Question 1

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

Accepted Answer

A) We cannot; we can only estimate a "best fit." 
B) We can test statistical confidence certain features of the tree are correct. 
C) In most cases, we can ascertain whether our tree is correct with 95% confidence. 
D) All of the above 
E) None of the above 
A) We cannot; we can only estimate a "best fit." 
B) We can test statistical confidence certain features of the tree are correct. 
C) In most cases, we can ascertain whether our tree is correct with 95% confidence. 
D) All of the above 
E) None of the above B

Question 2

Which of the following statements concerning trees is true?

Accepted Answer

A) Each unrooted tree corresponds to numerous rooted trees. 
B) An unrooted tree with k species has 2k-3 branches. 
C) An unrooted tree with k species has 2k-3 times as many rooted trees as unrooted trees. 
D) All of the above 
E) None of the above 
A) Each unrooted tree corresponds to numerous rooted trees. 
B) An unrooted tree with k species has 2k-3 branches. 
C) An unrooted tree with k species has 2k-3 times as many rooted trees as unrooted trees. 
D) All of the above 
E) None of the above D

Question 3

Phylogenetic trees are used to

Accepted Answer

A) construct hypotheses about common ancestors. 
B) construct hypotheses about how various species are related to each other. 
C) test hypotheses about the relationships between various species. 
D) All of the above 
A) construct hypotheses about common ancestors. 
B) construct hypotheses about how various species are related to each other. 
C) test hypotheses about the relationships between various species. 
D) All of the above D

Question 4

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

Accepted Answer

A) A maximum parsimony approach distinguishes among multiple alternative roots that correspond to the same unrooted tree. 
B) Any two rooted trees corresponding to the same unrooted tree will require the same number of character changes. 
C) The most common approach to rooting a tree is to use an outgroup. 
D) A and B 
E) B and C 
A) A maximum parsimony approach distinguishes among multiple alternative roots that correspond to the same unrooted tree. 
B) Any two rooted trees corresponding to the same unrooted tree will require the same number of character changes. 
C) The most common approach to rooting a tree is to use an outgroup. 
D) A and B 
E) B and C

Question 5

Does the Fitch algorithm indicate the most likely character states for the ancestral node?

Accepted Answer

No.The process of assigning st

Question 6

Computer programs for reconstructing large phylogenies

Accepted Answer

A) check all possible trees. 
B) only check a very small fraction of possible trees. 
C) make phylogenetic inference easy and certain. 
D) None of the above 
A) check all possible trees. 
B) only check a very small fraction of possible trees. 
C) make phylogenetic inference easy and certain. 
D) None of the above

Question 7

Evolutionary biologists have developed a number of different phylogenetic methods to find a tree that best corresponds to a number of character states for a given group of taxa.Describe the fundamental idea behind parsimony,and explain the strengths and weaknesses of this method.

Accepted Answer

The fundamental idea behind parsimony is

Question 8

If two sister species on the phylogenetic tree above 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?

Accepted Answer

A) One 
B) Three 
C) Two 
D) Four 
A) One 
B) Three 
C) Two 
D) Four

Question 9

Long-branch attraction is

Accepted Answer

A) the inferring of too close a relationship between rapidly evolving species or populations. 
B) the inferring of too close a relationship between slowly evolving species or populations. 
C) a method for inferring phylogentic ancestry of rapidly evolving clades. 
D) a method for inferring phylogenetic ancestry of slowly evolving clades. 
A) the inferring of too close a relationship between rapidly evolving species or populations. 
B) the inferring of too close a relationship between slowly evolving species or populations. 
C) a method for inferring phylogentic ancestry of rapidly evolving clades. 
D) a method for inferring phylogenetic ancestry of slowly evolving clades.

Question 10

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

Accepted Answer

A) We can form a rooted tree from an unrooted tree simply by picking a branch around which to root the tree. 
B) Both rooted and unrooted trees inform us about the polarity of character change. 
C) Knowing the root of a tree, along with information about species ranges, can tell us about the phylogeography of a group of species. 
D) A and C 
E) B and C 
A) We can form a rooted tree from an unrooted tree simply by picking a branch around which to root the tree. 
B) Both rooted and unrooted trees inform us about the polarity of character change. 
C) Knowing the root of a tree, along with information about species ranges, can tell us about the phylogeography of a group of species. 
D) A and C 
E) B and C

Question 11

One of the principle ways to understand the large-scale effects of natural selection is to compare traits across groups of species.However,there are many ways researchers can be misled by applying the comparative method without properly accounting for phylogeny-shared evolutionary history.Using the five-species tree illustrated above,list and describe or label all possible independent contrasts.

Accepted Answer

The answer of   One of the principle ways...

Question 12

Odds ratio testing

Accepted Answer

A) can be used with any technique for phylogenetic inference. 
B) can be used only with the model-based frameworks of maximum likelihood or Bayesian inference. 
C) does not yield statistical significance levels. 
D) can determine how strongly our character data support a given feature of a phylogenetic tree. 
E) B and D 
A) can be used with any technique for phylogenetic inference. 
B) can be used only with the model-based frameworks of maximum likelihood or Bayesian inference. 
C) does not yield statistical significance levels. 
D) can determine how strongly our character data support a given feature of a phylogenetic tree. 
E) B and D

Question 13

What does the "90" on the figure above indicate?

Accepted Answer

A) There is 90% certainty that species A₁, A₂, and A3 are a monophyletic clade. 
B) The monophyletic clade of species A₁, A₂, and A3 appears as a monophyletic clade in 90% of all bootstrap replicates. 
C) Both of the above 
D) None of the above 
A) There is 90% certainty that species A₁, A₂, and A3 are a monophyletic clade. 
B) The monophyletic clade of species A₁, A₂, and A3 appears as a monophyletic clade in 90% of all bootstrap replicates. 
C) Both of the above 
D) None of the above

Question 14

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

Accepted Answer

A) Three 
B) Four 
C) Two 
D) Seven 
A) Three 
B) Four 
C) Two 
D) Seven

Question 15

Use the Fitch algorithm to determine the minimum number of evolutionary changes required to explain the character states (square,circle,or star)of the seven species depicted on the tree in the figure above.Recall the rules for assigning character states as you work your way down the tree.
1.If each of the two daughters of a node shares one or more possible states for a trait,assign those shared traits to the node in question.
2.If the two daughters share no possible states in common,assign all possible states for both daughters to the node.(Note to instructor: The difficulty of this question can be adjusted by including or omitting the two rules above.)

Accepted Answer

The tally of the cha

Question 16

Based on the figure above,which of the following statements regarding the competing hypotheses is true?

Accepted Answer

A) The placentals and marsupials are sister groups under the Theria hypothesis, and the monotremes and marsupials are sister groups under the Marsupionta hypothesis. 
B) The monotremes and marsupials are sister groups under the Theria hypothesis, and the placentals and marsupials are sister groups under the Marsupionta hypothesis. 
C) The monotremes and marsupials do not form sister groups under either the Theria hypothesis or the Marsupionta hypothesis. 
D) The monotremes and marsupials form sister groups under both the Theria hypothesis and the Marsupionta hypothesis. 
A) The placentals and marsupials are sister groups under the Theria hypothesis, and the monotremes and marsupials are sister groups under the Marsupionta hypothesis. 
B) The monotremes and marsupials are sister groups under the Theria hypothesis, and the placentals and marsupials are sister groups under the Marsupionta hypothesis. 
C) The monotremes and marsupials do not form sister groups under either the Theria hypothesis or the Marsupionta hypothesis. 
D) The monotremes and marsupials form sister groups under both the Theria hypothesis and the Marsupionta hypothesis.

Question 17

Bootstrap resampling

Accepted Answer

A) can be used with any technique for phylogenetic inference. 
B) can only be used with the model-based frameworks of maximum likelihood or Bayesian inference. 
C) does not yield statistical significance levels. 
D) is used to determine the minimum number of character changes necessary to explain a given tree. 
E) A and C 
A) can be used with any technique for phylogenetic inference. 
B) can only be used with the model-based frameworks of maximum likelihood or Bayesian inference. 
C) does not yield statistical significance levels. 
D) is used to determine the minimum number of character changes necessary to explain a given tree. 
E) A and C

Question 18

Parsimony has the disadvantage of

Accepted Answer

A) being an inconsistent estimator. 
B) conceptual complexity. 
C) long-branch attraction. 
D) A and B 
E) A and C 
A) being an inconsistent estimator. 
B) conceptual complexity. 
C) long-branch attraction. 
D) A and B 
E) A and C

Question 19

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

Accepted Answer

A) use an odds ratio test, comparing the best possible tree overall with the best possible tree in which clade A is not monophyletic. 
B) use a bootstrap analysis. 
C) Both of the above 
D) None of the above 
A) use an odds ratio test, comparing the best possible tree overall with the best possible tree in which clade A is not monophyletic. 
B) use a bootstrap analysis. 
C) Both of the above 
D) None of the above

Question 20

In the figure above,the HIV that infected more than 400 children in a Benghazi hospital

Accepted Answer

A) is closely related to strains from Cameroon and Ghana. 
B) comprises many different strains of widely divergent origin. 
C) suggests a single introduction was responsible for the outbreak. 
D) A and C 
E) All of the above 
A) is closely related to strains from Cameroon and Ghana. 
B) comprises many different strains of widely divergent origin. 
C) suggests a single introduction was responsible for the outbreak. 
D) A and C 
E) All of the above

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

Which of the following statements concerning trees is true?

Phylogenetic trees are used to

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

Does the Fitch algorithm indicate the most likely character states for the ancestral node?

Computer programs for reconstructing large phylogenies

Evolutionary biologists have developed a number of different phylogenetic methods to find a tree that best corresponds to a number of character states for a given group of taxa.Describe the fundamental idea behind parsimony,and explain the strengths and weaknesses of this method.

If two sister species on the phylogenetic tree above 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?

Long-branch attraction is

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

Odds ratio testing

What does the "90" on the figure above indicate?

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

Based on the figure above,which of the following statements regarding the competing hypotheses is true?

Bootstrap resampling

Parsimony has the disadvantage of

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

In the figure above,the HIV that infected more than 400 children in a Benghazi hospital

An Overview of Evolutionary Biology

Early Evolutionary Ideas and Darwins Insight

Natural Selection

Phylogeny and Evolutionary History

Transmission Genetics and the Sources of Genetic Variation

The Genetics of Populations

Evolution in Finite Populations

Evolution at Multiple Loci

Genome Evolution

The Origin and Evolution of Early Life

Major Transitions

Evolution and Development

Species and Speciation

Extinction and Evolutionary Trends

The Evolution of Sex

Sexual Selection

The Evolution of Sociality

Coevolution

Evolution and Medicine

Filters

Exam 5: Inferring Phylogeny

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

Which of the following statements concerning trees is true?

Phylogenetic trees are used to

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

Does the Fitch algorithm indicate the most likely character states for the ancestral node?

Computer programs for reconstructing large phylogenies

Evolutionary biologists have developed a number of different phylogenetic methods to find a tree that best corresponds to a number of character states for a given group of taxa.Describe the fundamental idea behind parsimony,and explain the strengths and weaknesses of this method.

If two sister species on the phylogenetic tree above 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?

Long-branch attraction is

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

Odds ratio testing

What does the "90" on the figure above indicate?

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

Based on the figure above,which of the following statements regarding the competing hypotheses is true?

Bootstrap resampling

Parsimony has the disadvantage of

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

In the figure above,the HIV that infected more than 400 children in a Benghazi hospital

An Overview of Evolutionary Biology

Early Evolutionary Ideas and Darwins Insight

Natural Selection

Phylogeny and Evolutionary History

Transmission Genetics and the Sources of Genetic Variation

The Genetics of Populations

Evolution in Finite Populations

Evolution at Multiple Loci

Genome Evolution

The Origin and Evolution of Early Life

Major Transitions

Evolution and Development

Species and Speciation

Extinction and Evolutionary Trends

The Evolution of Sex

Sexual Selection

The Evolution of Sociality

Coevolution

Evolution and Medicine

Filters