Exam 02: the interactive key

In 1775, a severe typhoon reduced the human population of Pingelap Atoll to roughly 20 survivors. By chance, one survivor (the king!) carried a recessive loss-of-function mutation for achromatopsia (complete colorblindness). Today, roughly 10% of the island’s population is completely colorblind, compared to 0.003% globally.

1. What specific evolutionary mechanism caused this massive shift in allele frequency?
2. Compared to the pre-typhoon population, how did this event alter the inbreeding coefficient (F) of the modern islanders?
3. Before the typhoon why would this detrimental allele have existed in the population at all?
4. Do you expect this allele to be at Hardy-Weinberg Equilibrium?

In December of 2025, a new study came out looking at population genetics & demographics of two species of turtle found in the Midwest. These turtles are extremely similar, and for the purposes of this question, assume that they’re functionally identical for any trait you can think of that isn’t laid out in the table below. The researchers measured average census size (N), observed heterozygosity (H_o), expected heterozygosity (H_e), and two fitness components (percent of eggs that hatch and percent of hatchlings that survive their first year) across several populations of each of the two species.

1. Which species is more inbred?
2. What data let you answer (a)?
3. What is the most likely explanation for the hatching/survival rate differences?
4. Assume equal mutation rates. Which population should have higher genetic diversity?

Joe Thornton, an excellent first baseman, specializes in reconstructing ancient proteins & exploring how individual mutations that accumulated over time changed their function. This example is a simplified version of one of his types of analyses.

An ancestral sequence (CAGGTTACA) diversifies into three competing lineages in a population. Lineage A mutates to GAGGTTACA, Lineage B mutates to TAGGTTACA, and Lineage C mutates to AAGGTTACA. Each lineage then acquires the exact same mutations in the exact same order.

Despite all later mutations being the same, because that first base pair remains different (A/T/G), the entire structure of the three proteins is different. Each has a different biochemical activity (y-axis). For this question, assume receptor sensitivity is positively correlated with fitness.

The colored lines below show the “full” potential sensitivity curve for each trajectory across 8 subsequent substitutions. The solid black dots indicate the highest sensitivity each of these three allele trajectories can reach.

Imagine 10 populations that all start at the same allele & all start with the 3 of the 1-mutation alleles shown above.

1. At the start, when the three 1-mutation alleles are competing, which allele is most likely to go extinct in each of the 10 populations?
2. Which is least likely to go extinct in each?
3. What evolutionary force(s) would a population need to reach Lineage C’s peak?
4. What evolutionary force(s) would a population need to reach the highest peak?
5. How does the effective population size influence the probability a population that starts with all three alleles will ultimately end up with the best protein?

Researchers have monitored a wild population of bighorn sheep for decades, carefully measuring the mean adult male horn length (z̄) each generation. In 1995, the area became open to hunters. The hunting laws in this area put no restrictions on trait size, only the total number harvested. However, hunters preferentially target males with the largest horns. The average horn size trajectory over time is plotted below.

Presume how the horn size trait is transmitted has not changed.

1. How did the covariance of horn size & reproductive success change in 1995?
2. What was happening to the additive genetic variation for horn size before 1995?
3. What has been happening to the additive genetic variation for horn size since 1995?
4. Hunters specifically target males in bighorn sheep, but pay a fee to get their permits. The fees have allowed the park to expand each year, which means that the total population of bighorn sheep (N) has remained the same over time despite the hunting. How has neutral genetic diversity (θ) likely changed over this period?
5. If hunting is permanently banned in 2027, how do you expect horn length to change relative to the period before trophy hunting was legalized?

Your coolest friend comes up to you and says, “I’ve been reading a lot about Canine Transmissible Venereal Tumor (CTVT). It’s a contagious cancer that began long ago! It is a strictly asexual parasite spreading between dogs–when the dogs mate or lick or sniff a growth on another dog some of the tumor cells move into the new host and set up there. I took some notes on a cool paper by Baez-Ortega from 2019 where they sequenced hundreds of CTVT tumors from dogs around the world. I took some notes on mutation types in different genes and how many mutations tumors from different years had. I have some questions I was hoping you could help answer…”

1. “Papers keep saying the tumor began long ago but I can’t figure out what they’re using to determine that! There are no fossil tumors! Any idea how they estimate when these tumor cells diverged from healthy dogs using just the DNA?”
2. “If one cell in a tumor has a non-synonymous mutation to an immune evasion gene what is likely to happen to it?”
3. “If one cell in a tumor has a non-synonymous mutation to a housekeeping gene what is likely to happen to it?”
4. “A new paper that just came out in 2025 by Gori showed that CTVT sometimes steals chunks of nuclear DNA or even whole mitochondria from the host cells. Why would the tumor do this?”

Above is a diagram from a recent (Sept 2025) paper that looked at palliative care in pediatric cancer. They looked at alleles at a locus (here, two alleles A vs G at a single locus in the β-arrestin-2 [ARRB2] gene). The y-axis represents the dosage of fentanyl needed to relieve pain in the pediatric cancer cases, the x-axis represents the genotype at this specific locus. What (roughly) is the heritability of the fentanyl dosage for pain relief phenotype for the G allele?