Lecture 21 Phylogenetics Methods And Likelihood

Question 1

General procedures for Phylogenies

Answer 1

1. Choose species
2. Collect character data (create data matrix)
3. Find optimal tree (e.g., Parsimony or likelihood search
4. Root tree (establish character polarities or outgroup rooting)
5. Estimate confidence or strength of support (e.g., bootstrapping)

Question 2

Character polarity determines the

Answer 2

Direction of changes in character states

Question 3

Computer programs produce

Answer 3

Unrooted trees

Question 4

Outgroup method

Answer 4

Effectively same as “pulling: down the root on the branch between in-group and outgroup

Question 5

How do we test the hypotheses of a phylogeny?

Answer 5

Collect more data
Bootstrap

Question 6

Two ways to look at a tree

Answer 6

1. How confident should we be of the entire tree
2. How confident should we be of each one (hypothesis) in the tree?

Question 7

Phylogenetic history must be tested

Answer 7

indirectly

Question 8

Support for nodes (4)

Answer 8

Consensus trees
Congruence test
Character support
Bootstrapping

Question 9

Consensus trees

Answer 9

Summarize agreement among different Phylogenies
(Strict consensus and majority rule consensus)

Question 10

Strict consensus

Answer 10

Conflicts are collapsed on the tree to represent that we do not know 100% what is going on

Question 11

Majority-rule consensus

Answer 11

Put percentages on the tree to represent how sure we are of its placement

Question 12

Congruence test

Answer 12

A phylogenetic hypothesis makes predictions about the distribution of other characters
So to test you compare trees from different data sets to see if they are the same or not

Question 13

Character support

Answer 13

Numbers of synapomorphies

Question 14

Bootstrapping

Answer 14

Resamples a data set repeatedly to estimate confidence (robustness or repeatability)

Question 15

Likelihood

Answer 15

A general statistical approach applied to many areas of science
Optimality, way of choosing amongst alternatives

Question 16

Likelihood equation

Answer 16

L=P(D|M)

Question 17

Hypothesis =

Answer 17

History (tree topology and branch lengths) plus model of evolution

Question 18

Model =

Answer 18

Transition rates for character state transformation and for classes of characters (quantifying how the DNA sequence evolves; a general description of how things work)

Question 19

L = P(D|M, T)

Answer 19

If you hold D and M constant, one can compare the likelihood of different trees

Question 20

Parsimony is a

Answer 20

Special case of likelihood, where every character has its own model.
The phylogeny that makes the data most likely is preferred.

Question 21

Branch lengths are important when using

Answer 21

Likelihood to choose a tree (changes are more likely on long branches) but irrelevant to parsimony

Question 22

How to calculate Likelihood

Answer 22

1. Map characters (parsimony)
2. Ignore outgroup Branch
3. Assign Branch probabilities
4. Add scenarios on long branches
5. Multiply probabilities

Question 23

L = P(D|M, T) expanded

Answer 23

L=P(data|model, tree)