(over) 1 Integrative Biology 200B "PRINCIPLES OF PHYLOGENETICS: ECOLOGY AND EVOLUTION" Syllabus • Spring 2011 David R. Lindberg -- phone: 2-3926; email: [email protected] Brent D. Mishler -- phone: 2-6810; e-mail: [email protected] Graduate Student Instructor: Nicholas J. Matzke -- phone: 3-6299; email: [email protected] Class meeting time: Tu-Th, 12:30 - 3:30 pm in 3083 VLSB. This year lab exercises will be done on personal computers -- you need to have access to one to bring to class, preferably a laptop! Our class web page is: http://ib.berkeley.edu/courses/ib200b/ -- please check this often as it will have class announcements and answers to questions about the course material. Tentative Schedule of Topics: Jan. 18: Introduction to aims of course / Phylogenetic reconstruction in a nutshell: homology & characters (BDM) LAB: Get acquainted roundtable (all) Jan. 20 Phylogenetic reconstruction in a nutshell: trees (BDM) LAB: tour of systematics collections & resources in VLSB Jan. 25: What can we do with trees once we have them? 1. Classification classical and modern (DRL) LAB: Introduction to Statistical Thinking (all) Jan. 27: Qualitative character evolution within a cladogram (discrete states; ancestral state reconstructions; single characters - BDM) LAB: Introduction to Mesquite; Discrete character reconstruction (Matzke) Feb. 1: Qualitative character evolution (comparing two or more characters - BDM) LAB: Phylogenetic Conservatism and Correlation of Discrete Characters (Mesquite - Matzke) Feb. 3: Quantitative character evolution within a cladogram (intro; ancestral trait reconstruction; phylogenetic conservatism - BDM) LAB: Introduction to R (Matzke) Feb. 8: Evolution and development - heterochrony (DRL) LAB: Intro to R continued: Phylogenies; Continuous characters (Matzke) Feb. 10: Independent contrasts and trait correlations (Ginger Jui) LAB: independent contrasts (R) (Matzke) Feb. 15: Morphometrics (DRL) LAB: morphometrics applications (Matzke) Feb. 17: Fossil data in phylogenetics (DRL) LAB: PROJECT TOPIC DUE: discuss your potential project in class Feb. 22: Tempo in macroevolution (DRL) LAB: testing molecular clock, r8s, BEAST (Matzke) Feb. 24: Dating in the 21st Century: putting dates on nodes, characters, and events (DRL) LAB: discussion: the use of fossil data in phylogenetic reconstruction (all) March 1: Molecular evolution (BDM) LAB: analysis of molecular evolution; substitution models, Modeltest, etc (Matzke) March 3: Gene family evolution; comparative genomics (Matzke) LAB: tools for comparative genomics; BLAST, etc. (Matzke) March 8 Evolution and Development (DRL) LAB: tools for evo-devo (Matzke) March 10: Phylogenetics and adaptation (BDM) LAB: discussion of adaptation (all)(over) 2 March 15: Comparing sister clades within a cladogram: the shape of evolution (DRL) LAB: generating random trees; testing cladogram imbalance (Matzke) March 17: Adaptive radiations (BDM) LAB: lineages through time; diversification analyses (Matzke) March 21 - 25: SPRING BREAK March 29: Speciation and related issues: species revisited (BDM) LAB: QUIZ 1 March 31 Reticulation and phylogenetics; "phylogeography" and population biology (BDM) LAB: discussion of species (all) (your project data set should be complete) April 5: Phylogenetics and conservation biology (BDM) LAB: coalescence theory; applications in population genetics and phylogeography (Matzke) April 7: Modes in macroevolution - patterns of diversification and extinction (DRL) LAB: discussion on levels of selection (all) April 12: Comparing cladograms; supertrees; coevolution; symbiosis (BDM) LAB: consensus methods; Brooks parsimony (Matzke) April 14: Biogeography I -- basic principles; ecological vs. historical approaches; vicariance biogeography (DRL) LAB: Biogeographic software; DIVA, Lagrange (Matzke) April 19: Biogeography II -- New tools, databases, and research possibilities (Matzke) LAB: discuss progress on projects in class (hand in outline of project April 18th, details TBA) April 21: Interactions among clades in macroevolution (DRL) LAB: discussion of application papers (students to bring papers from their groups) April 26: Phylogenies and Community Ecology; Assembly of Regional Biota (Ginger Jui) LAB: phylocom, picante (Matzke) April 28: Glimpses of the future - comparative and functional genomics; integrating genetics, physiology, ecology and evolution (all) LAB: QUIZ 2 May 2 - 6: Reading/Review Week -- work on projects with help from instructors May 9-13: FINALS WEEK -- student minisymposium -- projects due (dates to be determined) Requirements & Grading: (1/3) Participation. Do the reading, come to each class and lab, and participate in discussions. A few homework assignments will also be given. (1/3) Quizzes. Two equally-weighted, one-hour quizzes will be given, that emphasize problem solving and conceptual understanding. (1/3) Project. This will be a substantive, comparative analysis of data from a group of the student's choice (with approval of the instructors; we encourage the study of thesis or other study groups). Based on phylogenetic trees (whether self-generated or from the literature), the project should apply all appropriate comparative methods to evaluate several types of comparative questions. There should also be a rigorous critique of previous comparative literature on the organismal group of choice. A written report will be turned in during finals week, in the form of a professional journal publication, that is, with an introduction (containing the literature review and critique), materials and methods section, results (using summary figures -- no raw data), and a discussion (being sure to compare results from the different methodologies applied, and to reach some biological conclusions). We will schedule a minisymposium at the end of the term where students can give a short presentation of their
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