Population Biology, Test 1. name ______•Most people will finish well before the 75 minutes are up, but those few who don't may without speaking follow me to the room next to my office where more time will be provided. If you want to use my dictionary or to say something to me, raise your hand. •Be very careful to not even look like you are peaking at other people's tests or your notes. If you even look suspicious I'll have to move you and it's disruptive. Also, the sequence of questions is different on neighboring tests, so you won't get very far cheating even if you try. •Don't worry tonight if you were unable to answer every question. This is a hard test meant to allow great students to show their stuff, but the grading system is lenient. You can miss quite a few questions and still get an okay grade. When two or more answers seem possible to you, I suggest guessing among them and moving on. 1. Populations that have plenty of resources a. are at carrying capacity. b. grow arithmetically (linearly). c. grow exponentially (geometrically). d. have discrete generations rather than continuous generations. e. are at Hardy-Weinberg equilibrium. 2. The study of quantitative trait loci (QTLs) a. is bringing together the ecology of population growth (focusing on N) and the study of population genetics (p's and q's). b. is a way of showing that hitchhiking has occurred whereby a neutral has changed in frequency by being linked to a that swept through the population by selection. c. is a way of accounting for the proportion of variance in quantitative traits that is explained by particular linkage groups in a mapped genome. d. was championed by Thomas Henry Huxley in England and Asa Gray in America. e. was used extensively in the empirical work of Fisher, Wright and Haldane who are remembered mainly for their contributions to gathering data of this sort. 3. Genetic load a. should decrease if there is an increase in mutation rate. b. is the effect of a single locus. c. should increase in organisms with smaller genomes. d. is mainly the result of that are lethal and not mutations that are deleterious, since the presence of a deleterious mutation does not necessarily mean the individual will die. e. is inevitable in every population because mutations are inevitable and elimination of inferior implies a reduction in mean fitness. 4. After Mendel's laws were rediscovered, a. the old problem that doesn't allow selection to get anywhere in a large population was quickly laid to rest. b. the Mendelians and Biometricians cooperated to form the so-called "Neo-Darwinian Synthesis". c. Darwin revised The Origin of Species to take particulate inheritance into account. d. Fisher, Wright, and Haldane conferred with Darwin and arranged to have Mendel's paper presented at a meeting with a paper by Darwin read immediately thereafter. e. there were a couple of decades when evolutionary and genetical research developed but when there was not a realization that "many Mendelian genes of small effect" could account for gradual quantitative . 5. Liebig's law of the minimum states a. all resources are more or less equally limiting.

1 b. conditions may be limiting, but resources will not be. c. biotic factors affect population size more than abiotic factors. d. populations tend to grow until limited by one factor or sometimes two. e. populations cannot go extinct because they would be saved by density dependence. 6. Under Haldane's model for selection against a recessive allele and for a dominant allele, write down the genotypic frequencies before and after selection given the chances of survival Haldane specified. Be sure that your frequencies are relativized. You may use the usual notation and shorthand of p, q, and W without going into how these are defined. (Note that the table does not strictly follow the presentation in the text–you have to understand what you're remembering).

Relative chances of Relative Frequency Relative frequency survival before selection after selection AA 1 Aa 1 aa 1-s

7. Regarding niches, a. A realized niche is one that is the result of , whereas a fundamental niche is the result of ecological fitting. b. Warblers have fundamental niches, whereas badgers have realized niches. c. The realized niche is fixed–its existence and circumscription are real even in the absence of a species to fill it. d. Charles Elton believed that the niche is partitioned by competition among all the species that happen to exist in that particular community. e. G. E. Hutchinson treated the niche as a hypervolumn in hyperdimensional space where each axis of the space represents an environmental factor. 8. a. can only occur by , by definition. b. can only occur by , by definition. c. is descent with modification when applied to microorganisms such as bacteria and yeast. d. is defined as change in allele frequency over time. e. usually proceeds by the inheritance of acquired traits. 9. Which of the following is not an "ultimate" explanation but rather is a "proximate" explanation? a. The reason the vas deferentia loop way over the ureters rather than connecting directly to the urethra is because evolution proceeds by gradual quantitative modifications not by saltatory anatomical reorganizations. b. Polar bears have a pelt of long translucent that are hollow and conduct light to their black skins where it is turned to heat, and short cream-colored hairs that are very good at retaining that heat. These features were selected for in the cold Arctic environment. c. In an experiment with 12 replicate lines of Escherichia coli, all evolved heightened glucose utilization efficiency (about 35% better than the ancestor) because selection favored parallel evolution in the glucose-limited environment provided by the researchers, but the 12 lines diverged in their latent abilities to use other sugars because of the randomness of mutations. d. If you had chickenpox as a child (or were vaccinated), you are very unlikely to get it again because exposure stimulated a specific lymphocyte in your system to proliferate into not only a large number of plasma cells that would have killed the chickenpox viruses but

2 also a large number of memory cells that are poised to attack any future chickenpox virus that is unlucky enough to be in your body. (The antigen-driven cloning of lymphocytes is called "clonal selection".) e. An experiment was done selecting for high bristle number in a population of flies. Bristle number went from 12 to 45 after 75 generations. Then selection was relaxed and bristle number went back down to 30 where it stabilized. The selection targeted on bristle number must have caused the evolution of deleterious alleles that were selected against through some unknown target after selection on bristle number was relaxed. 10. Given the same selection coefficient (s), when would evolution be the faster? a. Right after a new beneficial mutation arose as opposed to when it is near 50%. b. When the new allele that is selected for is recessive and the old allele that is selected against is dominant. c. When the allele that is being selected for is very near fixation (say q=95%). d. In an asexual haploid organism rather than a sexual diploid organism. e. a and b. 11. How has antibiotic resistance evolved since World War II? a. Many pathogenic bacteria have evolved resistance to one antibiotic after another because the use of antibiotics selects for resistance, and resistance spreads from strain to strain through transformation, transdunction, and conjugation. b. Because pathogenic bacteria had a long evolutionary history of flourishing in the presence of mold, they quickly evolved resistance to penicillin, but they have not evolved resistance to fluoroquinolones and other such modern antibiotics. c. Bacteria have such a short generation time, it takes them much longer to evolve than it takes humans and other large animals. d. Resistance to any one antibiotic has been selected for, but because bacteria don't have sex, bacterial lines don't mix their genes, and bacteria have not evolved resistance to multiple antibiotics. e. Bacteria have been around for much longer than other organisms. Some species are resistant to antibiotics and presumably have been for time out of mind. Others can be killed by antibiotics, and that hasn't changed in 65 years (and won't in hundreds of years). 12. Which of the following types of mutations is likely to be selected on, i.e., is not neutral or nearly neutral. a. a change in a nucleotide base that does not change the amino acid, i.e., is synonymous. b. a change in the nucleotide sequence in an intron. c. a change in a nucleotide that results in a bird having a song that humans notice as deviant. d. a deletion of several bases in a pseudogene. e. a change in a codon and the resulting amino acid that doesn't change charge or the active of the resulting enzyme.

13. Peter and Rosemary Grant and their students have studied Galapagos finches for many years. What do their results on selection on beak dimensions illustrate? a. The ecological causes of natural selection can be studied in the wild–during any one season in a small area selection might be measured as directional but averaged over many years it seems more stabilizing. b. It is essentially impossible to measure selection (at least in this system) because it is almost always minuscule–this is because organisms just don't vary to any measurable extent for characters that have been under selection. c. Spatial and temporal heterogeneity do not act to maintain variation because selection is always pushing characters in one direction. d. Stasis in quantitative characters (like beak length or any number of other dimensions) is

3 governed by selection on characters determined each by a single locus. e. You can measure the covariation between dimensions like beak length and fitness easily, but such quantitative variation almost never has much heritability, so it doesn't result in evolution. 14. You notice in a certain species of spider that the male is usually eaten by the female and even seem to have special behaviors that tempt the female to do this. You think... a. This couldn't be adaptive because natural selection always favors mechanisms that promote survival of the individual above all else. b. This must have arisen through Group Selection (not merely selection on individuals in groups) as a form of birth control–groups with a lower intrinsic rate of increase (r) would have survived better than groups that were frequently overshooting carrying capacity. c. I bet the energy in the male spider fortifies his offspring and is useful to them at least sometimes. d. There are probably other populations in which the male eats the female after copulation since nature is generally symmetrical. e. Probably this evolved in a population in which male spiders generally reproduced many times during their life before this behavior arose. 15. Inside a maturing fig, there are four types of gender-specific entities that are maturing–list them. 1______3______2______4______

16. h2 a. can be estimated by regressing offspring values on mid-parent values. b. is the total phenotypic variance as a proportion of the additive genetic variance. c. can be estimated as S/R, where S is the selection differential and R is the response to selection. d. is the square of broad-sense hertiability, and it is more usual to report h (not squared). e. is the variance among individuals that is due to heterogeneity in the environment; it gets smaller the less heterogeneous the environment is. 17. A population of clams is studied looking at the alcohol dehydrogenase enzyme. There are two alleles: the "fast" allele is found to be at frequency 0.60, and the "slow" allele at 0.40. What are the Hardy-Weinberg expected genotypic frequencies?

Genotype Expected Freq. fast-fast fast-slow slow-slow

18. In modern times, there have been a number of sudden crashes in populations of commercial fishes that previously seemed superabundant (e.g., Peruvian anchovies). This has been explained as being due to: a. harvesting below K/2, thus decreasing the populations ability to grow. b. harvesting near K, thus stimulating the population's ability to grow. c. harvesting above K, thus causing the population to undershoot its limits. d. stocking when the population was already near carrying capacity. e. stocking when the population was well below carrying capacity. 19. Which of the following seems not to be the case or at least is implausible as of the writing of

4 our textbook? a. Guppy populations can evolve in life history traits (like size at maturity) in a few dozen generations after a change in the predator environment. b. Orchids with extremely long and narrow nectar spurs (30 cm long) have probably been pollinated during their evolutionary history by animals (moths) with tongues that are that long. c. Kestrals lay an optimal number of eggs in a clutch–they can fledge more than they lay, but this comes at the cost of their ability to fledge offspring in subsequent years. d. The various aminopeptidase Lap alleles found in mussels are neutral and all function equally well regardless of temperature and salinity–there is no temporal or spatial pattern to their variation. e. Geographic variation in the production of cyanogenic compounds in Lotus corniculata is the result of local balancing the local costs of defense and impacts of herbivores, which vary with climate. 20. The sickle cell allele is a. selected for in homozygotes. b. neutral. c. found at higher frequency in people who are from northerly countries than from tropical countries. d. maintained at relatively high frequency in some populations because of heterozygote superiority. e. an example of the spread of a dominant allele that was strongly selected for. 21. Which is a good accounting of conditions affecting adaptive evolution by natural selection? a. Adaptive evolution is the result of heritable variation in traits and a relationship between that variation and fitness variation. b. Adaptive evolution is the result of a relationship between and fitness when there is no relationship between and phenotypes. c. Adaptive evolution is the result of a relationship between genotypes and phenotypes when there is no relationship between phenotypes and fitness. d. Adaptive evolution results from random sampling of alleles in finite populations by meiosis and fertilization. e. Adaptive evolution is not context dependent–if genes are selected for in one environment, they are going to be adaptive in any other environment where the organism can live. 22. Insects that eat the leaves of plants a. are generally considered competitors with the plants, although under odd circumstances they might be mutualists. b. are generally considered mutualists with the plants, although under odd circumstances they might be competitors. c. often have a more or less specialized digestive system that allows them to cope with the secondary compounds in the plants that they eat. d. generally produce secondary compounds that are not part of primary . e. are generally able to live on any kind of plant because plants are all basically the same in their chemistry.

23. What is the connection between and Alfred Russell Wallace? a. Wallace was a biometrician who defended the Darwinian view of gradual evolution after Mendel's laws were rediscovered. b. They independently discovered natural selection. c. They were both involved in the "Synthesis". d. They both realized that allows for natural selection to occur.

5 e. They both studied evolution for years before publishing their conclusions. 24. Draw the logistic growth curve starting at a small population size:

N

time

25. Which of the following is not a reason for the maintenance of genetic , rather is a reason for genetic monotony. a. Negative frequency dependent selection (as in those fish with left- or right-sided mouths). b. There is not enough time over geological periods of a few million years for quantitative genetic traits to be optimized (as from the time of the "first" horse to the "modern" horse for body size to change more than a few centimeters). c. Heterozygote superiority (as in sickle cell alleles). d. The recurrence of mutation at some rate with the hiding of recessive deleterious alleles in heterozygote carriers (as in innumerable genetic diseases each of which is at low frequency). e. fine-grained variation in the environment of selection with some alleles favored in some spots and other alleles in other spots (as with the blue tits nesting in downy and holm oaks). 26. The Hardy-Weinberg assumptions include all except which of the following? a. No meiosis or fertilization. b. No selection. c. Random mating. d. An infinite population size. e. No mutation or migration. 27. What are the limits to adaptive evolution? a. Mutations that cause big rearrangements, if they occur at all, are deleterious so evolution proceeds usually by many small modifications. b. You may find an organism in a novel environment (humans in L.A. schools) where there has not been enough time for selection to have fine tuned them. c. So many aspects of a species may be so coadapted to a way of life or a system of development as to constraint the lineage from spawning other species that are fundamentally novel. d. Natural selection cannot break the laws of physics and chemistry–a land mammal much bigger than an elephant would crush itself to . e. all of the above. 28. Which version is the least misleading as to the evolutionary process that fashions ?

6 a. "In the lineage that led to poinsettias, those plants with alleles that made their bracts red tended to reproduced more than those with alleles that made their bracts green." b. "Poinsettias evolved showy bracts because they needed to in order to survive." c. "The showy bracts of poinsettias arose for the good of the species." d. "The showy red bracts were designed with attracting pollinators in mind." e. "There was a random process that just happened to make all the poinsettias have red bracts." 29. Genetic drift is caused by a. large population sizes. b. natural selection. c. the sampling of gene copies during meiosis and fertilization. d. the opposite of a population bottleneck. e. the opposite of a founder event. 30. Regarding mutations and mutation rates... a. Mutations are not random in the sense of occurring at equal frequency in all locations and under all conditions, only in the sense of favorable mutations not arising in response to their usefulness. b. Mutations in the soma of animals (like in the bone marrow) are passed on to future generations at a higher frequency than mutations in the germ line because there are far more cells in the soma than in the germ line and they divide far more times. c. The point mutation rate per nucleotide is on average, very roughly about 10-5 (1 in 100,000 ). d. The mutation rate for known human genetic diseases is on average, very roughly about 10- 9 (1 in a billion gametes). e. The combined rate at which new neutral mutations arise and go to fixation is 2Neu, where u is the neutral mutation rate per individual, and Ne the effective population size: the population size affects this "substitution rate" because the more individuals there are in a population, the fewer opportunities for mutations and also the quicker they will spread.

7 Population Biology Fall 2000, Test 2 name: ______You may use a dictionary with no writing it. If you need to borrow mine, raise your hand. 1. As regards aging, which is not true? a. Senescence is the phenomenon in which rates of mortality increase with age. b. Selection acts only weakly against deleterious alleles that express themselves after most of reproduction has already happened. c. Selection will favor alleles that have a deleterious effect late in life if they have a beneficial effect early in life. d. Because survivorship inevitably declines, reproduction is selected to occur early in life, which in turn allows for mortality to accelerate with age. e. In experiments where one selects for long life, there is a correlated response to selection for earlier reproduction. 2. You observe the following pattern of overall similarity: A differs from B by only 3 characters, and C differs from D by only 2 characters, while A or B are quite different from C or D with the smallest pairwise difference being of 10 characters between B and C. Several phylogenies could give rise to this pattern. Place marks representing character changes on both the following phylogenies so that either would explain the patterns of overall similarity. A B C D A B C D

3. Parasites have been suggested to play the following role in the evolution of their hosts. a. Selecting for asexual lines over sexual lines as in the New Zealand snail Potamopyrgus antipdarum. b. Making showy male birds preferred by females over drab males based on the "handicap" principle. c. Causing the hosts to encourage great virulence thereby keeping the parasites from infecting others in their species (at least when the infection rate is low enough so that usually only one clone of the parasite is present in a host). d. Predisposing the hosts toward since hosts finding their parasites often causes genetic separation and phenotypic differentiation. e. Selecting for hosts to feed their parasites at some manageable level thereby favoring the harmony of living things. 4. Allopolyploidy involves a. allopatry. b. reduction of number. c. only one parental species. d. hybridization followed by chromosomal doubling. e. mostly birds and mammals, while it is thought to not occur in plants. 5. If tails were under to be as long as possible, they would evolve until a. the advantage in reproduction equaled the cost in survival. b. male-male interference set in. c. female choice was equal to male-male competition. d. variance in male reproductive success equaled the variance in female reproductive success in a large population. e. there was a sensory bias that pre-existed the long tails. 6. A series of populations are living in one extreme environment (say hot places) or another (cold places) with negligible among populations. By doing a series of transplants, it is determined that the various genotypes have reaction norms that cross, in fact, they cross to the degree of actually changing sign with some being – and others +. Under these circumstances, if you seeded both environments with equal frequencies of the various genotypes, what would happen? a. There would be no selection within any one environment. b. All other things being equal, body size would uniformly evolve to be larger regardless of environment. c. Adaptive evolution would proceed similarly in both types of environments, with the same "fittest" genotype similarly rising in frequency. d. Different genotypes would rise in frequency in the different environments. e. would be likely to evolve with no local adaptation. 7. The differentiation of local populations is counteracted by a. gene flow among the populations. b. independent drift in each of the small populations. c. selection that acts differently in each population depending on the differing local environments. d. the presence of heavy metals in mine tailings. e. elevational differences in habitats. 8. Fisher's runaway process for the evolution of mate choice (the sexy-son hypothesis) envisions a. a pre-existing sensory bias on the part of females for males with extravagant features. b. an increase in choosiness due to choosy females having attractive sons that sire more than their share of choosy granddaughters. c. the spread of a dominant allele by selection against a recessive such that the homozygous recessive individuals survive at a rate 1–s compared to other genotypes at a rate 1. d. the cost of males being one half the finite rate of increase per generation. e. a handicap that is selected for in males because it displays the quality of their genes at performing other functions, such as resisting parasites. 9. Which of the following would not represent an intrinsic isolating barrier between two biological species? a. The two populations live on different mountain tops, and they cannot live in the intervening desert, so they never come together, and that's the only reason they don't interbreed. b. The two populations interbreed at a frequency of roughly 1 in 1000 individuals, but the hybrids are less fit than pure breeds, rarely living to reproductive age. c. The two populations often live in the same place, but one blooms in spring whereas the other blooms in late summer, so there is almost no gene flow possible. d. The two populations have different courtship songs and plumage patterns, so females of each population will almost never mate with males of the other population. e. The two populations both have large ranges where they are pure (one has reddish feathers and the other yellower feathers in the males) but they meet in a narrow zone where they hybridize freely; the hybrids are strong but largely infertile because their often do not pair properly at meiosis. 10. Concerning male-male interference competition (contests), a. it can only occur if there is active female mate choice, as Darwin realized. b. typically when secondary sexual characters are present (sharp horns and tusks), males fight to the death, which results in a highly skewed sex ratio. c. Fisher's 1:1 sex ratio theory explains how this would only occur in hermaphroditic species. d. genes that make an animal disengage from battle once it has been proven he is weaker have been often selected for, and genes that make an animal not pursue the already-vanquished when he is retreating have evidently also been selected for. e. we would expect it to be more common in species that are strictly monogamous (where there is one female for every male) than in species that are strongly polygynous (where some males mate with several females). 11. Which of the following is thought to be a reason why sex should be selected against? a. Sons do not convert resources into grandchildren the way daughters do. b. Variation among offspring may reduce sibling competition. c. Muller's ratchet tends to remove sexual lines. d. Without the recombination that comes from sex, the capacity for polygeneic adaptation is reduced. e. Sex (as defined by population geneticists) only occurs in "higher" animals, mostly terrestrial vertebrates and insects, since selection favors external fertilization in most marine and aquatic habitats.

12. The "biological species concept" defines species as groups of ______or ______interbreeding natural populations which are reproductively isolated from other such groups. 13. Regarding Wright's F statistics, a. when FIS is high, there is little inbreeding within subpopulations. b. when FST is low, there is great differentiation among subpopulations. c. the higher FIS, the more heterozygosity within local populations. d. the lower FIS, the higher FST. e. the higher FST, the more differentiation among subpopulations. 14. Correlated response to selection a. is not usually invoked in arguments about life-history evolution. b. is not part of any standard model for . c. is not part of plausible models for . d. cannot be contingent on the environment of selection—whether toads are living in ponds of long or short duration, selection for longer larval period will increase body size. e. is caused by pleiotropy, close chromosomal linkage, and certain forms of epistasis. 15. A norm of reaction a. is the typical or "normal" way in which phenotypes evolve. b. implies that there is no phenotypic plasticity, at least with a steep norm of reaction. c. is the relationship between and environment for a single genotype. d. for one genotype may be different from those of other genotypes, in which case the phenotype is said to be canalized. e. is the relationship between genotype and phenotype regardless of environment. 16. What does it mean to be apomictic or parthenogenetic? a. Apomixis is facultative asexuality, whereas parthenogenesis is obligate asexuality. b. The organism has asexual reproduction. c. The organism is a bacteria that is pseudosexual. d. The organism is a that has meiosis and fertilization. e. The sexes are separate with male and female organs on different individuals. 17. What is the difference between an "adaptation" and an "exaptation"? a. An adaptation is caused by a single locus; an exaptation is polygeneic. b. An adaptation is a feature that is apt to a specified function because that function was involved in the origination of that feature; an exaptation is apt for a specified function but evolved by other means. c. An adaptation arose through the inheritance of acquired traits; an exaptation arose through natural selection. d. An adaptation is something that is apt no matter how it arose; an exaptation arose through natural selection because of the benefits it provided through the function that it now serves. e. An adaptation is a feature viewed from a genetical perspective; an exaptation is the same feature viewed from a purely phenotypic perspective. 18. The t-allele is mice a. is good for the organism as a whole and therefore good for the species. b. distorts meiosis such that when it is with a wild type allele more wild type sperm are produced than t sperm. c. has gone to fixation because it has no deleterious effects. d. is found in far more sperm than expect by Mendelian frequencies. e. causes the production of both a toxin and its antidote with the antidote being more persistent than the toxin. 19. Problems with the biological species concept include all except which of the following? a. It doesn't apply to asexual organisms. b. It doesn't explain how parapatric populations that extensively interbreed in a hybrid zone remain distinct. c. It allows for paraphyletic species. d. It is difficult to put into operation for candidate races that are entirely allopatric. e. It doesn't take into account whether or not the animals are interbreeding. 20. Obligate asexuality a. occurs mainly in a few large clades that are uniformly asexual. b. occurs mainly in tropical settings with little seasonality. c. is relatively common in mammals. d. assures that different genetic loci recombine freely. e. among higher animals and plants seems to not arise very often and to be lost to relatively quickly. 21. Gynodioecy is thought to have evolved by a. A cooperation between cytoplasmic and nuclear genes. b. A nuclear gene causing male sterility (making plants exclusively female). c. A cytoplasmic gene restoring male fertility (making plants hermaphroditic). d. b and c. e. A cytoplasmic gene causing male sterility and a nuclear gene restoring fertility. 22. Which of the following cladograms is not equivalent?

A B C D C D B A B D C A A D C B A B D C

a b c d e 23. Bateman's principal states a. sexual selection is usually stronger in males (the sex limited by mating opportunities) than in female (the sex limited by resources). b. female choice and male-male competition are mutually exclusive—if one is responsible for the evolution of an elaborate male character, the other was not involved. c. examples of sex-role reversals (such as seahorses and phalaropes) arise when females have very high parental investment per offspring and males have negligible parental investment. d. when population sizes are small and any one clone is likely to be eventually lost to drift asexuality (in previously sexual organisms) leads to a long-term mutational decay of the whole set of clones. e. selection acts in the same way on males and females. 24. In mammals the hormonal concentrations that mediate the interaction between fetus and mother in several cases are over an order of magnitude higher than other hormones normally are. This is explained by a. the placenta being poorly permeable to hormones. b. the mother's and the father's genes having an equal stake in the production of future offspring (siblings to the fetus). c. an evolutionary history in which fetuses initially got fed better when they secreted slightly higher hormone levels and in which mothers were selected who ignored the heightening of these signals. d. a long evolutionary history of strict life-long monogamy. e. a system of gene expression in which both gene copies are always expressed in any fetus. 25. Secondary reinforcement a. is the process by which a partial post-zygotic isolating barriers makes for selection for additional pre-zygotic isolating barriers. b. is the process by which a partial pre-zygotic isolating barriers makes for selection for additional post-zygotic isolating barriers. c. has often been demonstrated in experiments with fruit flies. d. is the best explanation for most cases of hybrid sterility (such as is found in mules). e. can only occur when the populations in question are allopatric. 26. Sketch the pattern of covariation you would expect if one were comparing various species of leaf beetles in terms of longevity and age at first reproduction: Age at First Reproduction

Average Longevity

27. When species are first described by alpha taxonomists, a. this has usually been done on the basis of studies on reproductive compatibility. b. this has usually been done with the goal of recognizing only monophyletic entities (whole clades) and recognizing all such entities that are diagnosable. c. at least in the past this has been done by looking for phenetic (morphological) gaps in multiple characters. d. "species concepts" have operationally and tightly followed concepts of "speciation" as treated by evolutionary biologists conceptualizing the processes that give rise to diversity. e. characters thought to be acted on by sexual selection have rarely proven to be useful. 28. Which of the following is not thought to be an instance of genomic conflict? a. Male-sterility genes in gynodioecious plants. b. The strictly Mendelian 50:50 segregation of chromosomes at meiosis. c. Plasmids that spread vertically through bacteria by killing daughter cells that lack them. d. "Petite" mutations in mitochondria in yeasts that divide rapidly themselves but cause the yeast cells to divide only slowly. e. Hypothetical organelles that were inherited biparentally and competed with one another to the detriment of the larger organism that contained them, thereby leading to the evolution of uniparental cytoplasmic inheritance. 29. What causes tradeoffs in life history? a. The way natural selection breaks the "laws" of mechanics and energetics. b. Selection for genes that make their bearers die young and reproduce late in life. c. The general lack of any genetic correlations between different life-history variables. d. The phylogenetic constraint that prevents asexuality from arising frequently from sexuality. e. Physiological constraints of time and energy that come to limit one aspect or another of the organism's survivorship and reproductive schedule. 30. Concerning sympatric speciation a. It was long thought to be unlikely (except in cases of major chromosomal changes) because continued interbreeding would prevent polygeneic differences from arising gradually, and reproductive isolating barriers were thought to be polygeneic. b. It has, however, been demonstrated with fruit flies that strong multifaceted disruptive selection can cause reproductive isolating barriers to arise despite continued opportunities for interbreeding. c. Host shifts that disrupt interbreeding seem to have allowed for speciation in Rhagoletis polmonella without geographic isolation. d. All of the above are true. e. None of the above are true. BIOL 322, Fall 2000 name ______Relax. If you need more time, you can follow me up to my office quietly. You can use a dictionary (as long as it doesn't have biology written in it). Exam 3 (This is the hard part—I know and I'm sorry, but it's my nature.) 1. In the following phylogeny, which character(s) is (are) synapomorphic for the group {A,B,C}? ______.

A B C D E F G H I J 5 - -19 3- -18 12 - 21 - -10 1 - - - 2 13 - 22 - 15 - 17 - 6 - 9 - 14 - 4 - 8 16 - - 20 - 7 11 -

2. Which is the correct order from oldest to most recent? a. Cambrian · Ordovician · Silurian · Devonian · Carboniferous · Permian · Triassic · Jurassic · Cretaceous · Tertiary · Quaternary. b. Triassic · Jurassic · Cretaceous · Cambrian · Ordovician · Silurian · Devonian · Carboniferous · Permian · Tertiary · Quaternary. c. Permian · Triassic · Jurassic · Cretaceous · Tertiary · Cambrian · Silurian · Devonian · Ordovician · Carboniferous · Quaternary. d. Cambrian · Jurassic · Cretaceous · Tertiary · Quaternary · Silurian · Ordovician · Devonian · Permian · Carboniferous · Triassic. e. Devonian · Tertiary · Quaternary · Carboniferous · Triassic · Permian · Jurassic · Cretaceous · Cambrian · Ordovician · Silurian. 3. Molecular genetic studies of human geographic variation a. suggest that when agrarian ethnic groups migrated from the Middle East to western Europe they interbred so much with the locals that the genes stayed in place while the agricultural practices moved north and west. b. confirm that the 5 conventional races (based on skin color) are real summaries of overall and are separated by sharp genetic boundaries indicative of deep divergence. c. suggest all people share a common ancestor more recent than 10,000 years (about the time of the origin of agriculture). d. indicate that all people share a common ancestor from about 200,000-300,000 years ago, although more recent common ancestors are also possible. e. place Europeans as the paraphyletic founding group from which all other people arose. 4. Individual animals often function as highly coordinated units with all the parts participating to make the whole work spectacularly well. The explanation for this involves which of the following? a. The germ line undergoes many more cell divisions than the soma (cells of the body), and representatives of the germ line are found throughout the body. b. The exact same genes expressed in all the various cells are in the germ line, so the level of replication upon which selection effectively acts is the individual, not the cell.

8 c. There is great genetic variance in terms differences in allele frequencies among the cells of the body, for instance, among different tissue types. d. Unlike in bacteria and simple single-celled , there are no epigenetic processes that allow for cell lines to differentiate non-genetically, such as through DNA methylation. e. The coefficient of relatedness among cells of the individual is much less than 1.0, around 0.5 for outcrossing species. 5. What is a reasons for character stasis? a. The various descendants of an ancestor have radiated adaptively. b. The genetic architecture of the characters in question are purely additive and without pleiotropy. c. All the descendants of an ancestor are adapted in many ways to a stable niche. d. There has been very little conservation of genetic architecture. e. There is a one-to-one correspondence between the genotypic plane, the phenotypic plane, and the fitness (adaptive) plane. 6. The best situation for use of molecular clocks is when all except which of the following is true? a. The molecules being used are evolving at different rates in the different lineages. b. There are several calibration points for geological events that have been dated by other evidence. c. The DNA sequences being used are thought to evolve mainly through neutral evolution. d. All the organisms have the same generation time. e. The probabilities of each kind of transition and transversion have been accounted for. 7. In , what is the differences between an exhaustive and a heuristic search? a. An exhaustive search is for large problems with lots of species; a heuristic search is for small lessons. b. An exhaustive search is not guaranteed to find the absolute shortest tree, but it often does; a heuristic search is sure to eventually find the shortest tree. c. An exhaustive search is a distance method that doesn't use parsimony (in the strict sense); a heuristic search is strictly programmed to find the most parsimonious tree. d. They are the same thing, just by different names, with Europeans calling it "heuristic" and Americans calling it "exhaustive". e. An exhaustive search looks at all possible trees; a heuristic looks among a wide array of trees and then tries to optimize without looking at every possible tree. 8. Although a fruit fly and a mouse are very different in body plan, they are similar in which of the following aspects of Hox genes? a. The genes have highly conserved nucleotide sequences. b. The have nearly colinear expression. c. They have conserved the aspect of function determining segmentation and the differentiation of segments. d. a through c. e. none of the above—a is false because the sequences are only weakly conserved, and b and c are false because flies and mice independently developed segmentation. 9. Regarding mass and their aftermath, a. origination rates are higher before the than after. b. there is no evidence for different groups of organisms going extinct simultaneously. c. radiations of major groups seem to happen after mass extinction events. d. they mostly affected organisms on land, with ocean organisms not going extinct. e. although they kill off species, there are few examples in which all the members of a higher

9 have gone extinct. 10. Background extinction a. has occurred in the past mainly when meteors have hit the Earth. b. is thought to have often been caused by a collapse of biogeochemical cycling. c. is statistically "selective" eliminating at a greater rate organisms with large range sizes who live in relatively stable environments than those with small range sizes who live in easily disturbed habitats. d. seems to happen to generalists more than to specialists. e. does not exact as much "clade selection" as mass extinction, i.e., it is more random with regard to the biogeographic and ecological features of the groups that do or don't go extinct. 11. What were the two biggest mass extinctions? a. The end of the Permian was the largest, and the end of the Cretaceous (K-T boundary) was next. b. Two waves of the ice age (Pleistocene), which was over just 13,000 years ago. c. The Cambrian (when many phyla of animals went extinct) and the Triassic (when many groups of and cycads went extinct). d. The one that caused the break up of Pangaea was the largest, followed by the one that caused the break up of Gandwanaland. e. The big bang was the largest (killing off many groups such as the dinosaurs), and the next largest was when people arrived in the Americas. 12. Regarding the evolution of eukaryotes, which seems to be the case based on recent molecular ? ("Extant" means still living, not extinct.) a. All eukaryotic genes and organelles seem to have arisen out of a particular line of eubacteria (the same group as the cyanobacteria), making extant eubacteria paraphyletic. b. All eukaryotic genes and organelles seem to have arisen out of a particular line of archaebacteria (the same group as the purples), making extant archaebacteria paraphyletic. c. Most of the nuclear genes arose from within the eubacteria, while most organellar genes are related to archaebacteria, making both domains of bacteria paraphyletic. d. For most nuclear genes, the branch leading up to eukaryotes is very long and not obviously nested within either the archaebacteria or the eubacteria. e. The symbiotic theory for the origin of extant eukaryotes has been proven incorrect. 13. Ecological communities a. typically consist of species that are all coevolved in the sense of their adaptations having been formed by natural selection through interactions with those specific species with which you now find them. b. contain mostly species that have lived with each other through not just the past few tens of thousands of years but for hundreds of millions of years. c. often are made up of species that arose at many different times and under many different circumstances. d. at a particular latitude have remained fairly constant for hundreds of millions of years. e. mostly have species in them with adaptations that all arose simultaneously. 14. What makes a gene useful in inferring a phylogeny? a. It being highly variable in the group. b. It being highly conserved in the group. c. It having an intermediate level of variability. d. It having been lost from several of the species being studied. e. It being prone to "horizontal transfer" through hybridization rather than being transmitted

10 only "vertically". 15. Mapping characters onto a phylogeny can be useful for all except which of the following? a. Distinguishing between different biogeographic hypotheses, e.g., stingrays in the Amazon arose from those in the Pacific not those in the Atlantic? b. Showing which innovations arose first and which later, e.g., Pit vipers became venomous and then rattles evolved. c. Revealing convergences, e.g., hummingbird pollination arose at least 12 times independently in Penstemon. d. Revealing the mechanistic causes of tradeoffs, e.g., life span is negatively correlated with age at first reproduction because of antagonistic pleiotropy. e. Showing how originations of a character state are associated with other characters or environments, e.g., the annualness arose always in desert species and was lost when a desert species gave rise to a montane species. 16. Major histocompatibility alleles a. are short lived, being selected out of the population very quickly. b. are completely different in humans and chimps. c. are few in number, with only 3 or 4 known for any one population. d. are related by a gene genealogy where the polymorphism predates speciation events, in some cases as old as the split between Old-world and New-world monkeys. e. have a gene genealogy that has the same arrangement as the species phylogeny they are inside of. 17. is the pattern in which a. many life forms go extinct simultaneously and are replaced by new ones. b. species are often static in the fossil record for a long time and then new forms appear quickly. c. mutations arise instantly but alleles are static. d. major innovations in life have been associated with new levels of selection. e. morphological evolution proceeds at a steady clock-like rate. 18. The method of independent contrasts a. allows one to test for correlations between characters removing the effect of common ancestry. b. allows one to look for correlations between characters without the phylogeny being known. c. rests on the assumption that species are all free to evolve and so are independent of one another. d. is more reliable the deeper into the phylogeny one goes, i.e., the contrasts near the tips are less reliable. e. is aimed at allowing one to tell a narrative about how one character changed and then another changed, and so on. 19. The most parsimonious phylogeny can be found by a. drawing all trees, mapping all characters on all trees, and choosing the shortest one. b. drawing all trees, mapping all characters on all trees, the choosing the one with the most homoplasy. c. using only data that you are sure is involved in a "syndrome" (like a pollination syndrome). d. assuming that the most come character state for each character is primitive and the rarer character states are derived from it. e. clustering based on overall similarity. 20. Pollen presentation theory asserts that

11 a. pollinators that remove more pollen are better pollinators than pollinators that remove less. b. the relationship between pollen removed in a visit and the amount of that pollen that makes it to stigmas is an accelerating curve (g>1). c. flowers pollinated by high-removal–low-deposition bees should have evolved anthers that open more rapidly and more thoroughly than flowers pollinated by low-removal–high- deposition hummingbirds. d. when pollinator visitation rates are high and g is low, selection favors gradual pollen presentation. e. the characteristics of flowers have been selected mostly through female function, i.e., through the advantages conferred in receiving pollen onto stigmas and setting seeds. 21. Jeannie Chari and I studied reproductive isolating barriers in Penstemon, following the work of Chris George and Richard Straw. List four possible barriers to hybridization that have been measured by one or another of us. ______

22. Map both the a and b characters on the phylogeny in a way that is maximally parsimonious. Place tick marks on the phylogeny. Next to each tick mark, label which character changed and how it changed (e.g., a 0’1). a b Sp. A 0 1

Sp. B 0 1

Sp. C 1 0

Sp. D 1 1

Sp. E 0 0

23. Cala Castellanos, James Thomson and I found what about Penstemon nectaries? a. When we removed nectar, more was secreted but not more than would have been secreted, i.e., there is a gradual fixed secretion schedule. b. When we removed nectar, resecretion was stimulated. c. When we added artificial nectar, resecretion was inhibited. d. The bird-pollinated P. barbatus resecreted more than the bee-pollinated P. strictus. e. b, c and d are all true.

12 24. A ______is a similarity due to inheritance from a common ancestor, whereas a ______is a similarity not due to common ancestry.

25. Hamilton's rule states that altruism will be selected for when the benefit to the ______times the coefficient of ______is greater than the ______to the donor. 26. Why are we seeing such a growth in research on phylogenetics these days? a. In the last three decades it has become clear that species are related to each other on an evolutionary tree. b. Development of our understanding of social evolution (particularly sexual selection and kin selection) has revolutionized the way phylogenies are inferred. c. Methods in molecular genetics (electrophoresis, restriction fragments, DNA sequencing) have provided vast new sources of information. d. Computers have become much faster allowing the implementation of algorithms that were programmed but not used shortly after the publication of The origin of species. e. The realization that we are causing a great number of species extinctions has led scientists to be interested in evolutionary trees rather than alpha taxonomy. 27. Eusociality is a. the living together of a bunch of individuals who all reproduce and share in the care of the young. b. group living where "castes" of individuals never reproduce but only help their parents to reproduce. c. more or less evenly scattered throughout many groups of animals. d. when there is no hierarchy among the individuals because everyone cooperates as one big happy family. e. unknown outside of insects. 28. When can reciprocal altruism be selected for? a. Only between close kin. b. Never between kin. c. Only when individuals know each other for long periods of time. d. Only when the cost to the donor is greater than the benefit to the recipient. e. Only if one individual is much stronger and can always be the donor, while the other individual can always be the recipient. 29. Haplodiploidy a. occurs only in mole rats, which explains why eusociality arose in that group. b. has as a consequence that a female is more related to a sister than to a daughter. c. means that there is an alternation of generations between a haploid stage and a diploid stage. d. is a reason for why reciprocal altruism rather than kin selection favored sociality in animals such as baboons. e. results in a decrease in rkin between sisters.

30. Which of the following is not a plausible reason why subordinant animals might be selected to stay in a group? a. Animals in groups are less likely to be surprised by a predator and are more likely to escape predation than solitary animals.

13 b. The animal may be helping to raise kin. c. The animal may be learning skills and building up strength that will allow it to eventually become a dominant member of the group. d. If food resources are concentrated, the animals should concentrate around the food. e. By remaining in a group, the subordinant will get out of having to reproduce because the dominant animal will do all the mating necessary.

Cumulative Final (This should be easier.) 31. What is systematics? a. The study of physiological systems in the body. b. The study of evolutionary processes, such as how natural selection works. c. The ethical position that ecosystems should be preserved. d. The study of patterns of diversity in the characteristics of organisms. 32. Which of the following is not a sensible reason for mate choice such as might cause sexual selection? a. There is generally more opportunity for variance in female reproductive success than male reproductive success. b. The sensory system of organisms is highly complex, biased, and prone to diverge for many reasons that are not related to variance among legitimate mates. c. Fisher's model for the runaway evolution of between male traits and female preference. d. Elaborate ornaments in a mate are indicators of good genes.

33. If there were selection for a shorter larval period in some toads and there were a negative genetic correlation between larval period and body size, we would expect a ______with body size becoming ______. 34. Field and lab studies have suggested what about the speed of evolution? a. Significant evolution can occur in ecologically important characters in a couple dozen generations. b. Evolution is essentially unmeasurable on the time span of dozens or even hundreds of generations. c. Microevolutionary rates when extrapolated to geological time and are just enough to account for observed macroevolutioary rates (such as increases in body size in horses). d. Microevolutionary rates when extrapolated to geological time are not nearly fast enough to account for changes in body size that have happened over the last 65 million years in mammals. 35. Which of the following are responsible for the loose coupling between genotype and phenotype? a. Canalization. b. Phenotypic plasticity. c. Crossing norms of reaction. d. All of the above. 36. What counteracts divergence? a. Allopatry. b. Gene flow. c. Disruptive selection.

14 d. Reproductive isolating barriers. 37. Convergence is often used as evidence for a. . b. adaptive syndromes. c. monophyly. d. common ancestry. 38. In animals that have separate sexes where the male contributes only sperm, sexual reproduction can be selected a. against because it makes species less adaptable. b. for because males get to play a role. c. for because then the female gets to have half her offspring be sons. d. for because it makes the offspring variable, which reduces sib competition. 39. The Lotka-Volterra model for competition concludes that a. no species is superior to any other species in all environments. b. the stronger interspecific competition is, the more likely the two species will be mutualists. c. species should evolve to be have more overlapping niches if they start out having less overlapping ones. d. complete competitors cannot coexist, i.e., if two species have stronger effects on one another than on themselves, one or the other will be driven to zero population size. 40. Regarding antibiotic resistance, a. it takes thousands or tens of thousands of years to arise. b. it has spread in recent years by purely random processes. c. it is prevented by people using only enough of a course of antibiotics for symptoms to be alleviated and then throwing away the rest of the pills. d. it has evolved in many strains in a matter of years, demonstrating the efficacy of selection and posing a major health problem. 41. Why do evolutionary biologists find sex to be such a mystery? a. It seems that it comes at a high selective cost (the cost of males). b. They are skeptical that any mutations could possibly arise that would allow for asexual reproduction. c. They think that sex has arisen many times through but is lost to extinction relatively rapidly. d. Facultative asexual reproduction seems to be impossible. All species are either one or the other. 42. Which of the following would be considered mutualistic? a. The relationship between a flower and a visitor that removes very large amounts of pollen but deposits little or none of it on stigmas (in the presence of other species of visitors that remove less but deposit more of it). b. The relationship between two species of barnacles one of which pushes the other off of rocks and the other of which can survive better (though suboptimally) at a higher tidal height. c. The relationship between a plant that makes seeds with removable oil bodies that thereby attracts ants who remove the seeds and carry them some distance before removing the oil body. This process results in the ant getting food, and the seeds being effectively dispersed. d. The relationship between a wasp and an aphid whereby the adult wasp ovaposits in the aphid and the larval wasp eats the insides of the aphid as it matures.

15 43. We have discussed both individual selection and clade selection. For sexually reproducing, outcrossing organisms, how are the two process thought to contrast? a. Clade selection has been responsible for forming most adaptations of organisms, such as the precise shape of your eyeball, the way its pupil adjusts to light intensity, and the position of the lens that allows you to focus an image. Individual selection is relatively weak and unimportant. b. Individual selection would almost always operate in a direction contrary to clade selection. c. Individual selection can act only on characteristics of species after nearly all individuals in the species are fixed for that character. Clade selection acts mostly within a species. d. Clade selection usually acts more slowly at a higher level, sorting out lineages in terms of their time to extinction. Individual selection is responsible for originating complex adaptations. 44. Although in common language, the word "adaptation" is often used similarly to "acclamation" to describe how an individual changes in response to its environment, I have avoided using "adaptation" in this way. Why? a. I think that changes between generations are the accumulation of acquired acclamation within the life of an individual. b. I do not think that natural selection can act on the capacity to be phenotypically plastic. c. Evolution focus on change from one generation to the next, so I use adaptation to mean a kind of evolution. d. Lamarck thought that the processes of acclamation had a different basis than those of adaptation. 45. Genetic load is caused by a. the inevitability of mutations and the huge number of loci at which they may occur. b. the mass of DNA inside of each cell (which adds up in a human since there are so many cells). c. competition between species for access to mates. d. a long history of selection followed by a relaxation of selection. 46. Mutations are random in what sense? a. They occur at a constant rate throughout the genome. b. The kinds of mutations that happen are not in response to what would be useful. c. They all have the same probability of affecting the phenotype regardless of where they occur in the genome. d. The mutation rate is the same in all types of organisms (it's the average for a certain type of mutation over a long period of time). 47. Response to selection R is equal to a. additive genetic variance divided by total variance. b. 1–sum(p2) where p's are allele frequencies. c. narrow-sense heritability h2 times the selection differential S. d. the average after selection minus the average before selection (all within a generation).

48. Micoevolution is defined as ______in ______over time, across generations. 49. A grouping that contains all the descendants of a common ancestor is said to be a. monophyletic. b. phenetic. c. paraphyletic. d. intrinsically isolated.

16 50. Which is a convention of biological nomenclature? a. Once you have written out the full name of a species, you may thereafter refer to it by only its epithet (second name). b. Species names are italicized or underlined. c. Both names of a species binomial are capitalized. d. The plural of "genus" is "genuses", and the singular of "species" is "specie".

51. If a population is censused for a variable locus, and two alleles are found, and the frequency of one allele is 0.6, then assuming Hardy-Weinberg, the frequency of homozygotes for that allele would be ______, the frequency of heterozygotes would be ______, and the frequency of homozygotes for the other allele would be ______. 52. The biological species concept states a. species are groups of actually or potentially interbreeding populations isolated from other such groups by barriers to interbreeding. b. species are whole clades that are diagnosable. c. species are morphologically distinctive units. d. species form through disruptive selection in sympatry. 53. Many TV shows used to speak of adaptations as being "for the good of the species". Why is it objectionable? a. Because most adaptations are due to genetic drift. b. Because most adaptations are caused by individuals doing what gets their genes into more than their share of the next generation even though this is frequently bad for the species. c. Because it is unscientific to imply that adaptations have "ultimate" causes. d. Because natural selection has foresight and shapes organisms to have the adaptations that they will need in the future even if those features are not particularly useful when they are formed. 54. The Darwinian principle of "gradualism" means, a. evolution occurs at a constant rate, and there are never periods when any lineage should be characterized as not evolving. b. we should assume the fewest changes of character state when inferring evolutionary history. c. those genotypes whose population size increases slowly are more likely to survive than those whose population size increases rapidly. d. as structures evolve from one state to another, they must function well in every intervening generation. 55. When does exponential growth occur? a. Whenever items—dollars, cells, individuals—increase as a proportion of the number that are there. b. When the population is at carrying capacity. c. When food or some other factor is limiting. d. When the organism is sexual; asexual species have populations that are only capable of linear growth. 56. Overall phenetic similarity between species in all characters a. is the best measure for inferring phylogenies. b. has not generally been used in arranging taxonomic classifications. c. is a poor measure for inferring phylogeny because a group can share many characters

17 while differing from another group whose exclusion made it paraphyletic. d. is the same as cladistic relationship. 57. For there to be lasting change in a quantitative character over generations, it is sufficient that there be a. additive genetic similarity between parents and offspring. b. a consistent difference between the mean of the population at birth and at reproduction. c. both a and b. d. either a or b. 58. Drift is a. a cause of adaptive evolution. b. equivalent to mutation. c. change in allele frequency due to reproduction being a sampling process. e. not a process that affects allele frequencies. 59. If you were to select a population of birds to have larger numbers of eggs, what correlated response to selection would I expect? a. An increase in annual mortality. b. An increase in egg size. c. An increase in the total reproductive output (lifetime fitness). d. Both b and c but not a. 60. Give an adaptationist hypothesis for how whales came to lack hind legs, being careful to not say anything I would consider misleading. ______

18