To foster international participation, this course will be held online

Phylogenetic comparative methods have now become both standard and necessary of many studies in fields as disparate as systematics, paleontology, ecology, behavior, anatomy and physiology. As many of these methods rely on the availability of ultrametric (time-calibrated) phylogenies, this course will introduce students, researchers and professionals to the theoretical and practical aspects of generating ultrametric trees, reconstructing trait evolution and investigating rates of lineage diversification. It will consist of both lectures to cover theory, as well as practical tutorials.

The course is aimed at advanced undergraduate students, graduate students, researchers and professionals interested in learning how to generate or interpret correctly ultrametric phylogenies ("chronograms or timetrees"), and how to use these trees with phylogenetic comparative methods to investigate both trait and lineage evolution.

This is not an introductory course on molecular evolution and phylogenetics, and will not cover aspects such as sequence generation, alignments, and inference other than Bayesian time-calibration. Students will thus be expected to have a basic knowledge of molecular evolution (a reading list of refresher literature can be made available to students before the course). Many of the hands-on practical exercises will require the use of packages running in R; for this reason some familiarity with R will be advantageous, even though the instructors will show how to set up R scripts to run the necessary programs.

The course is structured in modules over five days. Each day will include an introductory lecture with class discussion of key concepts. The remainder of each day will consist of practical hands-on sessions. These sessions will involve a combination of both mirroring exercises with the instructor to demonstrate a skill as well as applying these skills on your own to complete individual exercises. After and during each exercise, interpretation of results will be discussed as a group. Students will be provided with previously published datasets that have been selected to highlight some of the complexities of various types of methods and analyses, as well as to reproduce the type of dataset that they migh use in their own research. Students are also encouraged to bring their own dataset in case they want to seek input from the instructors on how to set up analyses of their own data

Monday - Classes from 2 to 8 pm Berlin time

✔ Introduction to the use of phylogeny in comparative methods (lecture)
✔ Likelihood and bayesian inference methods (lecture)
✔ Molecular clocks (lecture)
✔ Node dating relaxed clocks using Beast (tutorial)

Tuesday - Classes from 2 to 8 pm Berlin time

✔ Total-evidence dating using Beast (tutorial)
✔ Dating analyses using morphological/paleontological data (tutorial)
✔ Using remote servers for phylogenetic analyses (tutorial)
✔ Introduction to R for comparative methods (lecture)
✔ How to read, visualize and manipulate phylogenies and trait data in R

Wednesday - Classes from 2 to 8 pm Berlin time

✔ Evolution of phenotypic traits (lecture)
✔ Models or continuous and discrete traits evolution. Brownian motion and OU models (tutorial)
✔ Ancestral characters reconstructions (tutorial)
✔ Phylogenetic independent constrast, contrast regression, phylogenetic PCA (tutorial)

Thursday - Classes from 2 to 8 pm Berlin time

✔ Tree shape and lineage diversifications through time, adaptive radiations and key innovations (lecture))
✔ Models of diversification (tutorial)
✔ Using time-calibrated phylogenies to detect mass extinctions

Friday - Classes from 2 to 8 pm Berlin time

✔ Historical biogeography (lecture)
✔ BioGeoBear (tutorial)
✔ Troubleshooting analyses (lecture + tutorial)
✔ Extra tutorials to cover previously discussed topics (at request of students)
✔ Students can work on own data

Cancellation Policy:

> 30  days before the start date = 30% cancellation fee

< 30 days before the start date= No Refund.

Physalia-courses cannot be held responsible for any travel fees, accommodation or other expenses incurred to you as a result of the cancellation.