ID only (no name): 24.10.

2019

BIO 404 – MIDTERM 1 – 2019 FALL

Please be as brief as possible in your answers.

Q1. A beetle population found in Gokceada was compared to its sister population on the Anatolian mainland. The Gokceada
beetles were found to carry a long horn (mean 3 cm, sd 1 cm) compared to the mainland beetles (mean 1 cm, sd 0.5 cm).
Gokceada beetles are also genetically much less diverse than Anatolian beetles.

2 pt. Given this information, would you infer whether Gokceada beetles colonized Anatolia, or Anatolian beetles colonized
Gokceada? Explain how you make your inference.
Yes, Anatolian beetles probably colonized Gokceada, given lower genetic diversity in the latter (caused by drift/founder
effect).

3 pt. Describe an experiment to test the hypothesis that this difference in horn length represents an evolutionary change
(irrespective of being adaptive or neutral): Describe 2 possible findings and their interpretations:
Grow 100 beetles in the same environment (a common garden experiment): If beetles from both regions grow the same horn
size --> it is not evolution [the difference is not genetic]. If they retain their parental horn size --> evolution [the difference is
genetic] [suggesting an evolution experiment - this is both unnecessarily long and is actually testing for adaptation, not
evolution in general - 2pt].

4 pt. Describe an experiment to test the hypothesis that the long horn phenotype in Gokceada represents an adaptation. You
may use special microrecorders to track each individual's activity (feeding, mating). You can use plastic surgery but not
genetic means.
Add artificial extra 2 cm horns by surgery to 100 male Anatolian beetles. Subject 100 wild type male Anatolian beetles to
mock surgery. Release both groups in a cordened-off patch in Gokceada. Follow the survival and mating success of the
individuals using microrecorders. Test if long horn types have higher fitness than the control group [suggesting placing
Anatolian beetles on the island and vice versa and thus measuring fitness is NOT a good design: you cannot distinguish the
long horn effect from other confounding effects from the genotype - 2 pt only].

3 pt. Describe an experiment to identify which genes are involved in the long horn phenotype in Gokceada. Assume you do
not have candidate genes.
Sequence the genomes of the two populations [or some polymorphic markers scanning the genome], preferentially first
crossing Anatolian and Gokceada beetles and create an F2 [because otherwise too many differences will be linked - bonus 1
pt], find markers correlated with the phenotype, confirm effect with known-in / knock-out, use an outgroup [you would then
have to check the functions of the genes around the markers, because there may be multiple] [just saying "sequence
genomes" - 2p; "comparing gene expression" also 3 pt, but this is suboptimal because at the expression level many changes
are correlated].

1 pt. Will the experiment above be easier if there are many genes involved, or only a single gene? Explain briefly.
Single gene. [If all phenotypic variance is explained by a single variant: we will have more statistical power to find it.]

1 pt. Assuming in the experiment above you identified two alleles directly correlated with horn size differences. None of
them are located within protein coding sequence. How could you explain their effect on the phenotype?
They could affect gene expression. [Or they may be only linked with the causal mutation - bonus 1 pt.]

3 pt. Assuming you identified two alleles correlated with horn size. Describe an experiment to show that the long horn
phenotype represents an adaptation, using state-of-the-art molecular genetic tools.
Edit the 2 horn genes using CRISPR [bonus 1 pt] in Anatolian beetles to make them grow long horns, and release them along
with wild type Anatolian beetles in a cordened-off patch in Gokceada, and test if the edited beetles have higher fitness, as
above.
[or: Edit the 2 horn genes using CRISPR in Gokceada beetles to make them grow short horns, and release them along with
wild type Gokceada beetles in a cordened-off patch in Gokceada, and test if the edited beetles have lower fitness, as above.]

3 pt. Assume that, through these above experiments you found evidence that the long horn phenotype is genetic, but you
found no evidence that it is an adaptation. Provide three distinct (very unrelated) alternative hypotheses for the observed
phenotypic change.
Phenotypic change may be by drift.
It may have been adaptive in the past, but the adaptive effect may have been lost.
Adaptive function may not have been identified in the experiment [e.g. due to small sample size, side effects of DNA editing
or surgery, unique characteristics of the cordened patch, edited / artificial horns not being attractive to mates].
[Pleiotropy - also OK. Exaptation - 0.5pt].
Q2. 5 pt. Draw a hypothetical rooted phylogenetic tree that represents phylogeny and DNA differences of 9 mammals. These
are 3 marine mammals (A, B, C), 3 rodents (D, E, F), and 3 primates (G, H, I). Primates and rodents should both be
monophyletic, while the marine mammals should not be monophyletic. Primates and rodents should be sister clades in your
phylogeny. Rodents have evolved 2x shorter generation times than the other species, which your tree should qualitatively
represent.

2 pt. Given this description, what character must have

evolved convergently among some these mammalian
lineages? Explain.

Marine life, because they are not monophyletic.

1 pt. Show the most recent common ancestor of

primates on your phylogeny with an asterisk (*).

Q3. Humans like animals that like them, but many humans do not like animals that fear or bite them. Prof. Koc claims to have
invented a robot to automatically test and castrate (sterilize) animals that respond negatively towards human smell and
human appearance, and thus can select for nice animals. To show the robot's feasibility, the professor has applied for a 20
million TL grant from TUBITAK to conduct a 10-year selection experiment. TUBITAK asks you to review the professor's grant
application. Prof. Koc plans to apply the selection experiment on 4 captive populations, with characteristics summarised in
this table. He plans to maintain captive population sizes constant throughout the experiment. All 4 species have similar
generation time, about 0.3 years.
To measure the phenotype, the professor has devised a "human-liking" score that ranges from -Infinity to +Infinity. The initial
mean human-liking scores the professor has measured in founding populations are listed in the table. Each generation, the
robot will first measure the average human-liking score, and then castrate individuals who fall below the median.

Population size Initial genetic composition Genetic basis of Trade-off between human-
human-liking liking and survival
Guinea pig 100 A diverse population Exists Probably not
Hamster 1000 A diverse population Probably not Probably not
Rat 100,000 Inbred (homogeneous) Exists Exists
Mouse 100,000 Inbred (homogeneous) Exists Probably not

12 pt. Given this information, predict the phenotypic response of each population to the professor's selection robot over 10
years by choosing the most likely trajectories of the human-liking score, and writing the species names to the right. Mark the
species clearly at the end of the trajectories. Explain your reasoning in each case:

Guinea pig: genetic variance exists but population size small --

> early response, but variance will run out, response will slow
down

Hamster: no genetic basis --> no response

Mouse: no initial genetic variance, but variance will eventually

accumulate thanks to de novo mutations in large population
size --> response will be observed

Rat: no initial genetic variance, but will eventually accumulate

thanks to de novo mutations in large population size --> response will start but will be slowed down by survival trade-off, so
should be slower than mouse