2009 Workshop in Applied Phylogenetics


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Phylogenetic methods have revolutionized modern
systematics and become indispensable tools in evolution, ecology and comparative biology, playing an increasingly important role in analyses of biological data at levels of organization ranging from molecules to ecological communities. The construction of phylogenetic trees is becoming a methodology that is well-defined, with broad agreement on the central issues and questions. A nearly standard set of topics is now taught as part of the curriculum at many colleges and universities. On the other hand, application of phylogenetic methods to interesting problems outside of systematics is an area of special excitement, innovation, and controversy, and perspectives vary widely.

In March, 2009, for the tenth year, we will teach a workshop for graduate students interested in applying phylogenetic methods to diverse topics in biology. The one-week course will be an intensive exploration of problems to which modern phylogenetic tools are being applied. We cover a range of topics in biogeography, ecology, conservation biology, phylogenomics, functional morphology, macroevolution, speciation, and character evolution. The course starts with recent advances in phylogenetic methodology, and then focuses on methods and tools that can be brought to bear on these "applied" issues in the context of a given phylogeny.

The course will be held entirely at the Bodega Marine Lab on the Northern California coast, which has extensive computing resources and on-site housing. The course format will involve equal parts of lecture, discussion, and training in software and internet tools. One afternoon during the week will be left free for field trips to local natural areas.

Specific Topics to be Covered
* Finding, evaluating and interpreting phylogenetic trees; phylogenetic databases
* Recent advances in tree reconstruction: Bayesian inference; stochastic optimization strategies; divide-and-conquer methods; Garli; gene-tree species tree resolution
* Analysis of character evolution--theory: parsimony, likelihood and Bayesian approaches; null models and statistical testing
* Analysis of character evolution--form and function of complex character systems
* Phylogeography; coalescent methods for inferring migration rates and patterns
* Phylogenetic comparative methods
* Phylogenetic perspectives on biodiversity and conservation biology
* Data mining of sequence databases for phylogenetic analysis
* Estimation of divergence times from sequence data, analysis of diversification rates
* Ecological Phylogenetics, biogeography

Instructors for the main workshop.
* Peter Wainwright
* Brad Shaffer
* Brian Moore
* Michael Donoghue
* Bruce Rannala
* Jonathan Eisen
* Rich Glor
* Justen Whittall
* Greg Pauly
* Samantha Price
* Stephen Smith
* Phil Spinks
* Robert Thomson
plus guest lecturers!!

Prerequisites. Students should have some familiarity with phylogenetic methods through previous coursework. Some experience with PAUP, PHYLIP, or other programs for phylogeny reconstruction will be assumed.

Admission and Fees. Students will be admitted based on academic qualifications and appropriateness of research interests. The course fee is $450. This includes room and board at BML for duration of the course (arriving March 7, leaving March 14) and transportation from Davis to BML.

Application Deadline. Applications are due by January 4, 2009. Please send a completed application form (available at http://bodegaphylo.wikispot.org/2009_Course_Announcement)and one letter of recommendation from your major advisor.
Applications should be sent via email as PDFs to pqspinks@ucdavis.edu. Sorry, but due to the limited size of the class, postdocs and faculty are discouraged from applying. Students will be notified via e-mail by 9 January of acceptance.

Send all application materials to:
Dr. Phillip Q. Spinks
Department of Evolution and Ecology
2320 Storer Hall
University of California Davis
Davis, CA

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