[Select_Answers] WS2_Evolution_Fa23

Biology 1B Study Sleuth Evolution Worksheet 2 (Lecs 8-10) Fall 2023 For the schedule of future Study Sleuth sessions, please see weekly email announcements & the OH Calendar on bcourses. All answers can be found in your lecture material. 1. Rates of Evolution (2a) What is the difference between mutation and substitution ? (Lec 8, Slide 31) Mutation: nucleotide changes on individual level Substitution: mutations that become fixed over time Mutation Rate (μ) = Rate of un-repaired DNA changes per nucleotide position per year per individual. Substitution Rate = Rate that mutations become fixed in the population. Once fixed, a substitution becomes a characteristic ( synapomorphy (shared derived character) ) of that population For mutation rates: larger populations have more mutations compared to smaller populations. For substitution rates: larger populations have slower rates at which mutations become a substitution compared to smaller populations. For neutral (synonymous) changes, the substitution rate is independent of the population size, and equals the mutation rate (Kimura’s Neutral selection theory). (2b) Given the 5 lines of description below, match the one that is most appropriate to each type of mutation. (three won’t be used) (Lec 8, Slide 30) Synonymous mutation D Nonsynonymous mutation A A. A nucleotide mutation that alters the amino acid sequence of a protein B. A mutation in which a segment of a chromosome is reversed end to end C. A mutation affecting only one or very few nucleotides in a gene sequence D. A change in the DNA sequence that codes for amino acids in a protein sequence, but does not change the encoded amino acid E. A mutation in which parts of a gene, entire chromosomes, or an entire genome are duplicated (2c) For genic regions of DNA, which is neutral: synonymous mutation or nonsynonymous mutation? (And what does “neutral” mean in the context of selection?) Synonymous. “Neutral” means not subject to selection. (2d) How did Kimura’s neutral selection theory lead to the hypothesis of molecular clock? Because neutral (synonymous) changes in the substitution rate are independent of the population size and equals the mutation rate (Neutral selection theory by Kimura), the differences in the DNA between species should also accumulate at a universal rate, hence we can use the amount of changes in DNA across species to estimate when they diverged from each other.

Biology 1B Study Sleuth Evolution Worksheet 2 (Lecs 8-10) Fall 2023 (2e) Nowadays, we are in a post- molecular-clock era and can use relaxed molecular clock analysis ( rate smoothing ) to time-calibrate the phylogeny. In brief words, what is the purpose of the relaxed clock method? Brief explanation: To estimate divergence time. Long explanation: To convert the phylogram into a time-calibrated phylogeny (also called a timetree or a chronogram). - In the scenario where all tips are extant (living) taxa, rate-smoothing (i.e. relaxed clock algorithm) allows us to transform the phylogram (a cladogram with branch lengths proportional to amount of DNA changes) into a time-calibrated phylogeny (i.e. chronogram/time tree, in which branch lengths are proportional to time). The time tree (or chronogram) gives the relative divergence times between the lineages based on the molecular data. - Corresponding Study Guide Q: Can we use DNA distances to estimate divergence times even if there is no universal clock? What is the technique we use to do this? 3. Pre-adaptation (3a) Define pre-adaptation and give the 2 examples from lecture 9 about birds and humans. Definition of pre-adaptation: the scenario when a species evolves to use a trait/structure/morphology for a function that is different from the trait’s initial function. E.g. birds having feathers for insulation and display prior to a switch in the function to flight (as well as insulation and display); (*A to study guide Q: birds evolved dinosaurs, among which many are feathered!); flatter feet in humans used for squat feeding prior to bipedalism (3b) Was pre-adaptation involved in the formation of mammalian middle ear bones? Pre-adaptation was not involved in the formation of our middle ear bones, since the mammalian middle ear bones came from the reptilian lower jaw; even today, many reptiles rest their jaw on the ground to pick up vibrations. (3c) Complex eye: Label the steps of evolving a complex eye in chronological order and explain how living mollusks support the scenario for the major steps in the evolution of complex eyes. Steps of evolving a complex eye Order (1-5) Have light-sensitive cells (mollusk example: limpet) 1 Develop sophisticated controls of a complex eye (cornea, retina, etc…) (mollusk example: squid) 5 Fold eye structure into an eye cup (mollusk example: abalone) 2 Form primitive lens (mollusk example: marine snail) 4

Biology 1B Study Sleuth Evolution Worksheet 2 (Lecs 8-10) Fall 2023 LUCA stands for the last universal common ancestor: the most recent population of organisms from which all organisms now living on Earth share common descent. When we do a character analysis of the bacterial and archaeal locomotory structures (flagella and archaella) we see they are built from completely different sets of proteins. Bacterial and archaeal cell walls and membranes are also built from different molecules. Based on these character analyses, we would not consider bacterial and archaeal locomotory structures or cell walls and membranes as homologs. Character analysis thus suggests that archaea and bacteria became motile and cellularized independently and thus that the LUCA was neither cellular nor motile.

Biology 1B Study Sleuth Evolution Worksheet 2 (Lecs 8-10) Fall 2023 Part 3: Practice Questions Directions : Work on the following practice questions to get ready for your exam with the peers around you. 1. An example of a macroevolutionary event is: a. The changing frequency of light v.s. the dark phenotype of a species of moths on soot-covered trees in polluted forests. b. The mass extinction of nearly all non-avian dinosaurs. c. An isolated population of fruit flies grows exponentially and diverges from the parent population. d. A great reduction in population size of Alaskan salmon due to overfishing Baum, D. A. (2005). EVOLUTION: The Tree-Thinking Challenge. Science , 310(5750), 979–980. doi:10.1126/science.1117727 2. The tree above depicts inferred relationships among some major frog groups with branches drawn proportional to absolute time. Error bars on internal nodes depict confidence intervals on the dates of estimated nodes. Assuming this tree and the associated ages are correct, which of the following statements is true? A. No individual living before 70 million years ago is an ancestor of Raninae B. Raninae and Dicroglossinae shared a common ancestor about 75 million years ago C. The divergence of Raninae and Nyctibatrachinae occurred more recently than the 85 million year old separation of India from Madagascar D. The last common ancestor of Micrixalinae and Dicroglossinae lived before India and Madagascar separated (85 million years ago)