index.rmdUsing the data set we downloaded at the end of class (primates_and_galeopterus_cytb.nex ), do the following.
Make two copies of the MCMC_JC.Rev file. Call one MCMC_HKY.Rev, and MCMC_GTR.Rev.
Following the instructions in the Molecular Models lesson, edit the two model files you just made to correspond to the HKY and GTR models.
Run them in RevBayes and compute a summary tree.
Fill in the following table as you go through the tutorial.
Posterior probabilities under different analyses
| Model | Lemuroidea | Lorisoidea | Platyrrhini | Catarrhini |
|---|---|---|---|---|
| Jukes-Cantor | ||||
| HKY85 | ||||
| GTR |
Looking at your tree trace in Tracer, answer the following:
In your HKY model, is the inferred rate of transition substitutions higher than the rate of transversion substitutions? If so, by how much?
In your HKY model, are the resulting estimates of the base frequencies equal? If not, how much do they differ?
Under your GTR model, are the resulting estimates of the base frequencies equal? If not, how much do they differ?
Under your GTR model, are you able to tell which substitutions are more likley than others? If so, which?