2013 Bodega Applied Phylogenetics Workshop


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.

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, character correlation, 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

  • Jeremy Brown
  • Jonathan Eisen
  • Rich Glor
  • Tracy Heath
  • Mark Holder
  • John Huelsenbeck
  • Luke Mahler
  • Brian Moore
  • Samantha Price
  • Bruce Rannala
  • Bob Thomson
  • Peter Wainwright

Plus special guest lecturers!!


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 BML.

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 gbradburd@ucdavis.edu. Students will be notified via e-mail by December 1, 2012 of acceptance.


FAQ page with questions.

Send all application materials to:

Gideon Bradburd
Department of Evolution and Ecology
5343 Storer Hall
University of California Davis
Davis, CA
email: gbradburd@ucdavis.edu

Course Organizers
Brian Moore and Peter Wainwright