BIOL336-Midterm-2022W1Key

Given name FAMILY NAME (CAPS) Student Number: _____________________________ 1 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.] q = u/s q = 10^-7/0.002 q = 0.00005 è 2 pts for formula, +2 pts for plugging in numbers correctly, +1 for final calculation 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.] Prob fix = 2s =2(0.3) = 0.6 Prob loss = 1-Prob fix = 0.4 [Unlikely, but might also use Kimura’s formula: Prob fix = (1-exp[-2s])/(1-exp[-2sN]), in a large population = (1-exp[-2s]) = 0.45, for a prob of loss of 0.55. Answers are different because selection is so strong.] è 2 pts for formula, +2 pts for plugging in numbers correctly, +1 for final calculation

2 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 X 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 ࠵?[࠵?]/࠵?[࠵?] ] ࠵?[ ࠵?] ࠵? [࠵?] = ࠵? ! " ࠵? # " ࠵?[ 0] ࠵? [0] 0 .5 0 .5 = 1 .3 " 1 10 $% 1 − 10 $% 1 − 10 $% 10 $% = 1 .3 " è Logging both sides and solving for t: t =52.7 [Accept close solutions] Alternatively, could use the other formula: ࠵?[ ࠵?] = & ! " ([ *] & ! " ([ *] , & # " - [*. p[0]=10^-6 q[0] = 1-10^-6 = 0.999999 wA = 1.3 wa = 1 p[t] = WA^t p[0]/ WA^t p[0]+ Wa^t q[0] 0.5 = 1.3^t 10^-6 / 1.3^t 10^-6 + 0.999999 Can solve for t or estimate (t ~ 52) è 2 pts for formula, +2 pts for plugging in numbers correctly, +1 for final calculation 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

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 X 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: X 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 X 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.] ࠵?[ ࠵?] = ࠵? !/ [ ࠵?] ࠵? #0 [ ࠵?] − ࠵? !0 [ ࠵?] ࠵? #/ [ ࠵?] They can define any of the variants as AB, but they must choose the opposite to be ab. Using AB = STR12 (drug resistant & compensatory mutation) and ab = CAB281 (drug sensitive & non- compensatory mutation): D = (0.87 0.02) – (0.05 0.06) = 0.0144 If they define the lines differently and get -0.0144, that is OK, but the next part should be the same regardless: The pair of lines that are more frequent than expected are: _ STR12 and CAB281_ è 2 pts for formula, +2 pts for plugging in numbers correctly (defining opposite chromosomes to place in the 1 st and 4 th position), +1 for final calculation, +1 for finding that STR12 and CAB281 are more common 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. TWO EXAMPLES: While reducing the use of antibiotics is expected to slow the evolution of resistance, if resistance has already evolved and adaptation has led to compensatory mutations, then these adapted resistant lines may persist despite lowering the use of antibiotics. The evolution of reduced costs thus makes it challenging to reverse the rise of antibiotic-resistant strains. OR: There may be an initial cost to evolving drug resistance, but further adaptation can reduce this cost in drug-resistant pathogens. This reduced cost alleviates the fitness difference between drug-resistant and sensitive pathogens and thus may result in the persistence of drug-resistant pathogens even with reduced usage of drug treatments. è 5 pts for correctly interpreting the abstract: misunderstood = 0, partially understood =1- 4 (depending on extent of error), fully understood = 5 è 5 pts for writing proficiency (regardless of the argument being right or wrong): very hard to read and understand = 0, poorly argued =1-4 (depending on extent of error), well worded = 5. [Do not take off more than one point for minor grammatical errors if you can fully understand the answer.]

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. Tree as per slides in lecture. 1.5 marks taken off for each branch move required to fix the tree. MRCA of frog and human would be about 350 mya, but acceptable 450 to 200 MRCA of frog and crustacean would be from 600-1000 mya, but acceptable 550 to 2000 MRCA of fern and red alga must be 400 or before. 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 (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) (3) (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

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) worms (b) Please explain your answer to (a) in 1 to 3 sentences (4 marks) e.g. of good answer: The phylogeny of worm species matches the phylogeny of the dragons on which they live, implying co-speciation and thus vertical inheritance of worms within dragon families. Vertical inheritance implies the worm babies depend on the babies of their host dragon , selecting for cooperation . 1 mark: The worm tree matches the dragon tree (this is OK, but more precise would be: the clades in the worm tree match the clades of the dragons in which the worms live), but the other trees don’t match. [The second part of the sentence can probably be implicit.] Alternatively: the dragons and worms have parallel phylogenies. [If they go straight for co-speciation, it could be OK, but there has to be some implication that they derived this conclusion from the trees above.] 1 mark: Because the trees match, this implies the worms don’t move much among hosts, i.e. they have vertical inheritance . 1 mark: With vertical inheritance (assuming it’s at the mother-to-daughter scale), the fates of a worm and its host dragon are entangled (that’s how I phrased it in lecture). Alternatively: the success of the baby worms depends on the success of their host’s baby dragons. 1 mark: Entangled fates selects for cooperation 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 _____________________ (2) (b) When inferring phylogeny, probabilistic models are used to calculate ______________ (5) (c) Optimal adaptation is often prevented by _____________________________________ (1) (d) Vertical inheritance of a parasite within a host can lead to _______________________ (3) (1) ancestral constraint (2) bootstrap analysis (3) mutualism (4) coincidence (5) likelihood (6) parsimony (7) symbiosis (8) synapomorphy