Deck 24: Evolution of Genes and Genomes

Question 1

Use the following to answer questions:
In a hypothetical experiment, researchers split a bacterial colony in two, allowing each of the new colonies to evolve separately. They then sequenced a gene from colony 1 and colony 2.
In the common ancestor, the nucleotide at site 167 is T. In colony 1, it changes to C; in colony 2, it remains T. This is an example of a _______ substitution.

A) single
B) coincident
C) parallel
D) back
E) multiple

Answer 1

A

Question 2

Which of the following is true of the use of molecular evolutionary studies of human disease?

A) Molecular evolutionary studies are useful for identifying many diseases.
B) Molecular evolutionary studies are often used to determine the origin of emerging diseases.
C) Molecular evolutionary studies are important for developing vaccines against diseases.
D) Molecular evolutionary studies are used to track the effectiveness of polio vaccines in human populations.
E) All of the above

Answer 2

E

Question 3

Models of nucleotide sequence evolution, developed by biologists to estimate sequence divergence, include parameters that account for

A) substitution rates between different nucleotides.
B) differences in substitution rates across different positions in a gene.
C) differences in nucleotide frequencies.
D) All of the above
E) None of the above

Answer 3

D

Question 4

The rate of fixation of neutral mutations is

A) independent of population size.
B) higher in small populations than in large populations.
C) higher in large populations than in small populations.
D) slower than the rate of fixation of deleterious mutations.
E) None of the above

Question 5

A hypothetical protein sequence taken from humans is 161 amino acids long. The homologous sequence in chimpanzees is 160 amino acids long. Which of the following is most likely needed to align the sequences?

A) A single substitution
B) A parallel substitution
C) A gap
D) A similarity matrix
E) An amino acid replacement

Question 6

Fish use high-voltage discharges

A) to locate prey.
B) to communicate with other individuals.
C) to stun prey.
D) All of the above
E) None of the above

Question 7

Humans and chimpanzees both have large brains because their common ancestor had a large brain. Thus, their large brain size is considered a(n)_______ trait.

A) analogous
B) aligned
C) homologous
D) coincident
E) coordinate

Question 8

The capacity for an allele to interact well with other genes of the genome will affect whether this allele will persist in the population. This phenomenon is an illustration of which of the following evolutionary forces or principles?

A) Genetic drift
B) Genomic drift
C) Natural selection
D) Concerted evolution
E) Biased gene conversion

Question 9

Which of the following is not true of concerted evolution?

A) Concerted evolution refers to the nonindependent evolution of some repeated genes within a species.
B) Unequal crossing over may produce concerted evolution.
C) Biased gene conversion may produce concerted evolution.
D) Ribosomal RNA genes are an example of a gene family that has undergone concerted evolution.
E) Concerted evolution results in divergence of members of a gene family within an organism.

Question 10

Which of the following statements about molecular evolution is true?

A) Almost all genes evolve at the same rate.
B) All nucleotide substitutions give rise to amino acid replacements.
C) Changes in the amino acid sequence of a protein can change its charge, but not its secondary structure.
D) All of the above
E) None of the above

Question 11

A higher rate of synonymous relative to nonsynonymous substitutions in a protein-coding gene is expected under

A) purifying selection.
B) positive selection.
C) neutral evolution.
D) concerted evolution.
E) None of the above

Question 12

When a gene is duplicated, which of the following may occur?

A) Production of the gene's product may increase.
B) The two copies may become expressed in different tissues.
C) One copy of the gene may accumulate deleterious substitutions and become functionless.
D) The two copies may diverge and acquire different functions.
E) All of the above

Question 13

Genome size differs widely among different multicellular species of eukaryotes. What is the greatest contributing cause for these differences?

A) The number of protein-coding genes
B) The amount of noncoding DNA
C) The number of duplicated genes
D) The degree of concerted evolution
E) The amount of positive selection for change in protein-coding genes

Question 14

The precursors to the genes that cause the electric discharges in the electric organs of some fish evolved from _______ genes that were involved in _______.

A) calcium channel; muscle contraction
B) calcium channel; neuronal activity
C) sodium channel; muscle contraction
D) sodium channel; neuronal activity
E) NMDA channel; neuronal activity

Question 15

Genomes consist of

A) protein-coding genes only.
B) protein-coding genes and regulatory sequences.
C) protein-coding genes and noncoding DNA.
D) protein-coding genes, regulatory sequences, and noncoding DNA.
E) regulatory sequences and noncoding DNA.

Question 16

Use the following to answer questions:
In a hypothetical experiment, researchers split a bacterial colony in two, allowing each of the new colonies to evolve separately. They then sequenced a gene from colony 1 and colony 2.
In the common ancestor, the nucleotide at site 56 is A. In colony 1, it changes to C; in colony 2, it changes to T. This is an example of a _______ substitution.

A) single
B) coincident
C) parallel
D) back
E) multiple

Question 17

Which of the following statements about the "living battery" electric organ possessed by some fish is true?

A) It is composed of derived muscle cells called electrocytes.
B) Its development involved modification of sodium channels.
C) The signals produced by these organs are the same in all species with the organ.
D) Both a and b
E) Both b and c

Question 18

Before nucleotide and amino acid sequences can be compared in an evolutionary framework, they must be aligned to account for

A) deletions and insertions.
B) selection and neutrality.
C) parallelisms and convergences.
D) gene families.
E) All of the above

Question 19

Paralogous genes are genes that trace back to a common

A) speciation event.
B) substitution event.
C) insertion event.
D) deletion event.
E) duplication event.

Question 20

Which of the following is true of in vitro evolution?

A) In vitro evolution refers to bioprospecting for naturally occurring macromolecules.
B) In vitro evolution can produce new molecular sequences not known from nature.
C) In vitro evolution can only produce new proteins.
D) In vitro evolution only selects for changes that were present in the starting pool of molecules, and does not introduce any new mutations.
E) All of the above

Question 21

Which of the following statements about nonsynonymous substitutions is true?

A) They always affect the protein's shape and charge.
B) They occasionally confer a selective advantage to the organism.
C) The rate of their evolution is roughly the same among different genes.
D) They are unlikely to be influenced by natural selection.
E) All of the above

Question 22

Which of the following changes is a transversion?

A) A change from A to G
B) A change from C to T
C) A change from G to A
D) All of the above
E) None of the above

Question 23

Use the following to answer questions:
Suppose the size of a population of marmots is 300.
According to genetic drift theory, what is the probability that a newly arisen mutation will become fixed in this population?

A) 1/100
B) 1/300
C) 1/600
D) 1/1,200
E) None of the above

Question 24

According to the neutral theory of molecular evolution, the fastest rate of fixation of neutral mutations by genetic drift should occur in which of the following populations?

A) A population of 200 individuals
B) A population of 400 individuals
C) A population of 1,000 individuals
D) A population of 10,000 individuals
E) The rates of fixation should be roughly the same in all of the above.

Question 25

Which of the following statements about the Rainey and Travisano experiments on Pseudomonas bacteria is true?

A) The static cultures had a constantly uniform ­environment.
B) No phenotypic evolution occurred in the static cultures.
C) Molecular evidence showed that the same phenotype could arise from many genotypes.
D) Both a and b
E) None of the above

Question 26

Which of the following is not a reason that bacteria would be especially useful for laboratory studies of molecular evolution?

A) Substitution rates are related more to chronological time than to generation time.
B) They can be cultured in large numbers.
C) They have short generation times.
D) Their genomes can be sequenced more easily than those of multicellular eukaryotes.
E) All of the above make bacteria useful for laboratory studies of molecular evolution.

Question 27

A similarity matrix gives us a measure of the _______ number of changes that have occurred during the divergence between pairs of organisms.

A) minimum
B) maximum
C) most likely
D) All of the above
E) None of the above

Question 28

Which of the following represents the correct ordering (from fastest to slowest) of the average rate of evolution of nonsynonymous substitutions, synonymous substitutions, and pseudogenes?

A) Nonsynonymous substitutions, synonymous substitutions, pseudogenes
B) Nonsynonymous substitutions, pseudogenes, synonymous substitutions
C) Pseudogenes, nonsynonymous substitutions, synonymous substitutions
D) Pseudogenes, synonymous substitutions, nonsynonymous substitutions
E) All three evolve at roughly the same rate.

Question 29

According to the neutral theory of molecular evolution,

A) most alleles found in natural populations are neutral.
B) nearly all mutations have some effect on the organism.
C) the rate of fixation of neutral mutations is much faster in small populations than it is in large ones.
D) molecular clocks do not work.
E) None of the above

Question 30

Which of the following scientists proposed the neutral theory of molecular evolution?

A) Charles Darwin
B) Stephen Jay Gould
C) Albert Sabin
D) Chung-I Wu
E) Motoo Kimura

Question 31

Which of the following usually does not lead to undercounting the real number of substitutions?

A) Parallel substitutions
B) Back substitutions
C) Single substitutions
D) All of the above
E) None of the above

Question 32

Use the following to answer questions:
In a hypothetical experiment, researchers split a bacterial colony in two, allowing each of the new colonies to evolve separately. They then sequenced a gene from colony 1 and colony 2.
In the common ancestor, the nucleotide at site 327 is G. In colony 1, it changes to C; in colony 2, it also changes to C. This is an example of a _______ substitution.

A) single
B) coincident
C) parallel
D) back
E) multiple

Question 33

Use the following to answer questions:
Suppose the size of a population of marmots is 300.

-Assuming that the mutation rate for a particular gene is $\mu$ , the number of new mutations at each gene in this population is _______ $\times$ $\mu$ .

A) 100
B) 200
C) 300
D) 500
E) 600

Question 34

Which of the following statements about synonymous substitutions is false?

A) They do not change the amino acid sequence of the protein.
B) They are the same as silent substitutions.
C) They generally evolve at a faster rate than nonsynonymous substitutions.
D) They are less likely to be influenced by natural selection than nonsynonymous substitutions are.
E) All of the above are true; none is false.

Question 35

Which of the following changes is a transition?

A) A change from A to G
B) A change from T to C
C) A change from T to G
D) A change from C to G
E) Both a and b

Question 36

Use the following to answer questions:
In a hypothetical experiment, researchers split a bacterial colony in two, allowing each of the new colonies to evolve separately. They then sequenced a gene from colony 1 and colony 2.
Detection of which of the following types of substitutions requires knowing the sequence of intermediates between the common ancestor and the descendant colonies, in addition to that of the two colonies and the common ancestor?

A) Coincident substitutions
B) Back substitutions
C) Multiple substitutions
D) Both a and b
E) Both b and c

Question 37

Which of the following statements is true?

A) Transitions are more common than transversions.
B) A purine changing into another purine is a ­transversion.
C) A pyrimidine changing into a purine is a transition.
D) Both a and b
E) Both b and c

Question 38

The hypothesis of neutral evolution asserts that

A) the rate of molecular mutation is influenced by natural selection.
B) most variability in the structure of molecules does not affect their functioning.
C) closely related species have more similar molecular structures than do distantly related species.
D) organisms evolved through neutral changes in their molecules.
E) mutations neither add nor subtract amino acids from molecules.

Question 39

In the Rainey and Travisano experiments on Pseudomonas, cells with the "wrinkly spreader" phenotype

A) had a selective advantage under all conditions.
B) formed a mat on the surface of the medium in the static cultures.
C) had a selective disadvantage under all conditions.
D) were genetically the same as the original cells.
E) None of the above

Question 40

Regions of a DNA sequence that are invariant across diverse animals are most likely

A) subject to transversions.
B) under strong stabilizing selection.
C) incapable of alignment.
D) pseudogenes.
E) undergoing silent substitutions.

Question 41

Proteins can acquire new functions via

A) retrotransposons.
B) gene duplication.
C) bioprospecting.
D) biased gene conversion.
E) concerted evolution.

Question 42

Which of the following is not likely to occur after a gene duplication event?

A) One gene retains its function, while the other becomes a pseudogene.
B) Both genes retain their function, but they are expressed in different patterns or tissues.
C) Both genes become pseudogenes.
D) One gene retains its function, while the other evolves to have a new function.
E) All of the above are likely to occur.

Question 43

Which of the following statements about genome evolution is true?

A) Humans have between 10 and 20 times more genes than does Drosophila.
B) Many species have more than 500 times the number of protein-coding genes than the typical bacteria have.
C) Some salamanders have about 40 times as much DNA as humans do.
D) A larger genome always indicates greater complexity.
E) None of the above

Question 44

In a sequence of DNA taken from various species of snails, researchers have found that the rates of nonsynonymous substitutions and synonymous substitutions are roughly the same. What can we infer from this pattern?

A) Transversions are more common than transitions.
B) Most of the amino-acid changes are neutral.
C) Strong stabilizing selection is acting on this gene.
D) Strong selection for change is acting on this gene.
E) None of the above

Question 45

Genes from many isolates of the influenza virus have been sequenced. In certain regions of the genome, nonsynonymous substitutions occur much more frequently than do synonymous substitutions. What can we infer from this pattern?

A) A great deal of genetic drift is taking place.
B) Most of the amino acid changes are neutral.
C) Strong stabilizing selection is acting on this gene.
D) Strong selection for change is acting on this gene.
E) Mutations that change the amino acid are ­disadvantageous.

Question 46

In which of the following would you expect the greatest extent of lateral gene transfer?

A) Bacteria
B) Plants
C) Invertebrates
D) Vertebrates
E) Lateral gene transfer is roughly equally common across these groups.

Question 47

Which of the following would be the strongest evi­dence that most noncoding DNA is slightly deleterious?

A) Species with larger population sizes have more noncoding DNA.
B) Species with smaller population sizes have more noncoding DNA.
C) Species with larger genomes lose DNA more slowly than those with larger genomes.
D) Species with larger genomes lose DNA more quickly than those with smaller genomes.
E) There is an inverse relationship between the total amount of DNA in the genome and the percentage of the DNA that is noncoding.

Question 48

In which of the following animals would you find the enzyme lysozyme?

A) Only in foregut fermentators
B) Only in foregut fermentators and hoatzin
C) Only in hoatzin
D) Only in mammals and a few closely related organisms
E) In nearly all animals

Question 49

Which of the following statements is true?

A) Selection against the accumulation of junk DNA is more effective in species with small populations.
B) Noncoding sequences are thought to be slightly advantageous.
C) Large genomes can slow down the rates of ­development.
D) All of the above
E) None of the above

Question 50

Which of the following are foregut fermenters?

A) Lemurs
B) Langurs
C) Cattle
D) Both a and b
E) Both b and c

Question 51

Some birds have an enlarged esophageal chamber called a

A) hoatzin.
B) crop.
C) tranversion.
D) locazen.
E) vulva.

Question 52

Which of the following statements about genomes is true?

A) All plants have genome sizes that are smaller than those of all animals.
B) Humans have the largest genome size of all animals.
C) Most of the bacterial genome is noncoding.
D) All of the above
E) None of the above

Question 53

Researchers suspect that the gene FOXP2, which is involved in speech and cognition, has been under positive selection in the human lineage. Which of the following would provide the strongest support for such a claim?

A) The gene shows evidence of bioprospecting.
B) There is a higher rate of nonsynonymous substitutions than synonymous ones.
C) There is a lower rate of nonsynonymous substitutions than synonymous ones.
D) The gene evolves following the molecular clock.
E) There have been more transitions than transversions in the gene.

Question 54

Histones are proteins that play important roles in gene regulation. Between plants and animals, only two amino acid changes have occurred in the histone H4 protein, despite many synonymous changes. What can we infer from this observation?

A) A great deal of genetic drift is taking place.
B) Most of the amino acid changes are neutral.
C) Strong stabilizing selection is acting on this gene.
D) Strong selection for change is acting on this gene.
E) None of the above

Question 55

The best way to detect whether lateral gene transfer has occurred would be by

A) looking for orphaned LTRs in the genome.
B) looking for genes whose phylogenies differ from that of most of the genes.
C) bioprospecting.
D) comparing the ratios of synonymous and nonsynonmyous substitutions.
E) comparing the transition to transversion ratios.

Question 56

The human genome contains _______ genes.

A) less than 15,000
B) between 15,000 and 30,000
C) between 30,000 and 50,000
D) between 50,000 and 100,000
E) more than 100,000

Question 57

Which of the following were used by investigators to study the loss of genetic material in different insects?

A) Retrotransposons
B) Coding genes
C) RNAs
D) Noncoding regions of the globin gene family
E) Bioprospecting genes

Question 58

Which of the following statements about genomes is true?

A) The variation in genome size among animals is greater than the variation in the number of genes.
B) The variation in genome size among animals is less than the variation in the number of genes.
C) Most of the DNA in humans codes for proteins.
D) Both a and c
E) Both b and c

Question 59

Which of the following statements about lysozymes is false?

A) They do not have a function in mammals that are not foregut fermenters.
B) They have been subjected to convergent evolution in mammals.
C) At several amino acid positions of this enzyme, nonsynonymous substitutions have occurred at a faster rate than have synonymous substitutions in the lineage leading to foregut fermenters.
D) The changes that have occurred in the lysozymes of foregut fermenters have made the enzyme more resistant to attack by digestive enzymes.
E) All of the above are true; none is false.

Question 60

One reason that crickets (Laupala) have a larger genome size than fruit flies (Drosophila) is that crickets

A) lose DNA more slowly.
B) have a higher population size.
C) do not have retrotransposons.
D) do not have LTRs.
E) None of the above

Question 61

If one is interested in reconstructing the evolutionary history of species of birds, which of the following should be considered in the analysis?

A) Orthologs
B) Paralogs
C) Perilogs
D) Metalogs
E) Both a and b

Question 62

A biologist is examining the gene tree of a gene family of hormone receptor proteins. Which of the following should she compare when focusing on changes in function due to gene duplication?

A) Orthologs
B) Paralogs
C) Analogs
D) Both a and b
E) None of the above

Question 63

Gene duplication may involve

A) part of a gene.
B) a whole gene.
C) whole chromosomes.
D) All of the above
E) None of the above

Question 64

Which of the following can result from the misalignment of highly repeated genes?

A) Unequal crossing over
B) Biased gene conversion
C) Parallel substitutions
D) The production of paralogs
E) Transitions

Question 65

A biologist is examining species of plants found in Thailand in the hope of finding a naturally occurring treatment for cancer. This project is an example of

A) the application of the principles of concerted ­evolution.
B) bioprospecting.
C) bioremediation.
D) bioinfomatics.
E) the application of the principles of convergent evolution.

Question 66

Which of the following statements is correct?

A) All orthologs are paralogs.
B) All paralogs are orthologs.
C) All orthologs are homologs.
D) All homologs are orthologs.
E) None of the above

Question 67

Which of the following statements about the globin gene family is false?

A) Hemoglobin has a higher affinity for oxygen than myoglobin has.
B) Myoglobin is the primary oxygen storage molecule in the muscles.
C) Hemoglobin and myoglobin have evolved to have somewhat different functions.
D) Hemoglobin has a tetrameric structure that allows it to carry more oxygen molecules than does ­myoglobin.
E) All of the above are true; none is false.

Question 68

Investigations of the mechanisms and consequences of the evolution of macromolecules make up the field of _______.

Question 69

The globin genes are an example of

A) retrotransposons.
B) a gene family.
C) a gene tree.
D) synonymous genes.
E) None of the above

Question 70

Which of the following statements about gene duplication is false?

A) All duplications produce functional genes.
B) It can result in evolution of novel functions in proteins.
C) It created much of the diversity in our genome.
D) Ribosomal RNA genes arose from duplications.
E) It can result in increased complexity.

Question 71

The entire set of genes of an organism, along with all of its noncoding DNA, is known as its _______.

Question 72

Which of the following statements about ribosomal RNA (rRNA) genes is true?

A) Nearly all multicellular animals have hundreds (if not more) copies of them.
B) There is much variation within species in different copies of the rRNA genes.
C) They evolve through concerted evolution.
D) Both a and b
E) Both a and c

Question 73

The two globin gene clusters split _______ million years ago.

A) approximately 10
B) approximately 50
C) approximately 100
D) approximately 200
E) more than 300

Question 74

In order to estimate the age of the split between the globin gene clusters, scientists examined which of the following?

A) The fossil record
B) The molecular clock assumption
C) The ratio of nonsynonymous to synonymous substitution rates
D) Both a and b
E) Both b and c

Question 75

Copies of genes in the same or different species that are related as the result of gene duplications are known as

A) analogs.
B) orthologs.
C) paralogs.
D) heterologs.
E) None of the above

Question 76

Most emerging diseases are caused by

A) viruses.
B) bacteria.
C) in vitro evolution.
D) concerted evolution.
E) annelids.

Question 77

The hands of humans and the wings of bats are derived from a structure possessed by the common ancestor of both. Human hands and bat wings are thus _______ structures.

Question 78

The primary function of ribosomal RNA genes is

A) to carry oxygen.
B) protein synthesis.
C) DNA preservation.
D) to act as transcription factors regulating development.
E) lateral gene transfer.

Question 79

When researchers apply the principles of evolution to produce new molecules that can be used for pharmaceuticals, they are

A) bioprospecting.
B) performing in vitro evolution.
C) performing concerted evolution.
D) using biomes.
E) ribozyming.

Question 80

Biased gene conversion is a mechanism of

A) unequal crossing over.
B) convergent evolution.
C) concerted evolution.
D) bioprospecting.
E) None of the above