Fixations along phylogenetic lineages

Phylogenetic reconstruction: a simplification of the evolutionary process

Cladists and pheneticists

Anatomy of a phylogenetic tree

Edges and nodes

Depictions of phylogenetic trees Slanted Cladogram Rectangular Cladogram Phylogram

Circle tree Unrooted cladogram Unrooted phylogram

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

Branch lengths and phylogenetic trees Ultrametric trees Unequal branch lengths

Trees with and without branch lengths

A character matrix

Counting the number of steps on a phylogenetic tree

Sites 4 and 6 on the same tree

Rooted and unrooted trees

Convergence and homoplasy in mantids

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 ) Synapomorphies designate clades… But what if synapomorphies are reversed? Willi Hennig

The number of rooted, labelled, bifurcating trees

Informative and uninformative site patterns

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

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

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