Evolution Exam 2

What is the Hox paradox? Can you suggest a solution?

"The Hox paradox" came from the early evo-devo studies, where the surprising data showed high degree of conservation in the Hox genes. Since similar genes might be involved in the basic processes found in many groups of animals, how could we explain the diversity of life? Although these are divergent groups and very often we find the similarities based on homoplasy, the same transcriptional regulators are found to be used for what appear to be, similar purposes. A solution to this would be to look at all the aspects of Hox gene clustering, expression and function. In addition, some of them might be result of homoplasy. Modern developmental biology gives us a better insight in the underlying nature of such similarities.

What would health-care workers, patients, and healthy people do if they wanted antibiotic resistance to evolve as quickly as possible? Do you know of any cases where humans are (unintentionally) doing this?

. The surest way to accelerate evolution is to exert strong selection. In this case, that means using antibiotics routinely wherever possible. Unfortunately, this has been common practice in human and veterinary medicine. Some examples are the routine dosing of food animals with antibiotics, regular washing of surgery rooms with the same antibiotics after every surgery, unnecessary prescriptions of antibiotics for human patients, and widespread over-the-counter use of antibiotic soaps.

Two closely related plant species have dramatically different genome sizes. What are some possible biological mechanisms that could explain this phenomenon?

A difference in the amount mobile genetic element DNA is the most likely mechanism to explain a large difference in genome size. Dramatically different genome sizes could additionally be influenced by the amount of intron DNA within genes in the genomes, and by differing sizes of intergenic regions (which are themselves likely to contain mobile genetic element sequences).

What is a telomere? Describe how telomere shortening is thought to influence variation in life span among in- dividuals. Is telomere length associated with life span in zebra finches? In elderly humans? In different mammal species, after controlling for shared evolutionary history? What is different about the role of telomeres in the biol- ogy of aging in mice versus humans?

A telomere is the region at the very end of a chromosome, consisting of many repeats of a short, noncoding sequence of DNA. The telomere apparently serves to ensure the structural integrity of the chromosome, protecting the genes that are near the ends of the chromosomes from the small loss of DNA that occurs at the very end of chromosome during copying. The telomere-shortening theory of aging can be viewed as a subcategory of the rate-of-living theory. The rate-of-living theory states that aging occurs as an inevitable consequence of irreparable damage that occurs to cells during normal metabolic processes. The telomere-shortening theory states that this irreparable damage is, specifically, the shortening in telomeres that occurs with every cell division. According to this theory, once cells have divided so many times that telomeres have become too short, cells can no longer divide, organ damage can no longer be repaired, and aging occurs. In support of this theory, zebra finches with longer telomeres age 25 days had greater longevity, and humans over 100 years old and their children had longer telomeres than unrelated control individuals. However, in comparing different mammal species while controlling for the effects of body mass , telomere length did not correlate with life span. An important difference between mice and humans for the role of telomeres in aging is that if a mouse's lifespan is shortened, that mouse will have fewer offspring, but if a human's lifespan is shortened, this does not affect the human's reproductive success. Because humans live for many years after becoming post-reproductive, traits that affect human lifespan do not directly affect reproductive success.

Look at Figure 12.21 on page 472. a. What would have happened to the frequency of co- operators in the global population if all groups had two cooperators and one selfish individual? Why? b. What would have happened to the frequency of co- operators in the global population if the cooperators and selfish individuals had sorted themselves into groups like the Hadza do? Why? c. Now look at Figure 12.25 on page 475. What would have happened to the global frequency of cooperators if, instead of diluting the bacterial culture and trans- ferring a small number of individuals, the researchers had simply transferred a large aliquot? Why?

A) If all groups had two cooperators and one selfish individual, that means the starting frequency of cooperators is 2/3, or ≈0.67. After one generation, this frequency would fall to 5/8, or 0.625. So, if all groups start with two cooperators and one selfish individual, the frequency of cooperators will decline. B) The global frequency of cooperators would have increased, because groups composed entirely (or mostly) of cooperators would have had more offspring than groups composed of mostly selfish individuals. In the example shown in Figure 12.21, groups composed only of selfish individuals have especially low reproduction. C) The hypothesis of Chuang and colleagues (2009) that adequate variation for cooperative traits would arise by chance if each culture were established by a small number of individuals is an example of genetic drift combined with multilevel selection. If the researchers had transferred a large aliquot to start each of the 288 subcultures, each one would have started with many thousands of bacterial cells, with a frequency of cooperators of 10%. In that situation, cooperators would have been unable to form groups, and the frequency of cooperators would have decreased to zero in each subculture. The dramatic dilution step in the researchers' experimental design leading to Figure 12.25 is what allows cooperators to form groups, because each of the 288 subcultures founded by a small number of cells is an opportunity for cooperators to find themselves grouped together.

The cubs of spotted hyenas often begin fighting within moments of birth, and often one hyena cub dies. The mother hyena does not interfere. How could such a be- havior have evolved? For instance: a. From the winning sibling's point of view, what must B (benefit of siblicide) be, relative to C (cost of sibli- cide), to favor the evolution of siblicide? b. From the parent's point of view, what must B be, relative to C, for the parent to watch calmly rather than interfere? c. In general, when would you expect parents to evolve "tolerance of siblicide" (watching calmly while sib- lings kill each other without interfering).

A) Siblicide should evolve only when the benefit to the winning cub, B, is at least half of the cost of siblicide, C. This is because the winning cub is related to itself by r = 1.0 and is related to its sibling by r = 0.5. The winning cub must be increasing its chance of survival and reproduction markedly, enough to produce an entire additional offspring, in order to make up for the loss of the sibling. B) The mother is related equally to both cubs (r = 1/2). By tolerating siblicide, she loses an entire offspring. If this is an adaptive behavior, the death of the losing cub must be balanced by the survival of the winning cub. (It is also possible that the mother hyena may be able to produce a few additional future offspring herself, by not having to care for as many cubs in the present.) This implies that one or both of the cubs would have died anyway even if no siblicide had taken place. C) Generally, parents are expected to tolerate siblicide whenever reduction in the number of offspring greatly improves chances of survival for the surviving offspring. The most common reason for this is limited food.

When a Thomson's gazelle detects a stalking cheetah, the gazelle often begins bouncing up and down with a stiff-legged gait called stotting (see Figure 12.38). Stot- ting was originally assumed to be an altruistic behavior that distracts the cheetah from the gazelle's kin and also alerts the gazelle's kin to the presence of the predator, at considerable risk to the stotting gazelle. However, T. M. Caro reports that stotting does not seem to increase the gazelle's risk of being attacked. In fact, once a gazelle begins to stott, the cheetah often gives up the hunt. a. If Caro is right, how does C (the cost of stotting) for a gazelle compare to C (the cost of trilling) for a Beld- ing's ground squirrel? b. Do you think stotting is altruistic, selfish, spiteful, or cooperative (mutualistic)? If you are not sure, what further studies could you do to answer this question? c. With this in mind, make a prediction about whether a gazelle will stott when no other gazelles are around, and then look up Caro's papers to see if your predic- tions is right.

A) Since stotting doesn't increase a gazelle's risk of being captured, stotting has little cost to the gazelle (beyond the minor energetic expense) and may even have a benefit if it causes the cheetah to give up. Thus, for a gazelle, C, the cost of stotting is near 0 or below 0. In ground squirrels, the cost of trilling is substantially above 0, since trilling significantly increases a ground squirrel's chance of death. B) Many answers are possible. For perspective, stotting is now generally regarded as communication from prey to predator. In essence, the gazelle is saying to the cheetah, "I see you, and you're not going to take me by surprise. If you chase me, I will escape: See how fit I am and how high I can jump. So you might as well give up now." Once a gazelle has seen the cheetah, the gazelle's decision to stott appears to benefit both the gazelle and the cheetah, by communicating this information between the two of them and saving them both the energy of an unnecessary chase. Thus, stotting may be a cooperative behavior—a rare example of cooperation, and communication, between prey and predator. C) Caro reports that solitary gazelles will stott if they see a cheetah, even when no other gazelles are around. This is not in agreement with altruistic stotting, but is predicted if stotting is cooperative communication between gazelle and cheet

All teleost fish species have two copies of the sodium channel gene SCN4A: scn4aa and scn4ab. a. From the evidence in Figure 15.33a, did the duplica- tion of SCN4A happen just once in teleosts, or mul- tiple times independently? Explain your reasoning. b. In two lineages of electric fish, the expression of scn- 4aa is restricted to the myogenic electric organ. From the evidence in Figure 15.33b, did this change in ex- pression happen just once, or multiple times indepen- dently? Explain. c. From the evidence in Figure 15.33b, has scn4aa un- dergone adaptive evolution following the change in expression? Explain.

A) The evidence suggests that the duplication event occurred only once, in the common ancestor Channel catfish, Longtail knifefish, and Zebrafish. This is because the scn4aa genes from each species are more closely related to each other than they are to the scn4ab genes from the same species. Therefore, each species' scn4aa gene was inherited from a common ancestor. The same logic applies to the scn4ab gene. B) The change in scn4aa expression occurred twice independently in the tree shown in Fig. 1533b: once on the lineage leading to Mormyroid electric fish, and in a separate instance on the lineage leading to the Gymnotiform electric fish. C) Because some of the branches in Fig. 15.33b are colored bright red, indicating a dN/dS ratio near or above 1.0, this suggests that positive selection has acted on the scn4aa locus, which would indicate adaptive evolution.

It is often difficult to disentangle the roles of environ- mental factors and mating preferences in creating and maintaining species boundaries. This is why the cichlid example in Section 16.3 is so unique, and also why it can be difficult to understand. Study Figure 16.17 and answer the following questions by comparing the two most extreme island habitats of Marumbi (left column) and Makobe (right column): a. How do the two environments differ? b. What color are the male fish in these two habitats, and at what depth are the different colors of male fish found? c. What LWS opsin alleles are present in the two popu- lations, and what does it mean for a female to have a "blue" or a "red" LWS opsin allele? Finally, ask yourself why the environmental context is so important for these cichlids. What colors of male fish would be present in Lake Victoria if all habitats were similar to Marumbi (low water clarity)?

A) The water at Makobe is much clearer than the water at Marumbi (higher water quality values in Fig. 16.17a). B) At Marumbi, the male fish are blue, intermediate, and red class 3, and are all found in shallow water, at less than 4m depth. At Makobe, the males are either blue or red class 4, and blue males are found only in shallow water (less than 3m depth) while red males are found only in deep water (4 to 8m depth). C) At Marumbi, the LWS opsin alleles present are mostly "blue" and "Ooher," with a small proportion of "red." At Makobe, blue fish have mostly "blue" LWS opsin alleles and red fish have mostly "red" LWS opsin alleles. For a female to have a "blue" allele, it means she has either a preference for blue males as mates, or no preference between red and blue males. However, for females the "red" LWS opsin allele is correlated with a strong preference for red males as mates. If all habitats in Lake Victoria were similar to those at Marumbi—low water clarity—we can predict that the deeply red males (red class 4) would no longer be present in the lake, because there would be no way for females to preferentially choose them. In water of low clarity, red coloration is not visible to females, so it offers no selective advantage to males.

What is the difference between adaptation from new mutation and adaptation from existing genetic variation? Why is this distinction important?

Adaptation from new mutation occurs when a population is exposed to a new selective agent, and some time after this change in selection pressure a new mutation arises in the population that is adaptive, and this new adaptive mutation rises to fixation in the population. In contrast, in the case of adaptation from existing genetic variation, the adaptive allele is already present in the population at low frequency before the change in selection occurs. Once selection changes, the allele becomes adaptive and rises from low frequency to fixation in the population. This distinction is important because adaptation from existing genetic variation would be expected to result in similar adaptive trajectories among multiple isolated populations that are exposed to the same new selection pressure and share the same existing genetic variation. However, adaptation from new mutation has the potential to result in different adaptive trajectories among separate populations.

What does it mean to call a pair of closely related spe- cies "allopatric species" versus "sympatric species"? How do these definitions relate to the difference between the processes of allopatric versus sympatric speciation?

Allopatric species are those that became separate species while geographically isolated from one another and not exchanging genes; the outcome of speciation can be due to selection, drift, or both. Sympatric species are those that became separate species while living in the same geographic location. The process of sympatric speciation can only begin if there is some kind of barrier to gene flow that prevents two populations (which will eventually become separate species) from successfully interbreeding even though they live in the same place. Allopatric speciation does not require any barriers to interbreeding when the process begins, because geographic separation serves as such a barrier.

n what sense are the lens crystallins of elephant shrews and scallops homologous? In what sense are they homo- plasious? What about the red spots on the wings of Helico- nius melpomene xenoclea and H. erao microclea?

Although there is a great phylogenetic distance between shrews (mammals, vertebrates, Deuterostomes) and scallops (mollusks, invertebrates, Protostomes), the major lens crystalline in both scallops and elephant shrews is an aldehyde dehydrogenase. In that sense, these otherwise divergent groups of animals seem to be homologous. Although in vertebrates aldehyde dehydrogenases are enriched in the eyes and were predisposed for function as lens crystallin in elephant shrews, similarity between scallops and shrews probably evolved due to a homoplasy.The total set of possible proteins that fulfill all of the functional requirements for lens crystalline is small; evolution could repeat itself in these two groups. Parallel evolution is also defined as "the independent appearance of similar phenotypes via similar alterations of the same developmental mechanism". This seems to be the case of H. erato and H. melpomene, since they not sister species—they cannot hybridize—but rather resemble each other due to the co-mimics. The genes for wing-color pattern in this genus (Heliconius) map to loci of single genes or tightly linked gene clusters. Variation in the expression of a homeobox transcription factor, called optix, accounts for variation in red color pattern in both H. melpomene and H. erato across their geographic ranges. Depending on the optix allele a butterfly carries, optix is expressed in different places on the wings during chrysalis development, at the stage when color is determined.

Figure 11.12 shows the results of the experiment by Jones et al. (2000), in which broad-nosed pipefish mated in bar- rels in the lab. Each barrel contained either 4 males and 4 females, or 2 males and 6 females. Jones and colleagues also did experiments in which each barrel contained 6 males and 2 females. What do you think the analogous graphs from these experiments looked like? Why?

As the ratio of males to females increases, females will compete less for access to males. Most females should succeed in finding a mate, and the variance in female reproductive success should decrease (that is, the difference between the "winners" and "losers" will be smaller). The frequency distributions of the number of mates and the number of offspring become more even. The relationship between number of mates and number of offspring should be correspondingly shallower. A change in the ratio of females to males should have little or no effect on male reproductive success as they are already the limiting sex in this species. All males should garner at least some mates and all should have some reproductive success. Therefore, the graphs for male reproductive success should change minimally, if at all.

An evolutionary biologist once hypothesized that if evolu- tion has affected human social behavior, then a mother's brothers should take a particular interest in her children— more so than the father's brothers, and perhaps even more so than the father himself. Why did he hypothesize this? (As it turns out, there are many cultures in which men do, in fact, direct parental care primarily to their sisters' kids.)

As the reed bunting example shows, a male is not always the father of every offspring in his nest (or house). Evolutionarily speaking, mothers are always certain that they are related to their own children by r = 1/2, but fathers cannot be absolutely sure that they are really the father of the children. On average, fathers can expect to be related to the children in their house (or nest) by somewhat less than r = 1/2. By the same logic, men can always be certain that they are truly the uncles of their sister's children (r = 1/4) but cannot be certain that they are truly the uncles of their brother's children (r 1/4, on average). Thus, men are expected to direct extra care toward their sister's children (i.e., rather than toward their brother's children). In situations where uncertainty of paternity is particularly high, they may even direct more parental care toward their sister's children than toward their own children.

Suppose a researcher discovers a new population of mice with higher expression of retrotransposon RNA than wild-type mice. Can you predict the behavior of other molecular mechanisms in this new mouse lineage that may be related to retrotransposon activity?

Because methylation and RNA interference are both known defenses against retrotransposons, a logical prediction would be that the new population of mice has lower levels of DNA methylation (either throughout the genome, or specifically in retrotransposon sequences), and/or that the new population would have lower RNAi activity. Lower RNAi activity could be measured by evaluating what fraction of small RNAs in germline cells have sequences that match retrotransposon seuqences (as in Fig. 15.6). One prediction would be that the new population of mice would have a lower fraction of small RNAs that match to retrotransposons.

Mobile genetic elements are considered the best example of the prediction that natural selection can act on other levels besides individual organisms. Explain how herita- ble variation and differential success among transposable sequences can lead to evolution by natural selection.

Because most mobile genetic elements create copies of themselves when they transpose, variation in the gene sequences they encode will be heritable. That is, "offspring" elements will inherit their gene sequences from the "parent" element that generated them. If multiple versions of a mobile element exist, and some versions generate more "offspring" elements elsewhere in the genome, these more prolific elements will rise in frequency within the host's genome over time. Selection within the genome will favor mobile elements that have highest "reproductive success," which means the mobile elements that create the most copies of themselves per unit of time. Furthermore, if we consider mobile elements persisting through multiple generations of their host organsim, the mobile elements that are most effective at inserting themselves into the host's germline will have highest reproductive success across host generations. A mobile element that reproduces a lot in somatic cells of the host, but does not enter germline cells, will be favored within an individual host, but will not survive and persist in the host's offspring

Blue jays (Cyanocitta cristata) seem better than American robins (Turdus migratorius) at recognizing individuals. In one study (Schimmel and Wasserman 1994), blue jays raised with robins could distinguish strange from familiar robins better than the robins themselves. Do you think these species differ in occurrence of kin selection or reci- procity (or both)? Why?

Blue jays have a complex social system and remain in small family groups for several months after leaving the nest. They are suspected to have kin-selected altruistic behaviors and may also exhibit reciprocal altruism. Both of these behaviors (after leaving the nest) require the ability to recognize and identify individuals. American robins, in contrast, leave their families when they leave the nest, and are not known for any altruistic behaviors. In consequence, their ability to recognize and remember individual birds is not as highly developed as in blue jays.

What kinds of information can be gained by compar- ing gene trees and species trees? What kinds of questions about evolutionary history can be answered?

By comparing gene trees and species trees, one can evaluate whether particular alleles have been inherited from a common ancestor species, or whether alleles of interest have evolved independently within a particular species. This allows us to answer questions regarding whether particular adaptive changes evolved only once during evolutionary history, or whether a genetic change of interest evolved multiple times independently. Multiple independent occurrences of similar evolutionary changes are interesting because they suggest that certain evolutionary events are likely to occur repeatedly.

Do biases in developmental pathways limit evolutionary possibilities? How can this hypothesis be tested?

Darwin thought that variation is always present and that it is unbiased in direction. For example, when the mean phenotype shifts toward closer mimicry, the population still shows variation in all directions (including the better mimicry). However, evolutionary biologists discovered that developmental bias is a widely present constraint of the variation. This challenges the concept that variation has no directionality and that all directional evolution is due to selection. Since it is often difficult to distinguish developmental constraint from a case of strong directional selection, scientists test such hypotheses using biochemistry, genomics, systems biology and network modelling. Another source of data is experimentation with artificial selection, where evolutionary change proceeds more readily in some directions than others. Such results could be explained by the developmental bias, due to alternations in a developmental pathway.

Explain the difference between dispersal versus vicari- ance. Why might dispersal or vicariance events initiate speciation?

Dispersal occurs when individuals physically move to a new habitat and colonize it, forming a new population. Vicariance occurs when an existing population is fragmented into two or more isolated populations by changes in the habitat. Dispersal and vicariance produce geographic isolation, which reduces or eliminates gene flow between populations. Stated another way, geographic isolation leads to reproductive isolation.

The genesis of life is sometimes said to have required four things: energy, concentration, protection, and ca- talysis (for example, Cowen 1995). Explain why each of these four things was necessary for the generation of the primordial form.

Energy is necessary to produce the complex necessary for information storage and self-replication, fundamental characteristics of life. Concentration increases the likelihood that the constituents of those complex will be able to come together in synthesis reactions. Protection is necessary to maintain a chemical and physical environment appropriate for the chemical reactions at the foundation of life processes, especially when that environment is markedly different from conditions in the surrounding environment. Catalysis provides for precise control of chemical reactions, especially their sequence; without this precise control, the biochemical pathways necessary to minimally constitute life would be extremely difficult to maintain.

What does it mean to say that species are "evolutionarily independent" or that "species form a boundary for gene flow"?

Evolution is change in allele frequencies, and separate species experience changes in allele frequencies independently of one another. If species A has an increase in one allele's frequency as a particular locus, this is unrelated to whether or not species B does, or does not, exhibit a change in the frequency of the same allele. Allele frequencies change independently in separate species because there is no gene flow between species. For sexually reproducing species, no gene flow means that there is no interbreeding between species.

Some biologists regard our bodies as small ecosystems that exert selective pressure for the evolution of invasive meta- static cancer. If this is true, why don't we all get cancer? (Hint: Consider the speed of evolution.) However, these same biologists believe that humans have certain genes that have evolved specifically to prevent cancer. How is it pos- sible to have both strong selection for cancer and strong selection for anticancer genes? (Hint: Consider which pop- ulation is under selection in each case.)

Evolution of human cancers proceeds quite slowly compared to the human life span. For this reason, full-blown cancers are more common in the elderly, and many humans die of other causes before cancers get a foothold. The reason that evolution of human cancers proceeds this slowly, on a time scale of decades, is thought to be due to selection for anti-cancer genes in the human population. Note that we are discussing two kinds of selection: selection for invasive cancer itself is occurring within one body on individual cells and how fast they can replicate, counteracted by selection occurring in the population of humans, where the relevant factor is the reproductive success of each human. In human populations, natural selection in human populations has apparently favored the evolution of genes that prevent cancer until breeding can occur. Thus, in humans as well as in other species, cancers typically do not develop until after the average age of last breeding.

Why did the evolutionary synthesis not include develop- mental biology? What discoveries initiated the reconcili- ation of development and evolution?

Evolutionary synthesis refers to our understanding of the genetic basis of evolutionary processes, bringing together important ideas of Mendelian genetics with Darwin's theory. Fisher, Wright and Haldane were considered to be the leaders in this filed, since they led some major mathematical implications of the evolutionary synthesis. At the time of great synthesis (1930's to 1940's) geneticists did not have the tools of molecular genetics. Evo-devo became popular after the discovery of Hox genes in fruit flies and other advances in molecular and developmental genetics starting in the 1980's. In addition the discovery of gene sequencing, as well as many new techniques in molecular biology, opened the new insight on evolution.

Define exaptation and give an example. How do you know the trait you chose involved a change in function? Can you identify exaptations in your own body?

Exaptation is a word made by Gould and Vrba. It is used to describe the evolutionary novelty that arises from a structure that gains a novel function. For instance, the evolution of insect wing might be from a structure functioning as a body heat source. In many cases we could trace the change of function in a taxonomic lineage. Both vertebrates and insects evolved hearts independently, yet these structures came under the control of the same generic regulator of contractility. Therefore,, the human heart might be an example of expatation. There are many other examples both at the molecular and anatomical level (nervous system, gene clusters etc).

What are four reasons that females may choose males with particular traits and reject other males? Give one example for each. Does she always benefit from her choice?

Females may gain "good genes" for their offspring by choosing traits that indicate that the male is healthy and fit. An example is Welch's experiment on gray tree frogs, which demonstrated that offspring of long-calling males outperform those of short-calling males in several measures of health and rapid growth. Second, females may select males who provide them with a valuable resource, such as a food gift. An example is male hangingflies, who provide a food gift to the female. Third, females may have pre-existing sensory biases that can be exploited by males. An example is male water mites, which employ a mating display that appears to take advantage of females' tendency to turn toward vibrations—a trait that originally evolved for hunting, not for mating. Fourth, once a trait is preferred by a majority of females, the trait may become self-perpetuating because females that prefer that trait will tend to have "sexy sons". An example is spotted cucumber beetles, in which most females prefer fast-stroking males—a trait that appears to provide no advantage other than the fact that sons of those males will themselves be fast-strokers.

Look again at Figures 13.10 and 13.13, which show life- history trade-offs for a hypothetical species. Suppose you are studying these animals, and you discover a new mu- tation from the wild type that causes its carriers to have two offspring per year instead of one. The new mutation does not alter the age of maturation, which still occurs at 3 years. Your initial observations indicate that the new mutation may cause an early death, but you are not cer- tain exactly how early. You do notice, however, that the new mutation is increasing in frequency and the wild- type allele is decreasing. Make a prediction about the minimum possible age of death of organisms that carry this mutation, and explain your reasoning.

Given that the mutation is increasing in frequency, its benefits in terms of reproduction must outweigh its cost in terms of early death. The earliest possible age of death is five because individuals who live to that age and reproduce in their fifth year will have an average lifetime reproductive success of 2.49, slightly higher than the wild-type individuals. (This is easily verified by manipulating the data in a spreadsheet.)

Imagine an extremely primitive organism that has very primitive ribosomes with no proteins. Would it be pos- sible to place this organism on the tree of life shown in Figure 17.18? Why or why not? How about an or- ganism with no ribosomes? (Can you think of such an organism?) Is it conceivable that there are some as-yet- undiscovered primitive organisms that cannot be placed on these phylogenies? How would the discovery of such organisms affect our reconstruction of the cenancestor?

If an organism had primitive ribosomes that contained rRNA, it should be possible to at least place it on Figure 17.18 phylogeny, since the organism might have a small-subunit rRNA gene. The placement might be incorrect, however, if the function of this primitive ribosome is markedly different from typical ribosomes. That's because differences in function can cause rapid divergence of genetic sequences due to natural selection, not to neutral evolution, whereas phylogeny analyses assume that all sequence differences occur at the clocklike rate of neutral evolution. If the organism had no ribosomes, it clearly could not be placed on a tree based on ribosomal RNA. If it had no ribosomes, it would be unlikely to use tRNA, so it couldn't be placed on a tree based on tRNA synthase genes, either. This is the case with viruses, which are indeed difficult to place on many phylogenies because they lack the appropriate genes. It is conceivable-perhaps likely, given how little we know about most viruses-that undiscovered primitive life forms exist, and that some of them might not have the necessary genes for placement on some of these deep phylogenies. If that were the case, we would have to reconsider the reconstruction of the cenancestor to take that organism's characteristics into account. We would have to be sure, however, that its differences truly represented ancestral characters, not derived ones, which would be extremely difficult without an outgroup for comparison.

Red crossbills (Loxia curvirostra species complex) are small finches specialized for eating seeds pried out of the cones of conifer trees. They fly thousands of kilometers each year in search of productive cone crops. Despite their mobility, crossbills have diverged into several "types" that differ in bill shape, body size, and vocalizations. Each type prefers to feed on a different species of conifer, and each species of conifer is found only in certain for- ests. Bill size and shape affect how efficiently a bird can open cones of a certain conifer species. Explain how a highly mobile animal such as the red crossbill could have diverged into different types in the absence of any geo- graphic barrier. If crossbills could not fly, do you think speciation would occur more quickly or more slowly? If conifer species were not patchily distributed (i.e., in different forests), do you think crossbill speciation would occur more quickly or more slowly? Compare your an- swers to the analyses and data presented in Benkman (2003

If crossbill populations are specialized for feeding on certain types of trees, and each type of tree is found in a different location, then members of different populations usually would not occur in the same location and therefore would not have the opportunity to interbreed. If crossbills could not fly, speciation would likely occur more quickly because there would be even less opportunity for interbreeding among populations. If conifers were not patchily distributed and many types of conifers occurred within the same forest, this would result in crossbill speciation proceeding more slowly, because populations that specialize on different conifer types would come into contact in the same forests and would have opportunities to interbreed.

Males in many species often attempt to mate with strikingly inappropriate partners. Ryan (1985), for example, describes male túngara frogs clasping other males. Some orchids mimic female wasps and are pollinated by amorous male wasps—who have to be fooled twice for the strategy to work. Would a female túngara or a female wasp make the same mistake? Why or why not? (Think of general explanations that are applicable to a wide range of species.)

In general, the sex with the greatest reproductive investment should experience strong selection against making such mistakes, as any mistake in identifying an appropriate partner can cause a significant fitness cost. In contrast, the sex with minimal reproductive investment can, in effect, afford a few mistakes, and may benefit from a wider range of partners. A male frog that will mate with a large variety of females (various sizes, colors, behaviors, etc.) may occasionally make a "mistake" and stray completely outside its species. But the cost is minor (some sperm and a small amount of time), and may be offset by the benefit of being willing to mate with a large variety of females that are indeed the correct species. Females, in contrast, may benefit greatly from not only identifying the appropriate species, sex, and level of physiological maturity of potential mates, but also their overall quality. And for females, the cost of making a flawed choice and therefore wasting an expensive mating is extremely high.

In marine iguanas and red-collared widowbirds, what evidence is there that sexual selection acts contrary to natural selection? That is, what is the evidence that the sexually selected trait may reduce survival? What does this imply about survival rates of "attractive" males in many species, as compared to less attractive or less competitive males?

In marine iguanas, many males are larger than the "optimum" body size (size that can be maintained long-term), and experimental data confirms that survival rates are lower for the largest iguanas than for medium-sized iguanas. Similarly, in long-tailed widowbirds, males with intact long tail feathers lost weight at a greater rate than males with experimentally shortened feathers. These results indicate that sexual selection is working contrary to natural selection, and that "attractive" males may ultimately pay a price for attractiveness, in the form of lowered survival, shorter life spans, or reduced health.

What clues in the way RNA is used in modern cells hint that RNA may have an ancient role in cellular metabo- lism?

In modern cells, the most conserved component of cellular metabolism is the ribosome, which is built on an RNA framework, requires RNA adaptor molecules to work, and in which the actual catalytic step is performed by RNA, not by proteins. In addition, RNA subunits called ribonucleoside triphosphates are involved in many crucial aspects of cellular metabolism, including being the basic energy currency of all cells and the components of electron-transfer co-factors such as NAD and FAD. (Other recent research has found that cells contain several previously unknown types of RNA that play a crucial role in genotype remodeling and expression. Modern cells are now sometimes described as containing their own tiny "RNA World".)

Explain how the movement of mobile genetic elements can create mutations that are beneficial to hosts as well mutations that are deleterious.

In some cases, transposition events have led to the formation of genes with novel, beneficial functions. This can occur when a gene in a transposable element begins to serve a positive function for the organism (as in the SUN locus in Roma tomatoes), or when sequences attached to transposable elements fuse with other sequences to form a new gene. In most cases, though, insertion of transposable elements disrupts a gene and is deleterious.

What is the difference between intersexual selection and intrasexual selection? What kinds of traits do they each tend to produce? Give three examples of each.

Intersexual selection refers to sexual selection for increased attractiveness to members of the opposite sex. This form of sexual selection tends to lead to "display" or "advertisement" traits, such as showy or colorful body parts, or exaggerated mating displays. Examples include long tails in male red-collared widowbirds, calling in male frogs, and eye-stalk length in stalk-eyed flies. Intrasexual selection refers to sexual selection for increased ability to compete directly with members of the same sex for access to the opposite sex. Intrasexual selection tends to lead to weaponry, armor, fighting ability, and threat displays. Examples include large body size in iguanas, infanticide in lions, and antlers in deer. Note that some traits may serve both functions. For example, bird song often functions both as a display that attracts females and also as a threat that deters rival males.

In our discussion of rough-skinned newts, we inferred that tail crests in males evolved by sexual selection. Why is this a reasonable inference? Do you think the mechanism of sex- ual selection was male-male competition or female choice? Why? Design an experiment to find out.

It is a reasonable inference for any species that a morphological difference between males and females is probably a result of sexual selection. It is particularly reasonable for this species, since data show that male reproductive success is strongly affected by access to mates, and males must, therefore, be under selective pressure for traits that increase their likelihood of obtaining mates. However, either male-male competition or female choice could explain the crests. To test the hypothesis that female choice has selected for this trait, a sample of females could be given visual access to males with different crest sizes. If female choice is operating, females should consistently prefer the male with the largest crest. Male-male competition could be responsible for the trait if, for example, having a larger crest allowed those males to dominate access to preferred breeding spots. This could be tested with a combination of laboratory dominance trials and careful observations in the field.

What is Lack's hypothesis? Is it supported by most ex- perimental data? If not, why not?

Lack's hypothesis states that birds should produce an "optimum" clutch size each year, which should be the number of eggs that will result in the maximum number of surviving offspring for that year. This seems logical, but Lack's hypothesis appears to be wrong; most birds actually produce a clutch size smaller than the hypothesis predicts. This is probably because clutch size has effects that last well beyond one year, which Lack's hypothesis did not take into account. Data from several species shows that large clutch sizes in one year can reduce clutch size in subsequent years. Additionally, offspring from large clutches may suffer from poorer reproductive performance of their own in later years. Furthermore, clutch size may be phenotypically plastic: in some species, female birds can adjust the number of eggs that they lay, according to environmental factors and their own physiological health.

Suppose adult bee-eaters could raise only 0.3 more off- spring with a helper than without a helper. Would you still expect male bee-eaters to give in to the harassment of their fathers, or would male bee-eaters tend to fight off their fathers? Explain your reasoning.

Male bee-eaters should evolve to resist parental harassment and should tend to raise their own broods instead of helping at their parents' nest. If they try to raise their own broods, they will, on average, raise 0.51 nestlings (average nest success with no helpers), but if they help at their parents' nest, the helping will add only 0.3 more siblings, on average. Since 0.51 is substantially higher than 0.3, and since males are equally related to their own offspring and to their siblings (r = 1/2), males should try to raise their own offspring.

House sparrows often produce two successive broods of young. Males feed their first brood only briefly, but feed their second brood for much longer. Why do males feed first broods less than second broods? (Hint: Consider how C, the cost of feeding the current brood, changes.) How could you test your hypothesis? How is this situa- tion analogous to weaning conflict in mammals?

Males are thought to feed first broods for a shorter period of time because of the cost of not being able to start a second nest. Apparently, males cannot simultaneously feed one brood of young while also starting a second nest. Once B (benefit to the current young) declines below C (cost of not starting a new nest), the male should leave the first nest. The fact that males feed the second group of nestlings for a longer time implies that there is no cost of foregoing a possible third nest; perhaps house sparrows do not have enough time to raise three broods in a year. This could be tested in many ways, including removing males from nests to assess the benefit to nestlings of male feeding, hand-feeding nestlings to assess the additional benefit of prolonged feeding, investigating why and whether males cannot start two nests simultaneously, and investigating whether house sparrows can ever successfully raise three broods in one year. The trade-off of investing in future offspring, versus continuing to care for current offspring who are progressively less dependent on parental care, is exactly analogous to weaning conflict in mammals.

In many katydids, the male delivers his sperm to the fe- male in a large spermatophore that contains nutrients the female eats (for a photo, see Gwynne 1981).The female uses these nutrients in the production of eggs. Darryl Gwynne and L. W. Simmons (1990) studied the behav- ior of caged populations of an Australian katydid under low-food (control) and high-food (extra) conditions. Some of their results are graphed in Figure 11.55. (The graph shows the results from four sets of replicate cages; calling males = number of males calling at any given time; matings > female = number of times each female mated; % reject by M = fraction of the time a female approached a male for mating and was rejected; % re- ject by F = fraction of the time a female approached a male but then rejected him before copulating; % with F-F comp = fraction of matings in which one or more females were seen fighting over the male.) Based on the graphs, when were the females choosy and the males competitive? When were the males choosy and the fe- males competitive? Why?

Males were choosy and females competitive under conditions of low food availability (the control). Males called less (spent less energy trying to attract females) and rejected females a greater percentage of the time, while females tended to seek multiple matings and exhibited more competition with other females. When food is limiting, the male spermatophore represents a significant investment of energy on the part of the male. In this case, female reproductive success is limited by access to mates, whereas male reproductive success is limited by the ability to make spermatophores. When extra food is provided, male spermatophores represent much less of an investment by the males, returning the system to the more usual condition in which male reproductive success will be limited by access to mates and female success by the ability to lay eggs. Under these conditions, males become competitive and females choosy: males spend more time calling (advertising) and reject fewer females; females seek fewer mates, reject more males, and compete less with one another.

Compare and contrast the morphospecies concept, the biological species concept, and the phylogenetic species concept. What criterion does each use to identify spe- cies? What are the pros and cons of each?

Morphospecies are identified on the basis of phenotypic differences that biologists can observe and measure; biological species are identified by failure to produce viable hybrid offspring; phylogenetic species are the smallest monophyletic groups on a tree of populations. The morphospecies concept is widely applicable, but misses cryptic species and can become arbitrary when experts disagree. The BSC is sound theoretically but cannot be applied to extinct forms or the many species that reproduce asexually. The PSC is sound theoretically and widely applicable but the required data are only available for a relatively small number of species.

We have seen how aging can evolve due to two differ- ent phenomena: First, aging may evolve due to muta- tions that have deleterious effects only late in life. As a review, explain how such mutations could ever become common in a population. Second, aging may evolve due to mutations with pleiotropic effects that cause "trade- offs"—positive effects early and negative effects late. What would happen if a mutation arose with a reverse trade-off—that is, a mutation with negative effects early and positive effects late in life? Could such a mutation ever be selected for?

Mutations that have deleterious effects late in life may be maintained in populations via mutation-selection balance. As organisms live, they are continually exposed to a variety of mortality risks-disease, starvation, predation, etc. Even when the likelihood of surviving from one year to the next remains constant, the likelihood of living to an advanced age - the cumulative probability of surviving from year to year across a large number of years - is low. Therefore, the average reproductive benefit to an individual of living to an advanced age is also low (the benefit will be the average number of offspring produced by individuals of that age multiplied by the very low probability of surviving that long). If the benefit of living to an advanced age is low, the cost of failing to live to that age is equally low. And, if the mutation carries a relatively low cost, it may be maintained if it continues to arise in the population at the same rate it is selected out of the population. If the selection against the mutation is extremely low, genetic drift will cause some of these mutations to rise to quite high frequency. A mutation with harmful effects early in life but beneficial effects late in life may seem unlikely to increase in frequency, but in fact it could be selected for if the beneficial effects exceed the harmful ones when mortality is taken into account. That is, any reduction in survivorship must be more than compensated for by later reproduction. This may be the case in the large numbers of species with high rates of juvenile mortality and high adult fecundity.

After a gene is duplicated, what eventual evolutionary outcomes are possible? What is the most likely outcome?

Possible eventual outcomes for duplicate genes include: loss due to drift, gene conservation (duplicate copy retains the same function as the original), nonfunctionalization (duplicate copy acquires mutations and becomes non-functional), neofunctionalization (duplicate copy acquires mutations that give it a new function that differs from the original), and subfunctionalization (both original and duplicate copies acquire mutations such that each performs a separate function that were previously both performed by the ancestral gene). By far the most likely evolutionary fate of a duplicated gene is loss due to genetic drift.

What are the possible outcomes when species that have long been separated geographically come back into con- tact and begin hybridizing, and under what conditions does each outcome occur?

Possible outcomes include (but are not limited to: 1) reinforcement, which occurs when hybrids have lower fitness and therefore natural selection favors assortative mating; 2) hybrid speciation, in which a third species is formed because selection favors hybrids over both parental species in particular habitats, and 3) formation of a stable hybrid zone, in which hybridization is ongoing in a particular geographic area and hybrids are commonly found, but the parental species exist in isolation from each other outside of the hybrid zone. Reinforcement occurs when hybrids have lower fitness than parental species in all habitats, whereas selection that favors hybrids (i.e., hybrids have higher fitness than parental species) can lead to hybrid zones or hybrid speciation. The outcome of hybrid zones versus hybrid speciation, and the location and size of a hybrid zone, often depend heavily on environmental conditions.

How do the genomes of prokaryotes and multicellular eukaryotes differ? What is the evolutionary explanation?

Prokaryote genomes are small and compact, with no introns and few mobile genetic elements, and therefore short intergenic regions. Multicellular genomes, in contrast, are much larger and contain many mobile genetic elements (and therefore large intergenic regions) and many introns within genes. Also, prokaryote genomes have lower mutation rates than eukaryote genomes. One evolutionary hypothesis for the difference in mutation rates is that it results from effective population size, and that prokaryotes, with much larger effective population sizes, experience more effective selection (and less influence of genetic drift) for low mutation rates. However, the evolutionary significance of introns in eukaryote genomes remains unknown.

The examples of the chinook salmon and seed beetles indicate that females, in general, cannot produce many large eggs. Instead, they must choose between produc- ing many small eggs or producing a few large eggs (and sometimes, in unfortunate cases, just a few small eggs). Explain, then, how it is possible for a queen honeybee to produce a very large number of relatively large eggs. (Hint: Consider what the other bees are doing.) Does this suggest a general way in which a female can escape from the size-number trade-off?

Queen honeybees are likely able to produce large numbers of relatively large eggs because they can devote a large fraction of their energy to egg production. The other bees in the colony gather the food, feed the queen, and care for the larvae; her energy can therefore be devoted to a relatively few tasks: maintaining her own body and producing eggs. This suggests that females can, to some extent, escape from the size/number trade-off if they can rely on other individuals to help them maximize energy intake and minimize energy allocated to tasks other than reproduction.

Did the common ancestor of bilateral animals have a heart? Justify your answer by drawing an evolutionary tree and mapping hearts on it.

Recent studies show that regulatory genes in the insect-vertebrate ancestor with a basic function in rhythmic contractility, might have contributed to the development of the heart in both insects and in vertebrates. Based on the traits of its descendants, it is logical to infer that the common ancestor of all bilaterally symmetric animals was not segmented but had simple limbs, a simple eye, a nerve cord but no brain, and contractile blood vessels but no heart. In addition to using presence of heart on the evolutionary tree, think of the dramatic expansions of the Hox gene cluster at the origin of bilaterally symmetric animals, as well as the vertebrates, and the ray-finned fish.

What is reinforcement? Is it an example of genetic drift, natural selection, or sexual selection?

Reinforcement is the evolution of traits that reduce matings between previously isolated populations that have come into secondary contact, due to natural selection against production of low-fitness hybrid offspring. It is an example of natural selection.

Briefly summarize two studies on evolution of RNA populations in the lab. In each experiment, what ability(ies) did the RNA population develop during evolution (i.e., what was the change in phenotype)? Do you think these RNA populations qualify as "life"? Do you think that a self-replicating RNA population will be developed in the lab in your lifetime?

Spiegelman's experiment was one of the first to demonstrate that RNA populations could evolve. In his experiment, an RNA population was replicated repeatedly by an RNA replicase enzyme. The RNA population evolved over time, changing from a longer, more complicated structure that could infect bacteria to a shorter sequence that could not infect bacteria but could be replicated more rapidly. Beaudry & Joyce's 1992 study showed that a ribozyme from Tetrahymena could rapidly evolve the ability to cleave DNA, even though originally it had only been able to cleave RNA. Bartel & Szostak's ingenious experiment showed that RNA populations could evolve the ability to catalyze RNA synthesis, and Wendy Johnston's group has extended this line of research to evolve RNAs that can lengthen a growing RNA strand. "Life" has no agreed-upon definition-precisely because the boundary between nonlife and life is fuzzy. Thus, opinions differ about whether these evolving RNA populations can be considered "alive". Many would say that since these populations could not replicate themselves, they are not (yet?) alive. What do you think?

The scatterplot in Figure 11.54 shows the relationship be- tween the importance of attractiveness in mate choice (as reported by subjects responding to a questionnaire) and the prevalence of six species of parasites (including leprosy, ma- laria, and filaria) in 29 cultures (Gangestad 1993; Gangestad and Buss 1993). (Statistical techniques have been used to remove the effects of latitude, geographic region, and mean income.) What is the pattern in the graph? Does this pat- tern make sense from an evolutionary perspective? One of the parasitic diseases is schistosomiasis. There is evidence that resistance to schistosomiasis is heritable (Abel et al. 1991). What do women gain (evolutionarily) by choosing an attractive mate? What do men gain (evolutionarily) by choosing an attractive mate? Can you offer a cultural expla- nation that could also account for this pattern?

Taken at face value, the data in the graph illustrate a positive correlation between parasite prevalence and the importance of physical attractiveness, suggesting that, in populations where parasite infections are most likely, physical appearance is a mechanism of mate choice. This pattern is consistent with the hypothesis that selection favors mate choice mechanisms that enhance fitness. Under this scenario, males and females are selecting attractive mates because they are less likely to be carrying parasite infections than unattractive mates. This could be because the parasites themselves cause disfiguration, or because the features that are associated with attractiveness cannot be maintained if a portion of the body's energy is being used to fight an ongoing infection. By selecting an attractive mate, an individual reaps the benefit of obtaining a strong genotype (one that confers the ability to ward off parasitic infections) for his or her offspring. A possible cultural explanation for this pattern is that, while attractiveness is still associated with lack of parasites (for the reasons explained above), the mechanism protecting individuals from parasites is simply the wealth and education needed to avoid infection in the first place. Under this scenario, resistance to parasites isn't heritable. Rather, the most attractive individuals are the wealthiest and healthiest, and are preferred because of their material resources.

Briefly outline four possible hypotheses for the emer- gence of the three domains of life. Which is best sup- ported (at present) from the evidence? Which is your favorite hypothesis (this need not be the one you think is most likely to be true!), and why?

The "universal gene-exchange pool" hypothesis proposes a time when genomes were modular, and when organisms assembled their genomes from a common pool. It is not yet clear whether this system is stable and feasible, or whether it could give rise to Darwinian natural selection. The ring-of-life hypothesis proposes that eukaryotes arose from a fusion of archaeans and bacteria. However, this hypothesis cannot explain where eukaryotes got their unique genes, and how fusion could have occurred in the two groups that lack a cytoskeleton. The chronocyte hypothesis proposes that eukaryotes arose from a long-vanished lineage of "chronocytes", one of which engulfed an archaean that became the eukaryotic nucleus. No such chronocytes exist today, but perhaps the eukaryotes' unique genes represent a remnant of the genome of a chronocyte ancestor. Finally, the "three viruses, three domains" hypothesis integrates viruses into the picture, proposing that (a) viruses are a remnant of the RNA World, (b) viruses evolved DNA during arms-race coevolution with their hosts, and (c) three such viruses then converted the three domains from RNA to DNA. Evidence from viral genomes offers a modest amount of support for this hypothesis, though more viral genomes are needed to thoroughly test the hypothesis.

What is the canonical Hox gene expression pattern. Is is it maintained when the Hox genes are not found in a single cluster? What is the evidence?

The canonical Hox gene expression pattern refers to the co-linearity in the spatial patterns of cluster expression. In other words, spatial colinearity is the correspondence between genomic order of Hox gene loci and their spatial locations of expression along the body axis. Hox gene expression is highly conserved in the animal kingdom. However, scientists did not find single Hox clusters in the phylum's Porifera (sponges) and Cnidaria (sea anemones). This suggests that spatial colinearity might be ancestral, but is not essential to the proper Hox gene function. Some data support a scenario in which ancestral Hox genes were clustered, but that the ordered clustering has been lost multiple times. An alternative scenario is that different Hox genes arose early in animal evolution, in dispersed genomic locations, while clustering was a later event that linked these genes.

In some species of deep-sea anglerfish, the male lives as a symbiont permanently attached to the female (see Gould 1983, essay 1). The male is tiny compared to the female. Many of the male's organs, including the eyes, are reduced, though the testes remain large. Other structures, such as the jaws and teeth, are modified for attachment to the female. The circulatory systems of the two sexes are fused, and the male receives all of his nutrition from the female via the shared bloodstream. Often, two or more males are at- Figure 11.52 Distributions of lifetime reproductive success in male and female elephant seals From Le Boeuf and Reiter (1988). tached to a single female. What are the costs and benefits of the male's symbiotic habit for the male? For the female? What limits the lifetime reproductive success of each sex— the ability to gather resources, or the ability to find mates? Do you think that the male's symbiotic habit evolved as a result of sexual selection or natural selection? (It may be helpful to break the male symbiotic syndrome into separate features, such as staying with a single female for life, physi- cal attachment to the female, reduction in body size, and nutritional dependence on the female.)

The cost of male symbiosis for the male is that he can never change his choice of mate. If his female has reduced fertility or poor health, or cannot produce a large number of eggs, he is simply stuck with her (literally). In fact, if she dies, he will die, too. In addition, he may have to share the female with other symbiotic males, so he is not even guaranteed paternity of the eggs. The cost for the female of is that she bears a physiological and energetic cost of supplying energy and nutrients to the males, and the attached males also cause hydrodynamic drag while she is swimming. However, there are also benefits, primarily in mate-finding. It is very difficult to find mates in the vast and very sparsely populated environment of the deep ocean floor. Permanent attachment spares both sexes from having to find a mate or having to struggle to not lose each other. Overall, the males' symbiotic habit is likely the result of both natural and sexual selection. In this environment, sexual selection would favor traits that allowed a male to stay with one female for life, since mates are so difficult to find. Sexual selection, therefore, may have initially selected for the initial stages of the evolution of parasitism (physical attachment to the female). Subsequently, natural selection may have favored those aspects of male anatomy and physiology that allowed males to access energy and nutrient resources of the females. However, males that expropriated too much of the female's resources would bear a reproductive cost in terms of a reduction in the number of eggs the females could produce. Therefore, natural selection should also have favored a reduction in male body size to limit the amount of energy required by the male from the female.

The text claims that eusociality has evolved several times independently within the hymenoptera. What is the evi- dence for this statement? If it is true, in what sense is eusociality in ants, bees, and wasps an example of con- vergent evolution? (See Chapter 4.)

The evidence for independent evolution of eusociality in the hymenoptera is summarized in the phylogeny in Figure 12.37 on page 485. Eusociality evolved in two lineages that are quite distantly related to each other-the sphecid wasp / honeybee lineage, and the paper wasp / ant lineage. Evolution of similar traits in unrelated or distantly related lineages, due to similar ecological pressures, is convergent evolution.

Human siblings often show intense sibling rivalry that typically declines during the teenage years. Suggest an evolutionary explanation for this pattern.

The evolutionary explanation for sibling rivalry that lessens with age is that human siblings are (subconsciously) in conflict for parental resources during a time of life when parental care is especially important. Since a child is related to itself by r = 1 but is related to siblings by r = 1/2, evolutionary theory predicts that each sibling should try to get more than its share of parental resources (food, protection, living space, information, etc.). This puts siblings in direct conflict with each other. However, siblings should not try to completely monopolize parental resources-they should aim for siblings to have one-half the parental resources that they themselves get. Later in life, as children become less dependent on their parents, the benefits of monopolizing parental resources become less and less significant. Humans are then more likely to cooperate with or even assist their siblings.

What is the evolutionary theory of aging? What two ma- jor mechanisms are associated with it? Is natural selection crucial in both mechanisms?

The evolutionary theory of aging states that organisms are, in principle, capable of evolving longer life spans, and that if they have not done so it is simply because natural selection for increased life span has not been strong enough to counteract other, opposing, evolutionary forces. The two major mechanisms are thought to be: 1) accumulation of deleterious mutations, which are caused primarily by genetic drift, not natural selection; and 2) natural selection involving evolutionary trade-offs, usually between early and late-life effects, or between repair and reproduction.

Listed below are four possible causes of aging that were discussed in the text and in the questions above. As a re- view, name the theory that is associated with each cause, and describe whether selection for a longer life span is possible under each theory. What predictions does each theory make about the effect of ecological mortality (death due to external causes—predators, starvation, etc.) on aging rate? • "Wearing out" due to metabolic activity • Reduction in size of telomeres with each cell division • Mutations that have negative effects late in life • Mutations that have positive effects early and negative effects late in life

The first two, "wearing out" and telomere shortening, are subcategories of the rate-of-living theory. Under the rate-of-living theory, organisms should not be able to evolve longer life spans because they have already been selected to resist and repair damage to the maximum extent possible, and ecological mortality should have no effect on aging rate. The last two categories (deleterious mutations and antagonistically pleiotropic mutations) are associated with the evolutionary theory of aging, under which life span represents an evolutionary trade-off between repair and reproduction. According to this theory, organisms can and will evolve longer life span if subjected to appropriate selective pressures. In particular, populations with lower rates of ecological mortality should evolve delayed aging.

Under what conditions will sexual selection produce different traits in the two sexes (i.e., sexual dimorphism)? Why is one sex often "choosy" while the other is "showy"?

The fundamental cause of sexual dimorphism is an asymmetry in the amount of parental investment in a given mating and the care of any resulting offspring. The sex that invests less time and energy in this process tends to be limited merely by access to mates, and hence is under strong selective pressure to attract as many mates as possible. The result is evolution of showy traits that attract the opposite sex, and competitive traits for competition with the same sex. This sex is often (but by no means always) the male, since ejaculates tend to be relatively cheap and males of many species do not provide parental care. The sex that invests more time and energy in this process is usually not limited by access to mates, and hence is not under strong selective pressure to find as many mates as possible. Rather, this "parental" sex is under pressure to select just a few good mates, sometimes just one. This sex is often (but by no means always) the female, since eggs are relatively large and females often provide parental care

Which is more common in human cultures—eusociality (look back at the three requirements of eusociality; can you think of any human cultures that fit?) or a helper-at- the-nest social system? Which do you think is generally more common in social animals? Why?

The helper-at-the-nest social system is widespread in almost all human cultures; older siblings very often help with rearing young brothers and sisters, rather than starting their own families as soon as they are biologically able to. True eusociality, with specialized castes of worker individuals who never reproduce, is rare in humans, though some cultures have had slave or eunuch castes that may qualify. In general, the helper-at-the-nest system is much more common in social animals than is eusociality, because the helpers will almost always get a chance at reproduction eventually, whereas in true eusociality, a nonreproductive individual has almost no chance of reproduction.

Assuming that the grandmother hypothesis of meno- pause is correct, speculate on what aspects of a species' behavior and sociality may make menopause likely to evolve. For instance, is it important whether the spe- cies is highly social, or whether the species lives in kin groups? Might the age of independence of the young be important? Could menopause ever evolve in a species without parental care, such as aphids or willow trees? As fuel for thought, consider the likelihood of evolution of menopause in (1) orangutans, who live in small groups consisting simply of a female and her dependent young; (2) lions, in which females are very social and remain with their female kin for most of their lives; and (3) Ara- bian oryx, a species of antelope that lives in small family groups in arid deserts and must sometimes find distant waterholes known only to the older oryx.

The important underlying assumptions of the grandmother hypothesis for the evolution of menopause are that the reproductive success of young mothers increases with their ability to provision their weaned young and that, as women age, the benefits of having additional offspring are low relative to their costs. Under these circumstances, women past a certain age will increase their inclusive fitness more by helping their daughters provide for their older children than by having more children of their own. For this scenario to apply, species probably must be fairly social, as this is a general correlate of having long periods of juvenile dependence on adults. Living in kin groups is important at least to the extent that women should live with their own adult daughters and their offspring. Because the adaptive benefit of menopause is increased parental care for older offspring, menopause is unlikely to evolve via this mechanism in species that lack parental care. Menopause is unlikely to evolve in orangutans because grandmothers aren't part of the essential social group and therefore have no opportunity to increase their own fitness by helping with their grandchildren (chimpanzees would be a likelier species). It is more likely to occur in lions, but may be limited by the life span of adult females and, perhaps more importantly, the ability of the oldest females to contribute to providing for the young (it's likely that the oldest females will not be very good hunters). It is perhaps most likely to occur in the oryx (assuming that grandparents make up part of the social groups), where the oldest individuals can make a unique contribution to the fitness of younger individuals.

In the chain of events leading from the abiotic synthesis of biological building blocks to the evolution of eukary- otes (Figure 17.10), which transition appears to be the least characterized? Why do you think this is the case?

The intermediate stages between the formation of simple organic compounds and complex biological polymers seem to be poorly characterized; the problems of chirality and activation, as well as of catalysis seem to be particularly difficult to solve. One general problem seems to be that the chemistry of organisms is actually fairly precise and narrow (we use a vanishingly small percentage of the possible kinds of each of our major building blocks, for example) compared to the much more complex and variable world of organic molecules that exists outside of living systems. (Readers might consider some other step to be the least characterized step.)

When the Panama land bridge between North and South America was uncovered, some North American mammal lineages crossed to South America and under- went dramatic radiations. For terrestrial species, did the completion of the land bridge represent a vicariance or dispersal event? Did the recent construction of the Pan- ama Canal represent a vicariance or dispersal event for terrestrial organisms? For marine organisms?

The opening of the land bridge allowed terrestrial species to disperse from North America to South America (as well as the reverse); it represents a dispersal event for terrestrial species. The more recent construction of the Panamal Canal represents a vicariance event for terrestrial organisms because populations on either side are now separated by a barrier (the canal.) However, for marine organisms the opening of the Panama Canal represents a dispersal event because organisms can now disperse from the Atlantic Ocean to the Pacific Ocean, and vice versa.

Now suppose that during your research, you bring a large population of these animals into captivity. You notice that their annual survival rate immediately jumps from 0.80 to 0.95, primarily due to protection from predators. Make a prediction about whether the captive population will evolve changes in fertility or life span, simply due to this reduction in predation. Could this same process be occurring in zoo populations of captive animals today? Explain your reasoning.

The population will likely evolve a longer life span and delayed aging. Since more of the population is surviving to an advanced age, natural selection for survival and reproduction at advanced ages will be stronger. Due to the classic trade-off of repair versus reproduction, this increase in life span will likely be accompanied by reduced fertility or fecundity in early life (and it will be compensated for by increased fecundity later in life). These processes are almost certainly occurring in zoo captive populations, particularly those that are completely genetically isolated from wild populations. Unanticipated evolution in life-history traits of aging and reproduction is always a concern whenever a captive population experiences different patterns of mortality and reproduction than it would in the wild.

Pathogens require a minimum population size of potential hosts. If the host population is too small, in a short time the entire population has either been killed by the pathogen or has survived the initial infection and become immune. If this occurs, the pathogen dies out. What evolutionary changes in a pathogen might increase its ability to survive in a smaller population? For example, measles requires a host population of about 500,000 humans, while diphthe- ria can get by with only about 50,000 humans. Develop some hypotheses for why diphtheria can survive with just one-tenth the number of hosts. For example, how might these two diseases differ from each other in transmission rate, virulence, latency to infection, or mutation rate?

The problem that pathogens face in small host populations is that they must not "use up" hosts (kill them or cause them to become immune) any faster than new, vulnerable hosts appear (through birth, migration, or loss of immunity). One solution is for a pathogen to move through the population at a leisurely rate, infecting new hosts only occasionally and staying a relatively long time in each host. Alternatively, new hosts can be "created" if previously infected hosts cannot maintain immunity. In comparing diphtheria to measles in humans, diphtheria might be expected to have a faster mutation rate (so that hosts cannot maintain immunity), a less effective vaccine, lower virulence, a lower transmission, or a long latency period. As it turns out, diphtheria and measles have a similar latency and a low mutation rate, and diphtheria is more virulent. But diphtheria is much less contagious, and, in addition, many people vaccinated against diphtheria in childhood do not maintain lifelong immunity.

How did Darwin explain the "5% of a wing problem"? Was his explanation correct? On what evidence?

The question was: "How can evolution ever make a wing (in Darwin's gradualist view of natural selection), if 5% of a wing provides any benefit for flight?" Darwin himself explained this problem when he wrote: "Bear in mind the probability of conversion from one function to another can't possibly evolve via change in function." Although some of the evolutionary biologists disagreed, modern experimental evolution supports Darwin's answer. For example, Kingsolver and Koehltested proposed a hypothesis that the proto-wings of insects functioned in thermo-regulation, before flight evolved. They made physical models on which they could vary the size of the wings and found out that even a small increase in wing size improves model insect's ability to regulate its body temperature. Such proto-wings later begin to provide an aerodynamic function.

What are the two predictions of the rate-of-living theory of aging? What data exist to support or refute the two predictions?

The rate-of-living theory of aging holds that aging is an inevitable consequence of irreparable damage to cells that occurs due to normal metabolic processes, and that most organisms have already evolved the maximum life span possible, given their metabolic rates. The two main predictions of this theory are: 1) life span should be correlated with metabolic rate, such that total lifetime energy expenditure should be similar across species; and 2) species should not be capable of evolving longer life spans. Austad & Fisher's 1991 analysis of 164 mammal species refuted the first prediction. They found that there is high variation in lifetime energy expenditure across mammals. Several other experiments, including Luckinbill's fruit fly experiment, have refuted the second prediction by showing that species can evolve longer life spans, and can do so quite rapidly if selection is strong enough. Thus, though metabolic activity may have certain consequences for aging, life span in most species appears to not be limited by metabolic "wear and tear," but rather is an evolved trait that can change if selective pressures change.

doms" need to be revised and which are still valid? Has this new tree of life stood the test of time, as other genes have been studied?

The small-subunit rRNA analysis revealed that life on earth is best separated into 3 groups, not five; and that the "protists" and "bacteria" (which originally included the "archaeabacteria") need to be revised. Protists turn out to be several different groups of eukaryotes that are not closely related to each other at all. The "archaeabacteria" turn out to be a distinct group, and one that is probably more closely related to eukaryotes than to other bacteria. Plants and animals, on the other hand, are valid monophyletic groups. The fungi require a relatively minor revision-removal of the slime molds, which turn out to be an unusual group of eukaryotes. (This comes as no surprise to fungi researchers, who have always been rather puzzled by the peculiar biology of the slime molds.) The small-subunit rRNA tree is now recognized to be only one of many possible trees, due to extensive lateral gene transfer among early organisms. However, whole-genome analyses indicate that the basic outlines of the tree are probably valid.

In the experiment diagrammed in Figure 17.5, why was it important for the researchers to include a tag on the end of the substrate RNAs?

The tag sequence allowed selection to occur. The tag caused any pool RNA with the desired catalytic activity to be preferentially bound to an affinity column, allowing the scientists to separate these molecules from those that lacked the catalytic activity. The affinity column was, in effect, the selective agent determining which nucleotides would form the next generation in the selection experiment.

Do you think it would be possible, with artificial selec- tion, to breed fully-armored freshwater sticklebacks that grow fast? Why or why not?

The three spine sticklebacks exhibit pleiotropy in the alleles of the Ectodysplasin gene. This gene controls/contributes to the development of both body armor and body size. Thus, freshwater stickleback populations evolve larger body and less armor, because they don't have large fish as main predators and vice versa, marine populations tend to evolve more armor and as a trade-off, a smaller body. We could not breed a fully armored freshwater stickleback that grows fast, based on this gene. If we find another gene that contributes to the body size and select for it, along with the Ectodysplasin genotype that produces heavy armor (and smaller size), we could, at least in theory, create such a population.

AnavianinfluenzavirusoftypeH5N1hasrecentlyevolved a "high pathogenicity" (hp) strain that causes severe illness in most wild birds (except ducks) as well as in domestic poultry. A few humans have been infected. The World Health Organization (WHO) currently inspects every human case with particular attention to how the patients contracted the virus. Why is this virus a cause for concern, and why are WHO officials so interested in each patient's source of infection?

The worst human flu epidemics have been due to influenza A viruses that have moved to humans from another species (usually pig or bird). The worst epidemic of the last century was due to an avian influenza that may have moved directly into humans. Since H5N1 has recently developed the ability to move from birds directly to humans, and because it is a "high pathogenicity" strain, WHO officials are concerned that it could cause another epidemic. They are particularly interested in whether each human patient contracted the disease from a bird or from another human. If H5N1 evolves the ability to move from human to human, it will be much more likely to cause an epidemic.

Why has it been useful to study Hox genes in many taxa? What has it suggested about their original function?

There are many important findings that came from the studies of Hox genes in the past three decades. One is the discovery of the deep homology that occurs because some components of the regulatory network for a structure have been conserved, even while other components changed enough to result in a novel morphological structure. Another is the discovery that changes in the timing and location of certain Hox genes are associated with changes in segmentation of various arthropod groups, as well as with changes in where appendages occur—particularly in the evolution of the legless abdomen in insects. These studies also indicate that developmental biology should further integrate with evolutionary theory and genetics. Since animal Hox genes have in common canonical spatial expression and are always expressed in the nervous system, those might be their original function.

Speculate about why some greater ani couples form 2-pair coalitions when 3-pair coalitions have higher re- productive success. How could you test your idea?

There are many potential hypotheses for why some greater anis form two-pair groups rather than three-pair groups. For example, it could relate to access to resources—if greater anis are territorial, and three-pair groups need to defend larger territories in order to have enough food for their offspring, perhaps two-pair groups are a better strategy than three-pair groups when the group territory is small. Another example would be if nesting in a three-pair group has a hidden cost over time, such as reduced immune defense against parasites because being a member of a three-pair group is more stressful (chronically elevated levels of stress hormones are known to suppress immune function). Yet a third example would be if there is a benefit to males of nesting in two-pair coalitions—remember that the data shown in Figure 12.3 on page 457 indicate that females have higher reproductive success in three-pair groups, but we cannot assume the same for males until we collect appropriate data.

Within the past 50 years, soapberry bug populations in the United States have diversified into populations distin- guished by markedly different beak lengths. These bugs eat the seeds at the center of soapberry fruits. Native and recently introduced varieties of soapberries differ greatly in fruit size. Describe the experiments or observations you would make to launch an in-depth study of specia- tion in these bugs. What data would tell you whether they are separate populations evolving independently, or a single interbreeding population? Many museums contain insect specimens from decades ago. What would you examine in these old specimens? What information about the host plants would be useful?

There are many ways to design observational or experimental studies to answer questions about soapberry bug speciation. For example, it would be important to know what the feeding success of each population is on fruits from different soapberry varieties. There is an obvious hypothesis that the bugs' beak lengths have evolved in response to the size of the soapberry fruits from which they eat the seeds. To evaluate whether soapberry bug populations are evolving independently or are a single interbreeding population, DNA sequence data from neutral markers would be very useful, such as in the Audubon's warbler example in this chapter. In the museum specimens it would be informative to measure soapberry bug beak lengths from before and after certain soapberry varieties were introduced. It would also be important to know the average fruit size for each soapberry variety, in addition to their date of introduction.

Can evolution proceed in jumps? Give examples to sup- port your answer.

There is evidence that the tempo and mode of evolution might vary. In some cases the rate of evolutionary change might be higher than usual, and evolution seems to proceed in jumps, as it has been documented in both plants and animals. Among the mechanisms for evolutionary leaps is mutation in the genes encoding transcription factors. Strong positive selection on a genetic novelty or a genetic change in developmental genes might lead to speciation. This could explain relatively rapid diversification in the Animal kingdom. In plants speciation seemed to be promoted by similar genetic mechanisms, as well as with changes in chromosomal numbers (polyploidy). In addition, lateral gene transfer and impact of transposable elements might be a contributing factor of the seeming "jumps" in the evolutionary history of many clades, beyond plants and animals.

Examine closely Figure 17.4. Recall that mutations were introduced at 140 randomized nucleotide positions. By the ninth round of selection, 4 nucleotides were respon- sible for most of the evolutionary change. Look at the other 136 nucleotides. Many of these have reverted to their original state. Why?

These were presumably nucleotides in which the mutations that had been introduced were detrimental, not beneficial. The mutant forms were apparently eliminated by purifying selection, and only those ribozymes with the original wild-type nucleotides at those positions were able to function. (Some other nucleotide sites show mild accumulation of mutations that are probably due to genetic drift.)

Male butterflies and moths commonly drink from puddles, a behavior known as puddling. Scott Smedley and Thomas Eisner (1996) report a detailed physiological analysis of puddling in the moth Gluphisia septentrionis. A male G. sep- tentrionis may puddle for hours at a time. He rapidly pro- cesses huge amounts of water, extracting the sodium and expelling the excess liquid in anal jets (see Smedley and Eisner's paper for a dramatic photo). The male moth will later give his harvest of sodium to a female during mating. The female will then put much of the sodium into her eggs. Speculate on the role this gift plays in the moth's mat- ing ritual and in the courtship roles taken by the male and the female. How would you test your ideas?

This sounds like a case of female choice based on resources provided by the male. If so, selection would favor mechanisms that allowed females to reliably choose the males that provided the most sodium for her eggs. Those mechanisms should include, minimally, variation in male phenotype (morphological or behavioral) correlated with the amount of sodium he sequesters and neurological mechanisms in the female that allow her to assess phenotypic variation in the males and select the ones with the most sodium. These mechanisms, in turn, should be associated with a general courtship pattern in which males "advertise" to females and females select among rival males. To test these ideas, a first step would be to measure many aspects of male phenotype and explore them for correlations with the amount of sodium males can provide. If specific phenotypic features are correlated with sodium, then controlled mate choice tests should reveal that females prefer the phenotypes generally associated with high sodium levels. If the phenotypic trait in question is behavioral and flexible (i.e., males behave differently when they've been able to sequester large amounts of sodium than when they haven't), then we could do more sophisticated tests in which the amount of sodium available to a male is controlled and male behavior and female choice are assessed.

Why was the gene for small-subunit RNA particular- ly well suited for studies of the phylogeny of all living things? Do you think this gene is also useful for studying relationships among living mammals, such as for eluci- dating the family tree of humans, chimpanzees, and go- rillas? Why or why not?

To be useful in building a phylogeny of all living things, researchers needed a gene that (1) is present in all living organisms, and (2) has always been under very strong stabilizing selection, such that very few differences accumulate per year. Otherwise, the gene would have accumulated so many differences in the ~2 billion years that life has been evolving that its sequence would be unrecognizably different in distantly related groups. In addition, (3) the gene needed to perform the same function in all living things, since any changes in function could cause acceleration in genetic divergence due to natural selection for the new function. Small-subunit rRNA gene fulfills all these criteria. This gene, however, is useless for comparing groups of mammals to each other. Why? Because it changes so slowly that all mammals still share virtually exactly the same sequence. The very feature that makes it so useful for studying ancient phylogenies invalidates it for studying more modern phylogenies.

Consider Michael Lynch's hypothesis that mutation rates are determined by an interplay between natural selection and genetic drift. Now imagine an experiment in which you keep many different populations of E. coli bacteria, each at a different effective population size, for many thousands of generations. How would Lynch's hypoth- esis predict that mutation rates would evolve in popula- tions of different sizes?

Under Lynch's hypothesis, E. coli populations kept at large effective population sizes would evolve lower mutation rates, and populations kept at small effective populations sizes would evolve higher mutation rates (due to the greater influence of genetif drift in smaller populations).

It has now become clear that birds are the primary host of West Nile virus. If the virus reaches a human (or horse), it is not spread from human to human (nor from horse to horse) and is unlikely to be transferred back to birds. Is the virulence of the virus in humans and horses an example of coincidental evolution or shortsighted evolution? Explain your reasoning.

West Nile virus virulence in humans and horses is an example of coincidental evolution. Once the virus reaches a human or horse, it will not find another host-it has reached an evolutionary dead-end, is unable to spread any further, and that particular population of viruses will die out with that host. Thus, we can infer that the virus was not selected to cause disease in either mammal species. Instead, West Nile was selected to cause disease in birds. Its ability to infect some mammals appears to be a coincidental side effect of the similar physiology of birds and mammals.

Most domestic female rabbits will get uterine cancer if they are not spayed. The cancer usually appears after the age of 2 years. Describe a hypothesis for why rabbits have not evolved better defenses against uterine cancer. What do you think the average life span of a wild female rabbit might be? What do you think is a typical cause of death in wild rabbits? Why do you think that uterine cancer, and not (say) pancreatic cancer or throat cancer, is the most common cancer in female rabbits?

Wild rabbits most likely die from predation at a relatively young age; a wide variety of birds, mammals, and even snakes may prey on them. Specifically, the fact that uterine cancer usually appears after the age of 2 indicates that female rabbits in the wild usually die at or before the age of 2. That is, since natural selection has apparently been able to limit the occurrence of cancer before the age of 2, but not after, this indicates that much of the population survives this long, but not longer. Given a relatively high rate of ecological mortality, selection should favor traits that permit early maturation and the production of large numbers of offspring in a relatively short period of time. In mammals, repeated pregnancies involve repeated cycles of growth of the uterus. Rabbits have likely faced an evolutionary trade-off for rapid uterine growth early in life to support large litters of young, but at the cost of repair mechanisms that might have prevented uncontrolled rapid uterine growth later in life (i.e., uterine cancer).

Would glaciation in northern Europe and North Amer- ica have created vicariance events over the past 150,000 years? If so, how? (It may help to find a map showing the extent of the glaciers. Also think about the changes that took place in areas not covered with ice.) Which organ- isms might have been affected? For example, consider the different effects glaciation might have on small mam- mals, migratory birds, and trees.

Yes, because glacial sheets could split habitats into fragments separated by ice, or because climate change associated with glaciation could fragment large areas of forest or grassland. Fragmentation should reduce gene flow most in species that do not readily disperse long distances, such as salamanders, snails, and trees with large seeds.

In interactions between species, parasitism occurs when one species gains a fitness benefit and another suffers a fitness loss. In contrast to predation, parasites are small relative to their hosts and kill the host slowly if at all. Based on this definition, should mobile genetic elements be considered parasites? Should biologists still use the original term used to describe them—"junk DNA"?

Yes, because transposable elements increase in fitness by spreading to new locations, which reduces host fitness. "Junk DNA" is less appropriate to describe these sequences because they are not waste products or broken pieces of normal cellular genes.

Look again at Figure 13.4, which illustrates fertility and survival as a function of age in three different species. a. What similarities are there across all three species? What is the general trend in fertility and in annual probability of survival? Why are these trends consid- ered to be an evolutionary puzzle? b. Which species has the best probability of survival even in old age? This is a characteristic of this taxon. Do you remember another animal (a mammal, dis- cussed later in this chapter) that has a similarly high probability of survival in old age? What trait do these long-lived animals have in common? c. In red deer, how do patterns of survival and repro- duction vary with the two sexes? Why do you think these differences occur between males and females?

a. All three species show a reduction in fertility, and a reduction in probability of survival, with increasing age. These two trends constitute the central puzzle of aging, or senescence. Aging is an evolutionary puzzle because it obviously reduces fitness. Natural selection should (it seems) result in slower aging, or no aging at all, yet it has not. b. Of the three species shown in this figure, the bird has the best probability of survival even in old age. As it turns out, this is a characteristic of birds in general - most birds live much longer, and age more slowly, than other animals of similar body size. The mammals with the highest life span (relative to body size), discussed later in this chapter, are bats. The obvious trait that birds and bats share is flight. It is not clear why flight is associated with slow aging and long life span, but one possibility is that flight may offer protection against ecological mortality, particularly from predators. This may allow the survival of a greater proportion of the population into old age, which in turn should cause stronger selection for slower aging and increased life span. c. In red deer, males have much greater variation in reproduction across their life span, with a high peak in reproduction in the middle years, and very low fertility when young or old. Females have much more even reproduction across years, producing fewer young per year, but producing young for many more years than males do. These differences are related to the social system of red deer. The tendency of females to continue reproduction even into old age may have resulted in stronger selection for females to evolve greater resistance to aging. This may explain why females' probability of survival in old age does not decline as steeply as it does in males.

We have seen how the genetic diversity within a tumor can be used to estimate the tumor's history (see Figure 14.20). a. In what ways is this similar to the process of recon- structing the evolutionary history of organisms? In what ways is it different? Do the genetic traits we use to reconstruct a tumor's history need to be selectively neutral? Why or why not?

a. If some of the cells in a tumor population evolve a faster mutation rate, they will accumulate genetic differences from ancestral tumor cell lines at a faster-than-predicted rate, and they will appear to be older than they actually are. b. The genetic markers used in these analyses should be selectively neutral. As discussed in Chapter 7, loci that are under strong positive selection can accumulate new fixed mutations at a faster-than-expected rate (i.e., faster the neutral hypothesis). Strong selection, just like a change in mutation rate, can distort apparent ages and the timing of branching points in a phylogenetic analysis. (In their study, Shibat et al. studied selectively neutral microsatellite markers.)

. b. In the study of streptomycin resistance, why did Shrag and colleagues use genetically manipulated bacteria, instead of the original wild-type bacteria, to compare sensitive versus resistant strains? Summarize the key finding of Shrag et al.'s study. Why are these results worrying to the medical and veterinary professions?

a. Shrag et al. wanted to test whether a back-mutation to sensitivity would be favored after many generations of evolution in the presence of antibiotics. Comparing the resistant strain to a wild-type strain would not be a fair test of this question because the wild-type strain would lack whatever other genetic differences might have accumulated during the generations of evolving in the new environment. Their solution was to splice just the sensitive gene-the desired back-mutation-into the resistant strain. b. The key finding is that even after an antibiotic is withdrawn from use, bacterial populations may continue to be resistant. Back-mutations to sensitivity will not necessarily be favored. This is bad news for efforts to reduce antibiotic resistance by reducing use of antibiotics.

A common objection to genetically modified food, and to genetic engineering in general, is that it is "not natural for genes to cross the species barrier." Com- ment on whether this argument is logically sound. Whether or not it is "natural" for genes to cross spe- cies barriers, many people have additional worries about genetically modified food. One such concern is the possibility that the genetically modified or- ganisms might escape into the natural environment, where they could, conceivably, compete with other organisms and cause problems. Is this also a concern for research projects aimed at evolving self-replicating RNA populations? Which are more likely to survive if they escape into the natural environment: geneti- cally engineered modern organisms or self-replicating RNA populations? Why?

a. The tree-of-life phylogenies show clearly that, at one time, it was extremely common for genes to cross the species barrier. The "species barrier", in fact, may not have existed, and gene transfer was apparently more the rule than the exception. Lateral gene transfer continues to be quite common today among bacteria and archaea, and occurs occasionally in eukaryotes due to viruses. Therefore the "unnaturalness" of gene transfer, by itself, is an illogical argument against genetic engineering. (This does not negate other potential arguments.) b. Genetically engineered modern organisms are far more likely to survive in the wild than are self-replicating RNA life forms. This is because genetically engineering modern organisms retain, from their original genomes, a sophisticated battery of other genes that may allow them to survive and thrive in a variety of modern environments. In contrast, any young population of self-replicating RNA molecules would almost certainly be eaten instantly by bacteria the moment it "set foot" in the outside world, because it would lack all of the defenses that other existing life forms have evolved over the eons. If protected from being eaten, it would likely starve, since it would be dependent on a pool of abundant, easily accessible inorganic compounds for its metabolism-and these no longer exist in most modern environments. Genetically engineered modern organisms are far more likely to survive in the wild than are self-replicating RNA life forms. This is because genetically engineering modern organisms retain, from their original genomes, a sophisticated battery of other genes that may allow them to survive and thrive in a variety of modern environments. In contrast, any young population of self-replicating RNA molecules would almost certainly be eaten instantly by bacteria the moment it "set foot" in the outside world, because it would lack all of the defenses that other existing life forms have evolved over the eons. If protected from being eaten, it would likely starve, since it would be dependent on a pool of abundant, easily accessible inorganic compounds for its metabolism-and these no longer exist in most modern environments.

Suppose you discover a new gene family in your favor- ite study organism, which includes many similar but not identical genes that all arose from a single ancestral gene via duplication events. What data would you gather, and what calculations would you make, to explore the hy- pothesis that the expansion of the gene family was fa- vored by natural selection (i.e., adaptive)?

t would be useful to see if the gene family is present in closely related species. If so, one could gather gene sequences to compare the phylogeny of the species to the gene tree for all of the genes in the family, across species. This would allow one to infer when the gene duplication events occurred that resulted in the gene family. But the most informative approach regarding the role of selection would be to compare the individual gene sequences within the gene family, and to calculate the rates of nonsynonomous and synonomous mutations. A dN/dS ratio greater than 1.0 for this gene family would indicate positive selection, suggesting that the gene family expansion was favored by natural selection and is indeed adaptive.