Question 1

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

Accepted Answer

Phylogenetic inference is a difficult an

Question 2

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.

Accepted Answer

Two Xs should be drawn,showing

Question 3

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?

Accepted Answer

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

Question 4

The older the clade,the

Accepted Answer

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 
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 5

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

Accepted Answer

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

Question 6

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

Accepted Answer

Labels should match

Question 7

The method of independent contrasts

Accepted Answer

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 
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 8

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.

Accepted Answer

There should be three drawings

Question 9

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

Accepted Answer

Answers will vary but should include: Di

Question 10

For extinct taxa

Accepted Answer

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 
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 11

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

Accepted Answer

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 
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 12

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.

Accepted Answer

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

Question 13

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

Accepted Answer

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 
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 14

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.

Accepted Answer

One arrow should be drawn,indi

Question 15

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."

Accepted Answer

The answer of   In the spring of 1999,six...

Question 16

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.

Accepted Answer

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

Question 17

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.

Accepted Answer

Both parsimony methods and distance meth

Question 18

How many unrooted trees are possible for five species?

Accepted Answer

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

Question 19

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

Accepted Answer

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

Question 20

The role of organisms in impacting the external environment

Accepted Answer

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 
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

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

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.

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?

The older the clade,the

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

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

The method of independent contrasts

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.

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

For extinct taxa

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

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

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.

How many unrooted trees are possible for five species?

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

The role of organisms in impacting the external environment

An Overview of Evolutionary Biology

Early Evolutionary Ideas and Darwins 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

Sexual Selection

The Evolution of Sociality

Coevolution

Evolution and Medicine

Filters

Exam 5: Inferring Phylogeny

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

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.

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?

The older the clade,the

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

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

The method of independent contrasts

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.

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

For extinct taxa

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

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

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.

How many unrooted trees are possible for five species?

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

The role of organisms in impacting the external environment

An Overview of Evolutionary Biology

Early Evolutionary Ideas and Darwins 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

Sexual Selection

The Evolution of Sociality

Coevolution

Evolution and Medicine

Filters