INSTRUCTIONS: 1. Think before you write.

2. Write short, concise answers.

Lengthy answers will be selected against

Some formulas:

pt+1 = (p_t²w_AA + p_tq_tw_Aa)/(p_t²w_AA+2p_tq_tw_Aa+q_t²w_aa)

pequil = t/(s+t)

pequil = v/(u+v)

p_t+1= p_t(1-u)+q_t(v)

p² + 2pq + q² = 1

1/N_e = (1/t) (·1/N_e)

N_e = (4N_mN_f)/(N_m+N_f)

p_{pop1 t+1} = p_{popl t} (1-m) + p_{pop2 t} (m)

random variance in p = (pq/2N)^0.5

y = bx^a

log y = log b + a log x

1. Clearly define and state the significance of each of the following terms. (3 pts. each; ·=15)

Heritability

Mosaic evolution

Iridium spike

Endemic

Age of first reproduction

2. Clearly distinguish between each of the following pairs of terms. (5 pts. each; ·=35)

Isolation/recognition concepts

Homology / homoplasy

Stabilizing / disruptive selection

Adaptation / effect

3. Define species selection and describe three different modes by which it can arise. (15 pts.; ·=50)

4. You are trying to reconstruct the phylogeny of some distantly related organisms using a cladistic (e.g., parsimony) approach. What type of data would be more likely to give you reliable results?: neutral DNA sequences with nucleotides as character states or neutral protein sequences with amino acid character states. Clearly and briefly justify your answer. (10 pts.; ·=60)

5. One day God rewound the tape of life to run a little experiment: let the tape start again and see if the evolution of organisms follows the same path. To God's surprise the primates went extinct at the Cretaceous-Tertiary boundary (God arranged for an impact extinction event) and the dominant life form in the late Holocene (i.e., today) was sparrows. For each of the categories that follow, list one adaptation and one exaptation that clearly reflects the contingency inherent in the extinction of the primates and the rise of the sparrows: 1) acquisition of food, 2) shelter, 3) parental care, 4) communication and 5) technology. (10 pts.; ·=70)

6. You are interested in the ability of salt marsh plants to tolerate different levels of salinity in the soil. You have performed an experiment in a greenhouse where you grew three different genotypes (a, b and c) in each of three different species (1, 2 and 3) in three different salt treatments (Low, Medium and High). At the end of the growth period you measured plant height and concluded the following with regard to the effects of environment (E), genotype (G) and GxE interactions in determining plant height in each of the three species:

Species 1 showed no E effect, a clear G effect and no GxE effect.

Species 2 showed a clear E effect, a clear G effect and a clear GxE interaction.

Species 3 showed a clear E effect, a clear G effect and no GxE interaction.

On the graphs below draw the norm of reaction lines for the three genotypes in each of the three species. (20 points; ·=90)

7. A species of cichlid fish eats the scales off the sides of other fish by swimming up behind its prey on one side and taking a bite. In the scale-eating species there is a genetically based polymorphism for left-mouthed and right-mouthed morphologies which are related to the side of the prey on which the scale eater approaches: the left-mouthed morph attacks on the right side of the prey and the right-mouthed morph attacks on the left side. Below are some recently published data on the frequency of left-mouthed morphs over several years. Describe how selection is operating in this system. Your answer should address both the average frequency and the pattern of variation of the frequencies over the years. (15 points; ·=105)

8. G. C. Williams pointed out that the existence of facultative parthenogens (organisms that can switch between a parthenogenetic and a sexual mode of reproduction) strongly suggests that there must be a short term advantage to sex. Why? (hint: you do not need to describe the various advantages of sex to answer this question properly). (10 points; ·=115)

9. Data were collected on body size and brain size in graduates of three Ivy League Schools and their children. The data were log transformed and plotted as Log of body size (x) and Log brain weight (y). The following relationships were observed within each school and among graduates of all schools:

Graduate Interscholastic: y = 1.0 + 1.5x

From these data alone (don't assume anything other than what is given here!) answer the following questions and provide a one sentence justification of your answer:

i) Are big Brown children the same shape as small Brown Children? (4 points; ·=119)

ii) Are Princeton graduates the same shape as Harvard graduates? (4 points; ·=123)

iii) At which school do graduates most resemble children? (4 points; ·=127)

iv) Which comparison(s) show negative allometry? (4 points; ·=131)

iv) Using only the Graduate Interscholastic relationship, what additional information do you need to determine which graduates have the largest brains? (4 points; ·=135)

10. A former Bio 48 student who now works at Cafe La France has hypothesized that the piercing of body parts is governed by a single locus with two alleles. She has even gone so far as to estimate the social fitnes of various piercing patterns based on the observed frequencies of phenotypes "on the street". She did this using an approach from population genetics. Based on these data, determine the i) fitness of each genotype and ii) the selection coefficients for each genotype and 3) a name for this type of selection. If this selection continues will the L allele increase, decrease or stay the same frequency? Show your work. (15 points; ·=150)

11. Two identical populations of 100 individuals each experienced a population bottleneck. Population 1 went through three generations of a population size of 5 individuals, while population 2 went through six generations of population size of 10 individuals. After the bottleneck, both populations flushed up to 100 individuals, as indicated in the numbers below:

Population 1: 100, 5, 5, 5, 100

Population 2: 100, 10, 10, 10, 10, 10, 10, 100

Which population now has more variation? Show your work. (10 points; ·=160)

A Ph.D student at Brown university is studying the adpative significance of genetic variation in barnacles. Barnacles release their offspring (larvae) into the water column in January and these young spend 2-3 months in the water drifting at the whims of ocean currents. In April, the young settle on the rocky intertidal and metamorphose. They cannot move after this, so if they settle in a "bad" microhabitat, they're dead. In this apecies, settlement is approximately uniform across the rocky intertidal. The student is testing the hypothsis that natural selection is acting on certain alleles of several protein-coding loci which exhibit allozyme polymorphism as revealed by protein electrophoresis. These loci are on separate chromosomes, each has two alleles in natural populations, and the allele frequency is about 0.5 at each locus when barncles are collected from the water before settlement. The student also has identified two "anonymous" DNA loci in the nuclear genome, neither of which codes for any gene product, but both do show two alleles in natural populations at frequecnies of about 0.5. The DNA "alleles" appear as distinct bands on DNA gels after the DNA has been digested with a restrinction enzyme. To seek evidence for natural selection, the student is comparing the patterns of allele frequencey variation at these loci between barnacles collected at sunny and shady sides of a river in Maine. Below are some Fst values calculated from the allele frequency differences between samples of barnacles collected at sunny and shady sites at three sudy areas The Fst vales refer to the sunny vs. shaded sites within one study area (see figure). The student thinks he has evidence for natural selection.

Briefly describe what the Fst data "say".

During the student's Ph.D. exam, his professor asked him: what leads you to believe that your data are the result of natural selection and not, say, stochastic evolutionary forces such as gene flow or drift? What is it about the data, and this banancle system, that leads you to reject these alternative hypotheses?

The student slammed the professor with no fewer than three excellent answers having to do with 1) the number of study sites, 2) the patterns of Fst for the set of five loci and 3) the molecular and mendelian genetics of the different kinds of loci.

Please give your version of the student''s three answers. Clearly address each of these issues in your answer and state precisely why it provides evidence against the aternative hypotheses.

12. On the blank graph below, clearly label the axes and provide data points that illustrate the primary observation that lead Van Valen to propose the Red Queen hypothesis. Briefly describe the major points and significance of this hypothesis. (20 points; ·=180)

11. i) Draw and clearly label all axes of an adaptive landscape. ii) Describe the three important phases of the shifting balance theory of evolution proposed by Sewall Wright. iii) Describe the population structure of two different species in which shifting balance is likely to be important and unimportant, respectively. Answers should contain no more than i) a small drawing, ii) three short phrases and iii) one short sentence. (20 points; ·=200)