UC Davis

WORKSHOP IN APPLIED PHYLOGENETICS

at Bodega Marine Laboratory, Bodega Bay, California

March 2¡V9, 2013

Sponsored by the

University of California, Davis and Bodega Marine Laboratory

(additional financial support provided by the University of Rochester)

http://bodegaphylo.wikispot.org/Front_Page

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 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.

This Spring, for the fourteenth consecutive year, we will teach a workshop
for graduate students interested in applying phylogenetic methods to
diverse topics in biology. The one-week course is an intensive exploration
of problems to which modern phylogenetic approaches are being applied and
the most current statistical tools and approaches that are used to solve
those problems. 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 at the Bodega Marine Laboratory on the Northern
California coast, which has on-site housing. Our newly increased bandwidth
and access to computing clusters allows us to utilize computer-intensive
approaches even in a one-week course. The course format will involve
equal parts of lecture, discussion, and hands-on software training. One
afternoon during the week will be left free for field trips to local
natural areas.

Topics Covered
*       Estimating, evaluating and interpreting phylogenetic trees
*       Recent advances in Bayesian and Maximum-likelihood estimation
of phylogeny
*       Estimation of species trees, gene-tree/species-tree conflicts
*       Divergence-time estimation from sequence data: relaxed clocks,
fossil calibration
*       Analysis of character evolution: maximum likelihood and Bayesian
approaches, ancestral-state estimation, rates of trait evolution
*       Analysis of morphological form, function of complex
character systems
*       Inference of diversification rates: detecting rate shifts,
testing key innovation hypotheses
*       Model specification issues: model selection, adequacy and
uncertainty
*       Diagnosing MCMC performance

Instructors for the 2013 workshop
*       Carl Boettiger
*       Jeremy Brown
*       Jonathan Eisen
*       Rich Glor
*       Tracy Heath
*       Mark Holder
*       John Huelsenbeck
*       Luke Mahler
*       Brian Moore
*       Samantha Price
*       Bruce Rannala
*       Bob Thomson
*       Peter Wainwright

Prerequisites
Available housing limits course enrollment to ~30 students. Preference
is given to doctoral candidates who are in the early to middle stages of
their thesis research, and who have completed sufficient prerequisites
(through previous coursework or research experience) to provide some
familiarity with phylogenetic methods. Unfortunately, because of limits
on class size, postdocs and faculty are discouraged from applying.

Admission and Fees
Students will be admitted based on academic qualifications and
appropriateness of research interests. The course fee is $650. This
includes room and board at BML for duration of the course (arriving
March 2, leaving March 9) and transportation from Davis to

Application Deadline
Applications are due by November 16, 2013. Please send a completed
application form and one letter of recommendation from your major
advisor. Applications should be sent via email as PDFs to
[email protected]. Students will be notified via e-mail by December
1, 2013 of acceptance.

Application Forms and Information
Visit the Bodega website to for additional information and to download
an application form: http://bodegaphylo.wikispot.org/2013_Workshop

Send all application materials to:

Gideon Bradburd
Department of Evolution and Ecology
5343 Storer Hall
University of California Davis
Davis, CA
95616
email: [email protected]