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


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

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

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No.The process of assigning st...

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


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

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


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

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Odds ratio testing


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

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Long-branch attraction is


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.

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


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.

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


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

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


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

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Parsimony has the disadvantage of


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

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


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

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B

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.) 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.)

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The tally of the cha...

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


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

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Which of the following statements concerning trees is true?


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

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D

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


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

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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.

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The fundamental idea behind parsimony is...

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Bootstrap resampling


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

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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. 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.

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Computer programs for reconstructing large phylogenies


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

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Phylogenetic trees are used to


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

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D

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