Deck 23: Molecular Evolution

Question 1

Higher substitution rates are seen in ________ than in ________.

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

Answer 1

D

Question 2

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

Answer 2

True

Question 3

Which of the following types of proteins evolves at the slowest rate?

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

Answer 3

D

Question 4

Which of the following does not provide molecular evidence for evolution?

A)The 1,000-fold differences in nonsynonymous substitutions between some genes
B)The existence of pseudogenes
C)The fact that high-expression genes use amino acids that are less energetically costly than those used by low-expression genes
D)The fact that there is a lower rate of nucleotide substitutions in coding regions than in noncoding regions of genes
E)All these are molecular evidence for evolution

Question 5

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

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

Question 6

Which of the following statements about molecular evolution is true?

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

Question 7

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

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

Question 8

Which of the following factors does not interfere with the interpretation of evolutionary time using the molecular clock?

A)Horizontal gene transfer
B)Differences in generation time
C)Mutations due to background cosmic radiation
D)Different selection pressures on different taxonomic groups
E)Differences in DNA repair efficiency in different taxonomic groups

Question 9

_______ tend(s)to occur more frequently than ________.

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

Question 10

Which of the following mutations is considered a synonymous change?

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

Question 11

The greatest genetic differences found in humans are

A)found between individuals from different continents.
B)found between individuals of different racial groups.
C)found between island populations and mainland populations.
D)found between individuals of African descent.
E)found between individuals of European descent.

Question 12

Indels are

A)index deletions used to identify a species.
B)parsimonious trees.
C)transitions and transversions combined.
D)small deletions or insertions that produce gaps in sequence alignments.
E)the result of codon usage bias.

Question 13

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

A)2 times
B)5 times
C)10 times
D)50 times
E)100 times

Question 14

With regards to the sequence alignment G T C C A T C G G G T C G A T C - G,
Which of the following statements is not true?

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

Question 15

Codon bias suggests that

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

Question 16

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

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

Question 17

From the standpoint of evolutionary fitness,it is expected that genes with a high rate of expression will make use of amino acids that are ________ than those amino acids used by genes with a low rate of expression.

A)more common
B)more energetically economical
C)more energetically costly
D)rarer
E)None of these

Question 18

Synonymous changes that arise within coding sequences of genes

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

Question 19

Nonsynonymous substitutions

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

Question 20

What is the number of possible unrooted trees for 5 taxa?

A)5
B)10
C)15
D)20
E)25

Question 21

Distinguish between a gene tree and a species tree.

Question 22

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

Question 23

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

Question 24

Mitochondria and chloroplasts have genomes that have evolved from the nuclear genomes in eukaryotes.

Question 25

What is codon bias? If synonymous substitutions give the same amino acid,why should there be a bias in which codons encode that amino acid?

Question 26

High molecular similarity always reflects evolutionary relatedness.

Question 27

The fact that approximately 80% of the six codons that encode the amino acid leucine in yeast are UUG is an example of codon bias.

Question 28

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

Question 29

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 30

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

Question 31

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

Question 32

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

Question 33

What are the major weaknesses of the parsimony and distance matrix methods of phylogeny reconstruction?

Question 34

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

Question 35

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," in which the highly mutated lineages end up grouping together in a phylogenetic analysis even if they are distantly related.What do you think causes long branch attraction? How might it be compensated for?

Question 36

In the 1960s and 1970s,organisms were classified into five kingdoms,one of which was prokaryotes.In the 1980s,organisms were reorganized into three domains,with the prokaryotes split into Archaea and Bacteria,and all of the other four kingdoms lumped together into Eukarya.Why did this happen?

Question 37

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 38

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

Question 39

In most genes,the rate of synonymous mutations is significantly higher than that of nonsynonymous mutation.The MHC genes exhibit the reverse,having over twice as many nonsynonymous as synonymous mutations.Explain this phenomenon.

Question 40

Given the following aligned sequences
Sequence 1 ATA TGT ATA AAA
Sequence 2 ATA TGT TTA AAG
Sequence 3 ATC TGT ATA AAA
Sequence 4 ATC TGG ATA AAG,
identify any transitions and transversions as well as any synonymous and nonsynonymous substitutions.

Question 41

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 42

Humans have an extremely high level of genetic similarity,with greater than 99% 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.

Question 44

One of the lines of evidence supporting the theory that modern humans originated in Africa is that the modern-day human population of Africa contains the greatest diversity of genetic variants of any human population.Why is this consistent with the idea that humans first evolved in Africa?