PCB6675C Fall 2012 FINAL EXAM NAME:__________________________________
INSTRUCTIONS:
1.
Whenever possible, type your answer directly into the exam
2.
Please use complete sentences when answering questions (yes, you are being graded on your ability to
clearly and efficiently communicate your ideas, not just by answering correctly)
3.
With regard to answer length: as long as your answer is coherent and contains the necessary information, it is long enough.
4.
Whenever calculations are involved, show your work
5.
You may use any resource you desire, except other students (and other student’s resources). If you have questions, come and see me (really, I don’t mind).
6.
If you need more space, simply move the remaining questions down the page and expand the answer boxes.
7.
You may remove the highlighted yellow text prior to answering questions

PCB6675C Fall 2012 FINAL EXAM NAME:__________________________________
1. Prior to the publication of On The Origin Of The Species, many researchers had already published concepts of biological evolution, expounding on its underlying causes. What made Darwin’s contribution to evolutionary theory unique among contemporary evolutionary ideas?
2. Although Darwin’s evolutionary theory was revolutionary, it lacked a key piece of information that caused many biologists / naturalists to rebuke his theory. What were the missing pieces of information and how was this latter rectified?

PCB6675C Fall 2012 FINAL EXAM NAME:__________________________________
3. You are interested in reconstructing the phylogenetic relationships between species A, B and C, which are more closely related to each other than to the chosen outgroup, species D. You sequence the alpha-ketone pseudogene, which results in the following nucleotide sequence:
Species A
Species B
Species C
Species D
1
T
A
T
A
2
A
T
A
A
3
C
T
C
T
4
C
C
C
G
5
C
C
C
C
6
C
G
C
C
7
G
G
G
A
8
G
G
G
G
9
A
A
T
T
10
T
T
A
T
3a. Draw all possible phylogenies (remember, species D is the consistent outgroup). Please place and label the characters on each phylogeny to indicate when they should have evolved (use a hatch mark, “— “). Use the method of parsimony when placing characters. Assume that no evolutionary reversals have occurred, and that species D represents the ancestral genotype.
3b. Circle the most parsimonious tree.
3c. According to the most parsimonious tree, which character(s) appears to be the result of convergent evolution (if any)?

PCB6675C Fall 2012 FINAL EXAM NAME:__________________________________
4. Using MEGA, please construct a neighbor joining tree (using the Crab_rRNA.meg file in the MEGA examples folder) with the following criteria: Test of Phylogeny = none; Substitution type = nucleotide; Model/ Method = pdistance; Substitutions to include = d:Tranitions + Transversions; Rates among sites =Uniform rates; Pattern
among lineages = Same (homogenous); Gaps / missing data = complete deletion. Once the tree is constructed, select “options” under the “view” menu. Under the ‘branch’ tab, select ‘display branch lengths’ and set the ‘precision’ to 3 decimal places. Paste phylogeny into your exam.
4a. Time since Divergence – You have strong fossil evidence indicating that the Pagurus bernhardus and P.
acadianus group separated from Ellasochirus tenuimanus approximately 10 MYA. Based on your estimates of percent dissimilarity between the taxa (i.e. you branch lengths), when did P. acadianus separate from P. bernhardus?

PCB6675C Fall 2012 FINAL EXAM NAME:__________________________________
5. Discuss the fundamental similarities AND differences between the punctuated equilibrium and gradual evolution hypothesis. Please incorporate Ernst Mayer’s concept of peripatric speciation into your discussion.
6a. You have been examining eye color variation in a large panmictic lizard species found across Panama. Eye color is controlled by a single gene with two, co-dominant alleles (+ and -). Homozygotes produce either brown or yellow eyes (+/+ or -/-, respectively) and heterozygotes (+/-) produce green eyes. The Panama population possesses the following genotypic frequencies: +/+ = 0.09, +/- = 0.42, and -/- = 0.49 (the + allele frequency = 0.3 = p). Your colleague has just discovered a new lizard population on the small island of Po off of the Panamanian coast, with the following genotypic frequencies +/+ = 0.02, +/- = 0.22, -/- = 0.76. Your colleague suspects that the island population is suffering from severe inbreeding depression, considering that the lizards exhibit smaller body size, create smaller eggs and exhibit short lifespans. Based on these frequencies, do you support their claim?

PCB6675C Fall 2012 FINAL EXAM NAME:__________________________________
6b. Invigorated by the discovery of the new lizard population on Po, you set out to search for more. In all, you discover 2 additional islands with lizard populations, Kip and Chin. To obtain a robust estimate of population genetic structure, you develop 3 microsatellite loci that are hyper-variable. You collect 56 total specimens across the mainland and the three island populations (see website for GenAlEx file, “Panama Lizards). Using GenAlEx, answer the following questions:
6c. Does this appear to be one panmictic population or is it a metapopulation? Justify your answer by including the relevant population statistic(s).
6d. Do the microsatellite data support the eye-color generated estimate of F on the island of PO? Justify your answer.
6e. Which populations appear to be the most and least genetically similar? Justify your answer.

PCB6675C Fall 2012 FINAL EXAM NAME:__________________________________
6f. Let us assume that a new mutation for female preference for green eyes evolves in the mainland population, creating selection, s, against the brown and yellow genotypes such that s brown
= 0.15 and s yellow
= 0.10. At what frequency will the (+) allele eventually equalize?

PCB6675C Fall 2012 FINAL EXAM NAME:__________________________________
6g. How many generations will it take to reach equilibrium? (Note: this is a tough question and requires some thought. Use Microsoft Excel for this calculation, as you will need to conduct many iterative calculations. Print out the spreadsheet and attach it to your exam). THIS QUESTION IS FOR EXTRA CREDIT.

PCB6675C Fall 2012 FINAL EXAM NAME:__________________________________
7. Imagine a mountain-top population that can support only 100 individuals of species X. In this population, the Z1 allele provides a superior survival benefit by conferring increased cold resistance on its carrier, creating strong selection against all alternative alleles at the Z locus (s = 0.55). Assuming that the environment is stable, there is no migration from the low altitude population, and the population exhibits a relatively normal mutation rate at the Z locus
(µ = 1.5 x 10 -4 mutations / gamete / generation), can alternative alleles at the Z locus be maintained in the population? Explain.
8. When adaptive landscapes are rugged, populations tend to be ‘stuck’ on their local adaptive peak and unable to obtain the highest possible adaptive peak in the landscape. Please discuss how populations could move between peaks. What are the realistic constraints of these so called ‘peak shifts’.

PCB6675C Fall 2012 FINAL EXAM NAME:__________________________________
9. Discuss how the expression pattern of a new mutation (i.e. dominant or recessive) influences both its probability and rate of fixation in a population.
10. The potential for the evolution of altruistic behavior via reciprocity is limited. Still, altruism via reciprocity has evolved in many systems. Discuss the key traits that these systems are expected to have in common?

PCB6675C Fall 2012 FINAL EXAM NAME:__________________________________
11. As a researcher for the USDA, you are currently investigating whether enough genetic variation exists to artificially select for increased breast size in a population of domestic chickens. The population you are working with has a mean breast size of 108 grams and a mean thigh size of 58 grams. A preliminary analysis reveals the following additional parameters:
Trait Mean Phenotypic Variance Additive genetic
156.8 grams 2 variance
120.2 grams 2
Environmental
Variance
36.6 grams 2 Breast size 109.6 grams
You wish to employ strong truncation selection on breast size only, where s = 8.4 grams. How much is breast size expected to increase in the next generation? What is the new predicted breast size mean?
(show your work)
12. In the fall of 2012, you examined wing length in a population of seagulls in Long Island, New York.
Just after your recorded your data, hurricane Sandy decimated the population, killing 50% of the birds.
After the hurricane passes, you go back to the field and measure the surviving birds (Table 1).
Table 1: Long Island seagull population before and after hurricane Sandy:
Before
Hurricane
After
Hurricane
Trait mean var st dev mean var st dev heritability
Wing Length 178.8 cm 145.8
12.1
180.3 cm 81.8.
9.0
0.4
12A. Which mode of univariate selection (directional, stabilizing or disruptive) is acting on wing length.
As multiple modes may be acting (e.g. directional plus stabilizing), please identify the mode having the largest influence (show all of your work).

PCB6675C Fall 2012 FINAL EXAM NAME:__________________________________
13. There are several hypotheses regarding the underlying mechanisms for why animals age, including the accumulation of somatic mutations, oxidative damage and telomere shortening. But animals are capable of repairing this damage by producing DNA repair mechanisms, superoxide dismutase and telomerase, respectively. Thus, even though animals are theoretically capable of immortality, aging is the norm in nature. Please discuss why we age from an evolutionary perspective. Include the most prevalent theories covered in class (6pts).
14. There are theoretical costs to sexual reproduction. Despite these costs, the majority of animals and plants sexually reproduce. Please discuss the costs associated with sexual reproduction as well as 3 of the 5 theories suggested to offset these costs (6 pts).

PCB6675C Fall 2012 FINAL EXAM NAME:__________________________________
15. You’re on a cruise ship and the ship begins to sink. Three life boats are now adrift, each one containing a number of your relatives. You have the power to save one boat from a dire fate. According to kin selection theory, it would be in the best interest of your genome to save which of the listed boats
(assume that all individuals have equal reproductive potential and that you come from a really big family; show your work; 4
pts)?
Relative Boat 1 Boat2 Boat3
Full sibling 1 half sibling 2
Aunt/uncle 4
Full cousin 9
2
1
5
6
16. How might the evolution of an altruistic behavior evolve if kin selection is not involved? (be specific).
3
2
2
5

PCB6675C Fall 2012 FINAL EXAM NAME:__________________________________
17. According to Fisher’s Fundamental Theorem, natural selection erodes genetic variation. Mutation aside, how can genetic variation be maintained in a system? Note: there are several mechanisms.
Choose one and discuss.
18. You’re interested in a population of southeastern insects (Insectus makebelievous) where males use red wing spots to attract females. At the northern edge of their range, they are sympatric with their sister taxon Insectus imaginarious, who also use red wing spots to attract mates. Interestingly you notice that in the area of sympatry, I. makebelievous has yellow wing spots, instead of red. Although the two species do hybridize, their offspring are of reduced fitness compared with the parental populations.
Please discuss the most likely scenario to account for this phenotypic pattern (be specific).