Midterm Exam Guide: Biology 336 - Evolutionary Biology

Given name FAMILY NAME (CAPS) Student Number: _____________________________ 1 BIOLOGY 336 - Fundamentals of Evolutionary Biology Midterm 27 October 2022 Instructors: Sarah Otto, Wayne Maddison, and Jeannette Whitton 1. Some questions ask that you show your work or include the formula that you used. Marks may be deducted for not doing this, and part marks may be given for showing your work. 2. Short-essay questions will include a rough guideline (number of words or sentences) to help you know what we expect; this is not a strict limit. 3. If you think there may be a mistake in a question, if the meaning of a question is unclear, or if there is a word or phrase that you don’t understand, please ask for clarification. 4. The exam may be written in pen or pencil, but pencil answers will not be eligible for regrading. 5. Answer all questions in the space provided. Material written on other pages will not be read or marked unless you clearly indicate that you’ve completed the answer elsewhere. 6. You may use a non-programmable calculator (or be prepared to show that your programmable calculator has nothing in memory). 7. Students who write the exam during the normally scheduled time may not discuss the contents of the exam with students who subsequently take a make-up version of the exam. 8. Hand in all examination papers; do not take any examination material from the room. 9. Please follow any additional examination rules or directions communicated by the instructor. 10. Students are expected to behave honourably in completing their exams, submitting their own answers, and ensuring that others are not able to easily view their papers. I have read and fully understand these instructions, and I have checked that all 8 pages are present. Student signature ___________________________________________ Question Marks Possible Your Mark 1. 5 2. 5 3. 3 4. 5 5. 3 6. 3 7. A, B 10 7. C, D 16 8. 6 9. 10 10. 8 11. 6 12. 6 13. 6 14. 8 TOTAL 100

2 Background: The evolution of antibiotic resistance imposes a major health burden and cost, reducing the efficacy of medicines to treat bacterial and fungal infections. The above graph illustrates the number of years between the introduction of an antibiotic and early reports of resistance (start and end of bars, followed by the species in which resistance was first found, Buchy et al. 2020 IJID 90:188). Buchy et al. (2020) noted that antibiotic resistance accounts for >700,000 deaths annually and is one of the ten key threats to global health. In the first 7 questions of this midterm, you will explore several aspects of the evolution of antibiotic resistance. Assume in all questions Q1-Q6 that the organisms are haploid bacteria. We will track time with one “generation” representing the time course of a typical human infection (e.g., 2 weeks). Q1. (5 marks) Consider a new antibiotic that targets a particular site in the cell membrane. Before the antibiotic is used, mutations at that site that lead to antibiotic resistance will pre- exist at mutation-selection balance. If the mutation rate at that site is 10 -7 per generation and the selection coefficient against the resistant allele before antibiotic appears is 0.002, at what frequency do you expect the resistant allele to be present before the antibiotic is introduced? [Include the formula, show your work, and circle your final answer. Write the answer to five decimal places, e.g., 0.00011.] Q2. (5 marks) In a hospital where a single patient is infected with the resistant bacteria, what is the probability that that resistant allele is lost despite the fact that the mutation increases the ability of the bacteria to survive and transmit to another patient by 30% (i.e., s = 0.3). [Include the formula, show your work, and circle your final answer. Write the answer to one decimal places, e.g., 0.1, and assume that the population is large.]

3 Q3. (3 marks) Many antibiotic resistance genes are carried by plasmids, which are small circular genetic elements that can be transferred from bacterium to bacterium (Figure). Relative to genes in the main chromosomal genome, plasmids allow for [choose the best answer] : □ selection □ recombination □ disequilibrium □ hitchhiking □ epistasis Q4. (5 marks) When antibiotic resistance first appears, how many generations would it take for resistance to rise from an initial frequency of 10 -6 infections to a frequency of 50% if it increases the chance that an infection survives and transmits by s = 0.3. [Include the formula, show your work, and circle your final answer for t in generations. Write the answer to five decimal places, e.g., 0.00011. Hint: it can be easier to work with ࠵?[࠵?]/࠵?[࠵?] ] Q5. (3 marks) The form of selection in the previous question Q4 is □ Dominant selection favouring resistance □ Additive selection favouring resistance □ Heterozygote advantage □ Directional selection favouring resistance Q6. (3 marks) Which historical figure might have said that the frequency of antibiotic resistance rises because cells exposed to antibiotics practice eliminating the antibiotics and pass on this enhanced performance to their daughter cells? □ Carolus Linneaus □ Jean Baptiste-Lamarck □ Thomas Malthus □ Charles Lyell 2. 3. Relaxasome Transferasome DNA polymerase F plasmid F plasmid 4. Old donor New donor Chromosomal DNA F plasmid Chromosomal DNA Donor Recipient 1. Pilus Pilus Pilus By Adenosine - Own work, CC BY-SA 3.0, https://commons.wikimedia.org/w/index.php?curid=783186 4

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4 Q7. The abstract of “Adaptation to the fitness costs of antibiotic resistance in Escherichia coli ” by Schrag et al. (1997) in Proc. R. Soc. B 264:1287 reads [=with some wording help]: “Policies aimed at alleviating [=fixing] the growing problem of drug-resistant pathogens by restricting antimicrobial usage implicitly assume that resistance reduces the Darwinian fitness of pathogens in the absence of drugs. While fitness costs have been demonstrated for bacteria and viruses resistant to some chemotherapeutic agents [=drugs] , these costs are anticipated to decline during subsequent evolution. This has recently been observed in pathogens as diverse as HIV and Escherichia coli . Here we present evidence that these genetic adaptations to the costs of resistance can virtually preclude resistant lineages from reverting to sensitivity [=adaptations that lessen the cost of resistance can prevent the spread of mutations that eliminate resistance] . We show that second site mutations [=at other genomic positions] which compensate for the substantial (14 and 18%* per generation) fitness costs of streptomycin resistant ( rpsL ) mutations in E. coli create a genetic background in which streptomycin- sensitive, rpsL + alleles have a 4-30%* per generation selective disadvantage relative to adapted, resistant strains. We also present evidence that similar compensatory mutations have been fixed in long-term streptomycin-resistant laboratory strains of E. coli and may account for the persistence of rpsL streptomycin resistance in populations maintained for more than 10 000 generations in the absence of the antibiotic. We discuss the public health implications of these and other experimental results that question whether the more prudent use of antimicrobial chemotherapy will lead to declines in the incidence of drug-resistant pathogenic microbes.” A. (4 marks) The main message of this abstract is that [choose the best answer] : □ antibiotic resistance disappears rapidly in the absence of the antibiotic □ evolution can lead to the reduction of fitness costs of antibiotic resistance □ antibiotic resistance is likely to evolve □ second site mutations can occur □ the dollar costs of antibiotic resistance decline over time B. (6 marks) Their Figure 2 is illustrated on the right (CAB281 refers to the wildtype E. coli bacteria used in their experiments). The two bottom axes refer to streptomycin resistant ( Str R ) and sensitive ( Str S ) strains, with or without the compensatory second-site mutation. In the abstract, the phrase “substantial (14 and 18%* per generation) fitness costs of streptomycin resistant ( rpsL ) mutations” is referring to the heights of which bars: □ STR1 relative to CAB281 □ STR1 relative to STR12 □ STR12tr relative to STR12 □ STR12tr relative to CAB281 In the abstract, the phrase “streptomycin-sensitive, rpsL + alleles have a 4-30%* per generation selective disadvantage relative to adapted, resistant strains” is referring to the height of: □ STR1 relative to CAB281 □ STR1 relative to STR12 □ STR12tr relative to STR12 □ STR12tr relative to CAB281 [*Ignore this variation in costs, which was due to having different resistance mutations.]

5 C. (6 marks) When sampling the population near the end of their experiment, Schrag et al. might have observed the following frequencies of cells: 87% STR12, 5% STR1, 6% STR12tr, and 2% CAB281. What is the linkage disequilibrium in this population and which pair of lines are more frequent than expected? [Include the formula, show your work, and circle your final answer. Write the answer to five decimal places, e.g., 0.00011.] The pair of lines that are more frequent than expected are: ____________________ D. (10 marks) The study concludes “From a clinical and public health perspective, these results point to another potentially general reason why reductions in antimicrobial usage may not lead to rapid declines in the incidence of resistant pathogens.” In 50-100 words, describe the general reason implied by this abstract to another UBC biology student who has not taken 336.

6 Q8. (6 marks) This phylogenetic tree shows (correctly) relationships among vertebrates: A cell biologist studies variation in the enzyme MQSTR among vertebrates. They found two different forms of the enzyme, represented here by the black and white spots. (a) (2 mark) The biologist uses the phylogeny to reconstruct what enzyme form ancestors had. What is the most parsimonious estimate of the enzyme form in the MRCA of salamanders and lizards, ☐ black, or ☐ white? (choose one) What is the most parsimonious estimate of the enzyme form in the MRCA of zebrafish and crocodiles, ☐ black, or ☐ white? (choose one) (b) (4 marks) Mark whether each of the following phylogenetic trees is correct or not. ☐ correct ☐ incorrect ☐ correct ☐ incorrect ☐ correct ☐ incorrect ☐ correct ☐ incorrect salmon zebrafish lungfish frog salamander lizards crocodiles birds humans dogs crocodiles birds lizards dogs frog salamander lungfish salmon zebrafish lungfish lizards humans birds salamander zebrafish frog salamander humans dogs lizards crocodiles birds salmon zebrafish lungfish salmon zebrafish frog humans lungfish

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7 Q9. (10 marks) Draw the phylogenetic tree showing the relationships among these groups of organisms. Frogs Ferns Crustaceans (e.g., crabs) Snails Humans Red algae Fungi Sharks Spiders Draw them on the time scale below so that the 9 groups listed appear at time 0 (the present), and MRCAs appear at the appropriate times before the present. We won’t grade the placement of every single MRCA, just the MRCA of frog and human; MRCA of frog and crustacean; MRCA of ferns and red algae. We will grade all of the relationships implied by the tree. Millions of years ago 0 (present) 100 200 300 400 500 600 • • • 1000 2000 3000 Cambrian explosion Precambrian Paleozoic Mesozoic

8 Q10. (8 marks) Suppose a study is done of 2 Denisovans, 2 Neanderthals, 3 humans. Analysis shows that 4000 loci have a gene tree like #1 below, 3000 like #2, and 3000 like #3: (rooted with data from chimps) (a) Draw gene tree #3 in the species tree below, assuming discord is from incomplete lineage sorting (but as little as possible), not hybridization. The sampled gene copies are shown as spots on the species tree below. (4 marks) Gene tree #3 EXTRA TREE IN CASE YOU NEED IT. WILL NOT BE GRADED UNLESS YOU TICK HERE: ☐ USE THIS ANSWER FOR PART (a).

9 (b) These data imply incomplete lineage sorting in which lineage(s) of the species tree, the one(s) marked on the diagram as (1), (2), (3), or (4)? (The answer could be more than one.) (2 marks) (c) Assuming that lineage (1) of the species tree had a consistent population size throughout its history, and likewise for lineage (3), which population size for each lineage could reasonably explain the 1000 gene trees observed? The drawn width of the species lineages is not intended to show population size accurately, so you’ll need to infer the population sizes from the gene trees. [Choose one for each] (2 marks) Population size of Lineage (1): ☐ less than 1,000 ☐ more than 10,000 Population size of Lineage (3): ☐ less than 1,000 ☐ more than 10,000 Q11. (6 marks) A biologist friend of yours studies 12 species of fubonidians for two characters, whether they occur on basic soil or acidic soil, and whether they have spines or not. They find that five of the species (A, B, C, D, E) have spines and live on basic soil, while seven (F, G, H, I, J, K, L) lack spines and live on acidic soil. Your friend says, “I’m convinced this is good evidence that spines are an adaptation to basic soil!”. You say, “Not so fast! We need to know the phylogeny of the 12 species!”. To explain to your friend why it’s important to know the phylogeny, draw a possible phylogeny of the species that would strongly support their theory of a correlation between the evolution of spines and the preference for basic soil. Feel free to use abbreviations, e.g., s and ns (for spines and no spines) and a and b (for acidic and basic). Then, explain in 2 to 3 sentences how the phylogeny provides strong support for the theory of this correlation .

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10 Q12. (6 marks) Biologists exploring Planet Q have discovered 9 species of dragons, worked out their phylogeny, and also discovered organisms living on or in the bodies of each species of dragon. Biologists have given these different groups of associated organisms informal names: microbes, bugs, capsules, worms and spots. Dragon species D1 has microbe species m1, bug species b1, capsule species c1, worm species w1, and spot species s1. Likewise, species m2, b2, c2, w2, and s2 live on dragon species D2. Likewise for the others: the number in the name corresponds to the dragon species the organism lives on. They work out the phylogenies of each of the associated organisms: (a) There have been no studies of the interactions among these species, so it’s not known which of the associated organisms are parasites, commensals, or mutualists with the dragons. Based only on the phylogenies above, which of the associated groups (microbes, bugs, capsules, worms, spots) is most likely to be mutualists (i.e. cooperative with the dragons)? (2 marks) (b) Please explain your answer to (a) in 1 to 3 sentences (4 marks) D1 D8 D6 D2 D4 D5 D3 D7 D9 w6 w2 w1 w8 w4 w3 w5 w7 w9 c1 c6 c9 c8 c4 c3 c2 c5 c7 m 2 m 1 m 4 m 3 m 6 m 7 m 9 m 8 m 5 b4 b2 b1 b6 b5 b7 b8 b3 b9 s8 s6 s3 s2 s1 s7 s4 s9 s5 Dragons capsules worms microbes bugs spots

11 Q13. (6 marks) Complete this paragraph by indicating the correct choice in each of the three places: The antagonistic pleiotropy theory of senescence explains organisms' deterioration with age. According to this theory, [choose one] ☐ selection doesn't act. ☐ selection does act, pushing alleles to fixation. This happens because high rates of [choose one] ☐ extrinsic damage, i.e., accidents, ☐ intrinsic damage, i.e., from genes, lead to most individuals dying young, and thus not available to reproduce anyway. Therefore, [choose one] ☐ mutations that occur late in life ☐ mutations that act late in life can build up generation by generation. Eventually, the descendant organisms will not live to an old age even if they are protected from risk and given all the nutrition and care they need. Q14. (8 marks) Complete each sentence by selecting from the list of 8 choices below. Write the number or the phrase in the blank. (a) The repeatability or confidence in a clade can be assessed by ______________________ (b) When inferring phylogeny, probabilistic models are used to calculate ________________ (c) Optimal adaptation is often prevented by ______________________________________ (d) Vertical inheritance of a parasite within a host can lead to ________________________ (1) ancestral constraint (2) bootstrap analysis (3) mutualism (4) coincidence (5) likelihood (6) parsimony (7) symbiosis (8) synapomorphy

12 Biology 336 Formula Sheet – Midterm Exam Version Haploid selection: ࠵?[࠵? + 1] = ࠵? ! ࠵?[࠵?] ࠵? ! ࠵?[࠵?] + ࠵? " ࠵?[࠵?] ∆࠵?[࠵?] = ࠵?[࠵? + 1] − ࠵?[࠵?] = ($ ! %$ " ) ([*] ,[*] $ ! ([*]-$ " ,[*] Allele frequency after several generations: ([*] ,[*] = $ ! $ $ " $ ([.] ,[.] or equivalently ࠵?[࠵?] = $ ! $ ([.] $ ! $ ([.]-$ " $ ,[./ Mean fitness: ࠵? . = ࠵? ! ࠵?[࠵?] + ࠵? " ࠵?[࠵?] Diploid selection: Genotype frequencies when in “Hardy-Weinberg proportions”: ࠵? !! [࠵?] = ࠵?[࠵?] 0 , ࠵? !" [࠵?] = 2࠵?[࠵?]࠵?[࠵?], ࠵? "" [࠵?] = ࠵?[࠵?] 0 Genotype frequencies after selection ࠵? !! 1 = ࠵? !! ࠵? !! [࠵?] ࠵? . , ࠵? !" 1 = ࠵? !" ࠵? !" [࠵?] ࠵? . , ࠵? "" 1 = ࠵? "" ࠵? "" [࠵?] ࠵? . where the mean fitness is: ࠵? . = ࠵? !! ࠵? !! [࠵?] + ࠵? !" ࠵? !" [࠵?] + ࠵? "" ࠵? "" [࠵?] Allele frequency in the next generation ࠵?[࠵? + 1] = ࠵? !! ࠵?[࠵?] 0 + ࠵? !" ࠵?[࠵?]࠵?[࠵?] ࠵? !! ࠵?[࠵?] 0 + ࠵? !" 2 ࠵?[࠵?]࠵?[࠵?]+ ࠵? "" ࠵?[࠵?] 0 Formula for polymorphic equilibrium (used only for Heterozygote advantage or disadvantage): ࠵?̂ = $ !" %$ "" 0$ !" %$ !! %$ "" Mutations: Mutation alone (no selection, haploid or diploid model): ࠵?[࠵? + 1] = (1 − ࠵?) ࠵?[࠵?] + ࠵? (1 − ࠵?[࠵?]) Equilibrium: ࠵?̂ = 2 3-2 Haploid model: with mutations and selection ( ࠵? ! = 1, ࠵? " = 1 − ࠵? ) , the deleterious allele “a” approaches: ࠵? 8 ≈ 3 1 Diploid model: with mutations and selection, the deleterious allele “a” approaches: ࠵? 8 ≈ 3 41 if h>0 and ࠵? 8 ≈ : 3 1 if h=0 (i.e., if “a” is recessive to “A”) At the diploid mutation-selection balance equilibrium ( ࠵? 8 ≈ 3 41 ), the mean fitness is ࠵? . = 1 − 2࠵? , which does not depend on the strength of selection.

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13 Biology 336 Formula Sheet – Midterm Exam Version Genetic Drift: • The time for an allele in a single copy to become fixed: ~2 N generations in a haploid population; 4 N generations in a diploid population. Expected heterozygosity, ࠵?[࠵?] , the chance that two randomly chosen alleles are different, is a measure of genetic variation. ࠵?[0] = 2࠵?࠵? ࠵?[࠵?] = =1 − 1 2࠵? ? ࠵?[࠵? − 1] Expected homozygosity, ࠵?[࠵?] , is the chance that two randomly chosen alleles are the same, ࠵?[࠵?] = 1 − ࠵?[࠵?] . Haldane’s fixation probability: 2 s in haploids and 2hs in a diploid (assuming h >0). Two-locus model: Disequilibrium, D (also known as linkage disequilibrium or gametic-phase disequilibrium), measures genetic associations among two loci. ࠵?[࠵?] = ࠵? !5 [࠵?] ࠵? "6 [࠵?] − ࠵? !6 [࠵?] ࠵? "5 [࠵?] Recombination acts to break down linkage disequilibrium. Meiosis with recombination changes the chromosome frequencies by: ࠵? !5 7 = ࠵? !5 − ࠵? ࠵? ࠵? !6 7 = ࠵? !6 + ࠵? ࠵? ࠵? "5 7 = ࠵? "5 + ࠵? ࠵? ࠵? "6 7 = ࠵? "6 − ࠵? ࠵? When selection is absent (all ࠵? 89 = 1 ), genetic associations (D) decay by a factor (1 − ࠵?) each generation: ࠵?[࠵?] = (1 − ࠵?)࠵?[࠵? − 1] This means that over a number of generations, t, genetic associations decay according to: ࠵?[ ࠵? ] = ( 1 − ࠵? ) ࠵? ࠵? [ 0 ]

14 Biology 336 scrap paper – (not graded unless noted in an answer above)

15 Biology 336 scrap paper – (not graded unless noted in an answer above)

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16 Biology 336 scrap paper – (not graded unless noted in an answer above)

BIOL336-Midterm-2022W1

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