## Questions on Paul Lewis phylogenetics primer part 1 – Substitution
models

**Note: we won’t revisit codon models during this course so (if
you want) you can skip the last 15 minutes of this lecture. These models
are used rarely in the context of paleobiology. But if you have the
time, they are cool!**

- What are the assumptions of the following substitution models?
Consider the rate of change between character states and the state
frequencies.

- JC
- K80
- F81
- HKY
- GTR

- Can you briefly describe the following three approaches that account
for rate variation among characters? Don’t worry about the details, just
try to provide the general idea.

- Site specific rates
- Invariant sites model
- Discrete Gamma model

- For a given substitution model, what do the values in the Q matrix
and the P matrix represent?