Question 1

In a hypothetical experiment, researchers sequence a gene from a colony of bacteria at various times in the history of the colony.In the common ancestor, the nucleotide at site 998 is A.After 1,500 generations, it changes to G.After 5,000 generations, it changes back to A.We can infer that a total of _______ substitution(s) have occurred.Without knowledge of the sample taken at 1,500 generations, we would have inferred that _______ substitution(s) had occurred.

Accepted Answer

The correct inference is that two substitutions have occurred: first from A to G, and then back from G to A. Without knowledge of the intermediate state at 1,500 generations, we would have inferred zero substitutions, as the initial and final states are the same.

Question 2

A molecular evolutionist wants to study the dynamics of in vitro evolution for a particular gene.Which model system would be optimal for the experiment?

Accepted Answer

RNA viruses have a high mutation rate and a short replication cycle, which allows for rapid evolution and selection of advantageous genetic mutations in vitro. This makes them an optimal model system for studying molecular evolution. Bacterium and eukaryotic cell lines typically have slower replication rates and lower mutation rates compared to RNA viruses, while mouse or fruit fly cell lines may not be as relevant for a study of molecular evolution.

Question 3

Which model system for evolutionary research has a natural nucleotide substitution rate as high as 1 substitution per 1,000 nucleotides per generation?

Accepted Answer

Viruses have an incredibly high nucleotide substitution rate, with rates as high as 1 substitution per 10 nucleotides per generation for RNA viruses and 1 substitution per 1,000 nucleotides per generation for DNA viruses. None of the other model systems listed have such high rates.

Question 4

Below are shown segments of DNA from three species of flies.Species 1 is the common ancestor of species 2 and species 3, and we have access to its DNA because it was preserved in amber. 
Species 1: AACTACTGCACGCTCATA
Species 2: AACTAGTGCTCGCTCACA
Species 3: AATTACTGCACGCTCACA
There have been _______ single and _______ parallel changes as species 2 and 3 evolved from species 1.

Accepted Answer

To determine the number of single and parallel changes, we compare the DNA sequences of the species. Species 1: AACTACTGCACGCTCATA Species 2: AACTAGTGCTCGCTCACA Species 3: AATTACTGCACGCTCACA Single changes: 1. T to G in species 2 (position 6) 2. C to A in species 2 (position 17) 3. A to T in species 3 (position 4) These are changes that occurred uniquely in species 2 or 3. Parallel change: 1. T to A in the last position (18) for both species 2 and 3. This is a change that occurred in the same position in both species, indicating a parallel evolution from the common ancestor. Therefore, there are three single changes and one parallel change.

Question 5

The number of actual substitutions that have occurred between diverging lineages in a sequence will usually be _______ than the number of substitutions observed when sequences are compared, and this discrepancy should _______ with increasing evolutionary divergence.

Accepted Answer

The number of actual substitutions is usually greater than observed due to multiple changes at the same site, known as multiple hits, which are not always detectable. This discrepancy increases with evolutionary divergence as the likelihood of multiple hits at the same site increases over time.

Question 6

A mutation in a gene in which A is changed to G is called a _______, whereas a mutation of A to T is called a _______.The former type of mutation occurs at a _______ frequency than the latter.

Accepted Answer

A mutation in which a purine base (A or G) is changed to another purine base (A to G or G to A) is called a transition, whereas a mutation of a purine base to a pyrimidine base (A to T, A to C, G to T, or G to C) is called a transversion. The frequency of transition mutations is typically higher than that of transversion mutations because the former involves a simpler chemical change.

Question 7

Below are sequences of part of a gene taken from three species of plants. 
Plant A: AGATCTACGCGCAGTTTC
Plant B: AGATTAGGCGCAGTATC
Plant C: AGATTAGGCGCAGTTTC
To align these sequences, one should add a gap to species

Accepted Answer

By adding a gap to the second position in Plant A's sequence, it can align perfectly with Plants B and C. Therefore, gaps need to be added to Plants A and B to align with Plant C. This means the best choice is to add a gap to B and C only, which is option E.

Question 8

A parallel substitution occurs when

Accepted Answer

Parallel substitution refers to the same nucleotide change occurring independently in two different lineages. Choice C accurately describes this scenario with both lineages experiencing a change from A to T independently.

Question 9

Molecular evolutionists are able to study evolution directly using research models such as viruses, bacteria, and unicellular eukaryotes because substitution rates are related to _______ rather than to _______.

Accepted Answer

Molecular evolutionists are able to study evolution directly using research models such as viruses, bacteria, and unicellular eukaryotes because substitution rates are related to generation time rather than to absolute time. These models have short generation times, allowing for the accumulation of mutations and the observation of evolutionary changes over a relatively short time period. Absolute time, on the other hand, is more relevant for studying evolution in organisms with longer generation times and slower rates of evolution.

Question 10

A change from _______ is a reversion.

Accepted Answer

A reversion involves a change that is reversed to the original state. Only choice E describes a change followed by a reversal.

Question 11

Below are sequences of part of a gene taken from three species of plants. 
Plant A: AGATCTACGCGCAGTTTC
Plant B: AGATTGGCGCAGTATC
Plant C: AGATTAGGCGCAGTTTC
Align the sequences.If each added gap required to align the sequences represents two nucleotide differences, how many differences are between species A and species B?

Accepted Answer

To align the sequences, we can insert gaps as shown below:
Plant A: AGATCTACGCGCAGTTTC
Plant B: AGATTGGCGCAGTATC
Plant C: AGATTAGGCGCAGTTTC

Aligned sequences:
AGATCTACGCGCAGTTTC
AGATTGGCGCAGTATC-
AGATTAGGCGCAGTTTC

To calculate the number of differences between species A and B, we count the number of non-gaps that are different between the two sequences. There are four differences:
- ATCTACGCGC vs ATTGGCGCAG (difference at positions 5-14)
- T vs A (difference at position 17)

Each added gap represents two nucleotide differences, so the final answer is C) Four.

Question 12

A coincident substitution occurs when

Accepted Answer

A coincident substitution occurs when two or more independently evolving lineages undergo the same nucleotide substitution event at the same site in their DNA sequences. Option B describes such an event where nucleotide A changes to G in one lineage and A to C in the other lineage. Option A describes a synonymous substitution where the change in nucleotide does not affect the protein sequence. Option C describes parallel substitutions that occur independently in two or more lineages. Option D describes a successive substitution where one nucleotide is replaced by another and then another in the same lineage. Option E describes a reversal substitution where a nucleotide changes back to its original state in the same lineage.

Question 13

Under the conditions of an experiment, a particular virus has an expected substitution rate of 1 substitution per 5,000 nucleotides per generation and a genome size of 10,000 nucleotides.If the virus has one generation per hour, we would expect approximately _______ substitutions between 9 am on Monday and 1 pm on Friday of the same week.

Accepted Answer

The virus undergoes 1 substitution per 5,000 nucleotides per generation. With a genome size of 10,000 nucleotides, this results in 2 substitutions per generation. From 9 am Monday to 1 pm Friday is 100 hours, equating to 100 generations. Therefore, 100 generations x 2 substitutions per generation = 200 substitutions.

Question 14

Which scenario would tend to make obtaining correct sequence alignments difficult?

Accepted Answer

If a segment of DNA has frequent deletions, it would be difficult to determine the correct alignment of the remaining nucleotides, as it would be unclear which gaps are due to deletions and which are due to true evolutionary changes.

Question 15

Refer to the table.  Consider the first codon in the table, UUU.How many single nucleotide substitutions at any of the three positions are synonymous substitutions?

Accepted Answer

The answer of Refer to the table.  Consider the...

Question 16

In a hypothetical experiment, researchers sequence a gene from a colony of bacteria at various times in the history of the colony.In the common ancestor, the nucleotide at site 998 is A.After 1,500 generations, it changes to G.After 5,000 generations, it changes back to A.This is an example of a(n)

Accepted Answer

The change from A to G and back to A at site 998 represents a reversion, where a nucleotide returns to its original state after undergoing a mutation.

Question 17

Below are segments of DNA from three species of flies.Species 1 is the common ancestor of species 2 and species 3, and we have access to its DNA because it was preserved in amber. 
Species 1: AACTACTGCACGCTCATA
Species 2: AACTAGTGCTCGCTCACA
Species 3: AATTACTGCACGCTCACA
Having access to Species 1, we can infer that there have been _______ substitutions from Species 1 to Species 2 and Species 3.Lacking access to Species 1, we could infer that there have been _______ substitutions between Species 2 and Species 3.

Accepted Answer

There are five substitutions from Species 1 to Species 2 and Species 3. Without access to Species 1, we can infer three substitutions between Species 2 and Species 3.

Question 18

Transitions, which are changes from _______, occur _______ transversions.

Accepted Answer

Transitions are changes within the same type of nucleotide (purine to purine or pyrimidine to pyrimidine) and occur more often than transversions, which are changes between different types (purine to pyrimidine or vice versa).

Question 19

The nucleotide at a position in a DNA sequence changes from C to A to C.This is an example of a _______ substitution.

Accepted Answer

This is an example of a back substitution, where a nucleotide changes from one state to another and then back to its original state.

Question 20

The human and chimpanzee sequences for a particular DNA segment are being aligned.Both happen to be the same length, but you know that there is a three-nucleotide insertion in the chimpanzee sequence, relative to the human sequence.The most likely explanation is that there was a

Accepted Answer

A three-nucleotide insertion in the chimpanzee sequence would cause a misalignment with the human sequence. One way to restore the alignment is by assuming a deletion in the chimpanzee sequence that matches a gap in the human sequence. Alternatively, one could assume an insertion in the human sequence, but this would be less parsimonious as it would require postulating a mutation that did not occur in the chimpanzee lineage. The other choices (B, C, D, E) do not account for the observed difference in length between the sequences.

Quiz 23: Evolution of Genes and Genomes

A molecular evolutionist wants to study the dynamics of in vitro evolution for a particular gene.Which model system would be optimal for the experiment?

Which model system for evolutionary research has a natural nucleotide substitution rate as high as 1 substitution per 1,000 nucleotides per generation?

The number of actual substitutions that have occurred between diverging lineages in a sequence will usually be _ than the number of substitutions observed when sequences are compared, and this discrepancy should _ with increasing evolutionary divergence.

A mutation in a gene in which A is changed to G is called a ___, whereas a mutation of A to T is called a _.The former type of mutation occurs at a _____ frequency than the latter.

Below are sequences of part of a gene taken from three species of plants. Plant A: AGATCTACGCGCAGTTTC Plant B: AGATTAGGCGCAGTATC Plant C: AGATTAGGCGCAGTTTC To align these sequences, one should add a gap to species