Practical 4 - phylogenetic trees

Question 1

How do you calculate net diversification rate?

Answer 1

speciation rate (b) - extinction rate (d)

Question 2

What do you use to identify adaptive radiation / extinction events?

Answer 2

Medusa

Question 3

What is aic?

Answer 3

Measure of how well a model fits a real world process (larger = more info lost and worse model)

Question 4

What is r?

Answer 4

Diversification rate

Question 5

What are r low and r high?

Answer 5

The lowest and highest diversification rates

Question 6

What is eps?

Answer 6

Extinction rate

Question 7

What are eps low and eps high?

Answer 7

The lowest and highest extinction rates

Question 8

What does only one step indicate?

Answer 8

A non-significant result, no change in diversification rate across phylogeny from Medusa model

Question 9

What does more than one step indicate?

Answer 9

A significant result, a change in diversification rate across phylogeny from medusa model

Question 10

What does an increase in net diversification indicate?

Answer 10

Adaptive radiation across phylogeny

Question 11

What does a decrease in net diversification indicate?

Answer 11

Extinction event across phylogeny

Question 12

What could have caused radiation in the whale group?(speculation)

Answer 12

Echolocation from toothed whales, dolphins different to Odontocytes due to their intelligence and larger brains which gave them the ability to adapt to different niches

Question 13

In the body size over time model, what do longer branches mean?

Answer 13

More genetic change in the tree but not necessarily more evolved

Question 14

What does ancestral state reconstruction do?

Answer 14

Estimates ancestors body masses

Question 15

Problems with body mass analysis

Answer 15

Assumes we have complete data, assumes rate of body mass change is constant

Question 16

What does the Brownian motion model do?

Answer 16

Fit a model for how a trait changes over time

Question 17

In the Brownian single-rate model, what does s^2 mean?

Answer 17

Rate of evolutionary change

Question 18

In the Brownian single-rate model, what does a mean?

Answer 18

Reconstructive state

Question 19

In the Brownian single-rate model, what does u mean?

Answer 19

Parameters

Question 20

In the Brownian model, what does the p-value mean?

Answer 20

Likelihood test

Question 21

What does added fossil data help us to achieve?

Answer 21

A more accurate result

Question 22

What do the tips of a phylogenetic tree represent?

Answer 22

Species / populations / individuals described by the tree

Question 23

What do the branches of a phylogenetic tree represent?

Answer 23

Pattern of relationships between species

Question 24

What do the nodes of a phylogenetic tree represent?

Answer 24

Most recent common ancestor of the lineages that diverge from that node

Question 25

What is a clade?

Answer 25

A monophyletic grouping of lineages

Question 26

What makes a group monophyletic?

Answer 26

If all the members descend from a common ancestor to the exclusion of others

Question 27

What is a cladogram?

Answer 27

A tree where the lengths of the branches carry no meaning and if only useful for interpreting patterns of relatedness (not evolutionary change / time between nodes)

Question 28

What are time-calibrated phylogenetic trees?

Answer 28

A tree where the branch lengths represent time

Question 29

Apart from time, what else can branch lengths represent?

Answer 29

Evolutionary distance a the amount of change with longer branches meaning there have been more character changes (genetics, morphological, protein seq etc)

Question 30

What is the simplest form of diversifcation?

Answer 30

Pure birth model where each lineage had a constant probability of speciating

Question 31

What does the birth-death model do?

Answer 31

Incorporates extinction as well as speciation

Question 32

What is the general rule for aic's?

Answer 32

An aic of more than 2 indicated significant difference between models

Question 33

What is phylogeny?

Answer 33

Study of the evolutionary history of a group or species

Question 34

Utility of Ancestral State Reconstruction

Answer 34

Fossil data reduces uncertainty, ASR can highlight correlations but causation needs further study, more reliable with complete data