PLB 591D, Molecular Phylogenetic Analysis
Spring Semester 2002, 3 credit hours
Arizona State University, Main Campus

Instructor:   Martin F. Wojciechowski, Department of Plant Biology at ASU
Email: ; phone: 480.727.7767
Office/office hours:   LSE 711, Tuesday 3:00 pm to 4:30 pm, Thursday 10:00 am - 11:00 am, or by arrangement

Course description: Methods of phylogenetic analysis, particularly analyses using molecular sequence data, have provided a powerful tool for the study of the evolutionary history of organisms, their genes and genomes. The course will cover the basic theory and practice of currently used methods to infer phylogenetic trees, as well as practical information on obtaining molecular data for phylogeny reconstruction, with emphasis on their application to studies of the systematics and evolution of green plants. The course will also emphasize hands-on experience with software tools for obtaining sequence data, constructing trees (e.g., using parsimony, distance, and maximum likelihood methods) and related analyses of molecular data. Other topics will include resampling techniques and tree comparison methods, the advantages and disadvantages of common approaches for inferring trees, and recent advances in plant molecular systematics and evolution. Students will work on a phylogenetic analysis project using their own datasets, or using data obtained from the literature or existing databases, as a requirement for the course. This project will require computer work outside of class time.

Course goals: To familiarize students with modern phylogenetic methods used to analyze molecular sequence data for plant systematic or evolutionary studies. The laboratory sessions will provide hands-on experience with several software packages (e.g. PAUP*, MacClade, ClustalX) in widespread use for sequence alignment, phylogeny reconstruction, and evolutionary analysis.

Logistics. Lecture sessions will meet on Mondays, from 3:10 - 4:30 pm in LSE 204; computer lab sessions meet Wednesdays from 3:15 - 5:45 pm in Computing Commons 203. The purpose of the "laboratory" portion of the course is to acquaint you with some of the software that is available for phylogeny reconstruction and data analyses, tools you will need to complete the required phylogenetic analysis project (see below). Most of the lab sessions will be held in a Macintosh computer lab where phylogenetic software will be available for your use during the semester. The software will be set up on an "instructor volume" for this course. You will have access to this volume/software from certain computer sites on campus; a UserID and password will be given to you in the 1st lab session to enable access to this volume. Information on ASU computer labs location/availability outside of our scheduled lab time can be found on the following web site: You will need a Mac-formatted floppy disk/AFS drive space to save/transfer files from the computers in the lab.

Registration. All students attending class must register for credit. Postdocs and faculty are welcome to attend lectures, but because of the limited number of users allowed for some of the software we will be using (site license) I cannot guarantee non-registrants will have access to computers in the laboratory. However, handouts for the labs and/or datasets that are used as a basis for computer exercises will be made available.

Required/recommended texts: There will be assigned readings in Molecular Evolution: A Phylogenetic Approach, by R. Page, and E. Holmes, 1998, publisher Blackwell Science (ISBN 0-86542-889-1). The book Phylogenetic trees made easy, A how-to manual for molecular biologists, by B. G. Hall, 2001, publisher Sinauer Associates, Inc., Sunderland, MA (ISBN 0-87893-311-5) should prove indispensable for the laboratory part of the course and is highly recommended. Other relevant articles and handouts will be provided as necessary, or made available for copying in LSE 218, the Plant Biology departmental office.

Grading and required activities. Each registered student will be required to complete two class activities to receive a grade, both of which should be discussed/approved with the instructor beforehand. First, students must lead a 20-25 minute class discussion (during the last 3 weeks of class) on a topic not covered in lecture, but which has general implications for molecular phylogenetics or a closely related field (topics must be approved by the instructor). For example, students may lead a discussion on a topic that is covered in the textbook, but was not the focus of a lecture. To complete this activity, students must provide the class with limited required readings relevant to the topic of their presentation (we will have a folder where reading materials for the class are kept/borrowed for copying in LSE 218; alternatively, some reading materials may be distributed by email as .pdf files, if available). These readings must be made available at least 1 week prior to their scheduled discussion. Examples of readings include textbook pages, a short review article from a journal [such as one from Science or Trends in Ecology and Evolution] or other literature, but no more than 1 hour of reading material should be assigned. In addition, the discussion leader must prepare and distribute (due on presentation day) a summary of key concepts for the topic (maximum 2 single-spaced pages) and a list of relevant references for the topic.

Second, registered students must undertake a detailed phylogenetic analysis of a molecular dataset (this can be your own unpublished data, or data acquired from publically available databases such as GenBank, TIGR) in the context of using phylogenetic methods to test a particular hypothesis(es). For example, a project might involve a focus such as: comparing rates of evolution of different lineages; comparing rates and modes of evolution of different genes for the same taxa; reconstructing ancestral states of proteins and exploring implications for protein function; exploring the cost of "reconciling" different gene trees for the same organisms; exploring the performance of different inference methods/models relative to a "known" phylogeny; or estimating times of divergence using molecular calibration methods. For this project, hypothesis-testing cannot be limited to simply testing the monophyly of a taxon or assessing the sister-group of a clade. This project is to be presented in manuscript form (Molecular Biology and Evolution journal format, see following website for more details,, with emphasis on describing, presenting, and discussing the phylogenetic approaches used for hypothesis testing (project due by 5:00 pm on TUESDAY, May 7th; date of final exam). I recognize that analysis of this dataset may not yield a publication-quality outcome, however, a focused and detailed analysis (with proper interpretation) will serve to demonstrate your understanding of phylogenetic methods. Forty percent of the course grade will be based on the first class activity, and 60% based on the phylogenetic project.

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