1. Fixations along phylogenetic lineages

2. Phylogenetic reconstruction: a simplification of the evolutionary process

3. Cladists and pheneticists

4. Anatomy of a phylogenetic tree

5. Edges and nodes

6. Depictions of phylogenetic trees Slanted Cladogram Rectangular Cladogram Phylogram

7. Circle tree Unrooted cladogram Unrooted phylogram

8. Ultrametric tree Unconstrained tree Depicting trees with branch lengths Time Present Time

9. Branch lengths and phylogenetic trees Ultrametric trees Unequal branch lengths

10. Trees with and without branch lengths

11. A character matrix

12. Counting the number of steps on a phylogenetic tree

13. Sites 4 and 6 on the same tree

14. Rooted and unrooted trees

15. Convergence and homoplasy in mantids

16. Parsimony, Hennig and Occam’s razor “ One should not increase, beyond what is necessary, the number of entities required to explain anything.” William of Ockham (ca. 1285-1349) Synapomorphies designate clades… But what if synapomorphies are reversed? Willi Hennig

17. The number of rooted, labelled, bifurcating trees

18. Informative and uninformative site patterns

19. Long-branch attraction p, q probability of observing a change between nodes or From node to tip

20. Parsimony is consistent when p 2 < q(1-q) The “Felsenstein zone”

21. Parsimony: pros and cons Pros: Simple and fast (sometimes) Cons: Depends on a very simple ‘model’ of substitution Does not estimate branch lengths well Susceptible to long-branch attraction