Download Final Exam - UCF College of Sciences

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
GOOD LUCK!
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 sbrown = 0.15 and syellow = 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
Breast size
Mean
109.6 grams
Phenotypic Variance
156.8 grams2
Additive genetic
variance
120.2 grams2
Environmental
Variance
36.6 grams2
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:
Trait
mean
Wing Length 178.8 cm
Before
Hurricane
var
st dev
145.8
12.1
mean
After
Hurricane
var
st dev
heritability
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
Full sibling
half sibling
Aunt/uncle
Full cousin
Boat 1
1
2
4
9
Boat2 Boat3
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).