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BIO404 - EVOLUTION – MIDTERM 1 – NOVEMBER 4 2022

Please write clearly. Provide brief answers. Write explanations whenever you are asked for an explanation.

1) Among the cases below, choose the one that represents the most direct example of a trade-off, and the one
that represents the most direct example of an exaptation, and briefly explain both cases. 2 pt each

a- The evolution of photosynthesis in cyanobacteria

b- The evolution of a thorn structure in a plant from a leaf structure
c- The evolution of multicellularity independently in animal and plant lineages
d- The evolution of a full tail into a vestigial tail in the early ape lineage
e- The evolution of tumour suppressor proteins that reduce cancer risk and also limits regeneration capacity,
and thus reduces function at old age

Case e is the best example of a trade-off, because it involves opposite effects on fitness

Case b is the best example of an exaptation, because a previous adaptation evolves a new function

2) Killer whale females are known to undergo menopause at old age, like humans. Imagine a breast cancer
tumour-suppressor allele that shows its effect in breast tissue in killer whale females, only after menopause,
and increases longevity.
a. Name two tissues where the mutation creating this allele could have occurred first. 2 pt.
Sperm or egg stem cells, or embryonic gonads

b. Explain if this allele would evolve neutrally or whether it would be positively selected under the following
hypothetical conditions, b1 and b2. Write "neutral" or "selected", and add a brief explanation. 2 pt each

b1. Post-menopause killer whales are solitary (i.e. live alone):

Neutral, because it has no effect

b2. Post-menopause killer whales are social and support their own grand children, leading them to fish
sources:
Positively selected, because it increases fitness indirectly

3) a. Based on the protein sequence alignment below, create a distance matrix by filling in the table on the
right. Positions with differences are shown with asterisks. The sequence has 20 amino acids. 2 pt.

Cow LKTINADDKIKLGAAKDAAE Cow Human Gibbon Deer

Human LHTLNADDHIKLGAVKDAAE Cow
Gibbon LHTINADDHIKLPAVKDAAE
Human 4
Deer LHTINAEDKIKLGAAKEAAE
* * * * * * * Gibbon 4 2
Deer 3 5 5

Now draw an unrooted phylogenetic tree using this distance matrix and the UPGMA method.
You can also simply study the patterns in the alignment to draw the tree directly. You do not need to
explain/show the steps. You also do not need to show branch lengths on the tree. 3 pt.

Which of the four taxa represents an outgroup to the other three, or is there an outgroup at all? Remember
that an outgroup is equally distant to all other taxa. 1 pt.
None of them.

Given the alignment data, estimate the nucleotide-level substitution rate (i.e. the relative proportion of
changed residues) between human and gibbon. Assume each amino acid change is caused by a single
nucleotide change in each codon. Just report your answer as a ratio (e.g. 5/10). Bonus 1 pt.
2/(3*20) = 2/60
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4) Given the hominoid phylogeny, answer the below questions:

a. Are gorillas evolutionarily closer to chimpanzees or to humans? 1 pt

Equally distant.

b. Are humans an outgroup to chimpanzees and gorillas? 1 pt

No.

c. A gene duplication in modern-day humans is estimated to have occurred 8 million years ago. Which extinct
or extant species will be carrying it among bonobos, gorillas, and Australopithecus, and Neanderthals? 1 pt.
Bonobo, Australopithecus, and Neanderthal.

d. Both chimpanzees and bonobos have much larger relative testis sizes (0.27) than those of humans and
gorillas (0.06 and 0.02, respectively).
We do not know the relative testis size of the common ancestor of any of these groups.

A scientist suggests this could be explained by convergent evolution of small testes in humans and gorillas. Is
this a good explanation assuming parsimony? Say “yes” or “no” and provide a brief explanation. 2 pt.
No, it is not a good explanation. Because the same phenotypes could be explained by small testes being
ancestral, and large testes evolving only once in the chimpanzee lineage.

5) A group of scientists apply to TUBITAK with a grant proposal to perform a selection experiment on mice
(Mus musculus) to breed them as illegal drug detectors.
The plan involves performing two parallel selection experiments. One group of mice will be selected for
detecting methamphetamine derivatives, and a second group for detecting cocaine. Both experiments will
start with 10 inbred lab mice. In each generation, the researchers will test and choose the best 3 males and the
best 3 females. The experiment will continue for 3 years.
You are asked to review this proposal. You check the literature and notice that the heritability of detecting
amphetamine derivatives is <10% in mice, while the heritability of detecting heroine derivatives is 50%. You
also note that generation time is 3 months in mice.
You reject the proposal as unfeasible. However, being a nice researcher, you also propose changes that could
increase this experiment's success. Suggest 4 distinct modifications, removing or adding certain aspects of the
initial plan. 4 pt.
a. Increase the population size,

b. Use a more diverse population,

c. Focus on heroine instead of amphetamine.

d. Continue the experiment for a longer period.