Courses & Workshops
Biodiversity and the Tree of Life
Jonathan Eisen and I co-teach this course every spring quarter. In my lectures, I introduce students to tree thinking; how to interpret the information conveyed by phylogenies. Trees not only depict the evolutionary relationships among species, but may also provide estimates of the absolute timing of divergence events, allow us to infer the origin (and consequences) of important evolutionary novelties, and to understand the historical processes that have shaped the current geographic distribution of species. I also provide an overview of plant and fungal diversity. In these lectures, I draw heavily both upon examples from my own research, and also the research of my colleagues.
Phylogenetics, Speciation, and Macroevolution
Michael Turelli and I co-teach this upper-division undergraduate course on even years (next offered in the winter quarter of 2018). My lectures provide an unapologetically detailed treatment of modern statistical phylogenetic methods, but make extensive use of pedagogical techniques (such as computer simulation) to help students develop a strong intuitive grasp of complex mathematical and statistical concepts. Students leave the course with an advanced understanding of modern statistical phylogenetic methods, and develop some basic intellectual tools to understand models (and inference problems) that they have not encountered in class, and more generally, learn how to approach inference problems from a generic and rigorous statistical perspective. Dr. Turelli's lectures focus on speciation—who is the world's preeminent expert on the subject—and also on comparative phylogenetic methods for inferring character evolution and lineage diversification. Mike May leads the computer-lab component the course, where students apply the theory covered in lectures to now learn how to perform analyses of nucleotide sequence datasets using cutting-edge statistical phylogenetic methods.
Principles of Microevolution and Macroevolution
Annie Schmidt, Michael Turelli, and I co-teach the Population Biology Graduate core course every spring quarter. My lectures are essentially the industrial-strength, graduate counterpart of EVE 103. I introduce students to probability theory and provide an in-depth treatment of modern statistical phylogenetic methods (including a detailed treatment of continuous-time Markov models of DNA sequence evolution, and maximum-likelihood and Bayesian approaches for estimating the parameters of these models). Although a deep understanding of phylogenetic methods is directly relevant to most of the gradate students in the PBGG program, I have developed the presentation of this material so that it has a general utility beyond statistical phylogenetics. That is, phylogeny estimation also serves as a detailed case study of the procedures involved in (non-phylogenetic) statistical inference. My lectures are complemented by an optional computer lab (outside of class hours), where Mike May teaches students how to apply the methods from lecture to make inferences from real (generally their own) data.
Peter Wainwright and I co-teach (and co-organize) the Bodega Applied Phylogenetic workshop every spring (next offered in March 2017). This is an intensive, week-long immersion course held in residence at the picturesque Bodega Marine Lab that involves participation of ~12 expert instructors. Instructors give one or two lectures (and/or computer practicals) and mentor the students throughout the course to assist them with their individual research projects. The curriculum includes an introduction to core phylogenetic theory and methods, including Bayesian inference, phylogenetic CTMC models, model selection/hypothesis testing, MCMC diagnosis, and inference of phylogeny, divergence times, and species-tree estimation. The Bodega curriculum is somewhat unique in also covering a diversity of comparative phylogenetic methods, such as species delimitation, discrete- and continuous-trait evolution, biogeography, and lineage diversification. This is a hugely fun and wildly successful workshop. Graduate student feedback is effusive: students often express the sentiment that their participation has profoundly changed the way they approach their research.
Graduate Evolution Seminar
This is ten-week graduate-seminar course led by faculty in the Center for Population Biology that meets weekly (on Monday at noon in 2342 Storer Hall) to discuss fundamental and/or recent papers on topics that rotate each quarter. In previous iterations of the course, Graham Coop and I led a seminar where we reviewed literature "Exploring the phylogenetic/population-genetic interface in the genomic age," and I've also led a seminar where we reviewed literature on "New statistical phylogenetic methods for exploring correlations between character traits and diversification rates." I will be leading a new session in the winter quarter of 2017; please email me if you would like to suggest a potential topic.
Wellcome Trust/EMBL/EBI Advanced Course on Computational Molecular Evolution
This fantastic graduate course is held on odd years at the gorgeous Wellcome Trust Sanger Campus in Hinxton, UK. The course is organized by Nick Goldman, Laura Emery, Alexandros Stamatakis, and Ziheng Yang, and offers a comprehensive curriculum covering the statistical analysis of molecular sequence data sampled both different species (phylogenetics) and from different individuals of the same species (population genetics). An amazing faculty of international experts cover a range of topics in computational molecular evolution, including genomic informatics, sequence alignment, Markov models of sequence evolution, phylogeny and divergence-time estimation, hypothesis testing in molecular phylogenetics and evolution, coalescent models and inference from population data. This course will next be held in May 2017.
EMBO Practical Course on Computational Molecular Evolution
This fantastic graduate course is held on even years at the beautiful beach-side Hellenic Centre for Marine Research in Crete, Greece. The course is organized by Nick Goldman, Antonis Magoulas, Alexandros Stamatakis, and Ziheng Yang, with a comprehensive curriculum covering the statistical analysis of molecular sequence data sampled both different species (phylogenetics) and from different individuals of the same species (population genetics). An amazing faculty of international experts cover a range of topics in computational molecular evolution, including genomic informatics, sequence alignment, Markov models of sequence evolution, phylogeny and divergence-time estimation, hypothesis testing in molecular phylogenetics and evolution, coalescent models and inference from population data. This course will next be held in May 2018.
Short course on Bayesian inference of phylogeny using RevBayes
Mike May and I will offer a short, five-day intensive workshop introducing the theory and application of Bayesian inference of phylogeny using RevBayes. This course is intended for graduate students and postdocs, and will take place at UC Davis from June 11–15, 2016. Each day will include a lecture component and a practical component. The lectures will run from 9AM to noon, where I will introduce statistical phylogenetics, basic probability theory, CTMC models, Bayesian inference, MCMC algorithms, and model comparison. The practicals will run from 1:30PM to 5:00PM, where Mike will lead tutorials demonstrating how to perform analyses using the new program, RevBayes. Additional information is available on the course web page.