2019 Bodega Applied Phylogenetics Workshop

UC Davis

Workshop in Applied Phylogenetics

at Bodega Marine Laboratory, Bodega Bay, California, May 25–June 2, 2019

Sponsored by the
University of California, Davis and Bodega Marine Laboratory


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 all 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 eighteenth year, we will teach a workshop for graduate students interested in applying phylogenetic methods to diverse topics in biology. The 8-day course is an intensive exploration of problems to which modern phylogenetic approaches are being applied and the most current statistical tools and methods that are used to solve those problems. We cover a wide range of topics in comparative statistical phylogenetics. The course starts with recent advances in phylogenetic inference, and then focuses on methods for making inferences from phylogenies.

The course will be held at the Bodega Marine Laboratory on the beautiful Northern California coast, which has on-site housing. The course format will involve equal parts of lecture and hands-on software training with an emphasis on performing analyses using RevBayes: http://revbayes.github.io, with instruction in other inference software (MrBayes, BEAST, etc.) based on student interest. 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 inference of phylogeny
  • Model specification: model selection, adequacy and uncertainty
  • Diagnosing MCMC performance
  • Divergence-time estimation: relaxed clocks, fossil calibration
  • Species-tree estimation
  • Character evolution: discrete- and continuous-trait evolution
  • Lineage diversification: detecting rate shifts, testing key-innovation hypotheses

Instructor Team

  • Cécile Ané (University of Wisconsin-Madison)
  • Sebastian Höhna (LMU, Munich)
  • John Huelsenbeck (UC, Berkeley)
  • Michael Landis (Washington University)
  • Mike May (UC, Berkeley)
  • Brian Moore (UC, Davis)
  • Bob Thomson (U Hawaii, Manoa)
  • Peter Wainwright (UC, Davis)


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 generally discouraged from applying.

Admission and Fees

Students will be admitted based on academic qualifications and appropriateness of research interests. The course fee is $850. This includes room and board at BML for duration of the course (arriving on Saturday, May 25; departing on Sunday, June 2) and return transportation from Davis to the Bodega Marine Labs.

Application Information

Applications are due by Wednesday, December 12, 2018. Please fill out our application form and send your CV and one letter of recommendation from your major advisor. Applications should be sent via email as PDFs to jsigao at gmail dot com. Students will be notified via e-mail by December 14, 2018 of acceptance.

Send all application materials to:

Jiansi Gao
Department of Evolution and Ecology
5343 Storer Hall
University of California Davis
Davis, CA
email: jsigao at gmail dot com