Chapter 20 Genetics KSU

A path of gene duplication and mutation that produces paralogs with complementary functions.

Subfunctionalization

The principles of ______, ______, and ______ must all apply for evolution to take place through natural selection.

variation, heredity, and selection

Following a duplication event, describe four possible fates of the duplicated gene and its ancestral gene.

1. Gene is inactivated (pseudogenization) 2. Evolution of new function (neofunctionalization) 3. Function is divided between genes (subfunctionalization)

Walk through the steps of the McDonald-Kreitman method for detecting positive selection. Explain why the data in Table 20-3 shows that positive selection has occurred at the alcohol dehydrogenase locus.

1. The DNA sequence of a gene is obtained from a number of separate individuals from each of two species. The fixed nucleotide differences between species are then classified into nonsynonymous (a in the table below) and synonymous (b in the table below) differences. 2. The nucleotide differences among individuals within each species (polymorphisms) are then tabulated, and classified as either those that result in amino acid changes (nonsynonymous; c) or those that do not change the amino acid (synonymous; d). 3. If the divergence between the species is purely the result of random genetic drift, then we expect a/b to be equal to c/d. If, on the other hand, there has been selective divergence, there should be an excess of fixed nonsynonymous differences, and so a/b should be greater than c/d.

Identify four mechanisms that can expand the number of genes, parts of genomes, and entire genomes in an organism.

1. The formation of polyploids (individuals with more than two chromosome sets) 2. Gene duplication 3. Transposition (which can generate gene duplications 4. Retrotransposition

Select the statements that explain why duplication is a driving force for evolution and the generation of new genes (possibly multiple correct). A. Duplicated genes provide extra copies of DNA that are not constrained by an essential function. B. Duplication of a gene segment always results in novel gene functions. C. Genes duplicate and then diverge from the original sequence to create novel genes. D. Phenotypic variations can occur when random fixed mutations are introduced into a new chromosomal environment.

A. Duplicated genes provide extra copies of DNA that are not constrained by an essential function. C. Genes duplicate and then diverge from the original sequence to create novel genes. D. Phenotypic variations can occur when random fixed mutations are introduced into a new chromosomal environment.

What is the significance of the Dozhansky-Muller model? A. It explains how hybrid incompatibilities between species can evolve within species. B. It explains why purifying selection reduces genetic variation and preserves DNA over time. C. It explains why there is no proportionate relation between DNA change and functional change. D. It explains how reproductive isolating barriers can prevent gene flow between species.

A. It explains how hybrid incompatibilities between species can evolve within species.

Which is one of the key facets of the evolutionary process? A. Natural selection acts on whichever variation is available. B. Many genomes are the result of ancestral whole genome duplication. C. Most mutations are functionally neutral and fixed by genetic drift. D. Cis‑acting regulatory sequences play a critical role in the evolution of gene expression.

A. Natural selection acts on whichever variation is available.

Choose the correct statements about proteins and evolution (possibly multiple correct). A. The tertiary structure of a protein is more conserved than the primary structure. B. Orthologs are derived from a common ancestor but often have different functions. C. Percent identity for a random alignment of two nucleic acids is likely to be lower than the percent identity for an equal‑length random alignment of two polypeptide segments. D. Two proteins that have similar tertiary structures are said to be homologous. E. Lupine leghemoglobin and human α‑hemoglobin are only about 16% identical. This is an example of divergent evolution.

A. The tertiary structure of a protein is more conserved than the primary structure. E. Lupine leghemoglobin and human α‑hemoglobin are only about 16% identical. This is an example of divergent evolution.

How do evolutionary changes in cis‑acting regulatory sequences impact the evolution of gene expression? A. They circumvent the pleiotropic effects of mutations in the coding sequences of genes that have multiple roles in development. B. The allow for only advantageous mutations to occur within the genome. C. They allow duplicate genes to evolve into new functions. D. They maintain the proportional relationship between DNA change and change in function.

A. They circumvent the pleiotropic effects of mutations in the coding sequences of genes that have multiple roles in development.

Which of the following does not expand the number of genes or parts of genomes in an organism? A. neofunctionalization B. retrotransposition C. transposition D. gene duplication

A. neofunctionalization

Which reproductive isolating barrier can involve habitat isolation or temporal isolation? A. premating B. postzygotic C. infertility D. postmating

A. premating

In the evolutionary sense, some heritable feature of an individual's phenotype that improves its chances of survival and reproduction in the existing environment.

Adaptation

Using Figure 20-10, explain how gene duplication played a role in the evolution of placental mammals.

Adult hemoglobin is a tetramer consisting of two α polypeptide chains and two β chains, each with its bound heme molecule. The gene encoding the adult α chain is on chromosome 16, and the gene encoding the β chain is on chromosome 11. Both chromosomes have a pseudogene that has accumulated random, inactivating mutations.

Describe the evidence that led Tony Allison to infer that the HbS mutation has arisen independently multiple times.

Allison also noted a high incidence of HbS outside of Africa, including in Italy, Greece, and India. Other blood-type markers did not indicate strong genetic relationships among these populations. Rather, Allison observed that these were also areas with a high incidence of malaria.

With the aid of Figure 20-12, describe the role of whole genome duplication in the evolution of Saccharomyces cerevisiae.

Apparently, in the course of the evolution of Saccharomyces, the Kluyveromyces-like ancestral genome doubled, and so there were two sets, each containing the whole genome. After doubling occurred, many gene copies were lost from one set or the other, and the remaining sets were rearranged, resulting in the present Saccharomyces genome

The relative fitness of a new variant depends on the immediate selective conditions. Which is an example of relative fitness? A. Black rock pocket mice migrate into the sandy‑colored terrain to mate. B. Black rock pocket mice are a result of a new variant that allowed them to blend in with the lava outcrops. C. Black rock pocket mice become extinct due to lack of food within the lava outcrops. D. Black rock pocket mice are unable to mate with sandy‑colored mice due to habitat isolation.

B. Black rock pocket mice are a result of a new variant that allowed them to blend in with the lava outcrops.

How did the neutral theory impact the views of evolution? A. It shifted the views of evolution to state that it is only caused by adaptation. B. It shifted the views of evolution to include that evolution can occur without natural selection. C. It shifted the views of evolution to the idea that mutations can be beneficial. D. It shifted the views of evolution to the notion that it is not caused by natural selection.

B. It shifted the views of evolution to include that evolution can occur without natural selection.

Which is not a principle of natural selection? A. principle of selection B. principle of migration C. principle of variation D. principle of heredity

B. principle of migration

Which evolutionary outcome causes the duplicated gene to be invisible to natural selection? A. genetic drift B. pseudogene C. subfunctionalization D. neofunctionalization

B. pseudogene

Groups of individuals that actually or potentially interbreed with each other and that are reproductively isolated from other such groups.

Biological species concept

Which statements address why polyploidy is more common in plants than in animals (possibly multiple correct)? A. Polyploids only arise from gene doubling, which does not occur in animals. B. Polyploid plants are always fertile, whereas polyploid animals are sterile. C. The developmental process for plants is less complex than animals. D. Genome duplications, which result in polyploidy in plants, do not occur in animals. E. Behavioral isolation mechanisms prevent different animal species from interbreeding.

C. The developmental process for plants is less complex than animals. E. Behavioral isolation mechanisms prevent different animal species from interbreeding.

How does an increase in ploidy contribute to evolution? A. New species always arise when a haploid gamete fuses with a diploid gamete. B. All copies of the genes found in polyploids gain a new function. C. Sterile allopolyploids commonly pass down novel genes that evolve. D. New species can arise from crosses between two diploids followed by chromosome doubling.

D. New species can arise from crosses between two diploids followed by chromosome doubling.

Which two factors drive adaptation? A. habitat and temporal isolation B. neosubfunctionalization and pseudogenization C. gene duplication and retrotransposition D. survival and reproduction

D. survival and reproduction

Purifying selection is a pervasive aspect of natural selection that reduces genetic variation and preserves ______ and ______ over eons of time.

DNA and protein sequences

It is possible to detect signatures of adaptive evolution at the level of ______.

DNA sequences

_______ and ______ proposed a new explanation to account for the phenomenon of evolution. They understood that the population of a given species at a given time includes individuals of varying characteristics. They realized that the population of succeeding generations will contain a higher frequency of those types that most successfully survive and reproduce under the existing environmental conditions. Thus, the frequencies of various types within the species will change over time.

Darwin and Wallace

Explains the evolution of genetic incompatibilities between loci that result in hybrid sterility or hybrid inviability.

Dobzhansky-Muller model

_______, the change in populations or species over time, is the conversion of heritable variation between individuals within populations into heritable differences between populations in time and in space by population genetic mechanisms.

Evolution

Reproductive success, or the number of offspring that an allele, genotype, and/or individual contributes to the next generation.

Fitness

The duplication of genes or segments of DNA through misreplication of DNA.

Gene duplication

Give an example and describe how gene duplication contributes to postzygotic reproductive isolation.

Gene duplication can lead to the loss of one copy of the gene. If one copy of a duplicated gene is lost in one species, and the other copy of a duplicated gene is lost in the other species, hybrid progeny could result that completely lack a functional copy of the gene.

A set of genes in one genome, all descended from the same ancestral gene.

Gene families

Draw a diagram and explain how the Dobzhansky-Muller model works.

Genetic incompatibilities between two or more loci underlie hybrid sterility and inviability across a number of taxonomic groups.

State the specific mutation that has occurred that distinguishes HbA from HbS, and the resulting amino acid change in hemoglobin.

HbS was determined to be caused by a single point mutation (CTC → CAC) in the glutamic acid codon encoding the sixth amino acid of the β-globin subunit within the hemoglobin protein.

Using examples, explain how adaptive changes in morphology can result from mutations to gene regulatory sequences that result in either a gain or loss of gene expression.

If there is no selective pressure to maintain a character, it can be lost over time. But some losses are beneficial because they facilitate some change in lifestyle. Hind limbs, for example, have been lost many times in vertebrates—in snakes, lizards, whales, and manatees—as these organisms adapted to different habitats and means of locomotion.

Explain what it means that natural selection acts on whatever variation is available.

If there is variation, it is likely that one of the options is advantageous. Over time, natural selection will select whichever variation is advantageous.

Explain why the frequency of the HbS allele is declining among African Americans.

In African Americans, the frequency of HbS is declining because there is selection against the allele in the absence of malaria in North America.

Using the Hox genes as an example, explain the hypothesis that whole genome duplication events facilitate the evolution of novel traits.

In vertebrates, all four Hox clusters have been retained from the two rounds of ancient WGD, and up to eight Hox gene clusters are retained from the additional round of WGD in teleost fish. The retention of duplicate genes over long evolutionary times implies that they are maintained by natural selection and not by drift. Nonetheless, the function of most duplicate genes has not been directly tested. Thus, the evidence in support of the hypothesis that whole genome duplications have facilitated the evolution of novel traits remains mostly correlative.

A trait that allows a lineage to take advantage of a novel environment and rapidly diversify.

Key innovation

Compare and contrast random genetic drift and natural selection.

Most, but not all, mutations that are invariant or fixed between species are neutral or nearly neutral and any differences between species at such sites in DNA evolve by chance due to random genetic drift. So random genetic drift happens by chance while natural selection happens due to natural pressures selecting the best traits.

Contrast the effects of mutations in a cis-acting regulatory sequence and a coding sequence of a gene such as the Drosophila yellow gene.

Mutations in cis-acting regulatory sequence will change part of the organism. Changing the coding sequence of a gene will change the entire organism. Changes in cis-acting regulatory sequences play a critical role in the evolution of body form. Changes in the regulatory sequence rather than the coding sequence of this toolkit gene exemplify an important way in which evolution can occur. A mutation in the coding sequence that alters Yellow protein activity would alter Yellow activity in all tissues, which might be detrimental for fitness. However, because individual cis-acting regulatory sequences usually affect gene expression in only one tissue or cell type or at one developmental timepoint, mutations in these sequences provide a mechanism for altering gene expression at a specific time or a specific location while preserving the role of protein products in other developmental processes.

The differential rate of reproduction of different types in a population as the result of different physiological, anatomical, or behavioral characteristics of the types.

Natural selection

Describe how the sickle-cell mutation is under balancing selection in places where malaria is endemic.

Natural selection operating in favor of AS individuals is balanced by natural selection operating against AA individuals susceptible to malaria and SS individuals who would succumb to sickle-cell anemia. In other words, the heterozygote has an advantage over either of the homozygotes.

The evolution of a new function by a gene.

Neofunctionalization

Nucleotide-pair substitution within a protein-coding region that leads to the replacement of one amino acid by another amino acid.

Nonsynonymous substitution or missense mutation or nonsynonymous mutation

A reproductive barrier that acts after mating between species has occurred, but before hybrid zygotes have formed.

Postmating prezygotic isolating barriers

A reproductive barrier between species that acts after hybrid zygotes have formed.

Postzygotic isolating barriers

A reproductive barrier that prevents mating between species.

Premating isolating barriers

Identify the types of reproductive isolating barriers that can exist premating, postmating but prezygotic, and postzygotic.

Premating isolating barriers act before mating occurs. These barriers may involve differences in where species breed (habitat isolation) or when species breed (temporal isolation). Postmating, prezygotic isolating barriers can prevent the formation of hybrid zygotes. There may be incompatibilities between the mating structures of the two species (mechanical isolation), the mating behaviors of the two species (copulatory isolation), or between the sperm and eggs (gametic isolation). Hybrids may be formed but have reduced fitness (viability or fertility) due to postzygotic isolating barriers. In many cases, hybrid inviability or sterility is independent of the environment (intrinsic isolation). In other cases, hybrids are viable and fertile when created in the laboratory or a zoo, but in nature they suffer reduced viability or fertility that is dependent upon environmental conditions (extrinsic isolation).

A mutationally inactive gene for which no functional counterpart exists in wild-type populations.

Pseudogene

_______ selection is a pervasive aspect of natural selection that reduces genetic variation and preserves DNA and protein sequences over eons of time.

Purifying

Any mechanism that reduces gene flow between populations or species.

Reproductive isolating barrier

A reduction in the amount of gene flow between populations or species.

Reproductive isolation

State the focus of the biological species concept.

Reproductive isolation.

A mechanism of transposition characterized by the reverse flow of information from RNA to DNA.

Retrotransposition

Any sequence that enhances its own transmission to the next generation at the expense of other sequences in the genome, even if it has no positive or negative effects on organismal fitness.

Selfish genetic element

A change to the sequence of a codon that does not change the encoded amino acid.

Synonymous substitution or synonymous mutation or silent mutation

Give an example and describe how genetic conflicts contribute to postzygotic reproductive isolation.

There can be genetic conflict between the hsot and its pathogens or parasites. A type of genomic parasite is a selfish genetic element, which is an allele that violates the Mendelian rules of segregation and is transmitted to more than 50 percent of the gametes. Such alleles can rapidly increase in frequency in a population, although they are often are associated with reductions in fertility. In all of these cases, the host is engaged in an evolutionary arms race, in which the pathogen or parasite is evolving rapidly to escape the host's defense mechanism, and the host is evolving rapidly in response to reductions in fitness caused by the pathogen or parasite.

Explain how variation, heredity, and selection are critical for evolution to take place.

There must be different traits (variation) and some traits must be advantageous (selection). These traits must be passed on (heredity) for progress/evolution to occur.

Explain why the three proteins shown in Figure 20-7 have different substitution rates. Also, describe how this data illustrates a paradox that confronted scientists.

They observed that many substitutions were of one amino acid for another with similar properties. They concluded that most amino acid substitutions were "neutral" or "nearly neutral" and did not change the function of a protein whatsoever. At the time, this was confusing because they didn't believe there was such a thing as a "neutral substitute." They believed that every substitution must be due to natural selection.

Describe how four evolutionary forces affect genotypic and phenotypic variation in a population.

Variation - If all individuals are identical, no differences in the reproductive rates of individuals, no matter how extreme, will alter the composition of the population. Selection - If all variant types leave, on average, the same number of offspring, then we can expect the population to remain unchanged. Inheritance - the variation must be in some part heritable if these differences in reproductive rates are to alter the population's genetic composition. Time - Evolution is a slow process that requires change over multiple generations.

Describe the signature for purifying selection. Explain why the graph in Figure 20-8 illustrates purifying selection.

When the mutation/substitution rate deviates from u (rate of new neutral mutations), purifying selection is occurring. Nonsynonymous changes occur at a lower rate than synonymous changes.

The rate of neutral evolution for the amino acid sequence of a protein depends on the sensitivity of the protein's function to _______ changes.

amino acid

The sickle-cell hemoglobin allele, HbS, is under ________ in malarial zones and conveys a large survival advantage in heterozygotes over the first few years of life.

balancing selection

The ________ concept places the focus of speciation studies on the evolution of reproductive isolation.

biological species

Under the ________ concept, reproductive isolation between species does not need to be complete. Studying species pairs along a continuum ranging from little reproductive isolation to complete reproductive isolation provides insight into the mechanisms that promote speciation.

biological species

Evolutionary changes in ______-acting regulatory sequences play a critical role in the evolution of gene expression. They circumvent the pleiotropic effects of mutations in the coding sequences of genes that have multiple roles in development.

cis

Genes involved in genetic _______ within species often contribute to hybrid incompatibilities between species.

conflicts

Once a duplicated gene is ______ within a population and begins to acquire mutations, it can follow one of the following alternative evolutionary trajectories: pseudogenization, neofunctionalization, or subfunctionalization.

fixed

There is no proportionate relation between how much DNA change takes place in evolution and how much change in _______ results.

function

Adaptive changes in morphology can result from inactivation of regulatory sequences and loss of ______ as well as the modification of regulatory sequences and the gain of gene expression.

gene expression

Evolutionary changes in cis-acting regulatory sequences play a critical role in the evolution of _______. They circumvent the pleiotropic effects of mutations in the coding sequences of genes that have multiple roles in development.

gene expression

The neutral theory of molecular evolution proposed that most mutations in DNA or amino acid replacements between species are functionally neutral or nearly neutral and fixed by random ______. The assumption of neutrality offers a baseline expectation of how DNA should change over time when natural selection is absent.

genetic drift

The rate of substitutions in DNA in evolution resulting from the random ________ of neutral mutations is equal to the mutation rate to such alleles, μ.

genetic drift

Purifying selection is a pervasive aspect of natural selection that reduces _______ and preserves DNA and protein sequences over eons of time.

genetic variation

The sickle-cell hemoglobin allele, HbS, is under balancing selection in malarial zones and conveys a large survival advantage in ________ over the first few years of life.

heterozygotes

The Dobzhansky-Muller model explains how ______ incompatibilities between species can evolve within species.

hybrid

Genes involved in genetic conflicts within species often contribute to ________ between species.

hybrid incompatibilities

There [is/is no] proportionate relation between how much DNA change takes place in evolution and how much change in function results.

is no

Show why the rate of neutral substitution, k, is equal to the rate of new neutral mutations, µ.

k = rate of neutral substitution = 2Nμ × 1/(2N) = μ

The sickle-cell hemoglobin allele, HbS, is under balancing selection in ______ zones and conveys a large survival advantage in heterozygotes over the first few years of life.

malarial

Adaptive changes in ________ can result from inactivation of regulatory sequences and loss of gene expression as well as the modification of regulatory sequences and the gain of gene expression.

morphology

Once a duplicated gene is fixed within a population and begins to acquire _______, it can follow one of the following alternative evolutionary trajectories: pseudogenization, neofunctionalization, or subfunctionalization.

mutations

The neutral theory of molecular evolution proposed that most mutations in DNA or amino acid replacements between species are functionally neutral or nearly neutral and fixed by random genetic drift. The assumption of neutrality offers a baseline expectation of how DNA should change over time when _______ is absent.

natural selection

The ________ theory of molecular evolution proposed that most mutations in DNA or amino acid replacements between species are functionally neutral or nearly neutral and fixed by random genetic drift. The assumption of neutrality offers a baseline expectation of how DNA should change over time when natural selection is absent.

neutral

Evolutionary changes in cis-acting regulatory sequences play a critical role in the evolution of gene expression. They circumvent the ______ effects of mutations in the coding sequences of genes that have multiple roles in development.

pleiotropic

Once a duplicated gene is fixed within a population and begins to acquire mutations, it can follow one of the following alternative evolutionary trajectories: ________, ________, or ________.

pseudogenization neofunctionalization subfunctionalization

Adaptive changes in morphology can result from inactivation of _______ and loss of gene expression as well as the modification of regulatory sequences and the gain of gene expression.

regulatory sequences

The biological species concept places the focus of speciation studies on the evolution of ________.

reproductive isolation

Under the biological species concept, ________ between species does not need to be complete. Studying species pairs along a continuum ranging from little reproductive isolation to complete reproductive isolation provides insight into the mechanisms that promote speciation.

reproductive isolation

The ________ allele is under balancing selection in malarial zones and conveys a large survival advantage in heterozygotes over the first few years of life.

sickle-cell hemoglobin

The biological species concept places the focus of _______ studies on the evolution of reproductive isolation.

speciation

Many modern plant, animal, and fungal genomes are the result of ancestral ________ events.

whole genome duplication

There is no proportionate relation between how much _____ change takes place in evolution and how much change in function results.

DNA

The _______ model explains how hybrid incompatibilities between species can evolve within species.

Dobzhansky-Muller

Explain whether purifying selection is related to random genetic drift or to natural selection. Also, state the consequence of purifying selection.

Purifying selection is related to natural selection. A nonsynonymous change could change the protein which would not be beneficial. Purifying selection explains why we find many protein sequences that are unchanged or nearly unchanged over vast spans of evolutionary time.

The duplication of an entire genome leading to polyploidy.

Whole genome duplication (WGD)