Flashcards in Oct 16 Deck (25):

1

## How are timescales determined in a tree?

### molecular clock

2

## In the tree containing foxes, wolves, dogs, and bear, why is the dog group polyphyletic?

### Descendants of most recent common ancestor of dogs are not all dogs

3

## How do cluster methods work? Does order matter?

###
add taxa sequentially

ORDER MATTERS

4

## What are the 2 steps of optimality criteria?

###
a) model to explain changes between taxa

b) evaluate each tree

5

## Which is a quicker tree building method, cluster methods or optimality criteria?

### cluster methods

6

## What are 3 considerations for evaluating tree building methods?

###
1) efficient- will it break my computer?

2) power/consistency- minimum amount of data

needed to arrive at the correct tree all the time

3) robustness/falsifiability- how do violations of the assumptions impact outcomes and can it ‘report’ those effects

7

## Parsimony is sensitive to what type of species?

### rapidly-evolving

8

## What is long-branch attraction?

### dissimilar species are drawn together due to having more changes than their sister taxa

9

## How do distance methods work?

### quantify pairwise differences to yield a ‘distance score'

10

## What are the 3 steps of a DNA sequence alignment?

###
1) look for regions of homology

2) identify insertions and deletions (indels)

3) identify substitutions

11

## Multiple pairwise distances yield a...

### distance matrix

12

## How do sister taxa look in the tree representation?

### lines form a triangle NOT a trapezoid

13

## What are DNA substitution models of evolution?

###
Jukes-Cantor (homologous)

Kimura Two-Parameter

General Time-Reversible + Gamma +1

14

## What does the Jukes-Cantor model assume?

### equal probability of character (base-pair) change

15

## What does the Kimura Two-Parameter model assume?

### pur->pur changes more likely than pur->pyr

16

## What does the General Time-Reversible + Gamma +1 assume?

### accounts for diff. probabilities of substitutions/time; sites that remain unchanged; rates of change...at each site

17

## What does maximum likelihood predict?

### probability that the given tree explains the collected data

18

## What are 2 assumptions of maximum likelihood?

###
1) characters evolve independently

2) substitution rate is constant

19

## Statistical confidence provides

### level of certainty about how well the data supports monophyletic clades and the overall phylogeny

20

## What does bootstrap analysis do?

### ‘resampling with replacement’ to evaluate how data randomization affects tree topology; reorders character traits and duplicates some

21

## What are the steps of bootstrap analysis?

###
1) create many reordered character matrices with randomly replaced traits

2) trees are generated from each matrix

3) frequency of clade recovery is evaluated

22

## What does odds ratio testing do?

### compares the best tree with clade X vs. the best tree lacking clade X and reports a significance statistic

23

## What is phylogeography?

### Linking phylogeny and geological evidence to help explain migration/dispersal or adaptive radiation/speciation/extinction events

24

## What does comparative analysis do?

### Establishing evolutionary relationships to aid in making hypotheses about specific trait dynamics ie. association btw habitat and activity, testes size increases/decreases w/ age

25