Lecture 10 - Phylogenetics Part 2

Question 1

Monophyly

Answer 1

A group with all descendants of a single evolutionary origin

Question 2

Paraphyly

Answer 2

The group with most descendants of a single evolutionary origin

Question 3

Polyphyly

Answer 3

Group with multiple independent evolutionary origins

Question 4

Unrooted tree

Answer 4

No assumptions about ancestrty

Question 5

Rooted tree

Answer 5

One taxon acts as outgroup to all others

Question 6

Phylogram

Answer 6

Branch lengths correlate to the amount of evolutionary change

Question 7

Ultrametric trees

Answer 7

All tips equidistant from the root

Question 8

Will gene trees and species trees be the same?

Answer 8

No as gene mutation events are more rapid than speciation events

Question 9

How can gene duplication arise?

Answer 9

Processes such as unequal crossing-over of chromosomes can cause duplications of whole genes

Question 10

Homologous genes

Answer 10

Genes from the same ancestor

Question 11

Orthologous genes

Answer 11

Gene separated by speciation events

Question 12

Paralogous genes

Answer 12

Genes separated by gene duplication

Question 13

How can gene duplication cause species trees and gene trees to appear different?

Answer 13

As gene duplication followed by gene loss can cause them to be different

Question 14

Incomplete lineage sorting

Answer 14

Random sampling of population genes at each generation deep coalescence can lead to incomplete lineage sorting and then gene tree may not reflect the species tree

Question 15

Horizontal gene transfer

Answer 15

Genes can move horizontally rather than verticly mostly between closely related bacteria but can be in eukaryotes and can be between distant clades

This can then influence phylogenies to become more like branching networks

Question 16

Parsimony

Answer 16

The simplest explanation requiring the fewest assumptions should be preferred, therefore the tree topology requiring the fewest character changes

Question 17

Heuristics

Answer 17

Approximate the answer by subsampling and applying algorithms

Question 18

Random addition sequences

Answer 18

Adding each taxon in turn, choosing the shortest tree for the next step

Question 19

Branch swapping

Answer 19

Pruning and reattaching leaves and branches, keeping shorter solutions

Question 20

What is the problem with Parsimony?

Answer 20

There are so many trees it is hard to easily find the most parsimonous

Question 21

What is the problem with the hill-climbing scenario

Answer 21

As you start climbing you can get stuck on a peak

Question 22

What are two heuristic approaches to building a tree?

Answer 22

Random addition sequences and branch swapping

Question 23

Consensus tree

Answer 23

A summary of the most parsimonious trees found

Question 24

Likelihood

Answer 24

likelihood, like parsimony tries to find the tree with the fewest number of changes, but uses models to find the most likely tree

The tree that maximises sum of likelihood for individual characters is the most likely

Question 25

Substitution models

Answer 25

Specify different probabilities for each kind of change (mutation)

Different sites and genes have different mutation rates and can be used to find the most likely

Question 26

How do substitution models vary

Answer 26

They vary in complexity and number of parameters

Question 27

bootstrapping

Answer 27

Randomly take out and sample initial data to find if there are any groups with a large influence on the data

Question 28

Bayesian inference

Answer 28

Based on the probability and uncertainty of multiple factors: posterior and prior probabilities of the trees, the data, the models and their inter-dependency

Requires all trees which is impossible therefore Markov Chain Monte Carlo methods (MCMC)

Question 29

Markov Chain Monte Carlo Methods (MCMC)

Answer 29

Mechanism for sampling lots of solutions (trees with models) based on probability

Question 30

Long branch attraction

Answer 30

Distantly related taxa appear artificially similar by chance