Deck 2: Variations in Chromosome Structure and Number

Question 1

Given the following sequence alignment: G T C C A T C G G G T C G A T C-- G Which of the following is not true?

A) There is evidence of an indel.
B) There has been a transversion.
C) There has been a gene conversion.
D) There has been a base deletion.
E) There has been a base substitution.

Answer 1

C

Question 2

The average synonymous substitution rate in mammalian mitochondrial genes is ________ the average rate for nuclear genes.

A) ten times
B) fifty times
C) five times
D) twice
E) one hundred times

Answer 2

A

Question 3

The differences in evolutionary rates of change revealed by relative rate tests may be attributable to

A) differential exposure to mutagens.
B) average DNA repair efficiency.
C) differential strength of selection.
D) generation time.
E) all of the above.

Answer 3

E

Question 4

Nonsynonymous substitutions

A) do not lead to amino acid change.
B) lead to amino acid change.
C) lead to transversions.
D) affect only certain amino acids.
E) refer to substitutions in unrelated lineages.

Question 5

Synonymous changes that arise within coding sequences of genes

A) occur more frequently than nonsynonymous changes.
B) are usually detrimental to fitness.
C) generally have no effect on the phenotype.
D) may be eliminated by natural selection.
E) Both B and C are correct.

Question 6

The synonymous substitution rates across a given genome rarely differ by more than a factor of two, a difference that cannot account for the roughly 1,000-fold difference in nonsynonymous substitution rates observed between some genes. This observation strongly suggests

A) that nonsynonymous substitutions are more common than synonymous substitutions.
B) that natural selection has been acting on such genes.
C) that genetic drift is a stronger evolutionary force than previously believed.
D) that mutations rates are far more variable than previously believed.
E) that synonymous substitution rates are underestimated.

Question 7

Higher substitution rates are seen in ________ than in ________.

A) charged amino acid codons, noncharged amino acid codons
B) 5' flanking regions, 3' flanking regions
C) introns, exons
D) coding regions, noncoding regions
E) first codon positions, second codon positions

Question 8

Reconstructions of the evolutionary relationships of a set of taxa are called

A) evolutionary scenarios.
B) UPGMA networks.
C) classifications.
D) phylogenetic trees.
E) networks.

Question 9

Natural selection favors variability in ________ genes.

A) DNA pol
B) rRNA
C) prolactin
D) insulin
E) MHC

Question 10

Which of the following mutations is considered a synonymous change?

A) ACC to AUG
B) CUU to CUA
C) UUU to UUA
D) CUU to CUA
E) CUU to AUU

Question 11

It might be expected that highly expressed genes make use of ________ amino acids relative to rarely expressed genes.

A) energetically costly
B) energetically inexpensive
C) common
D) rare
E) None of the above

Question 12

Codon bias suggests that

A) some codons are selectively favored over others.
B) not all nonsynonymous substitutions are neutral.
C) some tRNAs are more abundant than others.
D) small fitness effects can make a large difference over time.
E) some codons evolved earlier than others.

Question 13

Substitutions in the 3' flanking region of a gene

A) do not affect gene expression.
B) increase the substitution rate elsewhere in the gene.
C) are always synonymous.
D) have a negative effect on fitness.
E) None of the above

Question 14

The rate of accumulation of mutations in homologous nucleic acids or proteins over time may be sufficiently constant on average to permit

A) dating of divergence times by a molecular clock.
B) identification of cases of homology.
C) use of sequences in molecular phylogeny.
D) all of the above.
E) none of the above.

Question 15

Homologous proteins

A) share a common amino acid sequence.
B) share a common ancestor.
C) are determined by alleles on homologous chromosomes.
D) A, B, and C
E) A and B only

Question 16

In molecular evolution analyses, the single most informative variable to estimate is

A) PN, the probability of a particular nucleotide occurring at a given site.
B) the relative number of indels per sequence.
C) the frequency of SNPs in aligned sequences.
D) the number of substitutions (K) observed between two aligned sequences.
E) the transition : transversion ratio.

Question 17

In the unweighted pair group method (UPGMA) of determining evolutionary relationships,

A) a distance matrix is first constructed.
B) a constant rate of evolution across all lineages is assumed.
C) each set of taxa is connected by the shortest genetic distance.
D) A, B, and C
E) A and B only

Question 18

Which of the following statements is true?

A) Genes in the same organism evolve at about the same rate.
B) Genes in different organisms evolve at about the same rate.
C) Homologous genes often evolve in the same way.
D) Different regions of the same gene evolve at different rates.
E) Nucleotide substitutions are nonrandom.

Question 19

Which type of protein evolves at the slowest rate?

A) Lipoprotein
B) Peptide hormones
C) Histones
D) Collagen
E) Insulin

Question 20

________ tend(s) to occur more frequently than

A) Transitions, transversions.
B) Genetic divergence, genetic convergence.
C) Synonymous substitutions, nonsynonymous substitutions.
D) A, B, and C
E) A and B only

Question 21

The counterpart to use of mtDNA to reconstruct maternal lineages is the use of chloroplast DNA to reconstruct paternal lineages.

Question 22

Maximum confidence is a procedure for reconstructing phylogenetic trees invoking the fewest number of steps or mutations.

Question 23

Nuclear DNA sequence is more abundant than mtDNA and is therefore preferable for use in reconstructing events like domestication or human migration.

Question 24

The five-kingdom taxonomic system is not especially old; for a long time, three kingdoms were recognized, then four, then (as of 1959) five. In light of Carl Woese's discovery of deep genetic divergence within the Kingdom Monera, why do you think he did not simply suggest adding a sixth kingdom rather than the supra-kingdom classification of domains?

Question 25

Pseudogenes tend to have lower average substitution rates than functional genes.

Question 26

Many viruses are helped along in generating antibody-evading capsid protein variations by replication error.

Question 27

In a molecular-evolutionary analysis, you estimate the number of base substitutions per site (K) at 0.82. Given an estimated divergence time (T) of 10 million years based on the fossil record, what is the substitution rate (r)?

Question 28

Distinguish between a gene tree and a species tree.

Question 29

The "three domain" classification advocated by Carl Woese and his colleagues is based on molecular-evolutionary data. What are the domains and the arguments for formally recognizing them in classification?

Question 30

Define codon bias. If synonymous substitutions give the same amino acid, why should there be a bias in which codons are used to encode that amino acid?

Question 31

High molecular similarity reflects evolutionary relatedness.

Question 32

The McDonald-Kreitman test is an important tool in molecular evolutionary analysis. What is this test, and what kinds of insights can it provide?

Question 33

What is the rationale behind the bootstrap procedure, where trees are repeatedly reconstructed following resampling with replacement of the original data?

Question 34

Of the six codons that encode the amino acid leucine in yeast, approximately 80 percent of them are UUG. This is an example of codon bias.

Question 35

It is not unusual for a phylogeny reconstruction to result in more than one equally robust phylogenetic trees that differ in their branching patterns. How can this be the case if evolution only took one true pathway?

Question 36

One problem commonly experienced in phylogeny reconstruction arises when two or more of the groups being compared have accumulated far more genetic changes (mutations) than the others in the comparison. This situation often results in a phenomenon known as "long branch attraction," where the highly mutated lineages end up grouping together in a phylogenetic analysis even if in fact they are distantly related. What do you think causes long branch attraction? How might it be compensated for?

Question 37

In the following alignment of 12 base pairs, which sites are phylogenetically informative? Sequence 1 ATTGGTATAAAA Sequence 2 ATTAGTATAAAA Sequence 3 ATTGGTATCAAA Sequence 4 ATTAGTATCAAA

Question 38

What are some weaknesses of (1) parsimony methods, and (2) distance matrix methods of phylogeny reconstruction.

Question 39

Genetic distance refers to the proportion of dissimilar nucleotides between two homologous sequences.

Question 40

The noncoding 5' flanking region of genes is more constrained by selection than the noncoding 3' flanking region.

Question 41

One of the lines of evidence supporting human origins in Africa is that African populations contain the greatest diversity of genetic variants of any human populations. Why is this consistent with human origins on that continent rather than stemming from some other process?

Question 42

Humans have extremely high genetic similarity, with greater than 99 percent sequence identity across populations. Yet, many people appear very different phenotypically. How do you reconcile these observations?

Question 43

Describe briefly the mechanisms that are thought to give rise to gene duplication and multigene families.