NAME: __________________________
Bio 418 – Advanced Evolution
Midterm
Spring 2015
_______
60 pts
Circle the best choice out of the options. Read all choices carefully before answering. (1 point each)
1. Which of the following are known to regulate gene expression after transcription?
a. promoters
b. transcription factors
c. micro RNAs
d. cis-regulatory elements
e. all of the above
2. What is gene duplication?
a. mutational process that produces an additional copy of a gene
b. process of DNA replication that occurs during meiosis
c. process of DNA replication that occurs during mitosis
d. lab technique that makes many copies of a targeted gene (aka PCR)
e. none of the above
3. Adaptation at the genetic level most commonly occurs by:
a. protein-coding mutations
b. mutations that affect gene regulation
c. physiological responses to the environment
d. frameshift mutations
e. both a and d
4. What is parthenogenesis?
a. formation of sperm cells
b. formation of egg cells
c. growth of a parasite population within its host
d. the replication of DNA during meiosis
e. development of an offspring from an unfertilized egg
5. What do we call the accumulation of deleterious alleles in an asexual lineage?
a. Muller’s Ratchet
b. Red Queen effect
c. purifying selection
d. Fisher’s runaway selection
e. none of the above
6. Anisogamy refers to:
a. equal-sized gametes within the same species
b. different-sized gametes within the same species
c. equal-sized gametes between different species
d. different-sized gametes between different species
e. both a and c
_______
6 pts
1
7. Due to unequal energy investment in reproduction, the operational sex ratio of a population is typically
expected to be:
a. less than 1
b. equal to 1
c. greater than 1
d. equal to zero
e. less than zero
8. Which of the following statements about mutation rates is not correct?
a. rates can vary 60-fold across a chromosome
b. rates are typically higher for chromosomes inherited from the mother than from the father
c. an average mutation rate for an animal species would be 10-8 changes per site per generation
d. humans are routinely born with 30 to 50 novel mutations not present in either parent
e. rates can vary among genes, among individuals within a species, and among species
9. Since their divergence from other primates, humans evolved larger brains and different reproductive
structures and functions, which may be at least partly attributed to:
a. loss of over 500 enhancers
b. widespread gains of adult lactase persistence
c. increased frequency of alternative splicing in those tissues
d. the need to avoid inbreeding
e. both a and c
10. In evolutionary terms, two distinct “populations” are groups that likely:
a. have significantly different allele frequencies
b. are separated by a river or mountain range
c. exchange migrants due to dispersal
d. do not compete for resources with each other
e. both b and d
11. Define each of the following in 1-2 sentences, and state their importance to evolution. (1 pt each)
transversion mutation – Transversions switch a purine for a pyrimidine or vice-versa,
causing a disruption in the DNA helix that is more likely to get fixed by
repair enzymes; although there are more ways to make a tranversion
substitution, they are seen more rarely in natural populations than
transitions.
genetic drift – a process in which alleles are randomly lost or fixed due to sampling
error in the production of offspring; responsible for steady loss of
heterozygosity; stronger in small populations
Bateman’s principle – because females invest more energy in gamete production, their
optimal strategy is to mate with the highest quality male; for males, the
optimal strategy is to mate with as many females as possible
2
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7 pts
Questions that require interpreting data.
30
12. Answer the following questions about the
graph shown to the left.
25
(a) What specific form of selection is acting on
this population? (1 pt)
20
15
disruptive selection
10
5
(b) Write a general equation for this kind of
selection (1 pt)
0
y = m1x2 + m2x + b
0
5
10
15
20
25
30
weight
(c) What is the general term for this class of model? (1 pt)
non-linear (produces a curved relationship)
(d) How will the mean value of weight change in the next generation? (1 pt)
no change, although individuals close to the mean have lowest fitness; extremes average
out and mean stays about the same
(e) How will the variance in weight change across this population in the next generation? (1 pt)
variance increases, as individuals farthest from the mean have high fitness
13. Answer the following questions about the
graph shown to the left. Solid dots indicate trait
values for individuals that failed to reproduce;
grey squares are values for individuals that
successfully reproduced.
(a) What form of selection is acting on this
population? How can you tell? (3 pt)
Correlational selection; fitness was
highest for individuals with a positive
correlation between height and weight.
(b) Do you expect the mean height to change very much in the next generation? Why or why not? (2 pt)
No, because equal numbers of tall and short individuals reproduced; what mattered was
the relationship between height and weight, not the value of either in isolation.
_______
10 pts
3
14. You produce this phylogeny by Maximum Likelihood analysis of DNA sequences from four genes:
(a) Which sister species evolved most recently
from their common ancestor? How can you tell?
(1 pt)
D. cathii and D. huggii because they
are joined to their common ancestor by
the shortest branches. Branch length is
a proxy for evolutionary time.
(b) Which species would probably most closely resemble the last common ancestor of this clade? Explain
your reasoning. (1 pt)
D. schmoopii, because no speciation events happened since it diverged from the
last common ancestor of the whole clade; other species will presumably show
adaptations arising after speciation events occurred (they must have gotten
different from each other, since we classify them as different species).
(c) All these species hide under beds, except M. nightmarus, D. cathii and D. huggii, which hide in closets.
Mark the branches where you think the character “hiding place” changed over the history of this group, and
indicate how it changed. There are 2 possibilities – why might your answer be better than the alternative
answer? (2 pt)
Either
“bed  closet” on #95 and “closet  bed” on #100(if it’s easier to lose a
trait than to evolve it in the first place)
OR
bed  closet on both branch #90 and M. nightmarus branch (if convergence
favors 2 origins of the same trait on long branches)
(d) Is the genus Dragon valid -- should it have its own name? Why or why not? (2 pt)
No - it is paraphyletic, leaving out the genus Monster with which it shares a common
ancestor.
(e) Can you confidently determine what the sister species of Monster grossus is? Why or why not? (2 pt)
No – the bootstrap support for this node is below 70%, meaning we cannot say
with confidence whether M. yikesus or M. scariius is closer to M. grossus (this
node is really a polytomy, or 3-way tie)
(f) Your rival Dr. Awful publishes a different phylogeny based on a neighbor-joining analysis of 2 genes, and
claims his phylogeny shows the “true” relationships. Why is your phylogeny more likely to be right? (2 pt)
A) NJ is a weak method for analyzing DNA; it throws out a lot of information.
Your ML analysis uses all the mutational information plus a model of sequence
evolution to find the best possible tree, given the data.
B) he only used 2 genes, whereas you used 4, meaning you had more data
4
_______
10 pts
15. You sample five snails from each of three parks, and genotype each one at a gene with two alleles (A, a).
1
p=
3
p=
a) Calculate p (the frequency of A) in each subpopulation. (1 pt)
aa
AA
AA
AA
AA
AA
aa aa
aa Aa
aa
aa
Aa
b) Calculate FST for this metapopulation. Show your work. (3 pt)
Hs = (2x1x0)+(2x0.1x0.9)+(2x0.1x0.9) = 0 + 0.18 + 0.18 = 0.12
3
3
2
p=
aa
1, p = 1; 2+3, p = 0.1
aa
Ht = 2(average p) (average q) = 2(0.4)(0.6) = 0.48
Fst = 1 – (Hs/Ht) = 1 – (0.12/0.48) = 1 – 0.25 = 0.75
c) Would you conclude there are likely to be >1, or <1, effective migrants per generation moving among
parks? Explain why. (1 pt)
I expect overall Nem <<1, given the high Fst value; the lack of migration allows the
allele frequencies to be very different in park 1 from the other two parks, which may
exchange migrants.
Short answer. Answer each numbered question in 3-4 sentences. (5 points each)
16. Are random changes to the DNA sequence of a gene more likely to result in a synonymous or a nonsynonymous substitution? Why? Which kind of change is more likely to persist in a population?
Based on the genetic code, the majority of possible DNA substitutions would result in
non-synonymous changes; only a subset of 3rd position and a few 1st position changes are
synonymous. However, non-synonymous changes will alter protein structure and
potentially function, and random changes to the amino acid sequence are more likely to
make a protein function worse than to improve its function; therefore, most nonsynonymous changes will be selected against. Synonymous changes are largely invisible
to selection and are thus more likely to persist in a population.
17. Explain how gene duplication can facilitate the evolution of novel adaptive traits, using the snake venom
gene for crotamine as an example.
Gene duplication creates redundancy in a gene’s function, i.e. two copies of a gene
doing the same thing. This redundancy allows one copy to continue to function properly
while the other copy can more readily assume a new function via mutations that would
otherwise be purged by purifying selection. The defensin gene codes for a protein
synthesized in the pancreas to fight infection. Duplication of this gene in the
ancestor of all snakes allowed it to specialize on different infections. A regulatory
mutation then caused one copy to be expressed in the mouth. Protein-coding changes in
this copy changed the protein’s shape in a way that made it damage muscle tissue.
Additional mutations made this protein more deadly, while additional duplications gave
rise to an entire family of crotamine venom genes.
_______
15 pts
5
18. Explain how ancestral E. coli populations helped researchers find evidence for the genetic adaptations
that allowed aerobic citrate metabolism to evolve in one lineage. Name and describe the three successive
steps of this complex adaptation?
Restarting the experiment by thawing samples that were frozen from different
generations allowed researchers to figure out at what point in time citrate metabolism
began to occur (actualization). After identifying the gene duplication event that
allowed this to happen, they discovered that the number of duplication increased up to
9 before leveling off at an optimal 4 copies (refinement). Going further back in time
prior to actualization, they discovered that an unknown mutation created a genetic
background that was necessary in order for the original gene duplication event to cause
citrate metabolism (potentiation).
19. Answer the following questions about Tishkoff et al. 2007, the first literature assignment, which dealt
with human lactase persistence in African versus European populations.
(a) What is a “SNP”? (1 pt)
Single nucleotide polymorphism; position at which some individuals in a population have
different DNA bases
(b) How did purifying selection on the LCT locus affect polymorphism at nearby genes, and why? (3 pt)
Extended “homozygosity tracts” show that selection on the LCT enhancer reduced
polymorphism for about a million bases on either side of the LCT gene. This reflects
genetic hitch-hiking due to linkage between alleles at nearby genes and the mutations
conferring adult lactase persistence: strong selection favoring mutations in the LCT
enhancer indirectly favored all linked variation, and decreased polymorphism upstream
and downstream. Only recombination over time can break down disequilibrium between the
favorable LCT mutations and linked alleges at other genes.
(c) The SNPs associated with adult lactase persistence did not affect the amino acid sequence of the lactase
protein itself. How then did they affect the phenotype? More generally, how does this type of mutation
contribute to evolutionarily significant changes in organismal phenotype? (3 pt)
The SNPs were mutations in a cis-regulatory element – in this case, an enhancer region
upstream of the LCT coding region that affects LCT expression by directing
transcriptional machinery to the LCT promoter through the “enhance-osome”
complex. Experiments using a luciferase expression assay confirmed that these
substitutions drive increased gene expression of LCT, and hence cause adult
lactase persistence. Mutations in enhancers contribute to phenotypic novelty by
restricting changes in gene expression to specific tissues or times, without
altering the protein itself; this modular effect insulates most tissues from a
change in expression, whereas coding region changes are expressed everywhere in
the body.
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12 pts
6