Deck 8: The History in Our Genes

Question 1

An important limit of molecular phylogenetics is that

A) DNA sequences hold little evolutionary relevant information.
B) they can only compare living and recently extinct species.
C) only closely related species can be compared with molecular phylogenies.
D) they can only compare species that went extinct more than 100,000 years ago.

Answer 1

B

Question 2

Gene flow among populations makes allele frequencies more _______, and genetic drift acts within populations, causing allele frequencies to ________.

A) similar; diverge
B) different; diverge
C) similar; coalesce
D) different; coalesce

Answer 2

A

Question 3

Which method would you employ to create a phylogenetic tree based on how different taxa are?

A) bootstrapping
B) distance-matrix method
C) maximum parsimony
D) maximum likelihood

Answer 3

B

Question 4

What mechanisms can create a mismatch between the history of genes and the history of species?

A) introgression
B) incomplete lineage sorting
C) genetic hitchhiking
D) a and b
E) a, b, and c

Question 5

Which of the following is supported by molecular phylogenetic studies?

A) Lobe-finned fish are more closely related to humans than to other fish.
B) Lobe-finned fish are more closely related to other fish than to humans.
C) Lobe-finned fish are tetrapods.
D) a and b
E) a and c

Question 6

Which of the following phylogenetic patterns supports the hypothesis that a disease was transmitted between partners?

A) The newly infected partner's strains are nested within the strains of the initially infected partner.
B) The initially infected partners strains are nested within the strains of the newly infected partner.
C) The newly infected partner's strains are more closely related to strains other than those carried by the partner.
D) Both partners' strains have identical phylogenetic trees.

Question 7

If the size of a population increases drastically,

A) more coalescent events occur near the tips.
B) more coalescent events occur near the base of the tree.
C) the rate of coalescence accelerates.
D) coalescent events are distributed evenly through time.

Question 8

BRCA1, Brca1, brca1, and PIGBRCA1 are examples of

A) homoplasy.
B) microsatellites.
C) orthologs.
D) paralogs.

Question 9

The correct species tree for the great apes shows that humans are most closely related to

A) chimpanzees.
B) gorillas.
C) orangutans.
D) bonobos.

Question 10

Which of the following is a mechanism that bacteria have for increasing their genome size?

A) horizontal gene transfer
B) genetic hitchhiking
C) introgression
D) a and b
E) a, b, and c

Question 11

Estimates of F_ST measure

A) differences between tree topologies.
B) gene flow between populations.
C) genetic drift in alleles.
D) ratios of substitutions.

Question 12

Which of the following is/are (a) pitfall(s) of trying to find the common ancestral allele of mitochondrial mutations?

A) There is no complete record of all the mitochondrial DNA in every living human.
B) There is no record of all the ancestors of humans going back millions of years.
C) Mitochondrial DNA is inherited only from mothers.
D) a and b
E) a, b, and c

Question 13

Scientist studying high-elevation adaptations in Tibetans discovered that the EPAS1 allele favored at high elevations first appeared in the Denisovan genome and entered the human genome when Denisovan and ancestral Tibetans interbred. This is an example of

A) genetic hitchhiking.
B) introgression.
C) incomplete lineage sorting.
D) linkage disequilibrium.

Question 14

The synonymous substitution rate is often assumed to represent

A) the rate of evolution by natural selection.
B) the rate of evolution by genetic drift.
C) the strength of purifying selection.
D) the rate of adaptive evolution.

Question 15

Phylogenetic studies of HIV-1 emergence that used molecular clock estimates demonstrate that:

A) the disease likely emerged with the growth of major settlements in central Africa.
B) the largest peak in SIV diversification rate occurred within the last 5 million years.
C) the common ancestor of the HIV-1 virus existed in the 1980s.
D) the virus hopped from chimpanzee to human hosts four separate times.

Question 16

All extant copies of a gene eventually coalesce; this occurs because

A) a particular allele becomes fixed in the population.
B) all extant genes coalesce at the same time in the same individuals.
C) the rate of coalescence speeds up as a population increases in size.
D) the original population consisted of only a single individual with the ancestral allele.

Question 17

Which of the following statements is supported by molecular phylogenetic studies of human populations?

A) Most human genetic diversity is found in Africa.
B) Non-Africans form a monophyletic group.
C) Africans form a monophyletic group.
D) a and b
E) a, b, and c

Question 18

Why can molecular homoplasy evolve more easily than morphological homoplasy?

A) Molecular homoplasy often results when many interacting genes mutate.
B) There are only four character states for molecular traits, each of the nucleotide bases.
C) Molecular traits are more subject to mutations than morphological traits.
D) Selection acts more strongly on molecular traits than morphological traits.

Question 19

Which of the following is not a characteristic of bacteria that are long-term obligate symbionts?

A) few pseudogenes
B) no mobile elements
C) a stable chromosome
D) interstrain recombination

Question 20

Which of the following statements is true about mitochondrial DNA?

A) Humans inherit mitochondrial DNA from both parents.
B) Mitochondrial mutations occur at different rates in different ethnic groups.
C) The time to coalescence for mitochondrial DNA was more than 5 million years.
D) Scientists have a complete record of the mitochondrial DNA for every human alive today.

Question 21

Maximum likelihood phylogenetic construction methods differ from distance methods in that

A) maximum likelihood methods incorporate specific models of molecular evolution.
B) distance methods use bootstrapping, while maximum likelihood does not.
C) maximum likelihood generates a tree with the shortest possible branch length, while distance methods do not.
D) all of the above
E) none of the above

Question 22

Which chromosome is the BRCA1 gene located on?

A) 2
B) 17
C) 23
D) X

Question 23

A woman who carries one G variant and one T variant of the BRCA1 gene would pass the T variant on to approximately how many of her children?

A) 100%
B) 67%
C) 50%
D) 0%

Question 24

The gene BRCA1 normally functions as

A) a gene that causes cancer.
B) a tumor-suppressor gene.
C) an oncogene.
D) a supergene.

Question 25

A neutrally evolving allele in a population of a constant size is expected to have

A) a linearly increasing number of coalescent events over time.
B) a linearly decreasing number of coalescent events over time.
C) an exponential decrease in the number of coalescent events over time.
D) an exponential increase in the number of coalescent events over time.

Question 26

The evolutionary tree of HIV-1 revels that

A) the virus jumped from chimpanzees to humans four times.
B) HIV is a monophyletic clade that originated from the same strain of SIV.
C) the SIV strain that infects gorillas is the same strain that infects chimpanzees.
D) western chimpanzees are more closely related to gorillas than eastern chimpanzees.

Question 27

Gene trees can be used to estimate times of coalescence for

A) only closely related alleles in a population.
B) only distantly related alleles in a population.
C) all populations where a single individual had the ancestral allele.
D) all possible pairwise combinations of different alleles in a population.

Question 28

New nonsynonymous mutations

A) occur randomly with respect to fitness.
B) are greater in number in a large population than a small population.
C) are most often deleterious.
D) all of the above

Question 29

If a biologist wanted to associate each node of a phylogenetic tree with a statistical measure of support for a particular grouping, what is one method she could employ?

A) distance-matrix method
B) maximum parsimony
C) maximum likelihood
D) neighbor joining

Question 30

Which of the following would cause incomplete lineage sorting?

A) The alleles of interest are all present before the divergence of species.
B) A hybrid offspring mates with individuals from the original species.
C) A favorable allele fixes in the population very quickly.
D) A substitution occurs that alters the amino acid sequence of a protein.

Question 31

Which of the following scenarios would be most likely to produce a gene tree that is discordant with a species tree?

A) long branch lengths; short coalescence time for alleles
B) short branch lengths; long coalescence time for alleles
C) long branch lengths; long coalescence time for alleles
D) short branch lengths; short coalescence time for alleles

Question 32

Which of the following statements is not true about lentiviruses?

A) The viruses infect mammals like cats, horses, and primates.
B) They typically infect by invading certain types of white blood cells.
C) Lentiviruses are a monophyletic group consisting of HIV and SIV.
D) HIV is most closely related to strains of lentivirus found in monkeys and apes.

Question 33

Knowing the structure of the HIV tree allowed scientists to pinpoint which specific adaptation that allowed HIV to infect humans?

A) an increase in virulence
B) an enzyme that allows the virus to break down white blood cells
C) a mutation in a gene that encodes the shell of the virus
D) a mutation changing the shape of the hemagglutinin stalk

Question 34

Studies show that despite causing a significant risk of hereditary breast cancer, the BRCA1 gene has undergone strong positive selection. One hypothesis for this is that

A) BRCA1 mutations prevent viruses from using human cellular machinery to replicate.
B) mutated BRCA1 genes provided some resistance to diseases like malaria.
C) the BRCA1 gene is on the same chromosome as the gene that controls lactose tolerance.
D) mutations in tumor-suppressor genes are usually favored by natural selection.

Question 35

Alleles that share a genealogical lineage in a gene tree are all

A) ancestral.
B) homologous.
C) mutations.
D) orthologs.

Question 36

In the following figure, what do circles with no lines extending from them represent?

A) pathogenic variants of alleles
B) points where two lineages converged
C) the occurrence of single nucleotide polymorphisms
D) alleles that were not transmitted to the next generation

Question 37

Which of the following has not been proposed as why the genomic structure of eukaryotes and prokaryotes is different?

A) Cells of eukaryotes were much larger than those of bacteria.
B) Populations of eukaryotes were smaller.
C) Genetic drift allowed mobile elements to invade genomes.
D) Eukaryotic genomes contain large amounts of non-protein coding DNA.

Question 38

Which of the following describes the McDonald-Kreitman test (MK test)?

A) The number of coalescent events in a population is compared to a null hypothesis.
B) The branch lengths of all trees are compared, and the one with the shortest branches is chosen.
C) The alleles of a species are compared within a species and to a homologous gene in another species.
D) Allele frequencies that are more different than expected are identified as outliers.

Question 39

When an allele increases in frequency because it is in close proximity on the chromosome to a positively selected allele, this causes

A) directional selection.
B) incomplete linkage sorting.
C) linkage disequilibrium.
D) synonymous substitution.

Question 40

Grouped together, paralogs form a

A) gene family.
B) gene tree.
C) molecular clock.
D) synapomorphy.

Question 41

In 2002, Trask et al. published a study showing that a high frequency of HIV transmissions in Lusaka, Zambia occurred between marriage partners. Specifically, they studied a cohort of married couples where, at the beginning of the study, one partner was infected and the other was not. Later, the uninfected partner became infected. If you were doing this study, how could you use phylogenetic methods to determine whether the newly infected individual was likely infected by his/her partner? Briefly describe your study design and results that would support and results that would refute (you can use drawings if you wish) the partner-partner transmission scenario.

Question 42

The codon TCA codes for serine. If a new mutation occurred that replaced the "A" with a "T," this mutation would be _______________, and its fate would most likely be determined by ___________.

A) nonsynonymous; genetic drift
B) nonsynonymous; natural selection
C) synonymous; genetic drift
D) synonymous; natural selection

Question 43

In a molecular phylogeny what can serve as a synapomorphy?

A) amino acids
B) insertions
C) homoplasy
D) orthologs

Question 44

Please explain why homoplasy is particularly problematic in the construction of molecular phylogenies from DNA sequence data.

Question 45

You are studying the relationships among a group of ten cichlid fishes that have speciated very recently (say, the last 5000 years). Would you choose to use intron or exon sequences in your phylogenetic analysis? Explain your answer.

Question 46

Please contrast the "out of Africa" model of human evolution with the "multiregional" model.

Question 47

Which bacterial niche is likely to favor having a large genome?

A) free-living bacteria
B) host-restricted symbionts
C) host-restricted pathogens
D) all of the above

Question 48

A free-living bacterium unrestricted by a host would probably have

A) few pseudogenes and few mobile elements.
B) few pseudogenes and no mobile elements.
C) many pseudogenes and few mobile elements.
D) many pseudogenes and many mobile elements.

Question 49

Please explain why the average rate of evolution differs between introns and exons, and why this is important for choosing genetic markers to be used in phylogeny construction.

Question 50

This is a true story. A gastroenterologist from Lafayette, LA was accused of infecting his girlfriend with HIV by injecting her with a syringe containing HIV-infected blood from one of his patients. The victim (the girlfriend) claimed that the doctor injected her during an argument. However, the victim was also a nurse and so conceivably may have had contact with HIV-infected blood through her job. Given below is a phylogenetic tree constructed using HIV sequences from the victim (denoted with a V in the label), HIV sequences from the patient whose blood was allegedly in the syringe that the doctor injected into the victim (denoted by a P in the label), and HIV sequences representing much of the diversity of HIV strains from the Lafayette area during the time of the incident (denoted by LA in the label). Is the tree consistent with the prosecution's case that the doctor injected the victim with HIV-infected blood from his patient? Why or why not?

Question 51

Why would bacteria that live in hosts have smaller genomes than free-living bacteria?

Question 52

Scientists have hypothesized that eukaryotic genome size may be related to

A) cell size.
B) mobile elements.
C) number of genes.
D) horizontal gene transfer.

Question 53

The ratio of the rate of nonsynonymous to synonymous mutations (dN/dS) is equal to one if a gene is evolving ______. A dN/dS ratio greater than one indicates that the gene is evolving _____.

A) neutrally; purifying selection
B) under positive selection; neutrally
C) neutrally; under positive selection
D) under purifying selection; neutrally
E) under purifying selection; under positive selection

Question 54

Proponents of the neutral theory of molecular evolution believe that most substitutions are fixed by _______.

A) sexual selection
B) natural selection
C) genetic drift
D) none of the above

Question 55

A substitution that changes one of the first two bases in a codon (e.g., AGT) is called a _______ mutation and will ______.

A) synonymous mutation; not change the resulting amino acid
B) nonsynonymous mutation; not change the resulting amino acid
C) nonsynonymous mutation; change the resulting amino acid
D) synonymous mutation; change the resulting amino acid
E) frameshift mutation; change the resulting amino acid

Question 56

F_ST estimates close to zero would suggest that a population

A) is fully homogenized.
B) is fully segregated.
C) has high rates of hybridization.
D) has low rates of introgression.

Question 57

When did Homo sapiens interbreed with Neanderthals and other extinct human populations?

A) before evolving in Africa for hundreds of thousands of years
B) after spreading across Asia, Europe, and the Americas
C) after migrating out of the African continent
D) none of the above

Question 58

Describe how incomplete lineage sorting caused confusion about the phylogeny of great apes and how the confusion was resolved.

Question 59

What is the working hypothesis for the origin of lactose intolerance? What evidence supports this hypothesis?

Question 60

Scientists have used F_ST outliers to

A) develop a hypothesis regarding selection for the lactose tolerance allele, LCT*P.
B) identify genes EPAS1 and EGLN1 as genes associated with high-elevation adaptations.
C) explain why the BRCA1 gene has undergone positive selection.
D) all of the above

Question 61

A few years ago, the avian influenza virus (H5N1) swept from Asia, across Russia, to Europe. Nigeria was the first African country to report detection of the virus in chickens. The phylogeny below depicts the relationships between H5N1 from Nigeria and samples from other parts of Asia and Europe. Samples from Nigeria are labeled either as Lagos or northern Nigeria. Given the phylogeny below, what is the minimum number of times H5N1 was introduced to Nigeria?

Question 62

Describe what information can be gleaned from gene trees created from within population sampling compared to. gene trees created from sampling individuals from different populations or species.

Question 63

You are studying the source of a new virus that has recently infected humans. You suspect that the virus was transferred from other primates (they exhibit a similar infection), specifically, chimpanzees, gorillas, or orangutans. You sample blood from several infected humans and sequence some viral genes. You then build a phylogenetic tree with the human sequences and all the known strains from each primate. Draw a hypothetical phylogenetic tree that would suggest that the virus came from gorillas and that this transfer occurred twice independently. Label chimpanzee sequences (c), gorilla (g), orangutans (o), and humans (h).

Question 64

A distribution of coalescent events for a population can be predicted from an estimated population size and randomly generated phylogenetic trees. What are ways for a population to violate this prediction?

Question 65

Please explain why synonymous sites typically evolve faster than nonsynonymous sites.