Question 1

Which of the following statements regarding rooted trees is FALSE?

Accepted Answer

The root of a tree represents the common ancestor of the taxa shown on the tree, but it does not necessarily represent the most recent divergence event. It is possible for a tree to be rooted at an intermediate point between two taxa that have diverged from a common ancestor, without including that common ancestor as the root. Therefore, statement D is false.

Question 2

Most computer programs for reconstructing large phylogenies

Accepted Answer

Given the vast number of possible trees for large phylogenies, it is computationally impossible to check all possible trees. As a result, most computer programs only check a very small fraction of possible trees through algorithms such as heuristic searches or Markov chain Monte Carlo simulations.

Question 3

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

Accepted Answer

A

Question 4

Which of the following is an advantage of parsimony analysis?

Accepted Answer

Parsimony analysis is conceptually simple and easy to understand, making it accessible to a wider range of researchers. A consistent estimator is not always guaranteed, and there is no assurance that parsimony will lead to the correct answer given enough data. Long-branch attraction is a potential problem in parsimony analysis that can lead to incorrect results.

Question 5

The older a clade is, the

Accepted Answer

As time passes, mutations accumulate in the DNA sequences of organisms within a clade, leading to sequence divergence. Therefore, the older a clade is, the more likely it is that its members will show sequence divergence.

Question 6

The basic conceptual approach to phylogenetic tree building assumes that

Accepted Answer

The basic conceptual approach to phylogenetic tree building is based on the idea that species with many character states in common are more closely related, as these shared traits are likely inherited from a common ancestor.

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?

Accepted Answer

Distance methods, also known as cluster methods, involve constructing a matrix of distances between pairs of taxa based on the number of shared characteristics or genetic differences. These distances can then be used to construct a dendrogram, which clusters closely related species based on their similarities.

Question 8

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

Accepted Answer

Distance methods are conceptually straightforward and easy to understand, making them accessible to researchers with different levels of expertise.

Question 9

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

Accepted Answer

An unrooted tree can correspond to multiple rooted trees, depending on where the root is placed. This makes statement D false, as there can be more than one rooted tree for every unrooted tree.

Question 10

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

Accepted Answer

For four species, there are three possible unrooted tree arrangements:
1) ((A,B), (C,D))
2) ((A,C), (B,D))
3) ((A,D), (B,C))

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?

Accepted Answer

The maximum likelihood tree shows two major clades: one containing marsupials (represented by the opossum) and one containing placental mammals (represented by all other taxa). This supports the Theria hypothesis, which proposes that all living mammals can be divided into two groups: those that have a placenta and those that do not. The tree does not support the Marsupionta hypothesis, which proposes that marsupials and placentals share a common ancestor that was separate from that of monotremes (represented by the platypus).

Question 12

Long-branch attraction is

Accepted Answer

Long-branch attraction is an artifact of phylogenetic analyses where rapidly evolving lineages are incorrectly inferred to be closely related due to their high rate of evolution, rather than their actual evolutionary relationships. This often occurs because the rapid accumulation of mutations can make these lineages appear more similar to each other than they are to more slowly evolving lineages.

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?

Accepted Answer

Only one evolutionary event (change in fur color) occurred in the lineage leading to the two sister species.

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.

Accepted Answer

Based on the phylogeny shown, the most parsimonious explanation for the distribution of beak color among the five species of magpie is that the ancestral state was black-billed. This is because only one species (yellow-billed magpie) has a yellow beak, while the rest have a black beak. The simplest explanation for this is that the ancestral state was black-billed, and that the yellow-billed magpie evolved a yellow beak independently. Option A is incorrect because it is possible to infer ancestral states from a phylogeny. Option B suggests that the yellow-billed magpie is the ancestral species, which is not supported by the phylogeny. Option D suggests an intermediate color of the beak as a possible ancestral state, but there is no evidence to support this hypothesis.

Question 15

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

Accepted Answer

We can use statistical tests such as bootstrapping and maximum likelihood to estimate the confidence level of different features on our inferred tree. This will give us an idea of how well-supported certain branches or nodes are and allow us to evaluate the likelihood of the tree being the best representation of our data. While we cannot be completely certain, statistical confidence tests can help us judge the reliability of our final tree.

Question 16

Which of the following is a DISADVANTAGE of parsimony analysis?

Accepted Answer

Parsimony analysis can suffer from a long-branch attraction which is a phenomenon where distantly related taxa may appear more similar to each other than they actually are due to multiple substitutions having accumulated on both branches. This can lead to incorrect or misleading results.

Question 17

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

Accepted Answer

The number of different unrooted tree arrangements for five species can be calculated using the formula (2n-5)!!, where "n" is the number of species. 
Therefore, for five species, the number of unrooted tree arrangements is (2x5-5)!! = 15. 
Thus, the correct answer is option B, with 15 possible unrooted tree arrangements.

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?

Accepted Answer

This method is known as the Fitch algorithm, which is based on the principle of parsimony (the idea that the simplest explanation is usually the correct one). The algorithm calculates the minimum number of changes necessary to explain the observed data on a phylogenetic tree, and assumes that the most parsimonious tree is the most likely one. Therefore, the Fitch algorithm uses the logic that the number of changes required to explain multiple characters is simply the sum of the number of changes required for each individual character.

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?

Accepted Answer

The answer of Killian et al. (2001) inferred a maximum...

Question 20

What is the fundamental idea behind parsimony?

Accepted Answer

Parsimony is based on the principle of Occam's razor, which states that the simplest explanation is usually the best. In the case of phylogenetic analysis, this means that the best tree is the one that requires the fewest evolutionary changes (e.g. mutations, deletions, insertions) to explain the observed data. This approach is often called "parsimony" or "maximum parsimony." Therefore, the correct answer is 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.

Quiz 5: Inferring Phylogeny