Instructions:  This review is worth 100 points (10% of your course grade) and will be due in class Wednesday, 2/16/04.  No exceptions, and late reviews will result in at least a 5% deduction.  You may not consult any references or any other person while working on this review.  Your signature at the bottom of the last page signifies that the work is yours alone and is pledged under the Honor Code.  When you break the seal on the envelope you will have three hours to complete the review!  Please print legibly; I can only grade what I can read!  For each question or part to a question, limit your answers to the space below each question, unless otherwise specified.  Any part of your answer outside of the space provided will not be graded.  You may type your answers separately, but use the same amount of space provided below each question.

1.      Consider the article by David Quammen (Was Darwin Wrong?) and our class discussions, and describe how the theory of evolution explains patterns of biodiversity on Earth (6 pts).

Evolution explains both the unity and diversity of life. Unity, in the shared traits that organisms have, and diversity, in the unique adaptations of each species. Biodiversity has increased over time, and diversity begets diversity. If there are more species, there are more opportunities for speciation events. These speciation events must be part of your answer, and can come in the form of adaptive radiations or modes of speciation. The way populations are structured in nature, and other factors, such as life history traits, that promote speciation can also be discussed. There are various mechanisms of evolution, and the theory of evolution encompasses them all. Microevolutionary processes lead to macroevolution, i.e., speciation, given enough time and separation of gene pools.

2.      Answer both of the following questions regarding the Hardy-Weinberg Equilibrium (10 pts total)
a.      Two assumptions of the Hardy-Weinberg equilibrium are that there is no migration and that populations are large.  For each assumption name the evolutionary mechanism that violates that assumption, and provide one example (real or hypothetical) of the consequences to genetic diversity of a population when that assumption is violated.

b.      Explain how the two mechanisms named in 4a work together or against one another to cause or prevent changes in allele frequencies. 

3.      Discuss in detail the most common means by which speciation is thought to occur.  Provide one example (hypothetical or real) supporting your discussion (8 pts).

Allopatric speciation must be defined or described as spatial separation of populations, separated by a barrier that is impassable or few cross it. This spatial separation causes the populations to evolve separately for a period of time, during which any of the mechanisms of evolution may act to cause the two populations to evolve along different paths. When, and if, the populations ever come together again, they must have evolved reproductive isolating mechanisms that prevent them from mating in order for allopatric speciation to have occurred. We discussed several examples, including Hawaiian fruit flies, Darwin's finches, Hawaiian honeycreepers, and more.

4.      Northern spotted owls live only in old-growth forests (forests uncut by humans).  They have long generation times, take 5-7 years to reach maturity, and thereafter mate for life and give birth to only 1 or 2 offspring each year.  95% of old-growth forests in the Pacific Northwest have been logged by humans in the past century, which has caused fragmentation of these former contiguous forests.  Spotted owls are extremely reluctant to cross open fields, and when forced to live in second growth forests (forests that grow after logging), have reduced production of offspring and higher mortality.  Answer the following two questions (8 pts).

a.      What would you predict might be a consequence to among-population variation and within-population variation for subpopulations isolated in such a manner?

We'd predict that subpopulations would become more isolated, and as gene flow decreased, within population variation should decrease, due to genetic drift, and among population variation should decrease, since without gene flow, subpopulations will drift away from each other in random directions.

b.      Despite the current disjointed distribution of subpopulations, list two traits of the owls (do not write an essay – list means list) that would prevent speciation in the Northern spotted owl?

Although gene flow will be disrupted, owls will still cross open spaces, albeit reluctantly, and they can still inhabit intervening second-growth forests despite the lowered reproductive success in those habitats. Because they have long life spans and few offspring per reproductive event, speciation would take a long time, and all that would be needed to disrupt that speciation is a little bit of gene flow.

5.      The following three factors may increase the probability of macroevolution.  Choose one and describe how it might lead to a speciation event.  Indicate how specific mechanisms of microevolution are at work in conjunction with the factor you choose (8 pts).

6.      Consider the graph on the next page and answer each of the following four questions (8 pts). 
a.      What is the mechanism that causes the trajectories shown and why might it be occurring here? 

Genetic drift, probably because of a small population size. Although drift can occur in all populations, its effects are stronger at smaller population sizes.

b.      What you see in the graph are six allele frequencies over time.  Each allele occurs at a different genetic locus.  If these alleles are all in the same population, how could they exhibit these changes that are so different from one another?

The process of independent assortment, and most are probably on different chromosomes.  So what happens to one allele at one locus during drift is not necessarily going to be mimicked by other alleles.

c.      Is there any evidence for gene linkage here, and if so, what is it?

There is some, in the case of the three traces that are colored blue, green, and black.  If you assume there’ll be some level of crossing over, this would explain why they might be on the same chromosome, and do not get lost or fixated at exactly the same time.

d.      If I ran this simulation again with the same exact parameters, would I get the same result?  Why or why not?

No, because genetic drift is random.

7.      Discuss one of the following two questions (10 pts):

a.      Describe Darwin’s argument that natural selection is the major mechanism of biological evolution of a population. Include some of the evidence he used to support this part of his thesis.  Be specific!

Darwin's influences were many, including the ideas that evolution did occur (LaMarck), populations grew exponentially (Malthus), geologic processes were uniform and gradual (Hutton, Lyell), and many of the examples he used influenced his thinking (artificial selection of pigeons, finches on Galapagos Islands, biogeography). His argument that Natural Selection was the mechanism boiled to 5 facts & 3 inferences. Individuals produce many offspring; if all survived population would increase exponentially forever. Most populations are stable in size, and although they can fluctuate no population increases indefinitely. Natural resources are limited; there are not enough resources for all to survive, so there must be a struggle for resources and few survive. In addition, he noted that individuals vary, yet resemble parents. Although he did not know the mechanism, he concluded that much variation is heritable. Survival therefore is not random; it depends on inherited characteristics.  Those with best fit to environment are more likely to survive & reproduce. This unequal ability leads to gradual changes in populations; favorable characteristics accumulate.

The mechanism can affect biological evolution by favoring certain characteristics over others.  The gene pool of the population changes over time to accumulate more and more copies of the alleles that code for adaptations that give their possessors higher fitness.  That is, those individuals have a better ability to survive and they produce more offspring that themselves survive to reproduce.

b.      Discuss how relative and absolute dating methods are used to determine the age of the Earth, and how both point to a very old age (determined to be about 4.6 billion years).

Stratigraphy and fossil evidence are relative methods that were used to show that the Earth and it's inhabitants have changed over time. Given that geologic processes are uniform and gradual, the many strata observed in cliffs and the Grand Canyon must have been laid down over long periods of time. The fact that many of the species of fossils are extinct and that the fossils in strata closer to the surface (are more recent) appear more similar to extant creatures is further evidence that the earth is much older than previously supposed. Use of radiometric data provides absolute dates to many rock formations and fossils. Using the fact that radioactive decay of a sample of radioactive isotope is constant and measurable, along with various facts about the formation of the rock from which a sample is derived, allows us to accurately data rocks from some strata. Use of multiple techniques validates estimates of age. All of these data point to an extremely old age for the Earth.

8.      In a population of the Common Sunflower Helianthus annuus, 100 individuals were sampled, and gel electrophoresis was used to determine the genotypes at the alcohol dehydrogenase (ADH) locus.  Three alleles were found, which we’ll call “a”, “b” and “c”; none was determined to be dominant to the others. The following genotypic frequencies were found in this sample; aa = 25, ab = 6, bb = 30, ac = 6, bc = 5, and cc = 28.  Answer each of the following questions (SHOW WORK – 9 points).

a.      Calculate the allele frequencies (set a = p, b = q, and c = r).

Use the equation [(2 x #aa) + #ab + #ac] / (2 x N) = [50+6+6] / 200 = 0.31 for a.
b = 0.355
c = 0.335

b.      Calculate the expected genotypic frequencies for the ADH locus in Phlox under Hardy-Weinberg equilibrium assumptions.

p2 = (0.31) x (0.31) = 0.096 (compare to aa = 0.25)
2pq = 2 x (0.31) x (0.355) = 0.22 (compare to ab = 0.06)
2pr = 2 x (0.31) x (0.335) = 0.208 (compare to ac = 0.06)
q2 = (0.355) x (0.355) = 0.126 (compare to bb = 0.30)
2qr = 2 x (0.355) x (0.335) = 0.238 (compare to bc = 0.05)
r2 = (0.335) x (0.335) = 0.112 (compare to cc = 0.28)

Do they add to 1?  Check it.

c.      Is there evidence for evolution occurring in this population?  If so, what microevolutionary mechanism may be in operation, judged by actual vs. expected genotypic frequencies? (If not, state that evolution is not occurring)

Yes, clearly the observed values of homozygotes are much higher than expected values.  So, possibilities include selection for homozygotes, selection against heterozygotes, or positive assortative mating.

9.      List two pieces of evidence that support the endosymbiotic theory of evolution in eukaryotes (6 pts).

10. Consider the following phylogenetic trees.  In the nematode worm phylum (Nematoda) both Caenorhabditis briggsae and C. elegans are self-fertile hermaphrodites (labeled Cbr and Cel on the trees, respectively).  Other Caenorhabditis species have separate sexes, including C. remanei (Cre) and C. spongiforma (Csp). Answer the following four questions regarding the three trees below (8 pts). 

a.      Which tree is most parsimonious?  A, it has only one evolutionary change in sexual reproduction.

b.      Which tree(s) presumes an evolutionary reversal? C, as it changes from separate sexes, to hermaphroditism, then back to separate sexes in species Cre.

c.      Which tree(s) shows convergent evolution? B (you can argue C as well, although it’s not as good an answer), as hermaphroditism evolved separately in Cbr and Cel.

d.      Of the two forms of sexual reproduction, which is the ancestral trait in all three trees? Having separate sexes is ancestral.

11.  Use the comparative approach to discuss convergent evolution of ichthyosaurs and sharks (from the Scientific American paper by R. Motani) (10 pts).  Include comparisons of at least two types of both taxa.

Variation in ichthyosaurs includes the three different types of ichthyosaurs discussed in the reading. The three are lizard-like, fish-like, and intermediate types. The full range of ichthyosaur diversity fell within this continuum.  Similarly, sharks have different body types, such as dogfish sharks and great whites.  The former were more similar to the lizard-like ichthyosaurs, and the latter more similar to the fish-like ones.  Body shape was more reptilian and vertebrae were longer and narrower in lizard-like ichthyosaurs and dogfish sharks.  In fish-like ichthyosaurs and open ocean sharks the body was bigger and more like a deep sea fish, and the vertebrae were shaped more like hockey pucks.  Ecological selective factors were primarily the different habitats in which the types lived and prey that they hunted. For instance, living near the coast in shallow water where prey was dense and plentiful, lizard-like ichthyosaurs retained some ancestral reptilian features. However, when ichthyosaurs evolved to live in the open ocean and hunt scattered prey that often lived deep and swam fast, the features discussed above led to their success, as it did with great white sharks.

12.  Consider the figure on the next page, which represents geographic distributions and phylogenetic relationships among five species of broadbills, a type of bird.  Answer the following questions (9 pts). 

a.      What evidence is there to suggest that species A and species B are closely related?

They belong to a monophyletic group, are separated by only 2 derived traits, and are sympatric.

b.      Explain the distribution of species C – what mechanisms of evolution might account for its distribution?

Probably a founder effect from species A, coupled with isolation and time, where mutations, natural selection, and gene flow were at work.

c.      What scenario of evolution might account for the distribution patterns of species D and E?

Species B, C, and D are monophyletic, and so one suggestion is that E came to inhabit its range in the Indonesia area, and then sometime after it had separated from B, C, and D’s ancestors, an ancestor of D came to that area and was already unable to interbreed with E.  It then subsequently inhabited a larger range than E, but was also sympatric with it for part of its range.  That’s one scenario.

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