Deck 5: Inferring Phylogeny

Question 1

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

Answer 1

E

Question 2

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

Answer 2

D

Question 3

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

Answer 3

D

Question 4

How many unrooted trees are possible for five species?

A)15
C)25
B)5
D)105

Question 5

The Fitch algorithm

A)determines how many evolutionary changes are required for a given tree and character.
B)does not find the best tree.
C)is based on a parsimony approach.
D)A and B
E)A and C

Question 6

Parsimony analysis offers the advantage of

A)being a consistent estimator.
B)conceptual simplicity.
C)ensuring that we get the right answer, given enough data.
D)All of the above
E)None of the above

Question 7

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

A)distance methods lack any sort of underlying evolutionary model.
B)the assumption is made that similarity is a reflection of homology.
C)Both of the above
D)None of the above

Question 8

How many unrooted trees are possible for a six-species tree and a seven-species tree,respectively?

A)6 and 7
B)15 and 25
C)105 and 945
D)More than there are stars in the universe

Question 9

Arrange the steps of constructing a phylogenetic tree using the distance method in the correct order.
1)A distance matrix is created.
2)Trees are constructed by arranging segments or branches derived from pair-wise distance comparisons.
3)The distance between species is measured using character state changes.
4)Phylogenetic inference software is used to choose the best tree.

A)1,2,3,4
C)3,1,2,4
B)2,3,4,1
D)4,3,2,1

Question 10

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

Question 11

The basic conceptual approach to phylogenetic tree building involves

A)the process of collecting information about character states.
B)the process of selecting taxa for inclusion in the tree.
C)the logic that species with many character states in common are more closely related than those without.
D)All of the above
E)None of the above

Question 12

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

Question 13

The basic conceptual approach to phylogenetic tree building assumes

A)that species with many character states in common are more closely related than those without.
B)That common characters are homologies.
C)Both of the above
D)None of the above

Question 14

The older the clade,the

A)more likely its members will share very similar sequences.
B)more likely its members will show sequence divergence.
C)less likely it has a common ancestor.
D)None of the above

Question 15

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

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

Question 16

The fundamental idea behind parsimony is

A)that the best phylogeny is the one that both explains the observed character data and posits the fewest evolutionary changes.
B)to provide a second approach to inferring phylogenetic relationships.
C)to compute the number of morphological or molecular differences between two or more species or populations.
D)that morphological traits cannot be used to reconstruct phylogenetic history.

Question 17

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
C)Three
B)Two
D)Four

Question 18

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

A)distance methods are conceptually straightforward.
B)distance methods are computationally among the fastest techniques.
C)Both of the above
D)None of the above

Question 19

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

A)parsimony methods.
B)distance methods.
C)maximum likelihood methods.
D)Bayesian inference methods.
E)All of the above

Question 20

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.

Question 21

How many unrooted trees are possible for a 22-species tree?

A)More than there are stars in the universe
B)22
C)945
D)1

Question 22

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

Question 23

In the spring of 1999,six medics were accused of purposely infecting over 400 Libyan children with HIV in a Benghazi hospital.Explain how a team of researchers were able to construct and use the phylogeny in the figure above to convince the Libyan Court to lift its death sentence for the "Bulgarian six."

Question 24

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.

Question 25

If two nonsister species on the phylogenetic tree in the figure above differ from the other two in a single character state (e.g.,dark or light fur),where would the likely evolutionary change(s)be? Indicate change(s)by drawing an X-or Xs-on the tree above.Be sure to label each X as a loss or gain.

Question 26

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

Question 27

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.)

Question 28

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

A)The Marsupionta hypothesis
C)Neither theory
B)The Theria hypothesis
D)Both theories

Question 29

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

Question 30

The method of independent contrasts

A)allows evolutionary biologists to use comparative methods for studying adaptations.
B)compares the best possible tree overall with the best possible constrained tree.
C)relies on running odds ratio tests.
D)A and C
E)All of the above

Question 31

The role of organisms in impacting the external environment

A)is the process of niche construction.
B)can feed back into evolutionary processes.
C)is evident when investigating fire ecology.
D)A and C
E)All of the above

Question 32

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

Question 33

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

Question 34

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

Question 35

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.

Question 36

If two sister species on the phylogenetic tree in the figure above differ from the other two in a single character state (e.g.,dark or light fur),where would the likely evolutionary change(s)be? Indicate change(s)by placing an arrow-or arrows-on the tree above.Be sure to label the arrow(s)as a loss or gain.

Question 37

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

Question 38

Arrange the following steps of bootstrap resampling in the correct order.
1)To assess the support for any feature of the original tree,the percentage of replicate trees that also display that feature are calculated.
2)Resampling is done from the original character matrix to create a collection of bootstrap replicate data sets.
3)A tree is constructed for the estimated phylogeny,based on the original character matrix.
4)The same tree-building methods used on the original character set are used to create a collection of bootstrap replicate phylogenies.

A)4,1,2,3
C)3,2,4,1
B)4,3,2,1
D)3,2,1,4

Question 39

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

Question 40

For extinct taxa

A)the fossil record is the primary source of data for constructing phylogenetic trees.
B)one would expect allied extant taxa from the same location to be very different.
C)it makes sense to use an ad hoc explanation of how natural selection produced changes in a lineage, even when it is uncertain how the biotic and abiotic environment changed over time.
D)A and C
E)B and D

Question 41

Why do some evolutionary biologists have philosophical concerns about using distance methods to construct evolutionary trees?

Question 42

On the figure above,number each of the seven change bars on the branches with the corresponding sequence change indicated on the sequence alignment.

Question 43

Using the evidence presented in the three figures above,describe how combining phylogeographic evidence-including geological processes such as continental drift,natural history (including distribution and dispersal of species),and phylogenies-worked to develop a hypothesis supporting the common ancestry of ratite birds.(Hint: Ratite birds are flightless,and tinamous can fly only weakly.)

Question 44

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.

Question 45

An unrooted tree,linking three species,is shown above.Draw all possible unrooted tree conformations when a fourth species,D,is added to the tree.

Question 46

Why is phylogenetic inference a difficult and computationally intensive problem? What solution do evolutionary biologists use to address this problem?

Question 47

While both parsimony methods and distance methods can be quite effective in inferring evolutionary history,both use tricks of sorts.Compare the assumptions,shortcomings,and methods of each.