Chapters 6-10

In a diploid population size of 1000, a new beneficial mutation arises with a selective coefficient of 0.0001. What is the probability that this mutation will go to fixation?

0.0005

Suppose you are studying a rare human genetic disease and find that the mutation rate for the disease causing allele is µ = 0.00012, and selection against the allele is s = 0.7. What would be the estimated equilibrium frequency for this recessive deleterious allele?

0.013

Suppose you survey a population in Hardy-Weinberg linkage equilibrium with two loci C and D (with allele C and c, D and d). The estimated frequencies of these alleles are f(C) = 0.6, f(c) = 0.4, f(D) = 0.8, and f(d) = 0.2 What is the frequency of the chromosome haplotype Cd?

0.12

Imagine that in a fishery laboratory experiment, you need to calculate h2 for the length of the caudal fin for a certain population of fish. If your average population measurement is 25 mm, the selected individuals have fins of 35 mm on average, and the offspring have fins of 30 mm on average, what is the narrow-sense heritability? Use the breeder's equation and the equations for R and S given in Figure 9.42 for your calculations.

0.5

Suppose that you are studying a population of African elephants and wish to learn more about its evolutionary history using the two linked loci (A with alleles A and a, and B with alleles B and b). You discover that haplotype frequencies in this population are as follows AB = 0.40, Ab = 0.10, aB = 0.42, and ab = 0.08 What is the frequency of the a allele in this population?

0.50

Human populations are polymorphic for the gene coding for myoglobin, with two alleles, A1 and A2. Tomoya Takata and his colleagues (Takata et al. 2002) found that in a small Japanese population, the frequency of the A1 allele was 0.755. If the population is in Hardy-Weinberg equilibrium, what are the frequencies of the A1A1, A1A2, and A2A2 genotypes, respectively?

0.57, 0.37, 0.06

In a population of birds, wing feather pigmentation is determined by a single gene with two incompletely dominant alleles, A1 and A2. Suppose genotype A1A1 confers dark brown wings, genotype A1A2 is light brown, and genotype A2A2 is light beige. In a population of 1000 birds, 350 have dark brown wings, 500 have light brown wings, and 150 have light beige wings. What is the A1 allele frequency in this population?

0.60

Imagine that in a large coastal population of plants, the frequency of the A allele is 0.7 and the frequency of the a allele is 0.3 at a neutral locus. If a small group of individuals from this population (with the frequency of the A allele as 0.9) manages to reach a distant island in a one-time colonization event, what is the probability that A will become fixed on the island?

0.9

An endangered animal species has an effective population size of 50. What is the expected loss of heterozygosity in each generation?

1%

If one human protein contains 400 amino acids, how many nucleotides need to be in the exons of the corresponding gene to properly code for it?

1200

In a population of about 50 walruses with 30 fertile females, only 4 males are mating, due to strong male-male competition. Suppose that you need to provide data for conservation efforts and are asked to calculate the effective population size (Ne). What would be your best estimate?

14

Consider a locus with two alleles in a population of 100 individuals, with the initial frequencies A1 = 0.7 and A2 = 0.3. If A1 and A2 are selectively neutral, what is the probability that the A2 allele will drift to fixation?

30%

The fruit fly (Drosophila melanogaster) has four pairs of chromosomes. How many chromosomes would you find in an unfertilized egg (female gamete or sex cell) of this species?

4

In a population of 200 diploid individuals, how long will it take on average for any two gene copies at a neutral locus to coalesce?

400 generations

Texas longhorn cattle have been bred to increase the tip-to-tip width of their horns, and the heritability of this trait has been well studied by Professor David Hillis at the University of Texas, Austin. In the current generation, the mean horn length is 52 inches. If only a subset of this population, with a mean horn length of 61 inches, is allowed to reproduce, and the narrow-sense heritability of this trait = 0.2, what approximately is the expected horn length in the offspring generation? Use the breeder's equation and the equations for R and S given in Figure 9.42 for your calculations.

54 inches

In mice that are homozygous for the dark-color Agouti allele (D), the effects of the Mc1R locus are entirely masked so that, irrespective of the genotype at Mc1R, the mice have fully dark coloration. However, if at least one copy of the light-color Agouti allele (L) is expressed, the different shades of brown Mc1R locus are revealed (with the particular shade depending on the number of copies of L). This is an example of __________.

epistatic effects of the two genes

An addition or deletion of one or two base pairs in a gene sequence results in a __________ mutation.

frameshift

he major genetic effect of inbreeding in a population is to increase the number of__________.

loci at which the average individual is homozygous

In sickle cell anemia, a point mutation leads to a replacement of one amino acid in a hemoglobin molecule, in a unit responsible for transportation of oxygen. This and any other mutation in a gene that causes a change in the amino acid sequence in a polypeptide chain is known as a __________ mutation.

missense

The proportion of phenotypic variance that results from additive genetic variance alone is called the __________ heritability.

narrow-sense

Which of the following lists four factors that can cause or create linkage disequilibrium in a population?

natural selection, migration, mutation, and genetic drift

In the southern European plains, a species of flower comes in two colors, purple and pink. When pink flowers are most common in a field, bees visit and pollinate the purple flowers more often, and vice versa. This switching of pollinator preference will result in __________.

negative frequency-dependent selection

Which of the following processes results in the maintenance of genetic variation within a population?

negative frequency-dependent selection

What allele frequencies result in the highest frequency of heterozygotes in a population at Hardy-Weinberg equilibrium?

p=q=0.5

In quantitative genetics theory, the value of a quantitative trait is sometimes given by the equation P = G + E. We could define P as the _________ of the continuous trait that we are studying.

phenotypic value

Small, circular DNA molecules in bacterial cells, which often code for resistance to one or more antibiotics and have the ability to move by the process of conjugation, are called __________.

plasmids

The purple flower of the F1 offspring of Gregor Mendel's parental generation crosses indicated that __________.

purple color in flowers is dominant to white color

Long interspersed elements (LINEs) make up about 17% of the human genome. What type of transposable elements are they?

retrotransposons

Which of the following breaks up or removes linkage disequilibrium from a population?

sexual reproduction

When narrow-sense heritability is calculated using similarities between parents and offspring, it will correspond to the __________.

slope of linear regression between the average phenotype of the two parents and the phenotype of the offspring

All of the following may be found in prokaryotic genomes except for __________.

spliceosomal introns

According to the neutral theory, most mutations are deleterious and most _______________ are __________.

substitutions ; neutral

Inbreeding depression is a reduction in the fitness of inbred individuals caused by__________.

the expression of recessive deleterious phenotypes due to increased homozygosity

Sunflower hybrids resulting from crosses between wild sunflowers and their domesticated relatives have high rates of survival. This would seem to suggest that the hybrids have a high fitness. However, before reaching this conclusion, you should next examine __________.

the number of offspring produced by hybrids

Which position in a codon shows the greatest degeneracy? In other words, if a change occurs in this codon position, it is less likely to change the amino acid that is specified relative to the other positions.

third position

One of the problems in hospitals is that some human pathogens, such as Streptococcus pneumoniae, Haemophilus influenzae, and Neisseria gonorrhoeae, have active mechanisms for acquiring DNA from the environment (which is released when other cells die). Such DNA can subsequently be incorporated into the genome by recombination and confer resistance to multiple antibiotics. This process of gene transfer is known as __________.

transformation

A type of mutation in which a region of one chromosome is moved to a different chromosome is called __________.

translocation

A mutation that results in a replacement of a purine with a pyrimidine is known as a __________ mutation.

transversion

A mouse population contains hybrids between New Zealand Black (NZB) and New Zealand White (NZW) mice. NZW homozygotes are healthy, but NZB homozygotes experience autoimmune disease. NZB/NZW heterozygotes experience even more severe autoimmune disease (so much so that they are used as a model for the human autoimmune disease lupus). This situation is an example of __________.

under dominance

In eukaryotes, protein-coding genes are typically composed of exon regions that code for protein products, interspersed with intron regions that are spliced out before translation. The exon theory of genes proposes an evolutionary explanation for this feature of eukaryotic genomes. Choose the best summary of this theory.

In the presence of introns, unequal recombination is likely to occur between the exons, creating new combinations of protein domains without disrupting the structure of the individual domains.

Drosophila melanogaster has a relatively short generation time (a couple of weeks) and is an easy species in which to score phenotypic markers for a number of linked loci. Consequently, an experiment was done with two pairs of linked loci to see how quickly sexual reproduction and random mating would break down linkage disequilibrium. Loci A and B are linked (A with alleles A and a, and B with alleles B and b) with a recombination rate (r) of 0.1. Loci C and D are linked (C with alleles C and c, and D with alleles D and d) with a recombination rate (r) of 0.01. If experiments were run for 25 generations, starting with a maximum linkage disequilibrium between the loci of 0.25, which two linked loci would have a faster decay of linkage disequilibrium?

Loci A and B

These are an assumption of the Hardy-Weinberg model

Mating in the population is not random with respect to the locus in question.

Which of Gregor Mendel's laws contradicts the blending theory of inheritance?

Mendel's first law, the law of segregation

The figure shows the ratio of nonsynonymous to synonymous polymorphism in humans and the ratio of nonsynonymous to synonymous substitutions between humans and chimpanzees. What do these data demonstrate about the nature of variation in human populations?

Much of the variation in humans is under purifying selection and therefore due to deleterious mutations.

Viral genomes tend to be extremely compact due to the effects of strong selection on genome size. Which of the following explains why such a remarkable degree of compression can be achieved?

Multiple genes may be packed into a single region of the genome

Consider two populations of fish that live in separate ponds, with no migration between them. How will mutation affect that degree of variation between these populations?

Mutation will increase the variation between populations.

Genetic drift tends to increase the homozygosity of a population, and if it were the only evolutionary process operating, any finite population would eventually become entirely homozygous. In practice, however, populations do not become entirely homozygous. Why not?

New mutations provide a continual supply of new genetic variation.

One important consequence of genetic drift is that it decreases the heterozygosity in a population from what is expected under Hardy-Weinberg equilibrium.What are the observed and expected heterozygosities in a population that has three genotypes with the following frequencies f(A1A1) = 100, f(A1A2) = 25, f(A2A2) = 100.

Observed = 0.1; Expected = 0.5

In an early study of black spruce trees in Canada's Hudson Bay area, researchers studying nuclear DNA found no reduction of genetic diversity in post-ice-age populations, and thus no evidence of founder effects. Why did a recent study, using mitochondrial DNA (mtDNA), show different results regarding the founder effects in black spruce?

Pollen, which carries nuclear DNA but not mtDNA, can disperse far in the wind, but seeds, which carry both nuclear and mtDNA, cannot disperse as far.

Which of the following is true of the nearly neutral theory of molecular evolution?

Population size plays an important role in determining the outcome of drift and selection

Which of the following is TRUE regarding prophage DNA in a prokaryotic genome?

Prophage DNA often encodes virulence factors.

Many mammals prefer mates that differ from themselves at the immune locus MHC. Why might this preference be advantageous for the offspring?

Such mating results in higher heterozygosity at the MHC locus, and therefore greater diversity in immune function.

What is the role of telomerase (a protein-based enzyme with an RNA template) in eukaryotic DNA replication?

Telomerase extends the 3' end of a chromosome, adding a specific repeat sequence.

Consider two populations of fish that live in separate ponds and differ in the frequency of alleles at a locus. After a flood, the two ponds become connected by a stream and some fish are able to move between the ponds. What will happen to allele frequencies at this locus in the two populations?

The allele frequencies in the two ponds will become more similar to each other.

In the 1850s and 1860s, Gregor Mendel bred pea plants and examined the way that traits were passed down across generations. His conclusions, although not accepted during his lifetime, established the foundation for the field of genetics. Of the choices listed, what is the most relevant summary of Mendel's conclusions?

The hereditary factors responsible for traits such as seed shape and flower color are inherited as discrete units.

If an mRNA sequence in the 5'-3' direction usually begins UGG AUG UCG CCC AUA, what would you expect to happen if the guanine in the third position is deleted from the mRNA sequence?

The mRNA will not be translated into a protein at all.

Manx cats are common on a remote island near Great Britain, though rare elsewhere. They have a reduced or absent tail and longer hind legs than forelegs. This phenotype is caused by a dominant allele, M, at an autosomal locus. Manx cats are always Mm heterozygotes because MM homozygotes are aborted prenatally. What is the best evolutionary explanation for the Manx cats' prevalence on this island?

The prevalence of the Manx phenotype on this island is a result of the founder effect and genetic drift.

The graph shows the distribution of fitness effects of Bacteriophage f1 mutants. Note that values greater than 1.0 indicate beneficial mutations, whereas values less than 1.0 indicate deleterious mutations. What is the best conclusion from this study?

The vast majority of the mutations had a deleterious effect, but some were beneficial.

Which of the following statements describes the C-value paradox?

There is an enormous variation in genome size across taxa, but organismal complexity does not correlate well with genome size.

When comparing the gene for elongation factor 1 between two species of rotifers, you find that the rate of nonsynonymous substitution is 0.026 and the rate of synonymous substitution is 0.81. Which of the following can you conclude from these data?

This gene has experienced strong purifying selection

What is an important difference between transmission genetics and population genetics?

Transmission genetics deals with genotypes of individuals, while population genetics deals with genotype frequencies in a population.

If a DNA sequence of the template strand (in the 3'-5' direction) reads ATG, what would be the corresponding mRNA codon (in the 5'-3' direction)?

UAC

Many models of the evolutionary consequences of mutation assume that the rate of back mutation is negligible. When is this a reasonable assumption?

When we are considering a protein where forward mutation leads to a nonfunctional protein and back mutation leads to a functional protein.

In a recent study on fitness consequences of antipredatory behavior and coloration pattern in garter snakes (Thamnophis ordinoides), the phenotype space was depicted as a three-dimensional graph where the highest points represent combinations of traits associated with the greatest fitness values. For such situations, we could use Sewall Wright's metaphor of the __________.

adaptive landscape

Genetic hitchhiking is a phenomenon in which __________.

alleles that are physically close to a locus under selection may change frequencies because of the linkage to a selected allele

Suppose that in wild rose plants, the A locus controls pigmentation of the flower petals. The A allele (for red flower coloration) is completely dominant to the a allele (for pale pink flower coloration). If purebred red-flowered plants were crossed with purebred pink-flowered plants, and their heterozygous offspring (the F1 generation) were grown so that such hybrids might be crossed among themselves, which of the following flower phenotypes might you expect in the F2 generation?

both red and pale pink roses (in a ratio of 3:1, respectively)

Gene expression in eukaryotes is strongly influenced by the local structure of the chromosome. In which of the following regions of a DNA molecule would you expect to find the highest levels of gene expression?

decondensed chromatin

One of the important facts learned from experiments in molecular genetics is that most amino acids can be encoded by more than one nucleotide triplet. For this reason, we say that the genetic code is __________.

degenerate

A mutation resulting in deletion of a protein-coding gene will most likely have a ___________ effect on fitness.

deleterious

Which of the following statements does resolve the C-value paradox to some extent?

-Genome size variation results in part from a balance between the proliferation of transposable elements and selection for replication speed. -There is an association between C-value and cell size, which may be one of the important aspects of selection as it affects genome size -In most cases, genome size differences result largely from differences in the quantity of noncoding DNA.

Which of the following statements regarding the eukaryotic genome structure is TRUE?

-In addition to the main nuclear genome, eukaryotic genome complexity is increased with the genes of mitochondria and chloroplasts. -Most eukaryotic nuclear genomes are made up of multiple linear chromosomes. -Transposable elements make up a large portion of eukaryotic genomes.

Which of the following is True regarding recombination across genomes, including the human genome?

-Some genomes, including the human genome, have small regions prone to serving as locations of crossover, or recombination hotspots. -Species with larger genomes tend to have lower recombination rates per base pair. -Haplotype blocks in human and other genomes are bounded by recombination hotspots, which help break down linkage disequilibrium.

These statements are TRUE regarding populations that have experienced a bottleneck?

-The population size is large for much of the time, only briefly becomes small, and again grows back to a large size. -Allele frequencies tend to fluctuate more during a bottleneck than before or after it. -Allele frequencies tend to vary between populations that have been through population bottlenecks

Which of the following statements is TRUE regarding syntenic dot plots?

-They are tools for comparing the gene order of two different strains or species of bacteria. -They provide us with a picture of the genomic reorganizations that have occurred. -They plot gene position in the clockwise direction beginning at the origin of DNA replication (ORI).

When a gene is first acquired by horizontal transfer, it will have a GC content and codon usage pattern characteristic of the species from which it was received. However, over time, different evolutionary processes drive GC content and codon usage toward patterns characteristic of the recipient species. Which of the following does facilitate that change over time?

-mutuation -gene conversion -natural selection

In selection experiments on quantitative traits, we often measure a value of the response to selection (R). What is R equal to?

(h^2)(s)

Which of the following is TRUE regarding the quantitative genetics study done by Steve Franks and his colleagues on a Brassica rapa population in the wilderness of southern California?

-Franks and his colleagues were able to measure both heritability and response to selection values in this natural population -The ability of plant species to respond will depend on whether there is a sufficient genetic variation, as well as strong selection, for traits such as reproductive timing. -This study has implications for global warming since it may teach us how plants will respond to ongoing changes in temperature and precipitation

Which of the following was found in the genome of the severe acute respiratory syndrome (SARS) coronavirus, which was responsible for an epidemic in 2002-2003?

-Gene segments for the replicase region -gene segment for structural proteins -a single linear chromosome

In both prokaryotes and eukaryotes, when we look at the protein-coding regions within a genome, we observe the codon usage bias, in which some codons occur more frequently than others yet specify the same amino acid. Which of the following is a possible explanation of this phenomenon?

A codon for which complementary tRNAs are common can be translated more quickly than a codon for which complementary tRNAs are rare

Consider three loci experiencing different selective conditions. Assuming the same initial number of gene copies and constant population size, which locus will have the longest time to coalescence?

A locus under balancing selection

Suppose that you collected genotype frequency data from a natural population. If you found that the expected genotype frequencies differed significantly from your observed genotype frequencies, which of the following could you conclude?

At least one evolutionary process is operating in this population.

In their experiment in 1943 using E. coli, Salvador Luria and Max Delbrück tested two alternative hypotheses. The random mutation hypothesis and the acquired inherited resistance hypothesis make different predictions about the distribution of resistant mutants that will be observed upon exposure to bacteriophage (viruses that can infect and kill E. coli). Which of the following predictions, if proven, would support the acquired inherited resistance hypothesis?

At the time of exposure to the phage, all E. coli cells will be phage-sensitive. The process of exposure to the phage will induce phage resistance in a small fraction of the bacterial cells.

Which of the following is TRUE regarding the difference between a DNA molecule and an RNA molecule?

DNA is a double-stranded molecule, whereas RNA is a single-stranded molecule.

For many years in the United Kingdom, people with urinary tract infections have been treated with sulfonamide antibiotics. These antibiotics used to be very effective against the common pathogen of the urinary tract, E. coli, but in the late 1990s, increased resistance among the E. coli strains was documented. In the meantime, worrisome side effects of these drugs were documented as well, so doctors curtailed their use. Which of the following statements is TRUE about the evolution of resistance to the sulfonamides in the last decade?

Despite the infrequent use of sulfonamides, there was little reduction in frequency of resistance among the bacteria.

Which of the following is a definition of evolution from the perspective of population genetics?

Genotype frequencies change over time

Which of the following correctly depicts the order in which whole genomes were first sequenced for the listed taxa?

Haemophilus influenzae, then Saccharomyces cerevisiae, then Caenorhabditis elegans, then Homo sapiens