Question 1

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

Accepted Answer

Both parsimony methods and distance methods are commonly used in inferring evolutionary history, but they have different assumptions, shortcomings, and methods.

Parsimony methods, such as maximum parsimony and maximum likelihood, assume that the simplest explanation is the most likely. They aim to find the tree that requires the fewest evolutionary changes, such as mutations or genetic rearrangements, to explain the observed data. This method is based on the assumption that evolutionary changes occur in the fewest number of steps, and it is often used for analyzing DNA or protein sequences. However, one of the shortcomings of parsimony methods is that they can be computationally intensive, especially for large datasets, and they may not always produce the most accurate tree.

On the other hand, distance methods, such as neighbor-joining and UPGMA, assume that the genetic distance between sequences is proportional to the time since they diverged from a common ancestor. These methods use a distance matrix to calculate the genetic distances between sequences and then construct a tree based on these distances. Distance methods are often used for analyzing molecular data and are relatively quick and easy to implement. However, they may not always accurately represent the true evolutionary history, especially if the assumption of a constant rate of evolution is violated.

In terms of methods, parsimony methods use character-based approaches to infer evolutionary relationships, while distance methods use a distance-based approach. Parsimony methods aim to find the tree that requires the fewest evolutionary changes, while distance methods aim to construct a tree based on genetic distances between sequences.

In conclusion, both parsimony methods and distance methods can be effective in inferring evolutionary history, but they have different assumptions, shortcomings, and methods. Researchers should carefully consider the nature of their data and the assumptions of each method when choosing which approach to use for their evolutionary analyses.

Question 2

The basic conceptual approach to phylogenetic tree building assumes that

Accepted Answer

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. 
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. A

Question 3

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

Accepted Answer

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. 
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. D

Question 4

What does the "90" on the figure 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)  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. 
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 5

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

Accepted Answer

The answer of In a paragraph, describe the data shown...

Question 6

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?

Accepted Answer

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 
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 7

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

Accepted Answer

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. 
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 8

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.

Accepted Answer

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. 
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 9

Based on the figure shown, 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 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. 
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.

Question 10

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. A

B

Accepted Answer

Labels should match

Question 11

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.

Accepted Answer

There should be three drawings

Question 12

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

Accepted Answer

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. 
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 13

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?

Accepted Answer

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

Question 14

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"?

Accepted Answer

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

Question 15

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

Accepted Answer

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

Question 16

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?

Accepted Answer

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

Question 17

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?

Accepted Answer

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

Question 18

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 character sta

Question 19

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

Accepted Answer

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

Question 20

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

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

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

The basic conceptual approach to phylogenetic tree building assumes that

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

What does the "90" on the figure indicate?

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

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?

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

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.

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

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. A B

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.

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

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

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?

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?

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.)

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

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

An Overview of Evolutionary Biology

Early Evolutionary Ideas and Darwin S 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

The Evolution of Sociality

Coevolution

Human Evolution

Evolution and Medicine

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Exam 5: Inferring Phylogeny

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

The basic conceptual approach to phylogenetic tree building assumes that

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

What does the "90" on the figure indicate?

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

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?

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

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.

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

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. A B

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.

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

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

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?

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?

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.)

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

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

An Overview of Evolutionary Biology

Early Evolutionary Ideas and Darwin S 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

The Evolution of Sociality

Coevolution

Human Evolution

Evolution and Medicine

Filters