Workshop in applied phylogenetics

Michael Sanderson mjsanderson at UCDAVIS.EDU
Tue Jan 11 12:27:57 CST 2005

UC Davis
at Bodega Marine Laboratory, Bodega Bay, California
May 7-14, 2005

Sponsored by the
Center for Biosystematics, Bodega Marine Laboratory, and Center for
Population Biology,
University of California, Davis

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 ecosystems. 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, applications of phylogenetic methods
to interesting problems outside of systematics is an area of special
excitement, innovation, and controversy, and perspectives vary widely.

In May, 2005, for the sixth 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, including topics in biogeography, ecology, conservation
biology, phylogenomics, functional morphology, macroevolution,
speciation, and character evolution. The course leads off with recent
advances in phylogenetic methodology, and then turns to methods and
tools that can be brought to bear to address these "applied" issues
in the context of a given phylogeny.

The course will be held entirely at 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 in the course include:

     * Finding, evaluating and interpreting phylogenetic trees;
phylogenetic databases
     * Recent advances in tree reconstruction: Bayesian inference;
stochastic optimization strategies; divide-and-conquer
     * 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
     * Phylogenetic biogeography and 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

Instructors for the workshop.

     * Dr. H. Bradley Shaffer
     * Dr. Michael Sanderson
     * Dr. Peter Wainwright
     * Dr. Tom Near
     * Dr. Amy Driskell
     * Dr. Rich Glor
     * Dr. Campbell Webb
     * Dr. Gordon Burleigh
     * Dr. Shelley McMahon
     * Dr. Justen Whittall

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 $375. This includes room and board at BML for the duration of
the course. UC Davis students may take the course for credit and can
apply for a partial waiver of this fee.

Application Deadline. Applications are available at the course
website: and are due by
February 28, 2005. Please send a completed application form, and one
letter of recommendation from your major advisor. We encourage
applications to be sent via email as PDFs to pqspinks at
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 March 18 of acceptance.

If sending application via surface mail, send all materials to:

Dr. Phillip Q. Spinks
Section of Evolution and Ecology
2320 Storer Hall
University of California Davis
Davis, CA 95616
email:pqspinks at

Michael J. Sanderson
Section of Evolution and Ecology
One Shields Avenue
University of California,
Davis CA 95616

lab web site:
Phylota project:
r8s software:


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