Download BIOL404/504 MOLECULAR EVOLUTION

BIOL404/504 MOLECULAR EVOLUTION: MIDTERM I
SEPTEMBER 26, 2008
Please answer the following succinctly; multiple choice questions may have >1 answer.
Number of points for each question in parenthesis after the question (60 points total).
NAME:__________________________
1. Define molecular evolution (do not use the words “molecular” or “evolution” in your answer). (2)
Change over time at the DNA, RNA, and protein levels.
2. List 4 (of 6) of Darwin’s postulates (i.e., necessary conditions for evolution). (4)
Any of the following:
1. there is individual variation
2. there is a mechanism for heredity
3. there is overproduction of offspring
4. there is a struggle for existence
5. only the fittest survive
6. there is change over time
3. Circle one of the following that was NOT a tenet of the modern synthesis? (2)
a) Evolutionary phenomena can be explained by existing genetic knowledge
b) Evolution generally relies on mutations with large effects
c) Selection is the primary process driving evolution
d) The population level is the primary level for understanding evolution
e) Micro and macro evolutionary explanations are fundamentally compatible
4. What does the term “ring of life” refer to? (2)
Eukaryotic genomes appear to be an Archaea-Bacteria chimera – so the early “branches” on the tree of
life may be more “ring-like” than “tree-like”
5. People generally simplify one of the principles of molecular evolution to “mutations are random”.
Please give 3 examples of why this is not strictly true. (3)
Mutations are not truly randomly distributed across:
1. species
2. organelles
3. genomes
4. environmental conditions
6. Please write the reverse complement of the following sequence: GTAAACCGTA (2)
TACGGTTTAC
7. What are 3 reasons that a population’s effective population size might be lower than its census
population size? (3)
Any of the following:
1. Generational overlap
2. Unequal sex ratios
3. Polygamous matings
4. Historical bottleneck
8. What is the difference between a synonymous and a non-synonymous substitution? (5)
Synonymous substitutions do not cause an amino acid change (only a nucleotide change) while nonsynonymous substitutions cause an amino acid replacement.
Which do you expect to see more of in a genome?
Synonymous substitutions
Why?
Synonymous substitutions are under less functional constraint than non-synonymous substitutions.
Mutations that cause amino acid replacements are more likely to have a (negative) functional
consequence and thus be weeded out by selection.
At which codon position do you expect to see the most synonymous substitutions?
3rd
9. You come across two populations of whoositwhats when searching for a study system. The populations
appear to be fairly distinct genetically. You decide to monitor these populations for the next 1000
generations. Please circle the correct choices below. (4)
How would you expect drift to affect the genetic variation within each local population?
a) increase variation
b) decrease variation
c) no change
How would you expect drift to affect the genetic variation between the two populations?
a) increase variation
b) decrease variation
c) no change
After the first 500 generations a new migration route is established between the populations. How
would you expect migration to affect genetic variation within each population?
a) increase variation
b) decrease variation
c) no change
How would you expect migration to affect the genetic variation between the two populations?
a) increase variation
b) decrease variation
c) no change
10. Why is selection considered “inefficient” at removing a recessive deleterious allele in a population? (3)
Because they are “hidden” from selection when heterozygous.
11. For a new neutral mutation which of the following are dependent on population size? (2)
a) Probability of fixation = 1/N
b) Rate of fixation = u
c) Interval between fixation events = 1/u
d) Average time to fixation = 4N (in a diploid)
12. Identify the following types of selection. The dotted line indicates the trait distribution before
selection and the solid line indicates the trait distribution after selection. (3)
Directional
Stabilizing
Disruptive or Diversifying
frequency
trait
13. Identify one major idea or advance associated with each of the following (3)
Motoo Kimura: neutral theory
Rosalind Franklin: DNA x-ray crystallography
Charles Lyell: geological uniformitarianism
14. Is there better evidence for the “RNA first” or the “RNA early” hypothesis? (3)
RNA early
What is the difference between the two ideas?
The RNA early hypothesis suggests that RNA preceded DNA and proteins in evolutionary history but
does not claim that RNA was necessarily the first complex organic compound.
15. What is the difference between overdominant and underdominant allelic interactions? (3)
In overdominance heterozygotes are more fit than either homozygote. In underdominance
heterozygotes are less fit than either homozygote.
Which is more likely to maintain multiple alleles in a population?
Overdominance (remember the graphs with stable vs unstable polymorphism)
16. You receive a phone call from a very detail oriented colleague who has been evolving bacteria for
many generations and sequencing the full genome of every individual. She started with a genetically
homogenous population but she has just discovered the first mutation in her population. She wants you
to predict for her what the fate of the mutation will be (i.e., whether it will ultimately be lost, fixed, or
maintained as a polymorphism). (6)
If you were a strict neutralist, what two pieces of information would you ask her for about the
mutation/population?
1. Population size
2. Initial mutation frequency
If you were a pan-selectionist what two pieces of information would you ask her for about the
mutation/population?
1. Strength of selection
2. Mode of allelic interaction
17. The neutral theory is easily misinterpreted. Which of the following IS a tenet (or ARE tenets) of the
neutral theory? (2)
a) organisms are not adapted to their environments
b) all morphological variation is neutral
c) all genetic variation is neutral
d) deleterious mutations are more common than advantageous mutations
18. The Hardy-Weinberg equation is useful for predicting the percent of a human population that may be
heterozygous carriers of recessive alleles for certain genetic diseases. Phenylketonuria (PKU) is a human
metabolic disorder that results in mental retardation if it is untreated in infancy. In the United States, one
out of approximately 10,000 babies is born with the disorder. Approximately what percent of the
population are heterozygous carriers of the recessive PKU allele? (6)
q2 = 1/10,000 so q = 0.1 so p = 0.99 so 2pq = 0.0198
so 1.98% of population are carriers
What are 4 assumptions of HWE equation?
Any of the following:
1. infinite population size
2. random mating
3. no mutation
4. no selection
5. no gene flow
19. So far how is the level and pacing of this course for you (i.e., too easy/hard, fast/slow)? (1)
What suggestions do you have for improving the course for the rest of the semester? (1)