3: Phylogenetics 2 Phenetics & Cladistics

3rd Lecture

There are three approaches to inferring phylogenies, what are they?

Phenetics, Cladistics, & Model-based approaches.

What are phenetics?

An approach that attempts to infer relationships by classifying organisms based on overall similarity

What are cladistics?

An approach that attempts to infer relationships by classifying organisms based only on shared derived characteristics; better than phenetics

What are model-based approaches?

An approach that attempts to infer relationships, allowing for possibility that not all character state changes are equally informative

Phenetics: What are the three steps?

1. Find most similar two taxa, link them together and treat them as a group

2. Find next most similar two taxa, link them, and treat them as a group

3. Continue until all species have been linked

use character state matrix to draw a neighbor-joining tree of the taxa

Phenetics: True or false. Phenetics reflects the true evolutionary history of the group

False.

Cladistics: What is the principle of parsimony?

The principle of parsimony- All else being equal, the explanation requiring the fewest number of steps is accepted

Cladistics: How do you map traits with parsimony?

• Show all hypothesized character state transitions

• Minimize number of hypothesized changes

Cladistics: What are the 5 steps to conduct a cladistic analysis?

1. Consider all possible unrooted trees

2. Map all character state transitions onto tree

3. Tree with fewest transitions is accepted as best hypothesis of descent relationships

4. Equivalent statement: the tree with the fewest apparent homoplasies is accepted.

5. Root tree using outgroup

Advantages of phenetics?

1. Simple

2. Doesn’t need an outgroup

Advantages of cladistics?

Most likely to give the true phylogeny

Problems with parsimony: What are the three general problems with parsimony?

• Parsimony minimizes the number of character state transitions

• Assumes that all character state transitions are equally likely

  • Between each possible character

  • Along each branch of a tree

• These assumptions are often not valid

  • Pyrimidines may be replaced by pyrimidines more often than purines

  • Some lineages evolve more quickly than others

Problems with parsimony: long-branch attraction

1. Branches with many autapomorphies will be similar to other long branches by chance alone

2. Long branches may also attract short branches, but small changes in the data may switch which short branch is attracted to

What is maximum likelihood? What does it not assume?

Maximum likelihood is a model-based approach to tree building. It does not assume equal probabilities of character state changes among all character states.

• It allows different probabilities of character state changes among all character states

• It accounts for different rates of evolution in different lineages.

Maximum likelihood: Advantages

• Takes into account varying rates

• May result in more accurate outcomes

• Reduces long branch attraction

Maximum likelihood: Disadvantages

• Computationally intensive compared to parsimony

• Estimates of probabilities of different kinds of change may be inaccurate

True or false? Homoplasies can make a big difference to patterns.

True

True or false? Homoplasy is more likely to affect results

False. Homoplasy is less likely to affect results.

Bootstrapping steps

• Make a new data set by randomly choosing loci from data set

  • Some are sampled repeatedly; some are omitted

  • Make new tree & see if patterns are the same

  • Clades that appear repeatedly are considered strongly supported; those that appear only occasionally are not considered to be reliable

  • Similar to P values, but higher numbers are better

• Must include all members and only members of the clade

• Relationship among the members in the bootstrapped clade is irrelevant