Oct 16 Flashcards Preview

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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

What does independent contrasts do?

compares changes along a branch, rather than character states