Flashcards in Chapter 5 Deck (34):

0

## The disadvantage of using distance methods to construct trees include the fact that

###
Distance methods lack any sort of underlying evolutionary model;

The assumption is made that similarity is a reflection of homology

1

## Phylogenetic trees are used to

###
-construct hypotheses about common ancestors

-construct hypotheses about how various species are related to each other

-test hypotheses about the relationships between various species

2

## The older the clade, the

### more likely its members will show sequence divergence

3

## The basic conceptual approach to phylogenetic tree building involves

###
-the process of collecting information about character states

-the process of selecting taxa for inclusion in the tree

-the logic that species with many character states in common are more closely related than those without

4

## The basic conceptual approach to p-tree building assumes (part two):

###
That species with many character states are more closely related than those without;

That common characters are homologies

5

## Phylogenetic methods developed by evolutionary biologists to find the best tree possible for the taxa being studied include:

### Parsimony methods; Distance methods; Maximum Likelihood methods; Bayesian Inference methods

6

## The fundamental idea behind parsimony is

### That the best phylogeny is the one that both explains the observed character data and posits the fewest evolutionary changes

7

## Parsimony analysis offers the advantage of

### conceptual simplicity

8

## Parsimony has the disadvantage of

### Being an inconsistent estimator; Long-branch attraction

9

## Long branch attraction is

### The inferring of too close a relationship between a rapidly evolving species or populations

10

## The Fitch algorithm is

### Determines how many evolutionary changes are required for a given tree and character; Does not find the best tree

11

## Which of the following statements regarding rooted trees is/ are true?

###
-Any two rooted trees corresponding to the same unrooted tree will require the same number of character changes;

-The most common approach to rooting a tree is to use an outgroup

12

## Which of the following statements regarding rooted trees is/are true?

###
-We can form a rooted tree from an unrooted tree simply by picking a branch around to which to root the tree.

-Knowing the root of a tree, along with info about species ranges, can tell us about the PHYLOGEOGRAPHY of a group of species

13

## Arrange the steps of constructing a phylogenetic tree using the distance method in the correct order

###
1. The distance between species is measured using a character state changes

2. A distance matrix is created

3. Trees are constructed by arranging segments or branches derived from pair-wise distance comparisons

4. Phylogenetic inference software is used to choose the best tree

14

## How many different unrooted tree arrangements are possible for a phylogenetic tree relating 4 species?

### THREE

15

## The advantage of using distance methods to construct trees include the fact that

### Distance methods are conceptually STRAIGHFORWARD; & computationally among the FASTEST techniques

16

## How many unrooted trees are possible for 5 species?

### 15

17

## Arrange bootstrap resampling in correct order

###
1. A tree is constructed for the estimated phylogeny, based on the original character mix

2. Resampling is done from original character mix to create a collection of bootstrap replicate data sets

3. The same tree-building methods used on the original character set are used to create a collection of bootstrap replicate phylogenies

4. To assess the support for any feature of the original tree, the percentage of replicate trees that also display that feature are calculated

18

## Bootstrap resampling

###
-can be used with any technique for phylogenetic inference

- does not yield statistical significance levels

19

## Once we have used character data to infer a tree, how can we be certain this tree is correct?

### We can test statistical confidence certain features of the tree are correct

20

## Computer programs for reconstructing large phylogenies

### only check a very small fraction of possible trees

21

## Which of the following statements concerning trees is true?

###
-Each unrooted tree corresponds to numerous rooted trees

-An unrooted tree with k species has 2k-3 branches

-An unrooted tree with k species has 2k-3 times as many rooted trees as unrooted trees

22

## How many UNrooted trees are possible for 22-species tree

### more than there are stars in the universe

23

## How many Unrooted trees for a 6-species and 7-species tree, respectively?

### 105 and 945

24

## For extinct taxa

### the fossil record is the primary source of data for constructing phylogenetic trees

25

## Odds ratio testing

###
-Can be used only with model-based frameworks of max-likelihood or Bayesian inference;

-Can determine how strongly our character data support a given feature of a phylogenetic tree

26

## The role of organisms in impacting the external environment

###
-Is the process of niche construction

-Is evident when investigating fire ecology

-Can feed-back into evolutionary processes

27

## The method of independent contrasts

### allows evolutionary biologists to use comparative methods for studying adaptations

28

## If two sister species on the p-tree differ from the other two in a single character state (say dark or light fur), how many character state changes (evolutionary events) are needed to explain this pattern?

### ONE

29

## In the figure of "The Libyan HIV Sequences", the HIV that infected more than 400 children in Benghazi hospital

###
-is closely related to strains from Cameroon and Ghana

-Suggests a single introduction was responsible for the outbreak

30

## The maximum likelihood tree constructed for the mammals in the figures above supports which of the following competing hypotheses for the evolutionary relationships among mammalian groups?

### The Theria hypothesis

31

## Based on the figure about "Two Competing hypotheses for the evolutionary relationships among mammalian groups" which of the following statements about competing hypotheses is true?

### The placentals and marsupials are sister groups under the Theria hypothesis, and the monotremes and marsupials are sister groups under the Marsupionta hypothesis

32

## To determine how strongly the character data support clade A (the grouping of species A1, A2, A3) on the tree above, we can

###
-Use an odds ratio test, comparing the best possible tree overall with the best possible tree in which clade A is not monophyletic;

-Use a bootstrap analysis

33