Q1 Explain the function of retroposition (retroduplication) in gene duplication. Describe the cellular mechanism used for this method of gene duplication, and the manner in which these typically nonfunctional pseudogenes can become active, functional genes.

Q2 Explain the relationship between genotype and phenotype with respect to the ability in humans to taste phenylthiocarbamide (PTC), and the correlation of this ability to the type 2 taste receptors (TAS2Rs). How does the conformation of the TASTRs receptors affect the ability to sense the bitter taste of phenylthiocarbamide?

Q3 Honey bees demonstrate morphological variations depending on the division of labor among the various morphotypes. Worker bees are quite different morphologically from the queens, who are different from the drones. Can you comment on which type of variation this might be, and the basis behind this variation?

Q4 What are reaction norms, and why do they matter? Draw your own reaction norm for mood as a function of the temperature outside. What kind of variation allows reaction norms to evolve?

Q5 Organisms that exhibit different phenotypes in different environments are said to exhibit pheno- typic plasticity. Using the tobacco hornworm, Manduca sexta, studied by Suzuki and Nijhout, describe the experiments done to illustrate the dependence of color on temperature. Be sure to explain the importance of using reaction norms in this type of study.

Q6 Chromosome inversions often have a major impact on evolutionary processes. Describe the process and causes whereby chromosome inversions occur. Describe the effect chromosome in- versions have on the process of meiosis, and provide a specific example of chromosome inversions discussed in the text.

Q7 Compare and contrast the evolutionary roles of point mutations, chromosome inversions, gene duplications, and polyploidization.
Q1: Retroduplication or retroposition is a type of gene duplication that occurs when a gene is first transcribed into mRNA and then reverse transcribed back into DNA, which is then integrated back into the genome at a new location, creating a new gene copy. This process is mediated by retrotransposons, which are mobile genetic elements that can move within a genome via a copy-and-paste mechanism.

The resulting duplicated genes are often initially nonfunctional, as they may lack regulatory sequences or contain mutations that disrupt the open reading frame. However, they can subsequently acquire new functions through the process of neofunctionalization, subfunctionalization, or exaptation. Neofunctionalization occurs when one copy of the duplicated gene acquires a new function that was not present in the ancestral gene, while the other copy retains the original function. Subfunctionalization occurs when the duplicated genes diverge in function, such that each copy retains only a subset of the ancestral gene’s functions. Exaptation occurs when a duplicated gene acquires a new function that was not present in the ancestral gene, but that is related to its original function.

Q2: The ability to taste PTC is controlled by a single gene, TAS2R38, which encodes a bitter taste receptor protein. TAS2R38 exists in two common allelic forms, PAV and AVI, which differ by three amino acid substitutions. Individuals who are homozygous for the PAV allele are highly sensitive to the bitter taste of PTC, while those who are homozygous for the AVI allele are less sensitive. Heterozygotes have intermediate sensitivity.

The genotype of an individual (i.e., their specific TAS2R38 alleles) determines their ability to taste PTC. The phenotype (i.e., the actual ability to taste PTC) is a result of the interaction between the genotype and the environment, as different levels of PTC in foods can affect an individual’s ability to detect it. The conformation of the TAS2R38 receptor affects its ability to bind to PTC and trigger a bitter taste sensation.

Q3: The morphological variations among honeybee castes are an example of polyphenism, where distinct phenotypes are produced by a single genotype in response to different environmental cues. The basis for this variation lies in differential gene expression patterns during development, which are controlled by environmental and hormonal cues. For example, queen bees are fed a special diet that includes royal jelly, which triggers the expression of genes involved in reproductive development and suppresses the expression of worker-specific genes.

Q4: Reaction norms are patterns of phenotypic expression that vary with environmental conditions. They matter because they reflect the ability of organisms to respond adaptively to changing environmental conditions. Reaction norms can be visualized as a graph of phenotypic values (e.g., mood) plotted against an environmental variable (e.g., temperature).

The shape of a reaction norm can evolve via genetic variation that affects the sensitivity or slope of the response to an environmental variable. For example, if individuals with a higher threshold for experiencing negative mood at low temperatures have higher fitness, then the average threshold for negative mood will increase in the population over time.

Q5: Suzuki and Nijhout conducted experiments on the tobacco hornworm to investigate how temperature affects the expression of the black coloration in their bodies. They found that hornworms reared at lower temperatures had darker bodies due to increased melanin production, while those reared at higher temperatures had lighter bodies due to decreased melanin production.

By plotting the hornworm’s body color as a function of rearing temperature, they were able to generate a reaction norm that illustrated how the phenotype varied with the environment. This allowed them to quantify the extent of phenotypic plasticity and determine the genetic and physiological mechanisms underlying the observed response. Using reaction norms is important because it allows researchers to study the degree of plasticity in a phenotype, as well as the extent to which genetic and environmental factors interact to produce phenotypic variation.

Q6: Chromosome inversions occur when a segment of a chromosome breaks off and reattaches to the same chromosome but in a reversed orientation. This can create a new gene order and alter the expression of genes located within the inverted segment. Chromosome inversions can arise spontaneously due to errors in meiosis or other genetic processes. They can also be induced by exposure to radiation or chemicals.

The effects of chromosome inversions on meiosis depend on the orientation of the inverted segment. Inverted heterozygotes may experience reduced recombination between the inverted and non-inverted chromosomes, leading to reduced genetic diversity in offspring. Additionally, meiotic crossing over within the inverted region can lead to the formation of chromosomal abnormalities such as deletions or duplications.

An example of chromosome inversion discussed in the text is the inversion polymorphism found in Drosophila melanogaster. In this species, two alternative arrangements of the X chromosome exist in natural populations, known as the standard (ST) and inverted (INV) arrangements. These arrangements have different gene orders and can affect the expression of genes involved in traits such as body size, wing shape, and fertility.

Q7: Point mutations, chromosome inversions, gene duplications, and polyploidization are all mechanisms that contribute to genetic variation and evolution.

Point mutations are small changes in DNA sequence that can alter the function of a gene. They can arise spontaneously or be induced by environmental factors such as radiation or chemicals.

Chromosome inversions alter the gene order and expression of genes located within the inverted segment. They can affect recombination rates and create genetic polymorphisms within a population.

Gene duplications create additional copies of a gene, which can then diverge in function through neofunctionalization or subfunctionalization. Gene duplications can contribute to the evolution of new traits and functions.

Polyploidization is the process of genome doubling, which can occur in plants and some animals. Polyploidization can increase genetic diversity and facilitate the evolution of new traits and functions.

While all of these mechanisms contribute to genetic variation and evolution, they differ in their magnitude and effects on the genome. Point mutations and small-scale duplications and deletions are relatively common and have modest effects on gene function. In contrast, chromosome inversions and polyploidization are less common but can have major impacts on gene expression and genome structure.