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BIOL404/504 MOLECULAR EVOLUTION: MIDTERM II
NOVEMBER 5, 2008
Please answer the following succinctly; multiple choice questions may have >1 answer.
Read questions carefully and be sure to use technical terms correctly.
Number of points for each question in parenthesis (52 points total)
NAME:__________________________
1. Which of the following type of sites do you expect to evolve the most quickly? (2 points)
a) nondegenerate
b) twofold degenerate
c) fourfold degenerate
d) first codon positions
e) pyrimidines
2. At equilibrium what parameter can Fst be used to infer? (2 points)
a) strength of selection
b) number of migrants
c) population size reduction
d) linkage disequilibrium
e) none of the above
3. Under neutrality pi equals which of the following? (2 points)
a) theta
b) 1/4Nm
c) Tajima’s D
d) 4Neµ
e) none of the above
4. What are 2 common inbreeding avoidance mechanisms and how do they help avoid
inbreeding? (2 points) Example full credit answer:
Heterostyly: self-incompatibility mechanisms in plants ensure outbreeding because an
individual cannot self-pollinate
Sex biased dispersal: if one sex disperses from the natal territory outbreeding will be
facilitated because females will always mate with unrelated males.
5. What is the name and basic characteristics of the simplest model of sequence evolution? (2
points)
The Jukes-Cantor model is the simplest model of sequence evolution. It has only one
parameter: alpha, which represents the rate of nucleotide substitution between all 4 states (ie:
transitions and transversions happen at the same rate.
6. What is one explanation for observed codon usage bias? (2 points)
Traslational efficiency: codons preferentially used that are recognized by the most abundant
tRNAs
Replicational/translational stability: codons with mononucleotide runs may be vulnerable to
slippage so selectively eliminated
7. What is linkage disequilibrium? (2 points)
L-D is the degree of nonrandom association between markers at different genomic locations.
Locus A is tightly linked to locus B. A new mutation at locus B is highly advantageous
and is associated with a mildly deleterious allele at locus A. Over the next several
generations, would you expect variation at locus B to increase or decrease in the
population? (1 points)
Decrease
Why? (1 points)
If locus A experiences a “selective sweep” and increases to fixation, it will take the
“attached” allele at locus B along with it. Thus other alleles at locus B in the population will
be replaced. In general, linkage tends to decrease genetic variation over time.
What are 3 synonyms for the phenomenon occurring at locus B? (2 points)
Any three of the following:
Selective sweep
Hitchhiking
Genetic draft
Selective interference
8. What does it mean for gene flow to be a “creative” versus a “conservative” force? (3 points)
Creative: Gene flow can spread advantageous alleles between populations – this is creative
because new beneficial alleles can be introduced to populations
Conservative: Gene flow can prevent local adaptation by introducing maladapted alleles into
a population
Do Morjan and Reiseberg consider the most important role of gene flow to be creative
or conservative? (1 point)
Creative
9. Euphilotes enoptes is an endangered butterfly species that occurs in fragmented habitat in
coastal California. This species is associated only with two host plants and adult butterflies
live for only one week. More than half of E. enoptes habitat has been destroyed by highway
development, human over-use, and invasive plants.
Given the fragmented nature of the habitat and the short time window available for
migration, would you expect this fragmented population to have a high or low Fst? (1
point) Lots of population structure/fragmentation will lead to high Fst.
What specifically does Fst measure? (1 point)
Fst is one of Wright’s F statistics that measures inbreeding. It specifically evaluates the
distribution of genetic diversity in subpopulations compared to the total population.
What are the extreme numerical ends of the Fst spectrum and what would it mean if
you found a population at each of the numerical ends? (2 points)
High: 1 = isolation (subpopulations are isolated from eachother with no migration)
Low: 0 = panmixis (random mating in the total population, no subdivision)
10. Many large vertebrates are endangered in Africa. For example, the black rhino population
declined by a staggering 96 percent between 1970 to 1992 due to illegal hunting. In 1970 there
were approximately 65,000 black rhinos in Africa, declining to a low of about 2,300.
In the current small population, would you expect genetic drift or genetic draft to play a
more important role? (1 point)
Drift
Why? (1 point)
In small populations stochastic forces like drift are more important. The fate of an allele is
more likely due to chance fixation or loss than selection or linkage. In larger populations
“sampling variation” due to drift is not as big an issue – so selection and linkage play a larger
role.
Luckily one of your swashbuckling collaborators has been taking genetic samples of
black rhinos for the last 40 years and you have obtained sequences from samples from
1970 and from 2010. Do you expect heterozygosity to have changed over the last 40
years and if so in which direction (increase vs decrease)? (1 point)
Decrease. Genetic diversity tends to decrease with population size reductions. Less
genetic diversity means fewer individuals will be heterozygous.
What pattern do you expect to observe if you calculate Tajima’s D? (1 point)
Positive D.
Why? (1 point)
With population size reduction, rare alleles will be lost more quickly. When total diversity
(theta) is lost faster than average diversity (pi) it leads to a positive D.
If you were given a significantly negative Tajima’s D value without any information
regarding the history of the population it was calculated from, what are the two
alternative explanations for the Tajima’s D pattern observed? (1 point)
A negative D could be due to population size expansion or purifying selection. One limitation
of Tajima’s D is that you can’t unambiguously distinguish the signature of selection from the
signature of demographic changes.
11. Answer the following questions with reference to the tree on the next page.
A
B
C D
E
F
G
What is the sister taxa to taxon “E”? (1 point)
F
Circle the common ancestor of taxa “F” and “G”. (1 point)
If you wanted to use a molecular clock to determine how long ago taxa “B” and “C”
diverged, what test should you do first to decide if using a molecular clock is justifiable?
(1 point)
Relative rates test
If you find that a molecular clock is not valid, what are 3 things that could explain this
deviation? (2 points)
Generation time
Mutation rate
Selection
Metabolic rate
Please draw the following as an unrooted tree (((A,B),C),(D, E)) (1 point)
A
D
B
C
E
12. What is the difference between the Ka/Ks ratio and the Dn/Ds ratio? (1 point)
Ka/Ks is the ratio of the numbers of nonsynonymous to synonymous substitution since
divergence of two sequences while Dn/Ds is the ratio of the rate of nonsynonymous to
synonymous substitution since divergence of two sequences
What type of selection would you infer for each of the cases listed on the top of the next
page? (1 point)
Dn >> Ds: Positive selection (nonsynonymous sites are evolving faster than expected)
Dn << Ds: Purifying selection (nonsynonymous sites evolving slower than expected)
Your lab mate has just sequenced the PhDwannabe gene from two different strains of
bacteria and needs help analyzing the data. He doesn’t know the frame of his
sequences so you do not need to worry about whether sites are synonymous or non
synonymous.
Strain A
Strain B
CCGTATATGA
CGGTATAAGA
What is your estimate of K? (1 point)
0.2 (There are 2 substitutions in a sequence of length 10 so 2/10 = 0.2)
What are 3 types of mutations will cause you to underestimate K? (2 point)
Any of the following:
Sequential
Parallel
Coincidental
Back
What additional information would you need to calculate D? (1 point)
Divergence time between the two sequences
13. You discover a new population of nocturnal snakes on Moscow Mountain that you have
named Nightus snakus. The snakes are quite unusual in that they have huge eyes and are able
to navigate well in the pitch dark. You desperately want to study the genetic basis of this
adaptive trait. The same night you find a genie in a bottle.
You ask your genie for a first wish and she grants you the ability to PCR amplify the
NightVision gene, a candidate gene for night vision. You sequence the NightVision
gene for 20 individuals from your population. What test for selection could you use for
this single locus in a population sample? (1 point)
Tajima’s D or Dn/Ds.
You ask your genie for your second wish and she finds you the closest diurnal relative to
your night snake, the Dayus snakus. Now you have sequences for the NightVision gene
from two different species.
point)
McDonald-Kreitman Test
What additional test for selection can you now conduct? (1
What 4 pieces of information will you need for this test ? (2 points)
1. synonymous polymorpisms
2. synonymous fixed differences
3. nonsynonymous polymorpisms
4. nonsynonymous fixed differences
You ask your genie for your final wish and she grants you the ability to sequence the
entire genome for 10 individuals of Nightus snakus and 10 individuals of Dayus snakus.
What additional test can you now conduct? (1 point)
Fst outlier test
Based on the graph below, how many loci look like good candidates for further study to
explain the difference between the two species (dashed lines are confidence intervals)? (1
point)
Four – only the deviations above the line are relevant – those genes are more different than
expected by chance. The five loci below the line are more similar than expected by chance
and so are not good candidates for explaining the differences between the species.
Fst
Genomic Location
14.
What are two ways that you can experimentally test whether the same genetic mechanism
underlies similar phenotypes in closely related species? (2 points)
Any of the following:
hybrid complementation
quantitative trait loci (breeding studies)
gene expression (gene chips)
gene sequencing (candidate genes)
transgenes