Chapter 5

Question 0

Phylogenetic trees are used to

Answer 0

• construct hypotheses about common ancestors
• construct hypotheses about how various species are related to each other
• test hypotheses about the relationships between various species

Question 1

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

Answer 1

Distance methods lack any sort of underlying evolutionary model;
The assumption is made that similarity is a reflection of homology

Question 2

The older the clade, the

Answer 2

more likely its members will show sequence divergence

Question 3

The basic conceptual approach to phylogenetic tree building involves

Answer 3

• 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

Question 4

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

Answer 4

That species with many character states are more closely related than those without;
That common characters are homologies

Question 5

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

Answer 5

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

Question 6

The fundamental idea behind parsimony is

Answer 6

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

Question 7

Parsimony analysis offers the advantage of

Answer 7

conceptual simplicity

Question 8

Parsimony has the disadvantage of

Answer 8

Being an inconsistent estimator; Long-branch attraction

Question 9

Long branch attraction is

Answer 9

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

Question 10

The Fitch algorithm is

Answer 10

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

Question 11

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

Answer 11

• 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

Question 12

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

Answer 12

• 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

Question 13

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

Answer 13

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

Question 14

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

Answer 14

THREE

Question 15

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

Answer 15

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

Question 16

How many unrooted trees are possible for 5 species?

Answer 16

15

Question 17

Arrange bootstrap resampling in correct order

Answer 17

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

Question 18

Bootstrap resampling

Answer 18

• can be used with any technique for phylogenetic inference

- does not yield statistical significance levels

Question 19

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

Answer 19

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

Question 20

Computer programs for reconstructing large phylogenies

Answer 20

only check a very small fraction of possible trees

Question 21

Which of the following statements concerning trees is true?

Answer 21

• 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

Question 22

How many UNrooted trees are possible for 22-species tree

Answer 22

more than there are stars in the universe

Question 23

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

Answer 23

105 and 945

Question 24

For extinct taxa

Answer 24

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

Question 25

Odds ratio testing

Answer 25

• 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

Question 26

The role of organisms in impacting the external environment

Answer 26

• Is the process of niche construction
• Is evident when investigating fire ecology
• Can feed-back into evolutionary processes

Question 27

The method of independent contrasts

Answer 27

allows evolutionary biologists to use comparative methods for studying adaptations

Question 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?

Answer 28

ONE

Question 29

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

Answer 29

• is closely related to strains from Cameroon and Ghana

- Suggests a single introduction was responsible for the outbreak

Question 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?

Answer 30

The Theria hypothesis

Question 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?

Answer 31

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

Question 32

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

Answer 32

• 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

Question 33

What does the “90” on the figure indicate?

Answer 33

The monophyletic clade of species A1, A2, and A3 appears as a monophyletic clade in 90% of all bootstrap replicates