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I. Cladistics and Phylogeny: What It Cladistics and How It Is Used to Test Phylogenetic Hypotheses

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I. Cladistics and Phylogeny: What It Cladistics and How It Is Used to Test Phylogenetic Hypotheses Bio 2.3 Study Guide Exam I Topics: I. Cladistics and Phylogeny: what it cladistics and how it is used to test phylogenetic hypotheses. What type of evidence is used to make decisions about cladograms and then phylogenetics? This topic applies to all of the other topics in this section of the course as it is the logical framework for the hypotheses about evolutionary relationships. Practice & Examples: given a character table make a cladogram create a character table or cladogram –good examples to practice; Fungi (all 5 phyla), the Stramenopiles, the 3 Domains, chloroplast and cyanobacteria I wouldn’t expect you to have memorized the characters of the classes Green Algae Be able to marshal an argument for or against a proposed cladogram/phylogenetic hypothesis (for example: lumping Fungi and Water Molds; Land Plants as part of Green Algae; Water Molds as part of Stramenopiles; Archea separated from Bacteria….etc) (potential essay?) Create a timeline showing the formation of the earth (solid rock), origins of life, Archea, Bacteria, Eukarya, photosynthesis and atmospheric concentrations of O2, etc II. Endosymbiosis and horizontal gene transfer: what is the impact of endosymbiosis (in our case mostly the plastids) on the evolution and ecology of the eukaryotes. How did this shape the evolution of the Eukarya- both primary and secondary endosymbiosis. This topic clearly relates to Cladistics and to Adaptation. Practice & Examples Know which phyla have primary vs. secondary endosymbiosis? Distinguish the origin of the chloroplast; cyanobacteria, green algae, red algae? What is the evidence? Can you distinguish between the host cell’s phylogeny vs. the plastid phylogeny? Make a cladogram of the chloroplasts found in eukaryotes. III. Adaptations of the Phyla we have studied. understand how adaptations can be explained in terms of o evolution and natural selection o phylogenetic o structure and function o adaptation to environmental niche o adaptive radiation These are all lenses through which we can view the same trait. For example endosymbiosis of a cyanobacteria is an adaptation that increases access to energy via photosynthesis. Organisms with this character outcompeted those without, leading to natural selection for chloroplasts in the ancestor of the Green and Red Algae. This in turn can be used to trace the phylogenetic history (evolutionary origin) of the photosynthetic Protists. The diversity of photosynthetic eukaryotes is also an example of adaptive radiation after acquisition of a new trait. Practice & Examples: Be able to give examples of mutualism that we have studied either in lecture or in lab, explaining the adaptations necessary and benefits to each party Give a specific example of adaptations in the different Phyla we have studied and be able to explain the how that increases the survival and reproduction of the individual in their ecological niche IV. Specific Life Cycles to Know Draw and label the complete life cycles below. Name all the structures, location of mitosis, meiosis, gamete production, spore production. Identify haploid vs. diploid vs. dikaryotic ( if any) parts of the life cycle Rhizopus Life Cycle Laminaria Life Cycle Ascomycete Life Cycle Oedogonium Life Cycle Basidiomycete Life Cycle V. Core Concepts Evolution and Adaptation Flow of Energy and Matter Structure and Function Systems/Biological Hierarchy Flow of Information Which did we emphasize in this section of the course? Practice: can you: a) define the core concept b) give a specific example from this section of the course c) explain how that example demonstrates that specific core concept. Cladistics and phylogenetics propose hypotheses for the evolution and origin of taxa based on vertical gene transfer, but we know that horizontal gene transfer has shaped the evolution of the protists. Explain how horizontal gene transfer has affected the evolution of photosynthetic eukaryotes. What is the evidence? What have been the implications ecologically and evolutionarily? (subtext: evolution and horizontal gene transfer) We have seen many examples of convergent evolution. Even though we focus on structure determining function, convergent evolution shows us that in reality it is the need for a particular function that selects for structures. Explain how the core concepts of structure/function and adaptation are really the same idea using an example of convergent evolution. (subtext: structure and function and evolution) Natural selection occurs when the genetics of a population intersects with the ecology of their environment. This in turn can lead to larger evolutionary changes such as speciation. Using a specific example, explain how novel genetic traits, natural selection and adaptations have led to adaptive radiation and the origin of higher level taxa such as phyla or clades. Which taxa would be a good example? (subtext: evolution, adaptation- adaptive radiation and speciation) Do you agree or disagree: Evolution is really one more example of the flow of information. Defend your opinion using evolution of photosynthesis as the specific example. You would want to include information about horizontal gene transfer vs. vertical; genetic information in the plastids vs. the nucleus; the idea that functions like photosynthesis occur due to structures and the genes that code for them….(subtext: evolution, horizontal gene transfer) .
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