals.org/content/63/4/534.full.pdf+html
I have also attached a paper which may be interesting...
I advise you to use Structure Harvester softwar, this softwar it's very easy to use and it's give you the exacte number of taxa you have. You can compare your two tree and choose ho have the great values of bootstrap.
Instead of posthoc comparing the two trees I'd rather suggest you use a method that simultaneously infers a species tree and assigns accessions to MSC species. DISSECT (and soon STACEY) exists as a plugin to *BEAST, here:
https://www.researchgate.net/publication/268874950_DISSECT_An_assignment-free_Bayesian_discovery_method_for_species_delimitation_under_the_multispecies_coalescent
Article DISSECT: An assignment-free Bayesian discovery method for sp...
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