Deck 5: Inferring Phylogeny

Question 1

Which of the following statements regarding rooted trees is FALSE?

A) The root of a tree represents the common ancestor of the taxa shown on the 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) The root of a tree represents the most recent divergence event for the taxa shown on the tree.

Answer 1

D

Question 2

Most 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) are not widely available, so many phylogenies are constructed by hand.

Answer 2

B

Question 3

Based on the figure shown, 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 a sister group under either the Theria hypothesis or the Marsupionta hypothesis.
D) The monotremes and marsupials form a sister group under both the Theria hypothesis and the Marsupionta hypothesis.

Answer 3

A

Question 4

Which of the following is an advantage of parsimony analysis?

A) it is always a consistent estimator
B) it is conceptually simple
C) it ensures that we get the right answer, given enough data
D) long-branch attraction

Question 5

The older a clade is, 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) less likely its members will show sequence divergence.

Question 6

The basic conceptual approach to phylogenetic tree building assumes that

A) species with many character states in common are more closely related than those with few character states in common.
B) shared characters are homoplasies.
C) vestigial traits are not relevant.
D) common ancestors are identified for each internal node.

Question 7

Which of the following phylogenetic methods involves counting up the number of commonalities among taxa and using this information to cluster closely related species together?

A) parsimony methods
B) distance methods
C) maximum likelihood methods
D) Bayesian inference methods

Question 8

Which of the following is an advantage of using distance methods to construct trees?

A) Distance methods are conceptually straightforward.
B) Distance methods are computationally among the slowest techniques.
C) Distance methods lack any sort of underlying evolutionary model.
D) The assumption is made that similarity is a reflection of homology.

Question 9

Which of the following statements concerning phylogenetic trees for a given group of taxa is FALSE?

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) There is only one rooted tree for every unrooted tree.

Question 10

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

A) one
B) two
C) three
D) four

Question 11

The maximum likelihood tree (the tree with the clades numbered) constructed for the mammals in the figures shown supports which of the following hypotheses for the evolutionary relationships among mammalian groups?

A) The maximum likelihood tree supports the Marsupionta hypothesis.
B) The maximum likelihood tree supports the Theria hypothesis.
C) The maximum likelihood tree supports both the Marsupionta and the Theria hypotheses.
D) The maximum likelihood tree supports neither the Marsupionta nor the Theria hypotheses.

Question 12

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 phylogenetic ancestry of rapidly evolving clades.
D) a method for inferring phylogenetic ancestry of slowly evolving clades.

Question 13

If the two sister species on the phylogenetic tree shown differ from the other two species in a single character state (e.g., dark or light fur), how many character state changes (evolutionary events) are needed to explain this pattern?

A) one
B) two
C) three
D) four

Question 14

In the phylogeny shown, which of the following hypotheses provides the most parsimonious explanation for the distribution of beak ("bill") color among the five species of magpie? The yellow-billed magpie has a yellow beak and the rest have black beaks.

A) There is no way to infer ancestral beak color using the phylogenies shown.
B) The ancestral state was yellow-billed.
C) The ancestral state was black-billed.
D) The ancestral state was most likely neither yellow nor black but rather some intermediate color of beak.

Question 15

Once we have used character data to infer a tree, how can we be certain this tree best represents our data?

A) We cannot be certain.
B) We can test the statistical confidence that certain features of the tree are correct.
C) In most cases, we can ascertain whether our tree is correct with nearly 100% confidence.
D) There are so many correct trees for a given data set that all options are equally good.

Question 16

Which of the following is a DISADVANTAGE of parsimony analysis?

A) it is a consistent estimator
B) it is conceptually simple
C) long-branch attraction
D) it ensures that we get the right answer, given enough data

Question 17

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

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

Question 18

Which of the following methods uses the logic that the number of changes required to explain multiple characters on a phylogenetic tree is simply the sum of the number of changes required to explain each individual character?

A) the Fitch algorithm
B) the maximum likelihood analysis
C) Bayesian inference
D) bootstrap resampling

Question 19

Killian et al. (2001) inferred a maximum likelihood tree (shown below) based on sequence data from the M6P/IGF2R gene. Numbers represent bootstrap support values for each clade. Based on their findings, you would expect that the clade comprised of mice, rats, and rabbits would have appeared in what percentage of bootstrap resampling replicates?

A) 100%
B) 74%
C) 91%
D) 64%

Question 20

What is the fundamental idea behind parsimony?

A) the best phylogeny is the one that both explains the observed character data and posits the fewest evolutionary changes for a group of taxa
B) the best phylogeny is the one that posits the greatest number of evolutionary changes for a group of taxa
C) the computed number of morphological or molecular distances between taxa indicates their relatedness
D) morphological traits cannot be used to reconstruct phylogenetic history

Question 21

Does the Fitch algorithm indicate the most likely character states for the ancestral node? Explain your answer.

Question 22

What does the "90" on the figure 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) The hypothetical common ancestor for species A₁, A₂, and A₃ lived 90 generations ago.
D) The hypothetical common ancestor for species A₁, A₂, and A₃ had 90 genes in its genome.

Question 23

On Figure B, number each of the seven hash marks on the branches (indicating synapomorphy) with the corresponding numbered sequence change indicated in Figure A.

Question 24

Bootstrap resampling

A) can be used with any approach for phylogenetic inference.
B) can only be used with the model-based tree-building methods of maximum likelihood and Bayesian inference.
C) must be used before a tree is constructed to ensure an accurate outcome.
D) is used to determine the minimum number of character changes necessary to explain a given tree.

Question 25

If the two sister species on the phylogenetic tree in the figure below differ from the other two species in a single character state (e.g., dark fur, whereas the other taxa have light fur), where would the evolutionary change(s) have occurred? Indicate change(s) by placing an arrow-or arrows-on the tree. Be sure to label the presumed ancestral state, and label the arrow(s) as a "loss" or "gain."

Question 26

If two nonsister species (any pair of species other than Species 2 and 3) on the phylogenetic tree in the figure below differ from the other two in a single character state (e.g., the nonsister species have light fur, whereas the sister species have dark fur), where would the likely evolutionary change(s) be? Indicate change(s) by drawing an X-or Xs-on the tree. Be sure to label each X as a loss or gain. In this case, assume that the ancestral state was "dark fur."

Question 27

The figure shows six pairwise genetic distances among four species (A, B, C, and D). Which of the following would be grouped as sister taxa on a tree constructed using distance measurements? A


B

A) Species A and B
B) Species A and D
C) Species B and C
D) Species B and D

Question 28

Both parsimony methods and distance methods can be quite effective in inferring evolutionary history. Compare the assumptions, shortcomings, and methods of each.

Question 29

The figure shown is a phylogeny created with DNA sequence data and has high bootstrap support values. The tree also includes observed phenotypes (in varying shades of gray) for the five taxa. The character states are indicated by "B" or "b," "G" or "g," and "P" or "p." Evaluate the hypothetical phylogenetic tree using a parsimony approach. For which of the following taxa were there the FEWEST state changes if the inferred ancestral state was "bGP"?

A) Taxon 2
B) Taxon 3
C) Taxon 4
D) Taxon 5

Question 30

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 31

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 32

From the DNA sequence data for the eight species (A through H) shown below, what is the genetic distance between Species B and Species G?

A) 4
B) 5
C) 6
D) 7

Question 33

The figure shown is a phylogeny created with DNA sequence data and has high bootstrap support values. The tree also includes observed phenotypes (in varying shades of gray) for the five taxa. The character states are indicated by "B" or "b," "G" or "g," and "P" or "p." Evaluate the hypothetical phylogenetic tree using a parsimony approach. How many state changes were required for Taxon 5 ("BGP") if the inferred ancestral state was "bGP"?

A) one
B) two
C) three
D) four

Question 34

The figure shown is a phylogeny created with DNA sequence data, but it is NOT well-supported with bootstrap analysis; in other words, all clades of the tree have very low (<50%) bootstrap values. The tree also includes observed phenotypes (in varying shades of gray) for the five taxa. The character states are indicated by "B" or "b," "G" or "g," and "P" or "p." Evaluate the hypothetical phylogenetic tree using a parsimony approach. If a more parsimonious tree were to be drawn based only on phenotypes (excluding the DNA data), which of the following would be grouped as sister taxa on the new tree?

A) taxa 1 and 2
B) taxa 1 and 3
C) taxa 2 and 3
D) taxa 2 and 4

Question 35

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

Question 36

DNA sequences are the most frequently used character for phylogenetic construction today, but DNA may not always be available. For which of the following would a phylogeny have to be constructed with nonmolecular methods for collecting character data?

A) Ebola isolates from strains collected in Guinea, Sierra Leone, and Mali by Hoenen and his colleagues in 2014
B) data collected by Killian and his colleagues to create a phylogeny of mammals that supports the Theria hypothesis
C) fossils of Tiktaalik roseae discovered by Daeschler and his colleagues
D) HIV isolates from the 1999 Benghazi Hospital AIDS outbreak

Question 37

The figure shown is a phylogeny created with DNA sequence data and has high bootstrap support values. The tree also includes observed phenotypes (in varying shades of gray) for the five taxa. The character states are indicated by "B" or "b," "G" or "g," and "P" or "p." Evaluate the hypothetical phylogenetic tree using a parsimony approach. What is the minimum total number of state changes necessary to describe the observed distribution of characters in the taxa?

A) four
B) five
C) six
D) seven

Question 38

Why do evolutionary biologists say that Tiktaalik roseae is a "transitional species"?

A) It is an extinct species whose DNA sequence indicates that it is intermediate between fish and tetrapods.
B) It is an extant species whose DNA sequence indicates that it is intermediate between fish and tetrapods.
C) It is an extant species whose skeletal structure indicates that it is a morphological intermediate between fish and tetrapods.
D) It is an extinct species whose fossils indicate that it was a morphological intermediate between fish and tetrapods.

Question 39

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 below to convince the Libyan Court to lift its death sentence for the "Benghazi six."

Question 40

The method of independent contrasts

A) allows evolutionary biologists to use phylogenetic 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) relies on the logic of bootstrap analysis.

Question 41

An unrooted tree linking three species (A, B, and C) is shown. Draw all possible unrooted tree conformations when a fourth species, D, is added to the tree.

Question 42

In a paragraph, describe the data shown in the figures with regards to sequence alignment.

Question 43

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

Question 44

Describe how fossils of Tiktaalik roseae discovered by Ted Daeschler and his colleagues in 2005 help biologists "fill the phylogenetic gap" between fish and tetrapods.

Question 45

The phylogenetic tree shown was constructed using a nucleotide distance matrix of Ebola isolates from Guinea in March 2014 ("G"), Sierra Leone ("S"), and Mali ("M") in October/November 2014. Describe what the phylogeny revealed regarding the three Ebola outbreaks.

Question 46

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 shown, list and describe or label all possible independent contrasts.