When running jmodeltest on my chloroplast dataset of the genus
Mosannona the substitution model GTR+G is predicted to be the best
fitting model. Accidently, I performed BEAST analyses with a GTR model
without gamma. These analyses remarkably show a significantly higher
support value (0.91 instead of 0.74) for one of the basal nodes of
interest compared to the same analyses with a GTR+G model.
Jmodeltest gives a –lnL of 11.314,459 for GTR+G and 11.362,524 for
My question is whether it is more likely that the analyses with the
GTR model find an incorrectly high support value or that jmodeltest
fails in finding the model best describing the data.
Has anyone had a similar experience in BEAST? Comments are welcome!