End of Chapter Questions



End of Chapter Questions

1. HIV entered the human population several times, from SIV strains found in several primates. From comparisons of genetic sequence data in different strains of HIV and SIV, it is clear that HIV-1 is derived from a form of SIV found in chimpanzees, and that it has moved to humans at least three different times (because the three different groups of HIV-1 are each more similar to a chimpanzee strain than they are to each other). Similarly, HIV-2 appears to be derived from a form of SIV found in sooty mangabeys, and has moved to humans at least twice. The age of the last common ancestor of group M of HIV-1 has been estimated by calculating how quickly the group M strains diverged from each other throughout the 1980s and 1990s, and, assuming this rate of evolutionary divergence has been constant, back-calculating to estimate the year when they all diverged from their last common ancestor. The last common ancestor-that is, the SIV strain that had just moved from a chimpanzee to the first human host-probably existed between 1915 and 1941.

2. HIV has a very high mutation rate, a rapid reproductive rate, and an enormous population size. This means that at any given time, a human infected with HIV is carrying tens of millions of HIV virions with millions of different random mutations. Inevitably, sooner or later, a mutation will occur that confers resistance to AZT. (This will typically be a mutation that causes greater selectivity in the active site of the reverse transcriptase enzyme.) Notice that the HIV population has heritable variation for resistance to AZT before exposure to AZT. However, at this stage the resistance to AZT occurs only in one or a few virions, out of the billions.

Step two is for the patient to begin taking AZT. This prevents or slows replication of most HIV virions, and those strains die out. But the lucky virion with the right mutation will survive and will be able to replicate. In more general terms, there is differential reproductive success that is linked with a heritable trait.

The surviving HIV virions then repopulate the host. Soon the entire HIV population is composed of resistant virions. Formerly, there was only 1 resistant virion among millions; now all of the millions are resistant. The population has evolved.

The process is identical in almost every detail for evolution of antibiotic resistance in bacteria. The only difference will be in the specific nature of the mutation-it will not be occur in the gene for reverse transcriptase, but in some bacterial gene.

3. These patients had been infected by other patients who had HIV and were receiving AZT treatment for it, and yet continued to engage in unprotected sex (or needle-sharing, transfusions, etc.). Unprotected sex by HIV-positive patients who are undergoing retroviral therapy is the primary means by which resistant strains of HIV "escape" to the general population.

4. The key to HIV's rapid evolution is that it can generate the key "lucky" (or unlucky) mutations extremely quickly. This is because HIV has a very high mutation rate, an extremely fast reproductive rate, and a very large population size (within one host). This makes it virtually inevitable that at least one HIV virion within one patient will, by chance, acquire a key mutation that will cause increased replication or resistance.

5. The patients were probably not given higher doses because of the serious side effects of antiviral drugs. Since viruses use their host cell's molecular machinery, any drug that can stop viral replication usually interferes with normal healthy cells as well. AZT can disrupt cell division because it interferes with DNA transcription in healthy cells, not just in HIV-infected cells.

6. No. The unfortunate result would likely be development of resistance to all the drugs. This is because the HIV population would only have to develop resistance for one drug at a time, which is quite easy for it to do. The key to multiple drug therapy is that the drugs are given simultaneously, so that an HIV virion must have four or five simultaneous mutations (one for each drug) to survive. Even with HIV's high mutation rate and large population size, the simultaneous occurrence of multiple resistance mutations in one virion is unlikely.

7. From an evolutionary perspective, this is a bad idea. Recall HIV's high mutation rate and large population size. A break in multiple drug therapy allows the surviving HIV virions-most of which will be those with partial resistance to one or two of the drugs -to multiply and generate billions of offspring with new mutations, some of which will confer mutations to additional drugs.

8. HIV has so far shown no tendency to evolve into a more benign form. Within one host, HIV almost always evolves to become more virulent, as demonstrated by the multiple studies reviewed in this chapter on AZT resistance, epitope evolution, replicative speed, etc. Across hosts, the form of HIV that has spread most widely is the more virulent one, HIV-1. It appears that the same traits that cause increased virulence also cause increased transmission to new hosts. A virus must only keep its host alive long enough to spread to a new host; once it has spread, it doesn't matter (for the virus's continued survival) if the first host dies.

9. A. Spock has gotten some things correct: Many parasites do live "in amity" in their host, or in other words, they have evolved to have very low virulence or even have become beneficial. (If they are beneficial, they are not called "parasites"-parasites, by definition, cause damage to their hosts.) However, this is not the only path to evolutionary success. A parasite with high virulence can thrive, and spread, if it can move to new hosts before the current host dies. Many virulent parasites do indeed reproduce "with tremendous rapidity" as Spock suggests, and many have also evolved to spread through body secretions, feces, water, or even secondary host species.

B. Robots, HIV virus, and any entities, can and will evolve if (and only if) all of the following conditions are met: They must vary. They must reproduce (or in the case of robots, build copies of themselves). Their variations must be inherited by their offspring. And there must be some environmental factor that causes differences in survival and reproduction, so that some of the robots (or viruses, etc.) that vary in certain heritable ways will leave more surviving offspring than others. If any of these factors is missing, evolution cannot occur.

10. HIV-2 is a less virulent virus than HIV-1. It causes less damage to the host, and has a longer progression between initial infection and onset of AIDS. However, it also is transmitted less often to new hosts, and has not played a major role in the global pandemic. These two traits-virulence and transmission-appear to be linked: HIV-2 has lower viral load (number of virus particles in blood and bodily secretions), which lowers virulence but also apparently lowers transmission rate to new hosts.

11. (Many answers are possible.) It is widely thought that any widespread epidemic that affects reproductive rate will eventually cause counterrevolution in the host. HIV is certainly widespread enough, and virulent enough, to cause evolution in its host. However, it is not clear whether HIV's low prevalence in many countries will be enough to cause evolution, and whether the infections in North American and Europe, which primarily circulate in the homosexual population, will have any affect on reproductive rate. However, in Africa the disease is so widespread, and so clearly affects reproductive success, that it appears likely that humans will evolve in response to HIV, perhaps within a few generations.

Many studies could be designed to test this prediction, likely involving comparisons of genetic diversity in human populations for as many immune-system-related genes as possible. The comparisons should be done across many generations in several world regions, including Africa and other regions, and tested for correlations with HIV prevalence, AIDS mortality, and actual reproductive success.

12. All the SIV strains from monkeys and chimpanzees would cluster together, branching off from the one HIV strain that jumped from humans to other primates. Other HIV strains will be more distant branches on the tree (branching off closer to the base of the tree).

13. The three hypotheses discussed in this chapter were: (1) Short-sighted evolution: Within each patient, competition between HIV virions results in evolution of HIV strains that are more aggressive, replicate more rapidly, and can evade attack by that host's T cells. This evolution is not to the virus' long-term benefit, however, because it ultimately kills the host-and kills all virions within that host. (2) Evolution for transmission to new hosts: Traits such as high viral load that can cause high virulence may also allow HIV to spread to new hosts. (3) Host has not had time to counterevolve: HIV is a new disease for humans, and our species has not yet had time to evolve defenses. We are still within the first generation of humans to be exposed to HIV.

CHAPTER 2

End of Chapter Questions

1. Evidence available to Darwin:

Some examples of vestigial structures

The fact of extinction

The law of succession in the fossil record

Structural homology

Developmental homology

The occurrence of closely related species in groups of islands

Age of Earth known to be much greater than 6,000 years (but absolute dates not known)

Not available to Darwin:

Many more examples of all the above

Transitional fossil forms

Direct observation of populations in the wild changing through time (however, Darwin did know about, and paid close attention to, the changes that animal breeders can cause in domestic animal populations)

Ring species

Genetic and molecular information of any kind, including vestigial molecular traits, molecular homologies, and basic genetics

Radiometric dating and absolute dates for the geologic time scale

2. The answer to this question is entirely subjective and is left to the reader. For perspective, however, we can offer that the discovery of Archeopteryx was quite influential and convinced many people, both scientists and laypeople, that the theory of common ancestry was probably correct. However, most people, including biologists, doubted that natural selection was a significant factor in evolution until the "modern synthesis" of the 1930s united genetics with natural selection.

3. Many different approaches are possible. Anatomical traits of dogs or cats (e.g., snout length in dogs, ear shape, leg length, and so on), could be traced through time examining archeological remains of the domesticated dogs and cats throughout history, and assessing whether the anatomical changes appear to lead back to the putative wild ancestor. The question can also be tested with molecular data-for example, by comparing DNA sequences in modern dogs and cats and in wild canids and felids. In either case we would use the data to construct a phylogenetic tree, as discussed in further detail in later chapters. If all modern breeds are descended from a common ancestor, the phylogeny should show that all modern breeds are more closely related to the purported wild ancestor than to any other wild canid or felid. Furthermore, the modern breeds should show a branching phylogeny indicating the pattern and relative timing of their divergence from each other.

4. Many answers are possible. Several examples that paleontologists are eager to find are: a common chimp-human ancestor from approximately 7-8 mya (just before the hypothesized split of chimps and humans); a transitional bat fossil showing incipient development of bat wings; a transitional turtle fossil demonstrating an intermediate stage in development of the turtle shell; and very early representatives of the major animal phyla. (Some possible examples of these cases have been discovered, but are still controversial.)

The fossil record is a case of "Absence of evidence is not evidence of absence." Many species do not leave any discoverable fossils at all, due to such factors as our lack of access to deeply buried strata and the complete destruction of large sections of the earth's crust in subduction zones. Thus, presence of a fossil obviously proves that the predicted species once existed, but absence of known fossils does not prove that it did not exist.

5. Birds are endothermic ("warm-blooded"), and their body feathers are critically important as insulation. Feather coloration is also important in species and sex recognition, and feathers are frequently used in behavioral displays. Any of these functions may have played a role in the feathered dinosaurs, with insulation generally suspected to have been particularly important. Mathematical models of the thickness and potential insulative value of the dinosaur feathers and close inspection of other anatomical and locomotory features associated with endothermy could clarify whether the dinosaurs' feathers had a thermoregulatory benefit.

6. Under the modern definition of homology, a kiwi's wing is homologous to an eagle's wing, and the rubber boa's spurs are homologous to a kangaroo's hind legs. Owen's classical definition is only applicable if the organs are subjectively judged to be "the same organ." Owen would likely have agreed that a kiwi's wing and kangaroo's wing are the same organ, but he might not have perceived the rubber boa's spurs as being essentially the "same organ" as a quadruped's hind legs.

7. a. Analogous

b. Homologous

c. Analogous

d. Homologous

e. Homologous

f. Analogous

8. Both types of trees show relationships, and show patterns of descent from ancestors. However, phylogenetic trees are fundamentally about populations, while genealogical trees are about individuals. Phylogenetic trees cover much huger spans of time than genealogical trees. In phylogenetic trees, all living representatives, even "elderly" ones, are shown at the tips of the tree; in genealogical trees, "elderly" living individuals will be in the middle of the tree, not just at the tips. Phylogenetic trees branch only when populations acquire distinct new traits; genealogical trees develop a new branch for every individual. Branches of genealogical trees merge when parents mate; branches on phylogenetic trees never merge. In general, phylogenetic trees tend to be a bush that begins from a single oldest point (the common ancestor), and develops branches going forward in time, while genealogical trees typically begin with a bush (all the individual ancestors) and converge on a single point, or just a few points, in the present (the individual under study, and perhaps his or her siblings).

9. Jaguarundis are more closely related to tigers than to bobcats, because the common ancestor of jaguarundis and tigers lived more recently than did the common ancestor of jaguarundis and bobcats. (The easiest way to see this on the phylogenetic tree is to imagine all other branches removed, so that the phylogeny just shows bobcats, jaguarundis, and tigers.)

10. The assumptions behind relative dating were clearly correct. The clean consistency of these two dating systems is widely viewed as an impressive testament to the meticulous fieldwork and logical reasoning of the 18th- and 19th-century geologists who developed relative dating. Interestingly, many of these early geologists were creationists who were expecting to find evidence of worldwide floods (see next).

11. If most fossils were formed by worldwide floods, as the Theory of Special Creation proposes, fossils should be found in thick bands of flood-type sediment (i.e., no annual layers of slow sedimentation, as are seen in deep ocean deposits, rivers, and lakes). In any given worldwide flood, fossils should also be either not sorted at all (i.e., all species mixed together), or possibly sorted according to body size or buoyancy (e.g., dinosaurs and elephants together in the lowest layers, small beetles and trilobites higher up). Fossils should not be sorted by tiny internal anatomical details. Extinct and modern species should be mixed together. The Theory of Evolution, in contrast, predicts that fossils should be highly sorted, according to their order of descent from a common ancestor. The existing fossil record, with its clear "law of succession," the very precise order in which various animal taxa are found (no elephants in the lowest layers; no trilobites in the upper layers; ichthyosaurs always in Mesozoic sediments, but dolphins always in Cenozoic sediments; etc.), and the common occurrence of slowly deposited riverine and oceanic sediments, refutes these predictions of Special Creation.

CHAPTER 3

End of Chapter Questions

1. The everyday meaning of "adaptation" refers to a change that occurs in a single individual's lifetime, while the evolutionary meaning refers to a trait that has developed via natural selection over many generations. An evolutionary adaptation is also defined strictly in terms of relative reproductive fitness, while the everyday meaning can refer to changes that do not necessarily affect reproduction.

2. a. The four postulates are, briefly: variation exists, the variation is heritable, survival & reproduction are not equal, and survival and reproduction are not random. In the snapdragon experiment, if there had been no variation, all flowers would have been the same color. If variation had not been heritable, the colors of the best-reproducing plants would not have been passed to their offspring. If there had not been unequal survival and reproduction, all plants would have attracted equal numbers of bees, and produced equal numbers of seeds. If survival and reproduction had been random, some plants would have had more bee visits and produced more seeds than other plants, but the difference would not be related to plant color. In any of these four cases, the snapdragon population would not have evolved.

b. If the four postulates are true, a population is virtually certain to evolve, unless selection is extremely weak and genetic drift is very strong. Since the four postulates are almost always true, virtually all populations are probably evolving today, at least some genetic loci.

3. a. If bill depth was not variable, Figure 3.9 would show one skinny, high bar - all finches would have had exactly the same bill depth.

b. If bill depth was not heritable, the two graphs in Figure 3.13 would look the same. The1978 post-drought birds would still have the same average bill depth as the 1976 birds (even though the 1978 chicks had thicker-billed parents). The population would not have evolved.

c. In Figure 3.10, the strongest overall trend is clearly that thick-billed parents have thick-billed chicks. This demonstrates heritability of beak depth. But the fact that one line is slightly higher than the other shows that a small part of the variation in beak depth is not heritable. Parents with a given average bill depth had slightly thicker-billed chicks in 1978 than in 1976. This is probably due to a slight environmental effect on beak depth.

4. The claim that the vanished finches probably died of starvation is certainly reasonable, given the data in Figure 3.11, and the absence of obvious other causes such as increased predation or disease. The graphs in Figure 3.11 show that most small, soft seeds disappeared between about July and October of 1976, the same time that the bird population began to decline. Seeds were still abundant at first, but they were predominantly large seeds. Then, even the large seeds began disappearing, and the bird population continued to decline sharply. The birds did not all die instantaneously because it takes time for an animal to starve to death, and some individuals were likely able to scratch for the few remaining small seeds for several months before succumbing.

5. Many answers are possible. Though it may be "just" microevolution, the shape of a bird's bill is not a minor feature for the bird-it is the bird's one and only food-handling tool. Furthermore, microevolution and macroevolution are not a dichotomy-macroevolution is simply microevolution carried out for a long time. The changes that most laypeople would consider "macroevolution" typically require hundreds of thousands of years to evolve, so it is not logical to expect to observe them in a single field study. Evolutionary biologists generally regard long-term studies of microevolution as highly informative for learning how natural selection happens in a natural environment, and for a close-up look at the causes of small changes that, eventually, can add up to macroevolution.

6. Many answers are possible. A first step would be to identify some traits that affect the plant's survival or reproduction if rainfall changes, such as drought tolerance or resistance to root rot. We would then want to measure current variability in those traits, carefully assess the heritability of that variation, and explore the genetic and developmental underpinnings of the traits as much as possible. Over time, we would measure survival and reproduction (seed set, pollinator visits) of all the plants on the island. We would, of course measure changes in the amount of rainfall, and also keep an eye on other environmental factors that might affect our results. Over many years, we would inspect our growing dataset to see if certain genotypes were changing in abundance due to differences in survival and reproduction, and if these changes can reasonably be linked to rainfall.

7. Krontiris is referring to "group selection": selection of a trait that is detrimental to the individual carrying the trait, but that is favorable to other members in the group. Unless the individual in question is closely related to other members of the group (kin selection - see chapter 12), this cannot happen. Natural selection eliminates traits that are detrimental to the individual carrying the trait. Even if others in the group would benefit, the trait will quickly be eliminated from the population.

8. Three major objections to Darwin's theory were: there is not enough variability for evolution to continue for very long; new traits would disappear by "blending" with other traits; and, the earth's temperature implies that the earth is too young for evolution to have occurred. These were resolved by the discoveries of mutation, genes, and radioactivity, respectively. The message is that a theory should not be discarded if it cannot answer all questions, especially if it is clearly better than all alternative theories ("better" meaning that it agrees with more data, makes more successful predictions, and has fewer unanswered questions). The unanswered questions should instead be regarded as topics deserving intensive research.

9. The answer to this question is left to the reader.

10. a. The "irreducible complexity" argument states that if a complex biological process or entity cannot function without the presence of many interdependent parts, then that process cannot have evolved. This is not a logical argument, because complex processes do not evolve all in one step. Specifically, they can evolve in two stages, first slowly accumulating the different parts (each new part being, at first, helpful but not essential), and only later refining the process so that the parts become interdependent. The argument does not apply to the eye or the flagellum in any case, since some types of simplified eyes and flagella do, in fact, function. Though they do not function as well as an advanced eye or flagellum, the simplified versions are clearly more useful than having no eyes or no flagella.

b. The major logical flaw with the "argument from personal incredulity" is that it can be due simply to ignorance or lack of imagination. Furthermore, it tends to discourage research into interesting questions.

11. The answer to the first question is left to the reader. As for the second question, any objection to evolutionary theory on the grounds that it occurred in the past and/or is not directly observable must, logically, also apply to all other theories regarding processes that occurred in the past or are not directly observable. This includes all historical sciences, (including geology, astronomy, and archeology), as well as sciences that infer the existence of particles that cannot be observed directly (such as particle physics today, and, in the past, cell theory and germ theory).

12. The answer to this question is left to the reader.

13. The answer to this question is left to the reader.

CHAPTER 4

End of Chapter Questions

1. A characteristic that is shared by species and derived-meaning that it was modified in a common ancestor and then inherited by the descendant species.

2. Similarity in traits that is not due to inheritance from a common ancestor.

3. Homoplasy is misleading because it makes species that are not closely related appear as if they are closely related.

4. Homoplasy occurs due to reversal and the independent evolution of similar traits. Because parsimony minimizes the total number of evolutionary changes that occur on a tree, it minimizes the chance that reversals and independent evolutionary events are responsible for the relationships described by the tree.

5. If the genetic and developmental basis of a morphological trait is known, then researchers can distinguish homology from homoplasy. Morphological traits can also be measured in fossil species. Compared to morphological traits, DNA sequence data are relatively easy to acquire in large amounts, but can be subject to extensive homoplasy.

6. Homology can be claimed if traits have a similar genetic and developmental basis, or if a large number of other traits also link the species in question.

7. Frequently the fossil record documents which traits appeared earlier versus later during evolution. Comparisons with traits in outgroups can also help establish the direction of evolutionary change.

8. Traits usually converge when natural selection favors similar structures in response to similar environmental challenges. There are many examples, including the eyes of octopuses and vertebrates and the placement of eyes in the skulls of crocodiles and hippos.

9. A monophyletic group contains a common ancestor and all of its descendants, but a paraphyletic group contains a common ancestor and some but not all of its descendants. Mammals are a monophyletic group; fish are not.

10. Because they are derived from a common ancestor, synapomorphies accurately reflect shared evolutionary history and identify the species that descended from that common ancestor.

11. Cladistic approaches to phylogeny inference are based on clustering groups by distinctive traits (synapomorphies). Phenetic approaches are based on clustering groups by some measure of overall similarity.

12. In this case evolution was not parsimonius. The trait was gained in artiodactyls and then lost when whales became aquatic.

13. Molecular clocks convert measures of sequence divergence into estimates of time of divergence. They should work for changes in sequences that are not due to natural selection, because these changes accumulate at a steady rate.

14. It did not serve as a synapomorphy that distinguished any of the lineages on the tree from other lineages.

15. Convergent evolution. It is likely that this tooth shape evolved independently in the 5 groups due to selection for chewing grass. The alternative hypothesis is that the tooth shape evolved early in mammalian evolution and then was lost many times.

16. The arrangement of bones is homologous because all tetrapods have a similar arrangement. But because bats are the only mammals that fly and because birds are descended from dinosaurs, it is logical to infer that flight evolved independently in the two groups.

17. Ungulates are not monophyletic and the name should not be used. It is most likely that hooves evolved at the base of the group that includes the two lineages mentioned in the question and that hooves were lost in the ancestor of carnivores and pangolins.

18. For the species that are common to all three trees, the relationships and order of branching are the same. Because English is read from left to right, people tend to read trees from left to right and infer that evolution proceeds from left to right. As a result, the tree in (b) appears to show humans as the "highest" primate. The trees in (a) and (c) do not give this false impression.

19. Because the branching patterns for the ants and the fungi they farm match exactly, the authors of this study argued that cospeciation has occurred in every instance.

20. Evolution is a branching process, not a linear or progressive process. There are lineages that appeared earlier in evolution and thus are considered more basal relative to lineages that appeared later and are considered more derived, but no species is any higher or lower than any other.

CHAPTER 5

End of Chapter Questions

1. A silent site mutation does not change the amino acid specified by a codon; a replacement mutation does.

2. Chromosome inversions result from two breaks in DNA, a flipping of the broken segment, and then reannealing of the segment at the breakpoints.

3. See Figure 5.11.

4. See Figure 5.6.

5. Most mutations have small deleterious effects on fitness.

6. Transitions replace a purine with a purine or a pyrimidine with a pyrimidine; transversions replace a purine with a pyrimidine or a pyrimidine with a purine. Transitions are much more common than transversions.

7. Point mutations affect a single point in a DNA sequence; duplications produce a duplicated segment of DNA.

8. Evolution by natural selection cannot occur unless heritable variation exists. Heritable variation is based on variation in the alleles present among individuals in a population.

9. Mutation rates vary among individuals because the enzymes responsible for copying and repairing DNA vary in accuracy. Mutation rates vary among species because trade-offs occur between the speed and accuracy of copying and repairing DNA, and because higher or lower mutation rates may increase fitness in certain environments.

10. See Table 4.2., right-most column.

11. Duplicated genes may become 1) extra functioning copies of the original gene due to selection for additional gene product, 2) pseudogenes due to mutations that make the gene product non-functional, or 3) new genes with a distinct function due to mutations that are favored by natural selection.

12. Genes are claimed to be homologous if they have high sequence identity at the DNA or amino acid sequence level, they have introns of similar size in similar positions, and products with similar structure and function.

13. Yes, because the DNA sequence has been altered. This is a new version of the gene for beta-globin.

14.

• This hypothesis is logical, because the genes are located in tandem, they have high sequence similarity, and more basal groups (New World monkeys) have only one X-linked pigment gene.

• This hypothesis is also logical, because all of the lineages in the Old World have two pigment genes on the X chromosome, while all of the lineages in the New World have only one.

• If a human male has a knock-out mutation in the gene for one of the X-linked pigment genes, then that individual cannot make the red or green pigment. That person's vision would be more similar to ancestral primates or New World monkeys than to other humans.

15. The most likely explanation is that the long chromosome found in domestic horses split into two pieces in the ancestor of Przewalski's horse. If the two smaller segments still synapse with the long chromosome during matings between hybrids, then it is likely that gene number and order is unchanged. ence identity at the amino acid sequence level, and they have similar function.

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