Workshop: Bodega_California.AppliedPhylogenetics.Mar2-9

Workshop: Bodega_California.AppliedPhylogenetics.Mar2-9

16 October, 2012

at Bodega Marine Laboratory, Bodega Bay, California

March 2-9, 2013
Sponsored by the

University of California, Davis and Bodega Marine Laboratory

(additional financial support provided by the University of Rochester)


Phylogenetic methods have revolutionized modern systematics and become

indispensable tools in , ecology and comparative biology, playing

an increasingly important role in analyses of biological data at levels

of organization ranging from molecules to 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 -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

* Gideon Bradburd

* Jeremy Brown

* Jonathan Eisen

* Rich Glor

* Tracy Heath

* Mark Holder

* John Huelsenbeck

* Luke Mahler

* Brian Moore

* Samantha Price

* Bruce Rannala

* Bob Thomson

* Peter Wainwright

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, and 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, 2012. Please send a completed

application form and one letter of recommendation from your major

advisor. Applications should be sent via email as PDFs to 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:
Send all application to:
Gideon Bradburd

Department of Evolution and Ecology

5343 Storer Hall

University of California Davis

Davis, CA



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