chapter 15 learning curve

In the absence of purifying and positive selection, the ratio of the rate of synonymous substitutions to the rate of nonsynonymous substitutions should be near

1

Suppose the size of a population of crickets is 1,500. According to genetic drift theory, what is the probability that a newly arisen neutral mutation will become fixed in this population?

1/3,000

A gene family that codes for various hormone receptors has been accumulating nucleotide substitutions at a rate of 0.4 per million years. On average, there have been 60 substitutions between the common ancestor of this gene family and each of the various living forms of this gene. Based on these figures, this hormone receptor gene family likely originated _______ million years ago.

150

If the effective rate of reproduction of an asexual lineage is 6 per year, what would be the effective rate of reproduction of a sexual lineage that was identical to the asexual lineage in every way except reproduction type?

3

Two species of rodents that diverged 15 million years ago have accumulated an estimated 20 nucleotide differences in a gene. Both of these species produce one generation each year. Suppose sequence analysis of offspring and parents shows that the actual total mutation rate is 1.5 per million generations. Assuming that all mutations are either deleterious or neutral, approximately what percentage of mutations are neutral?

44

Suppose that the size of a population of midges is 20 million and that the mutation rate of a gene is 1.5 per million midges per generation. How many new mutations of this gene should appear in the next generation of the population?

60

Which genetic effect is an example of heterometry?

A gene whose expression causes legs to become shorter and wider

_______ is most likely to lead to an increase in the rate that pseudogenes accumulate in a population.

An increased rate of gene duplication

Which correctly ranks organisms from most to least in terms of the expected amount of coding DNA in their genomes?

Bacterium, vertebrate, Drosophila, single-celled eukaryote,

Refer to the table. Lignin is a macromolecule that provides support to plant and tree stems. Two genes involved in lignin biosynthesis, C4H and CAD, were studied in populations of two different tree species. As shown in the table, changes between the two species (substitutions) in these genes were classified as synonymous or nonsynonymous. (Click image to enlarge.) what can be inferred from these data?

Both C4H and CAD genes are under purifying selection.

Refer to the figure. Members of the JAK family of nonreceptor kinases are involved in signaling pathways. The four gene copies JAK1, JAK2, JAK3, and TYK2 are found in humans, mice, chickens, and fishes, as shown in this phylogenetic tree. (Click image to enlarge.) According to this phylogenetic gene tree, which statement is true about mouse Jak1 and mouse Tyk2?

Both copies exist because of a gene duplication that took place prior to the split between humans and mice.

Refer to the table summarizing codons for selected amino acids. (Click image to enlarge.) Starting from TTA, a change to which codon would most likely be a neutral one?

CTT

The odd skipped gene in Drosophila received its name because mutations in that gene often lead to embryos missing the odd-numbered segments. Based on this information, what is the most likely class of gene to which odd skipped would belong?

Pair rule

Sexual reproduction is least likely to evolve when

DNA repair is exceptionally good.

A yeast mostly selfs but very occasionally engages in sexual reproduction. Which change would most likely reduce the rate of Muller's ratchet?

Decreasing the mutation rate

Which statement about genomes is true?

Due to the role noncoding DNA plays in genome evolution, the variation in genome size between organisms is greater than the variation in the number of genes in those organisms.

A gene in fruit flies is found to be a gap gene that is expressed in the abdomen. What is the most likely consequence of reducing its expression using RNA interference?

Many abdominal segments will be missing.

BMP4 and Gremlin are both involved in whether the feet in birds are webbed. What is the relationship between BMP4 and Gremlin?

Gremlin inhibits BMP4.

What accounts for the giraffe's long neck as compared with the necks of other vertebrates?

Heterochronic growth

Refer to the figure showing a phylogenetic tree of the engrailed gene family. (Click image to enlarge.) Which gene is the same evolutionary distance from chicken En1 as is chicken En2?

Human En2

A and B are loci on the same chromosome in a plant population. Some alleles at A work well together with particular alleles at B, but not with other alleles at B. Given that selection is operating on combinations of alleles, which would you expect to most likely evolve?

Increased selfing

A mutation causes a change in the physical properties of an enzyme in a bird. At sea level (under normal oxygen concentrations), this change has no effect on the survival or reproduction of a bird. At high elevations where there is limited oxygen, bearers of this mutation have an increased rate of survival. What sentence best describes this mutation?

It is neutral at sea level, but not at high elevations.

A normally asexual lineage experiences sexual reproduction, and as a result, the amount of genetic variation increases and deleterious mutations are purged from the lineage. This purging is a reversal of

Muller's ratchet.

A fly embryo is already far along in its development, to the point that the segment polarity and Hox genes have been turned on. What would be the most likely effect of repressing expression of maternal effect genes that turn on gap genes that are normally expressed in the head?

Nothing; their normal time of action has already passed.

What is the difference between ducks and chickens with respect to Gremlin?

The Gremlin gene is expressed in the webbing cells of ducks, but not chickens.

Lateral gene transfer is occurring between strains of bacteria that are found together in contaminated meat. As a result of this, which is most likely to occur?

Phylogenetic patterns across different genes will become more different.

Which manipulation would most likely result in increasing the webbing of a chicken's foot?

Providing more Gremlin

The lab, the pb, and the Dfd Hox genes are all expressed in the heads of developing Drosophila. The region where lab is expressed is anterior to the region where pb is expressed, which, in turn, is anterior to the region where Dfd is expressed. Which result would be most likely?

The chromosomal location of Dfd would be nearest that of pb on the chromosome in flies.

Refer to the table. In a series of experiments on chick embryos, researchers applied different concentrations of BMP4 (in standard units) to the embryo's beak growth region in chickens of different populations (A-D). They measured the size of the beak cartilage at a later stage of development. The table shows the extent of growth (increase in size in millimeters) between the two time points for different concentrations of BMP4. Note that the source of BMP4 is identical for all treatments. (Click image to enlarge.) Which statement about the role of BMP4 in beak development is most likely correct?

The differences between populations are heterometric.

Which scenario would be the least likely result of gene duplication?

The gene produces less of its product than it did before duplication.

Consider the case of in vitro evolution used to generate RNA molecules with ligase activity. If the researchers used a DNA polymerase in the PCR that was more accurate, which result would be most likely?

The mutation rate would be lower.

A nematode has a gene that is not found in any closely related nematode species. A similar gene, however, is found in a variety of bacteria. What is the most likely explanation for this?

The nematode acquired the gene via lateral transfer.

Mutations in the third position of codons are the least likely to affect the amino acid sequence. Mutations in the second position are most likely to change the amino acid sequence, while first-position mutations are intermediate. Based on what you know about molecular evolution, predict the relative rates of evolution for first-, second-, and third-position codon nucleotides, from highest to lowest.

Third, first, second

If a gene is a Hox gene, what is its most likely normal function?

To instruct a segment regarding what organ to form

A gene in fruit flies is found to be a segment polarity gene that is expressed in the head segments. What is the most likely consequence of reducing its expression using RNA interference?

The posterior structures of an abdominal segment will be missing.

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

There is a higher rate of nonsynonymous substitutions than of synonymous ones.

Suppose humans and chimpanzees have four copies of a gene. Mice, cows, and whales have only two copies of the gene. Birds, frogs, and crocodiles have only one copy of the gene. Which statement is most likely true about the four copies of the gene family in humans?

They are due to two gene duplications: one since humans and chimpanzees diverged from other mammals, and one since mammals diverged from other tetrapods.

Which statement about synonymous substitutions is true?

They are less likely than nonsynonymous substitutions to be influenced by natural selection.

Which statement about pseudogenes is true?

They do not affect an organism's phenotype.

What is the primary function of the products of the globin genes?

They transport oxygen.

Refer to the figure. (Click image to enlarge.) Based on the information provided in this phylogenetic gene tree, multiple gene duplication events followed by mutations have created _______ that consist(s) of JAK and TYK2 genes.

a gene family

Suppose mutations in a set of genes affected the bones of the inner ear in mice, but they did not affect other structures. The bones of the inner ear would then be acting as

a module.

There are two lineages of beetles: lineage A has four times the population size as does lineage B. Assuming that the mutation rates for a given gene are the same in the two lineages and all mutations are neutral, then we should expect the probability that any particular new mutation will be fixed in lineage A to be _______ the probability that any particular mutation will be fixed in lineage B.

a quarter of

Humans, mice, rats, chickens, and all other bony vertebrates have two groups of developmental genes. The most likely explanation for this is that these two groups of genes arose from a gene duplication event in the common ancestor of

all bony vertebrates.

Biologists use a chemical derived from a bacterium to help treat sewage waste. This is an example of

bioprospecting

Refer to the table. A study of organisms of the same species revealed that some individuals had a duplicate set of gene X, while others did not. The table summarizes the results from an analysis of three different individuals, including quantification of the protein product of gene X in each individual. (Click image to enlarge.) Following duplication of gene X in organisms B and C,

both copies in organism B retained their original function, while one copy in organism C retained its original function and one copy became a functionless pseudogene.

Refer to the figure showing a phylogenetic tree of the engrailed gene family. (Click image to enlarge.) The divergence between gene copies chicken En1 and mouse En1

did not involve a gene duplication.

Sexual reproduction often is favored in natural populations because it

enhances the elimination of deleterious mutations.

The presence of pathogens tends to _______ the evolution of sexual reproduction because _______.

favor; populations require more genetic variation to evolve defenses against pathogens

There are two lineages of beetles: lineage A has four times the population size as does lineage B. Assuming that the mutation rates for a given gene are the same in the two lineages and all mutations are neutral, then we should expect _______ of new mutations each generation in lineage A as in lineage B.

four times the number

A mutation leads to death of developing Drosophila flies as early embryos because the abdomen and part of the thorax are missing. This mutation is recessive, and its phenotype is due solely to the genotype of the individual possessing it. This is most likely a mutation in a _______ gene.

gap

Developmental modules based on a common set of genetic instructions can evolve separately in a lineage because _______ control how the toolkit is used.

genetic switches

Knowledge of sodium channel structure in puffer fish benefits humans by

helping scientists understand protein structure-function relationships that can be applied to human diseases involving mutations in proteins.

A change comes about via a change in the relative timing of different developmental processes. This is called

heterochrony

Suppose a crab species has short appendages, while a related species has long appendages, and this difference resulted from the level of expression of a signaling molecule. This would be a case of

heterometry

In one species of beetle, a transcription factor is expressed in the first and second thoracic segments, whereas in a related species, the transcription factor is expressed only in the first thoracic segment. This difference, one of _______, results in altered coloration patterns.

heterotopy

Suppose biologists working with cactus finches wanted these birds to develop beaks like large ground finches via changes in the expression of key genes. Assuming that the expression changes took place at the appropriate time and place, the best course of action would be to _______ the usual expression of BMP4 and _______ the usual expression of CaM.

increase; decrease

One of the species of Darwin's finches that previously lived on a mixed diet now feeds mainly on large, hard seeds. Based on the currently existing birds, one would expect _______ BMP4 expression and _______ in CaM expression in these birds.

increased; no change

The rate of fixation of neutral mutations, m, is

independent of population size.

Refer to the figure showing a phylogenetic tree of the engrailed gene family. (Click image to enlarge.) The divergence between gene copies zebrafish En2a and zebrafish En2b

involved a single duplication that occurred after the duplication that led to human En1 and human En2.

Refer to the figure showing a phylogenetic tree of the engrailed gene family. (Click image to enlarge.) The divergence between gene copies zebrafish En1b and zebrafish En2b

involved a single duplication that occurred at the same time as the duplication that led to human En1 and human En2.

A mutation in a gene causes little or no effect on the viability of its carriers, even when in a homozygous state. Females that are homozygous for this mutation, however, never produce viable offspring, because their progeny (regardless of genotype) all die early in embryonic development. Based on this information, this gene is most likely a _______ gene.

maternal effect

Cytoplasmic determinants are most often the product of _______ genes.

maternal effect

In Drosophila early development, the _______ genes are primarily responsible for establishing the dorsal-ventral body axis.

maternal effect

Processes occurring in the developing liver are largely independent of those in the developing brain. This is an example of

modularity

As the amount of lateral gene transfer in a taxon increases, it becomes _______ difficult to infer relationships among lineages within the taxon, and ability to infer species boundaries ____

more; becomes more difficult

As the amount of lateral gene transfer in a taxon increases, it becomes _______ difficult to infer relationships among lineages within the taxon, and ability to infer species boundaries _______.

more; becomes more difficult

The central hypothesis of the neutral theory asserts that

most variability observed in a population does not affect the survivability of organisms in the population

Consider the case of in vitro evolution used to generate RNA molecules with ligase activity. If the researchers repeated the investigation using a higher-fidelity DNA polymerase during PCR, the _______ would most likely be _______.

mutation rate; lower

Early development in Drosophila is unusual because

no cytoplasmic division occurs.

A missense substitution is the same as a _______ substitution.

nonsynonymous

Refer to the table summarizing codons for selected amino acids. (Click image to enlarge.) Starting from TTT, how many single nucleotide substitutions at any of the three positions are synonymous?

one

Bacteria in the ocean after an oil spill evolve new enzymatic functions to increase the rate at which they can detoxify the oil. Most likely the genes encoding these enzymes will be under _______ selection and will have an increased number of _______ substitutions.

positive; nonsynonymous

A Galápagos finch has an elongated beak. It would most likely use this beak for _______ and have _______ CaM levels.

probing; high

The primary use of in vitro evolution is to

produce new molecules.

The population size hypothesis for genome size proposes that _______ selection on noncoding DNA is _______ effective in large populations, and thus species with large populations should have _______ genomes than those with smaller populations.

purifying; more; smaller

Refer to the figure showing a phylogenetic tree of the engrailed gene family. (Click image to enlarge.) The divergence between gene copies lamprey En and zebrafish En2b

required at least two gene duplications.

Pair rule genes most directly activate _______ genes. They are most directly regulated by _______ genes.

segment polarity; gap

Consider the great diversity of genome size among organisms. As genome size increases, the relative proportion of noncoding DNA

steadily increases.

Respiratory syncytial virus (RSV) is a human-specific virus that causes infections of the lungs and respiratory tract and commonly infects infants and young children. In the young and immunosuppressed it can cause bronchiolitis and pneumonia. There are multiple strains of RSV, which has made it difficult to develop a protective vaccine. To better understand the evolution of different RSV strains, scientists should

study cross-species transmission

Some puffer fishes possess a chemical called _______ that acts as a toxin by blocking _______.

tetrodotoxin; sodium channels

Certain developmental mechanisms have been conserved over long periods during the evolution of multicellular organisms. These mechanisms are controlled by conserved specific DNA sequences known as

the genetic toolkit.

There are two lineages of beetles: lineage A has four times the population size as lineage B. Assuming that the mutation rates for a given gene are the same in the two lineages and all mutations are neutral, then we should expect the long-term substitution rate of mutations in lineage A to be _______ the long-term substitution rate of mutations in lineage B.

the same as

Noncoding DNA takes up a small proportion of the genomes of _______, which tend to have _______ population sizes.

unicellular organisms; large

A researcher is interested in determining what nucleotide substitutions in TTX-resistant puffer fish sodium channels are critical for resistance. To facilitate her research, she uses PCR-based in vitro evolution to generate altered versions of the puffer fish sodium channels. To increase the possibility of generating genes that are not resistant to TTX, the researcher should

use a DNA polymerase that has low fidelity.