06-Mar-2010 - 13-Mar-2010
University of California, Davis and Bodega Marine Laboratory (additional financial support provided by the University of Rochester, and NESCent)

at Bodega Marine Laboratory, Bodega Bay, California

March 6-13, 2010

Sponsored by the

University of California, Davis and Bodega Marine Laboratory
(additional financial support provided by the University of Rochester,
and NESCent)

Introduction. 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 estimation of phylogenetic
trees is now a well formalized statistical problem, with general
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 novel problems outside systematics is an area of special
excitement, innovation, and controversy, and perspectives vary widely.

In March, 2010, for the eleventh 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 approaches are
being applied. We cover a range of topics in ecology, 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

* Estimating, evaluating and interpreting phylogenetic trees
* Recent advances in tree estimation: Bayesian inference;
stochastic optimization strategies; divide-and-conquer methods; gene-
tree species tree inference
* Estimation of divergence times from sequence data: relaxed
clocks, calibration issues
* Analysis of character evolution-theory: maximum likelihood and
Bayesian approaches; ancestral-state estimation; character
correlation; rates of trait evolution
* Analysis of character evolution-form and function of complex
character systems
* Inference of diversification rates: detecting rate shifts,
testing key innovation hypotheses
* Phylogenetic perspectives on biodiversity and conservation biology
* Phyloinformatics: mining sequence databases for phylogenetic
* Ecological Phylogenetics: community composition and historical
Instructors for the main workshop.

* Peter Wainwright
* Brian Moore
* Michael Sanderson
* Bruce Rannala
* Jonathan Eisen
* Sharon Strauss
* John Huelsenbeck
* Rich Glor
* Justen Whittall
* Thomas Near
* Jean Burns
* Greg Pauly
* Samantha Price
* 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 estimation will be assumed.

Admission and Fees. Students will be admitted based on academic
qualifications and appropriateness of research interests. The course
fee is $550. This includes room and board at BML for duration of the
course (arriving March 6, leaving March 13) and transportation from
Davis to BML.

Application Deadline. Applications are due by January 8, 2010. Please
send a completed application form (available at http://bodegaphylo.wikispot.org/Front_Page)
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
22 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