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FA2008 - BILD 3 - Lecture 06 (Phylogenetic Trees - 02)

FA2008 - BILD 3 - Lecture 06 (Phylogenetic Trees - 02) -...

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10/21/08 1 Midterm Tuesday October 28 8 AM – 9:10 AM (same room as lecture) 5 PM – 6:10 PM Will cover all lecture, associated reading, and discussion section activities from Sept 25 – Oct 24 Please be on time for exams. If you arrive after other students have started to leave, you may not be able to take the exam at all. During exams all backpacks, water bottles, hats, etc. will have to be left in the front of the room. If you are concerned about valuables, please do not bring them to class on exam days . No calculators, cell phones, or any electronic devices during the exam. We will check picture IDs at the exam You must take the midterm and final in the lecture time for which you are enrolled Know your correct discussion section date/time/TA name when you come to the exam (5 points) If you have any confusion about the day/time/TA name for your discussion section, please clear up the confusion BEFORE the exam. You can check your discussion section enrollment at http://sections.ucsd.edu/ . TA names are on WebCT (“Discussion section TAs”). Questions may be multiple choice, fill-in-the-blank, T/F, and free response. There are no old exams posted. NO scantron needed. S uper office hours : Monday October 27 12 noon - 5 PM 2130 Bonner Hall No discussion section Oct 27 – 31 (Also no discussion section Nov 10 – 14 Nov 24 – 28) Overview I. What is a phylogeny? II. History III. How do we read trees? IV. How do we build trees? A. characters B. reasons for similarities 1. homology 2. homoplasy 3. shared & derived homologies C. tree building techniques 1. outgroup comparisons 2. parsimony 3. maximum likelihood V. Is there such a thing as a fish? VI. Why are phylogenies useful? VII. Molecular clocks Usually don’t have any idea what is shared, derived How do you find out? D. Tree building techniques 1. Outgroup comparisons 2. Parsimony 3. Maximum likelihood
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10/21/08 2 Outgroup comparisons Ingroup – a group of taxa that are of interest, assumed to be monophyletic Outgroup – one or more taxa assumed to be phylogenetically outside the ingroup, although related Example - Conifers – outgroup to flowering plants Outgroup comparisons can distinguish between ancestral and derived character states Outgroup comparisons amniotes - animals that have an egg membrane, amnion, during development Outgroup comparisons
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FA2008 - BILD 3 - Lecture 06 (Phylogenetic Trees - 02) -...

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