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BBio466 Week 1 Study Guide Jensen, Spring 2016 Meeting 1: Darwinian view of life. Pattern and process, evidence and conflict Short narrative: I wanted you to get a sense that Darwin’s view of the natural world was very different from that of his contemporaries, and that even today we have trouble seeing the world in Darwinian terms (e.g. we impute design and direction to nature). People had limited understanding of the depths of time in Darwin’s day, and we spent some time describing how we know what we know about the age of the Earth and its organisms. Finally, we contrasted naturalism in sciences vs. naturalism in metaphysics to point out that they are not the same thing. Evolution is consistent with atheism (“God is not a necessary hypothesis”), but evolutionists take many different ontological stances (ranging from Atheism (e.g. Richard Dawkins) to evangelical religious beliefs (e.g. Francis Collins). Some key terms: Pattern vs. Process Catastrophism vs. Uniformitarianism Stratigraphy Relative vs. Absolute dating Geologic Time scale Radiometric dating and half-­‐life Extinction vs. Mass extinction Comparative evidence – phylogeny Homology vs. Analogy Vestigial structures Methodological vs. Ontological Naturalism Concepts/examples: How can we reconstruct pattern? Relative vs. Absolute Relative timing of events known before absolute timing of events – stratigraphy Law of Succession – Marsupials Historical constraint and tinkering Skills: Can you describe what radioactive decay is, and how it can be used to provide absolute dates? When would you use 14C vs., e.g. 236U? Why? Can you describe the kinds of insight fossils can reveal into historical pattern? Can you describe how pattern can illuminate process using examples from the fossil record? Can you verbally define homology and homoplasy? Can you illustrate each on a phylogeny? How does homology generate similarity? By what process? How does analogy arise? What is the process? Can you define vestigial “structures” and provide examples? How do vestigial structures support descent with modification relative to separate creation? Is this support different from that of homology in general? Can you explain why science relies on methodological Naturalism? Is it possible to be a methodological naturalist and an ontological supernaturalist? Meeting 2: Deep History – Major features in the long history of life Short narrative: I wanted you to come away a sense of how different Earth and its life forms was in the past, to describe some of the major features of the origin and diversification of life, how we know what we know about past ages and organisms, and to be able to place some approximate dates on major events. Rather than give a lengthy rundown on the history of life, we formed groups to summarize information describing important events in the history of life. The papers are still posted, I’ve posted images of the Post-­‐it notes you produced, and some of the key terms/ideas associated with each are indicated below: Origin of Life: Second Law of Thermodynamics Open system vs. Closed system “Darwinian Takeover” Dissipation driven organization Ribozyme Zircon crystals Fractionation (I described this in class) Cell membranes are highly ordered – can they form spontaneously? Why are cell membranes and genetics thought to have evolved together? Why is the fact that bases and sugars can be spontaneously formed as a unit (rather than being formed separately and linked) a “major advance” in prebiotic chemistry? Why are RNA polymers difficult to form under typical natural conditions? How did the researchers use “test tube evolution” to develop a more effective ribozyme? 2) Early Life Cambrian explosion and date Evolutionary origins vs. first appearance Molecular clock Extrinsic vs. Intrinsic influences on diversification (term I used) Permissive environment “Boring billion” Oxygen revolution Eukaryotes What is the Cambrian explosion? Was it really explosive? Is so, in what way; if not, how would you justify your answer? What is a molecular clock? What are its assumptions? How can it be used to date the origins of animal diversification? How do these results compare with what we see in the fossil record? Explain. How do explanations invoking “Genetic innovation” versus “environmental factors” relate to the idea of intrinsic versus extrinsic explanations of diversification? How have oxygen levels changed, and how is this potential related to diversification? 3) Mass Extinctions Prior to the Permian-­‐Triassic extinction, what large vertebrate group was dominant on land. We think of extinction as paving the way for mammals, but what role has extinction played in the rise and demise of dinosaurs? What are “extrinsic factors” and how do they differ from intrinsic (or extrapolationist) explanations for patterns of diversification and extinction? See 4/4 meeting. 4) Diversifications (and extinctions) How long ago did mammals appear? How does that relate in time to the diversification of most modern mammal groups? The standard current explanation for the extinction of dinosaurs is asteroid impact. What is the evidence that volcanoes played a role? How were zircon crystals useful? Skills: Can you describe some features that distinguish life from non-­‐life? Can order arise from disorder? If so, how is this not a violation of thermodynamics? Can you describe the general circumstances under which early life arose and diversified? Can you provide approximate dates for the following? Origin of life; Oxygen Revolution, Cambrian explosion,, Permian-­‐Triassic extinction, Cretaceous-­‐Tertiary extinction, boundary dates of the Paleozoic, Mesozoic, and Cenozoic periods? What is fractionation, and how is it relevant for recognizing early life? Can you distinguish between Extrapolationist and Hierarchical views of macroevolution? What is the role of chance in each? BBio466 Week 2 Study Guide Jensen, Spring 2016 Meeting 3+4: Phylogeny reconstruction and Tree Thinking Short narrative: Tree thinking is an essential part of modern biology and, although Darwin developed the Tree as a nice metaphor it is only relatively recently that we’ve figured out how to reconstruct it. These lectures are about understanding what a phylogeny is, how we go about reconstructing it, why we can’t assume the organisms are closely related just because they are similar, and how we use phylogenies to understand character evolution and relationships. Some key terms Phylogeny vs. Cladogram Groups-­‐within-­‐groups Synapomorphy, Homoplasy, Plesiomorphy Monophyletic, Polyphyletic, Paraphyletic Outgroup, Ingroup Outgroup analysis, Parsimony Molecular clock Concepts/examples Darwin’s metaphor of a “Tree of Life” – what it means, why it’s useful, some limitations Was Linneaus an evolutionist? If not, how could he come up with a classification scheme that is still useful? Value of knowing pattern to help understand process Phylogeny reconstruction as a way of looking into the past – reconstruction of relationships and describing evolution of characters. Monophyly – e.g. mammals; Synapomorphy – e.g. Hair Polyphyly – e.g. birds and bats; Homoplasy – e.g. wings Paraphyly – e.g. “protists”; plesiomorphy – e.g. unicellularity Unequal rates of evolution – e.g. whales vs. other artiodactyls How can knowing the phylogeny allow us to trace character evolution on a tree? Character tracing – e.g. spider webs, transmission of HepC, etc. Dating historical events – using molecular clocks. E.g. divergence of human head/body lice. Skills Can you describe and give some examples of how phylogenies are used to test evolutionary hypotheses? Can you describe the relationship between phylogeny and the hierarchical organization of variation in nature? How does this relate to classification? I was able to reconstruct three phylogenies created by you guys … even the though the likelihood of doing so by chance was less than on in a million. Can you describe how I did? Can you describe why overall similarity may not be a reliable guide to relationships? If you had a monophyletic group, would the feature used to unite it be found in the common ancestor of that group? What about a polyphyletic group? A paraphyletic group? Can you explain why we avoid using paraphyletic groups? Can you identify monophyletic, polyphyletic, and paraphyletic groups on a tree? Which of these groups would include the ancestor? What’s wrong with the depiction of paraphyletic groups in Fig. 4.13? Can you describe, both verbally and using a tree diagram, how outgroup analysis allows us to distinguish between plesiomorphy and synapomorphy? Do you understand how parsimony allows us to recognize homoplasy? Do you understand that trees should be read from the base to the tips or tips to the base, but never across the tips? Do you understand that branches can be swiveled around nodes without changing the information they contain? See the Baum et al. article or go to UCMP web site for more help. How can you tell if a gene is evolving in a clock-­‐like fashion? How can you calibrate molecular clocks? Can you use the features of living organisms to reconstruct the features of long-­‐dead ancestors using the phylogeny? BBio466 Week 3 Study Guide Jensen, Spring 2016 Meeting 5: Natural Selection and Design Short narrative: Here we confront Darwin’s answer to the Argument from Design. Natural selection is fairly simple to describe, and explains a lot relative to what it assumes, and yet there are many misconceptions about natural selection. Natural selections rests on a few propositions – if these are valid in a given situation then evolution will inevitably occur. We evaluated how we test these propositions, using finches as an example, and what the consequence would be if one or more of these propositions does not hold (using EvoDots). Natural selection is powerful, but is constrained by history to a much greater degree than is human engineering. Some key terms Paley, Watchmaker analogy Natural Selection – Variation, heritability, Differential survival, non-­‐random reproduction Phenotype vs. genotype Historical constraint Preadapation/exaptation Concepts/examples What is the Watchmaker analogy? Demonstrating the postulates of natural selection – Darwin’s finches How does history constrain evolution – e.g. QWERTY, recurrent laryngeal nerve. Functional tradeoffs – e.g. tails in peacocks, coloration or gonopodia in guppies. Skills Can you explain the Paley’s interpretation of complexity and integration in nature? Can you explain Darwin’s argument for the appearance of design from natural processes? Can you explain why each of the following is necessary in order for natural selection to operate? Variation, Heritability, Differential survival/reproduction? Can you describe what heritability is and how it is measured? Can you graph high and low heritability given offspring traits on one axis and parental traits on the other? What are some of the limitations of the way we described measuring heritability? In what sense is natural selection a “Blind Watchmaker” (to borrow a term from Dawkins) Although organisms may look designed, their “design” is constrained by history in ways that human designed machines usually are not. Can you explain how, and provide examples? Is natural selection a tautology? Can you explain how populations change even if the individuals within them do not? Can you explain how selection can act very strongly on phenotypic variation, and yet result in no evolution of the population? Can you explain why natural selection cannot produce perfect designs? Can you explain how a random process such as mutation can be the foundation for a non-­‐
random process like adaptation? Can you explain how natural selection can produce wonderful adaptations without being goal oriented or forward looking? Meeting 6: Genetic Variation Short narrative: Ultimately, evolution depends on variation. We discussed the nature of information flow between genotype and phenotype, how the source information may be changed via mutation, how changes in DNA translate to changes in phenotype, and how this relates to fitness. We ended with the observation that rates of heterozygosity in nature are much higher than selectionists had predicted. Some key terms Complementary base pairing DNA polymerase, RNA polymerase The central “dogma” Codon: first, second, and third positions Redundant code Synonymous vs. nonsynonymous substitutions Transitions vs. Transversions Fitness Retrotransposition Unequal crossing over Ortholog vs. Paralog Gene families Pseudogenes Inversions Supergenes Polyploidy Fusion Purifying selection Phenotypic frequency, Genotypic frequency, Allele frequency Heterozygosity Concepts/examples DNA as information storage Mutations may be silent or not silent – example of latter is sickle cell Historically we’ve recognized mutations with strong phenotypic effects (e.g. eyeless) but have been less able to recognize synonymous substitutions or mutations with subtle effects on the genotype. Not all substitutions are equally likely – transitions (within pyramidines or within purines) are more likely than transversions (between pyramidines and purines) Polymerases vary in accuracy and speed (a tradeoff) and can be the focus of natural selection. How do new genes arise? E.g. point mutation, gene duplications (e.g. globin) Expectation: Purifying selection will keep levels of variation low Observation (starting in 60’s): Genetic variation surprisingly high Skills Can you explain the flow of information from genotype to phenotype? Can you explain why some base pair changes are “silent.” Why is this more likely to be true of 3rd position substitutions that 1rst position substitutions. Can you predict when selection would favor DNA polymerases with high accuracy vs. high speed? Can you explain why most mutations are either neutral or deleterious? Creationists sometimes refer to mutation as “negative variability” because mutations are often deleterious. Even when a mutation is demonstrably beneficial, such as antibiotic resistance in the presence of antibiotics, creationists claim the benefit is only “context dependent” and that the mutation will be disadvantageous in the natural environment. What is the logical flaw in the argument? Can you explain how gene duplication provides evolutionary potential? Humans have 46 chromosomes, other great apes have 48? Can you explain what happened and use both phylogenetic and chromosomal evidence supporting your argument? If you know the population size and the number of each of the genotypes, can you calculate genotypic frequency? If you know the genotypic frequencies, can you calculate allele frequencies? What does it mean if p + q = 1? Can you define heterozygosity, and contrast selectionist versus neutralist explanations for why heterozygosity is so high? BBio466 Week 4 Study Guide Jensen, Spring 2016 Meeting 7: Hardy-­‐Weinberg: Selection and Mutation Short narrative: Hardy-­‐Weinberg tells us what the genotypic frequencies will be for a given p and q assuming that no evolution is occurring. That’s great, because if our expectations from HWE are not met, it clues us into that fact the something interesting must be going on. We explored Hardy-­‐Weinberg as a null model and how to incorporate selection into population genetics models so we could predict changes in allele frequencies under selection. We spent most of our time discussing the general selection equation, and introduced the idea that there are specific cases in which the general selection equation can be expressed more simply – e.g. 1) selection against recessive homozygotes; 2) selection against dominant phenotypes; 3) Selection favoring heterozygotes. We did not (and will not) do the algebra linking the general selection equations to the simpler equations, but if you like algebra puzzles (and who doesn’t!) and want a deeper understanding of how the equations work, I encourage you to do so. We will also consider the balance between mutation introducing deleterious alleles into a population and selection removing them. Finally, we will return to the question of the role of selection in explaining high levels of heterozygosity in nature. Some key terms Allele frequencies: p and q Hardy-­‐Weinberg: p2 + 2pq + q2 Null Model Agents of evolution: Mutation, migration, drift, selection Genotypic fitness: w11, w12, w22 Average fitness: 𝑤 = 𝑝! 𝑤!! + 2𝑝𝑞𝑤!" + 𝑞! 𝑤!! p vs. p’; q vs. q’ 𝑝 = equilibrium value for p with heterozygote advantage 𝑞 = equilibrium value for q under mutation selection balance Meeting 8: Hardy-­‐Weinberg: Drift Short narrative: Most of this period will be devoted to exercises with incorporating selection and mutation into models of allele frequency change – little new material will be presented. We will introduce drift, though, and will take it up more fully after exam 1. Drift is an important evolutionary force but, unlike selection, it is random and does not generate adaptation. Drift is particularly important in small populations, and in populations that are reduced in size by a bottleneck or founding event. In small populations, the effects of drift can be larger than, and in opposition to, selective forces. We will briefly discuss the implications of drift for heterozygosity. Some key terms Genetic drift Population/Genetic bottleneck, Founder effect Heterozygosity Concepts/examples Drift is random changes in allele frequencies across generations Unlike natural selection, drift does not lead to adaptation Drift can actually operate against selection, especially in small populations. When populations become very small, drift can lead to loss of genetic diversity and reduced heterozygosity – e.g. prairie chickens Skills Can you verbally explain why drift plays a greater role in small populations than in large populations? Can you explain why drift poses a problem for conservation of endangered species? Can you calculate the changes in heterozygosity from one generation to the next due to drift? A note about equations: I will not expect you to memorize the equations -­‐ I will provide them for you on the exam. I will also not require you to do the algebra to get from one form of the equation to another (except for very simple cases). I will not tell you which equation to use for what, however, so you’ll need to know enough about how they work that you’ll know which one to apply. Working through the algebraic treatments in your book may be helpful. We used a few different equations, but not all the ones described in your book) –
you can download and equations sheet from the Meeting Information page. I will give you the necessary numbers, you will be expected to identify and deploy the relevant equations (bring a non-­‐graphing calculator). Concepts/examples Hardy-­‐Weinberg describes expected genotypic frequencies for a given p and q assuming that no evolutionary forces (e.g. mutation, migration, drift, selection) are acting. Evolutionary forces violate the assumptions of HWE If we know the genotypic fitnesses (wxx) we can calculate expected allele frequencies (p’ and q’) even if selection is acting. Selection may remove alleles from a population, but acts differently on dominant alleles than on recessive alleles. Alternate alleles will reach an equilibrium value if heterozygotes are favored. Removal of deleterious alleles from a population will be balanced by addition of alleles back into the population via mutation. Selection and mutation will reach a balance, the value of which depends on the mutation rate and strength of selection. Skills Can you verbally explain why the expected (under HWE) frequencies of homozygotes is p2 and q2, incorporating probability into your argument? Can you do the same for expected values of heterozygotes being 2pq? Do you understand how to determine whether Hardy-­‐Weinberg conditions apply by comparing expected and observed genotypic frequencies? For a two allele system with dominance, do you know how to calculate p and q if all you know is the phenotypic frequencies? What do you need to assume for this to work? What does it mean if p + q = 1? If p2 + 2pq + q2 = 1? Under selection, the equation for delta p includes the “Average Excess of Allele A1” term. Can you verbally explain this term? Is it possible for delta p to be positive even if A1A1 homozygotes are strongly selected against (i.e. w11 << ŵ)? Can you describe, both verbally and with reference to an equation, why it takes a very long time to entirely remove deleterious recessive alleles from a population? Can you describe, both verbally and with reference to an equation, why 𝑝 is larger when the selection coefficient for the other allele is large? Can you describe, both verbally and with reference to an equation, why 𝑞 is larger when the selection coefficient for the allele is small? Why 𝑞 is larger when the mutation rate the allele is large? Can you verbally explain how these equations relate to the observation of high levels of genetic variation in populations? !"#$"$#%&'()*+,-.%/%00+,122%3%4$-.$-%
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