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LIFE230 > Practical 4 - phylogenetic trees > Flashcards

Practical 4 - phylogenetic trees Flashcards

1
Q

How do you calculate net diversification rate?

A

speciation rate (b) - extinction rate (d)

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2
Q

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

A

Medusa

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3
Q

What is aic?

A

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

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4
Q

What is r?

A

Diversification rate

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5
Q

What are r low and r high?

A

The lowest and highest diversification rates

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6
Q

What is eps?

A

Extinction rate

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7
Q

What are eps low and eps high?

A

The lowest and highest extinction rates

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8
Q

What does only one step indicate?

A

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

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9
Q

What does more than one step indicate?

A

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

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10
Q

What does an increase in net diversification indicate?

A

Adaptive radiation across phylogeny

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11
Q

What does a decrease in net diversification indicate?

A

Extinction event across phylogeny

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12
Q

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

A

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

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13
Q

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

A

More genetic change in the tree but not necessarily more evolved

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14
Q

What does ancestral state reconstruction do?

A

Estimates ancestors body masses

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15
Q

Problems with body mass analysis

A

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

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16
Q

What does the Brownian motion model do?

A

Fit a model for how a trait changes over time

17
Q

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

A

Rate of evolutionary change

18
Q

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

A

Reconstructive state

19
Q

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

A

Parameters

20
Q

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

A

Likelihood test

21
Q

What does added fossil data help us to achieve?

A

A more accurate result

22
Q

What do the tips of a phylogenetic tree represent?

A

Species / populations / individuals described by the tree

23
Q

What do the branches of a phylogenetic tree represent?

A

Pattern of relationships between species

24
Q

What do the nodes of a phylogenetic tree represent?

A

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

25
Q

What is a clade?

A

A monophyletic grouping of lineages

26
Q

What makes a group monophyletic?

A

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

27
Q

What is a cladogram?

A

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)

28
Q

What are time-calibrated phylogenetic trees?

A

A tree where the branch lengths represent time

29
Q

Apart from time, what else can branch lengths represent?

A

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

30
Q

What is the simplest form of diversifcation?

A

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

31
Q

What does the birth-death model do?

A

Incorporates extinction as well as speciation

32
Q

What is the general rule for aic’s?

A

An aic of more than 2 indicated significant difference between models

33
Q

What is phylogeny?

A

Study of the evolutionary history of a group or species

34
Q

Utility of Ancestral State Reconstruction

A

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

LIFE230 (4 decks)

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