Discuss how bottom-up effects may have been expressed in the experimental lake food web during the experiment by describing the potential changes at each trophic level.

Questions

Question 1: The distribution of various biomes across the globe is determined by global climate patterns, which influence the availability of abiotic resources.

A) Describe how global climate patterns, such as solar radiation, air circulation, adiabatic lapse rate, and the seasonal movement of the intertropical convergence zone, influence the climate and consequent availability of abiotic resources across the globe.

B) Discuss why there is generally a greater diversity of plant species in tropical biomes and why that might lead to more diversity of animal species, through both ecological and evolutionary processes.

C) Discuss a few ways in which global climate change may alter the geographic distribution of organisms and the biomes in which they are found.

Question 2: Demonstrate how a density-independent event could result in a bottleneck effect:

A) Give an example of a density-independent effect. Explain how it is different from a density-dependent effect.

B) Draw a graph of genetic diversity (y-axis) over time (x-axis) that shows the genetic diversity in the population before the event, directly after the event (1 generation), and 1000 generations after the event. Your graph should show trends; you do not need to show specific values for genetic diversity.

C) Give a justification for your graph. List and define all 5 microevolutionary forces and include a discussion of how each one has (or has not) influenced the patterns shown in your graph.

D) Explain how genetic diversity is defined and might be measured. Explain why it is important to this population.

Question 3: Describe different scenarios under which alleles sort into gametes during meiosis using pipe cleaners.

A) Talk through the phases of meiosis using pipe cleaners.

B) Explain where and how meiosis results in the shuffling of genes and increased genetic variation, and why this is evolutionarily important.

C) When given a genotype, label the genes and alleles on pipe cleaner chromosomes for independent and/or dependent assortment.

D) Show how nondisjunction in meiosis could result in offspring with Down Syndrome.

E) Draw a Punnett square based on gametes produced for any of these scenarios (independent assortment, dependent assortment, nondisjunction).

Question 4: Darwin’s finches in the Galapagos Islands are used to illustrate many concepts in ecology and evolution, largely because Peter and Rosemary Grant and their students have studied these species for > 30 years. Use Darwin’s finches to explain the process of adaptive radiation by:

A) listing the three requirements that must have been met in the original finch population in order for evolution by natural selection to occur,

B) describing the data you would gather to demonstrate each of these requirements

C) describing how interactions among the finch species may have led to character displacement of beak shape, and

D) discussing how that character displacement could have driven the evolution of a behavioral isolating mechanism in this species.

Question 5: In California, Ensatina eschscholtzii salamanders west of the Sierra Nevada Mountains mimic toxic rough-skinned newts, whereas E. eschscholtzii salamanders east of the mountains are darkly camouflaged. Describe how Batesian mimicry of the rough-skinned newt by E. eschscholtzii salamanders could result in reinforcement of pre-zygotic isolating mechanisms by:

A) describing why hybrid offspring of a cross between the mimicking (west) and non-mimicking (east) salamander subspecies would be likely to have low fitness, and

B) explaining how low hybrid fitness results in reinforcement of pre-zygotic isolating mechanisms.

C) Describe some possible pre-zygotic isolating mechanisms that could be at play in this system.

Question 6: Scientists have observed that the males of guppy populations in Trinidadian streams look quite different depending on if they live above or below a waterfall. For example, adult male guppies are typically brightly colored when they live above waterfalls but dull colored when they live below waterfalls. (Juvenile guppies of both sexes are dull colored in all populations. So are adult female guppies). Scientists have hypothesized that these differences in male guppy color are related to the type of predator at each site. Pike-cichlids, a large predator that eats adult guppies, are found below waterfalls. Killifish, a small predator that can only eat small (juvenile)guppies, are found above waterfalls. Design an experiment to test the question:

Does the type of co-occurring fish predator affect the evolution of guppy color?

Be sure to include:

A) Your null and alternative hypotheses

B) At least one testable prediction

C) Key methods for your experiment, including your dependent (response) and independent (predictor) variables, and how you will incorporate control and replication

D) A graph of what your data would look like if your null hypothesis is true

E) A graph of what your data would look like if your alternative hypothesis is true

Question 7: Sickle-cell anemia provides an interesting real-world example of important concepts in genetics and evolution, such as codominance, natural selection, and evolution. Use what you know about this disease to complete the following exercises.

A) Suppose a man who is heterozygous for the sickle-cell gene mates with a woman who is homozygous recessive for this disorder. What is the expected phenotypic ratio of their children? Demonstrate your reasoning with a Punnett Square.

B) Choose one of the children from part A (circle it) and draw a cell of this child that is in metaphase I of meiosis. You only need to draw 3 different kinds of chromosomes (not all 23 that would really be in a human cell). Draw one way that the alleles of the sickle-cell gene could be arranged on the child’s chromosomes. Be ready to draw the alleles of a second gene that is either linked or unlinked to the sickle cell gene if I tell you to. Also be ready to identify homologous chromosomes, sister chromatids, and maternal and paternal chromosomes.

C) This child grows up to be a MD-Ph. D. and wants to learn more about the relationship between sickle-cell anemia and blood-borne diseases. She already knows that heterozygous individuals for the Hemoglobin S gene have some resistance to malaria, and she wants to study if this gene also affects resistance to other blood-borne illnesses. During her background research, she reads an interesting paper in which the authors examine if Hemoglobin S affects a person’s susceptibility to infection of the blood by bacteria (called bacteremia). In this study, the authors determined the genotypes of children off the coast of Kenya who had bacteremia and a comparable uninfected control group. Their data are below. Assume that bacteremia, while detrimental, is not lethal. Children with genotype AA are homozygous for normal blood cells, children with genotype AS are carriers of the sickle-cell allele, and children with genotype SS are homozygous for the sickle-cell allele. (These are real data from a published paper, by the way).

Group	AA	AS	SS
Control	1252	218	10
Bacteremia	1280	134	83

I. Use a chi-square test to determine if the control group is in Hardy-Weinberg Equilibrium. Use another chi-square test to determine if the Bacteremia group is in Hardy- Weinberg Equilibrium.

II. Does the Hemoglobin S gene affect a child’s resistance to bacteremia? If so, which genotype(s) are more or less resistant to bacteremia? Explain your reasoning.

Question 8: Advances in technology that have allowed faster and more widespread genetic testing of individuals has also spurred a new profession. Genetics counselors are specially trained in genetics and counselling and they help people, usually parents-to-be, make informed health decisions when family genetics increase risk factors for certain conditions. A couple comes to you for genetic counseling. Both of them have a genetic disorder, but they already have one child who does not have the disorder. They want to have more children and were told by a friend that since their first child was normal all of their future children would be normal as well.

A) Explain to them the probability of future offspring being normal or having the disease (assume that this is an autosomal disease). Be sure to tell them whether the disease is brought about by a dominant or recessive allele and what fraction of their children (if any) could be carriers for the disease.

Suppose a couple has come to see you to discuss the probability of their children having cystic fibrosis (CF). CF is known to be an autosomal recessive disease caused by a single gene mutation that has pleiotropic effects including thick mucus in the lungs and excessively salty sweat. After discussion with the couple, you learn that they both have a history of the disease in their families. Both the man and his wife are phenotypically normal, but both have one parent and one sibling with CF. The other parent in each case is phenotypically normal.

B) Explain to the couple the probability of their children having CF or being carriers for the CF gene. Explain to them why their children can have the disease even though neither of them do. Draw a Punnett square to help illustrate your points.

You face an uncomfortable situation with a couple who comes into your office to discuss potential color blindness in their children. The man is not color blind, but his wife is. They already have one daughter who is color blind and want to know the probability of future children having the disorder.

C) Explain the difference between sex chromosomes and autosomal chromosomes to the couple, and explain how sex linkage affects this trait. Once they understand this, you can explain to them the probability of their other offspring having the disorder and you can also explain the other dilemma in this case.

Question 9: The pygmy rabbit (Brachylagus idahoensis) is the smallest rabbit species in North America. It is patchily distributed in sagebrush-dominated habitats of the western United States and the Columbia Basin in Washington, and it forms underground burrows in areas where big sagebrush grows in dense stands. It is one of only a few species that feed on sagebrush, which makes up most of its diet. The WA population has been isolated from the rest of the species for at least 10,000 years, but degradation of the eastern WA shrub-steppe (by over-grazing, conversion to crop land, etc.) has led to significant habitat loss for this species, and it is now confined to one small remnant population (<150 individuals). It is currently listed as an endangered species and recovery efforts are underway.

Pygmy rabbit (Brachylagus idahoensis)

A) Explain how this species could be genetically distinct from other populations in the western United States, and explain how and why genetic drift and non-random mating may be driving WA pygmy rabbits into an extinction vortex.

B) What should conservation biologists do to save WA pygmy rabbits? Describe one realistic conservation solution for increasing genetic variation in WA pygmy rabbits.

C) Draw a food web of the shrub-steppe ecosystem that includes big sagebrush, pygmy rabbits, sagebrush gall-forming insect larvae, sage grouse (primarily eats sagebrush), coyotes (eat most small mammals and birds), songbirds (eat gall larvae), and two additional species that you learned about but are not on this list. Use arrows to indicate energy flow. Label primary producers, primary consumers, secondary consumers, and show how material is cycled.

D) Discuss how pygmy rabbit extinction might affect the other species in its ecosystem.

Question 10. A single ancestral cichlid species has given rise to a wide array of different cichlid species within Lake Tanganyika in Africa. The ancestral species was almost certainly a generalist, feeding on many different types of food. The resultant species differ dramatically, particularly in the shape of their lips and jaws. A second ancestral cichlid species has independently given rise to a wide array of different cichlid species within Lake Malawi in Africa. The forms of these Lake Malawi species are remarkably similar to those in Lake Tanganyika (Fig. 1). Lakes Malawi and Tanganyika are hydrologically isolated so the populations cannot intermix.

A) Draw a phylogenetic tree that includes the uppermost 6 species shown in figure 1. On your tree, circle and label the most recent common ancestor of all 6 species. Circle and label a speciation event on the tree. Circle and label two sister species (species that are most closely related to each other). Indicate which area of the tree represents the present day, and which area represents the earliest time period.

B) Discuss how competition, resource partitioning, and character displacement could account for the pattern of speciation shown by your tree. Discuss whether this pattern supports or refutes the idea that each species inhabits a specific niche in its ecosystem. Does this system demonstrate convergent evolution or not?

C) Identify the microevolutionary forces that were most likely involved in the speciation events that gave rise to Lake Tanganyika and Lake Malawi cichlids. Explain your reasoning.

Figure 1. Species of cichlids from Lake Tanganyika and Lake Malawi in Africa.

Question 11. In a famous experiment on nutrients in freshwater, researchers divided a single lake in half using a vinyl curtain so that each side had a volume of approximately 500,000 m3. They fertilized one side with carbon, nitrogen, and phosphorus, and they added carbon and nitrogen to the other half. Almost immediately, the lake with phosphorus added supported 4-8x the phytoplankton as the lake with no phosphorus added. Researchers stopped adding nutrients after 10 years and phytoplankton levels quickly returned to background levels.

Draw and label a generalized food web in the lakes that terminates in a predator that eats an herbivore.

Explain how energy moves through the ecosystem.

Discuss how bottom-up effects may have been expressed in the experimental lake food web during the experiment by describing the potential changes at each trophic level.

Discuss the limitations and strengths of this experimental design.

Imagine a lake system that you could divide into three roughly equal parts. The third part receives carbon, nitrogen, and phosphorus as above, but you manipulate the consumers to test for top-down effects.

Design and describe this experiment

State your null and alternate hypotheses and your null and alternate predictions.

Draw a graphic that you would see if your data supported your null prediction, and do the same for your alternate prediction.

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Lake Tanganyika Species Lake Malawi Species

Julidochromis ornatus

Tropheus brichardi

Bathybates ferox

Cypholapia frontosa

Lobochilotes labiatus

Melanochromis auratus

Pseudotropheus microstoma

Ramphochromis longiceps

Cyrtocara moorei

Placidochromis milomo