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BBio466 Study Guide Exam2 Jensen, Spring 2016 I’m a bit behind so the meeting numbers don’t always match up with the syllabus. The content is the same, though. Some of the specific examples may change. Meeting 9: Finish up single locus; Evolution at multiple loci: Linkage, linkage disequilibrium, sex Short narrative: So far we have considered single locus models – we had HWE as a null model, and we introduced wxx to incorporate in predict the effects of selection. We continued single locus models to consider substitution rates and to contrast (again) neutral and selection models. We considered the relative effects of population size, generation time, and selection on rates of substitution. The nearly neutral model addresses the roughly constant rate of substitution (in absolute time) regardless of generation time by suggesting that selection on slightly deleterious alleles reduced substitution rates in large populations (with short generation times) but that drift is more important in small populations (with longer generation times). These effects balance each other out in absolute time. We also introduced multilocus models of evolution and, in particular, the idea of linkage disequilibrium. This will be relevant to us as we discuss the evolution of sex. Some key terms: Mutation Substitution Neutral mutations Neutral Theory Nearly neutral theory Synonymous vs. nonsynonymous substitutions Linkage Fixation Hitch hiking Haplotype Linkage equilibrium/disequilibrium Inbreeding depression D = gABgab - gaBgAb Concepts/examples: Relative rates of beneficial, neutral, deleterious mutations Substitutions versus mutations Red Queen Hypothesis Relationship between population size and the relative strengths of selection and drift How populations are moved out of linkage equilibrium, and why we care to know Skills: Can you explain the difference between mutations and substitutions? What does substitution rate depend on? Can you explain why large and small populations have similar rates of substitution even when variation is neutral? Shouldn’t substitution rates be higher in small populations? Can you explain why are deleterious and neutral mutations more common than beneficial mutations? Can you explain the difference between synonymous and non-synonymous substitutions? Why would you expect rates of divergence to generally be lower for nonsynonymous substitutions than for synonymous substitutions? Why would you expect rates of substitution to be dependent on generation time? Can you explain why rates of divergence are roughly independent of generation time? What is the nearly neutral theory, and why did neutralists modify their neutral theory to include some selection? 1 Can you explain the significance of this equation? 𝑠 ≤ (2𝑁 ) 𝑒 Can you explain how it is possible for selection to be effective at some population sizes but not others? Can you explain why the rate of synonymous substitutions serves as a good baseline for detecting selection? What does it mean if (dN/dS) = 1? (dN/dS) < 1? (dN/dS) > 1? Is it possible for selection to affect rates of substitution for a synonymous mutation? If so, how? Can you explain what inbreeding does to heterozygosity, and why? What is linkage equilibrium? Can you explain how populations can be out of equilibrium, and why populations tend to return to equilibrium? Do you know how to calculate D for a population? Do you understand why values for D range from -0.25 to +0.25? What does is mean when D = 0? Why would finding neutral alleles at linkage disequilibrium suggest positive selection on adjacent alleles? Meeting 10 was Exam1 Meeting 11: Review of Disequilibrium, Sex, and Introduction to Quantitative Genetics Short narrative: We reviewed linkage disequilibrium, and the “paradox of sex.” Sex is costly in terms of reproduction and yet predominates in eukaryotes. There are organisms that are obligately sexual, facultatively sexual or asexual, and obligately asexual. Asexuality does not appear to be difficult to evolve, and facultatively sexual organisms often reproduce sexually despite the obvious cost. This suggests that sex must have an advantage, at least under some circumstances. We considered several ways in which sex could be advantageous, including breaking Muller’s ratchet and promoting offspring survival in varied or variable environments. The beetle example illustrated conditions under which asexual or sexual reproduction would be favored. Some key terms: Sexual vs. asexual Obligate vs. facultative Sexual reproduction Muller’s Ratchet Genetic Load Continuous variation Blending inheritance Multiple loci Segregation and independent assortment QTL mapping Genetic markers Concepts/examples: When two populations of beetles were placed in competition, but one was manipulated to mimic asexual reproduction and the other was allowed to reproduce sexually, asexual beetles won under standard conditions but sexual beetles won in the presence of malathion. Explain these different outcomes. What happens to variation in small populations? How does sex help? Why is sex advantageous in variable environments? How does this relate to the Red Queen Hypothesis? Can you explain how genetic markers are used to find quantitative trait loci? What does this have to do with linkage disequilibrium? Skills: Can you explain several ways in which sex is costly? Why are males disadvantageous in terms of producing offspring? How might males be advantageous in viability of offspring? Is asexuality difficult to evolve? Can you explain Muller’s ratchet, and how sex can break it? Can you explain the linkage (har har) between sex and linkage equilibrium? What does sex do to linkage disequilibrium? How? Meeting 12: More with Quantitative Traits (haven’t gotten to all of this yet) Short narrative: We illustrated the difference between complete linkage (fully dependent assortment) and no linkage (independent assortment). If we look at offspring of crosses (e.g. of double heterozygous for a trait and a marker), we can see whether and how our offspring deviate from the null model of no linkage. Fully linked traits would obviously be very different from unlinked traits; traits that are linked but are far apart will not look like unlinked traits, but will also not look like fully linked traits. Some intermediate level linkage will best describe the distribution of genotypes in offspring. The LOD score describes how well a particular linkage model explains the distribution of offspring (relative to a no linkage model). We can use outcomes of matings and look for traits and markers that have a high LOD scores – these will be close to our marker in the genome. We also revisited the idea of heritability, and broke down genetic variance into additive and dominance components – we used this to distinguish between broad sense and narrow sense heritability (we are concerned with the latter). We reviewed strategies for estimating heritability, including an example of cross fostering. Once we have estimated heritability, we can use this information to predict the response of the population to a given level of selection (or, alternatively, estimate S if we know R and h2, or estimate h2 if we know S and R). We used the Bugsville simulation to estimate h2, set up selection, and estimate R. Some key terms Independent assortment Dependent assortment LOD score (know what this means and how it’s used, not how to calculate) How LOD scores are used to identify quantitative trait loci VG, VA, VD, VE 𝑉𝐴 𝑉𝐴 = 𝑉𝑃 𝑉𝐴 + 𝑉𝐷 + 𝑉𝐸 𝑉𝐴 𝑉𝐴 ℎ2 = = 𝑉𝑃 𝑉𝐴 + 𝑉𝐷 + 𝑉𝐸 Cross fostering Response to selection Selection differential = 𝑆 = 𝑡 ∗ − 𝑡̅ Concepts/examples Broad sense vs. Narrow sense heritability – Don’t worry about the distinction. Review the example of cross fostering (song sparrows). Do you understand what cross fostering accomplishes? How to estimate h2 from matings and twin studies The meaning and application of LOD scores The relationship among R, S, and h2. Skills Can you describe high vs. low heritability graphically? Verbally? What is the relationship between heritability and selection? Can you describe and explain expected similarities between monozygotic and dizygotic twins if heritability is high vs. low? Can you explain what crossfostering studies are, and how they reveal the relative influence of genes and environment on phenotypic variation? Can you verbally and graphically describe the relationship between h2, R, and S? What is the difference between h2 and r2 in a regression of mid offspring against mid parent? Remember, the response to selection is R, not r. Can you describe how R will differ if h2 is large vs. small? Can you describe how R will differ if S is large vs. small? Given phenotypes for a group of parents and values for their offspring, can you calculate h2? If you know S and R, can you estimate h2? If you know S and h2, can you predict R? Meeting 13: Adaptation Short narrative: It’s easy to look at structures/behaviors that are useful to organisms and assume that natural selection has molded them for that “purpose.” In reality, the relationship between phenotype and selection is much more complicated than that. Evolutionary biologists have been rightly criticized for telling “Just-so stories” – plausible but untestable narratives for how natural selection has molded lineages into their current form. In this meeting we considered how we could make a stronger and testable case for features being adaptations. We considered approaches ranging from verifying how a feature is actually used in nature to how it may affect current fitness to the circumstances under which the feature actually evolved. We marshaled observational, experimental, and comparative information in this endeavor. Finally, we considered phenotypic plasticity as a potential complication in studies of adaptation, and as an adaptive feature in itself. Some key terms: Adaptation Just-so stories Exaptation The comparative method Phylogenetically independent contrasts Norm of reaction Phenotypic plasticity Concepts/examples: Oxpeckers and oxen – Do oxpeckers eat ticks? Do they actually help oxen? Shaving the hooks off pigeon bills – what did this demonstrate? What did it not demonstrate? Rock choice in garter snakes – what did this demonstrate? What did it not demonstrate? Fly wings (and moth wings) and jumping spiders – what did this demonstrate? What did it not demonstrate? Anolis limb proportions and habitat Bat testes vs. social structure Daphnia behavior in the presence and absence of visual predators Skills: Can you define adaptation? Give structure or behavior X, how would you construct at strong argument that it is an adaptation for Y? What kinds of evidence would you use in your argument? How would you acquire it? Can you explain how phylogenies were used in assessing adaptation of limb proportions in Anolis lizards? Can you explain why simply drawing a regression line between two traits is not sufficient to determine whether they evolve together? How do phylogenies help? Can you explain why phenotypic plasticity may confound us in assessing adaptation? Can plasticity itself evolve? Meeting 14: Sexual Selection Short narrative: We begin with observation that many species are sexually dimorphic, and that it is usually the males that are most brightly colored, larger, etc. This raises two questions: 1) how does sexual dimorphism arise? and 2) why is it males that are usually brighter, larger, etc.? We framed this in terms of different levels of investment in offspring and different strengths of sexual selection (i.e. variation in reproductive success) in males and females. Males often show extreme variation in mating success, but invest relatively little in offspring – what limits their reproductive success is mating opportunities, not the costs of producing/rearing offspring. Females are typically the reverse. This means males will generally be competitive for mating opportunities (intra or intersexual selection) and females will tend to be more selective. We reviewed examples of intrasexual and intersexual selection, and considered why females should even care about the sometimes comical displays and ornaments of males. Finally, we considered a case where females are competing for mating opportunities, and males have a great investment in producing offspring. Some key terms: Sexual dimorphism Fundamental asymmetry of sex Sexual selection Intra- vs. intersexual selection Combat, sperm competition, infanticide Mate guarding, copulatory plug, nuptial gift Sexy Son hypothesis Runaway sexual selection Good genes hypotheses – Handicap, parasite, developmental stability Direct benefits Pre-existing biases Concepts/examples: Elephant seals, rough skin newts – male vs. female mating success Intrasexual selection – Elephant seals, iguanas Infanticide – Gorillas and lions Parental investment Intersexual selection Female choice Widowbirds – costs/benefits of long tails Gray tree frogs – female preferences and quality of offspring Seahorses and pipefishes Skills: Can you explain why, as Darwin noted, it is usually the males that the brighter, larger, more ornamented, etc. when species are sexually dimorphic? Can you generalize this phenomenon? I.e. is it a feature of males, or is there a more general explanation that might apply to cases in which the females are the brighter, larger, more ornamented, etc. sex? Can you explain why mating success is usually less evenly distributed in males than in females? How is sexual selection different from natural selection? Why would selection on males and females be different, and how does this lead to sexual dimorphism? Can sexual selection act in ways that compromise survival? How might size be advantageous in intrasexual selection? How might it be costly overall? Can you provide examples? How can infanticide in lions be good for the species? Is that even a sensible question? Can you explain why features that have no value in intrasexual selection might still be sexually selected? Why would females tend to be more discriminating than males when mating? Can you provide counterexamples? Can you explain why females would even care about elaborate displays and ornaments in males? What are males actually advertising? What did Alison Welch’s experiment with breeding long-call and short-call male frogs with females demonstrate? How is this relevant to theories of sexual selection? Can you explain why the sex subject to strong sexual selection will tend to be competitive, and the sex subject to weak sexual selection will be choosy? Can you explain how seahorses and pipefish reverse the usual sex roles, but still uphold the general pattern of sexual selection? Meeting 15: Kin Selection and Social Behavior Short narrative: Behavior is a phenotype, and like most phenotypes, it has both genetic and environmental components. Because behavior can satisfy all of the premises of natural selection, behaviors can represent adaptations. A particularly challenging behavior to think of as being adaptive is altruism. Nevertheless, apparently altruistic behavior is quite common. There are two main explanations for the existence of such behavior: 1) inclusive fitness, where one helps others who share their own alleles, thus indirectly increasing the chance of theirs being passed on. Hamilton’s rule dictates that the more closely related two organisms are the more likely the other organism is willing to help. Eusociality is an extreme example of this in which there is an overlap in parent and offspring generations, specialized castes for reproduction and other tasks, and cooperative care for offspring; 2) Reciprocal altruism occurs not because the actor and recipient are closely related, but because individuals help each other under circumstances in which the favor may be repaid in the future. Reciprocal altruism is more likely when the benefits to the recipient outweigh the cost to the action; there are stable groups so individuals will see each other multiple times; there are repeated opportunities for the act to be practiced (and reciprocated); cheaters can be recognized and punished; and there is a symmetrical relationship, meaning that there is no expectation that one will always be the donor or the recipient. Some key terms: VP = VG + VE Altruism Group selection Inclusive fitness, direct fitness, and indirect fitness Relatedness (r) Hamilton’s Rule: Br – C > 0 Kin recognition Eusociality and its three characteristics: Parent/offspring overlap, cooperate care, specialize reproductive/nonreporductive casts Reciprocal altruism Cheaters Concepts/examples: Group selection models – difficult to see how cheating would not be favored. Benefits, costs, relatedness. Black-tailed Prairie dogs White fronted Bee eaters Eusociality in hymenoptera and naked mole rats. Altruism in vampire bats Skills: Can you explain how altruistic behavior might be favored by natural selection when it occurs between related individuals? Would it make a difference how closely related the individuals are? Can you explain how altruistic behavior might be favored by natural selection when it occurs between unrelated individuals? Can you explain why behaviors that confer an advantage to the group but not the short term interests of the individual would be difficult to maintain by selection Can you explain the logic behind Haldane’s statement that he would gladly give up his life for “two siblings or eight first cousins”? To which model of the evolution of altruism does this statement apply? Can you explain what it means if Br – C > 0? If Br – C < 0? What would prompt a prairie dog to send a warning signal if a predator is near? Under what circumstance would a prairie dog “decide” not to call? Can animals besides humans recognize their kin? Examples? What about plants … can they recognize kin? How does this relate to Hamilton’s rule. Can you describe circumstances in which it makes more sense (in terms of fitness) to help your parents raise offspring than to attempt to raise your own? What kind of fitness is being maximized here? Can you explain why haplodiploidy is not considered a strong explanation for the evolution of eusociality in hymenoptera? Can you explain why a large r in naked mole rats facilitates the evolution of eusociality? Can you explain why each of the following help promote the evolution of altruistic behavior even in unrelated individuals? Stable groups, repeated opportunities to commit altruist acts, memory, symmetrical interactions? Do any or all of these apply in humans? Is altruism in vampire bats an example of kin selection, reciprocal altruism, or both? How can you distinguish reciprocal altruism from altruism based on kin selection? The cost to a well-fed bat regurgitating blood for a starving bat is less than the benefit received by the starving bat. Can you explain why this is true? How would this favor the evolution of altruism?