Phylogenetic analyses are central for understanding the ecological and evolutionary processes shaping present-day biodiversity patterns.
In this course participants will learn phylogenetic analyses with the RPANDA R package. They will also have a quick introduction to Julia and to the jPANDA Julia package.
The RPANDA package contains tools for macroevolutionary analyses on phylogenetic trees, in particular for the analysis of diversification and trait evolution from comparative data.
The instructors will introduce the theory behind these analyses, run practicals with illustrative examples, and guide the interpretation of the output of these analyses.
This workshop is primarily intended for (but is not exclusive to) graduate students and postdocs. Participants are encouraged to bring their own phylogenetic datasets (with potentially matching trait, biogeographic and paleoenvironmental datasets).
Graduate or postgraduate degree in Life or Earth Sciences. Basic knowledge of phylogenetics and R at user level is need it to follow the course.
Participants must have a personal computer (Windows, Mac, Linux). The use of a webcam and headphones is strongly recommended, and a good internet connection.
Click here to see the full program
Session 1 (Sophia Lambert & Hélène Morlon):
- Introduction to birth-death models and their use for estimating speciation and extinction dynamics from extant phylogenies
- Running and interpreting constant & time-dependent diversification models
- Optional: estimating diversity-through-time
Session 2 (Fabien Condamine & Hélène Morlon):
- Introduction to environment-dependent diversification models for testing if and how past environmental changes influenced diversification rates
- Running and interpreting environment-dependent diversification models
- Testing for diversification rate shifts using RPANDA
Session 3 (Ignacio Quintero & Hélène Morlon):
- Introduction to the Cladogenetic Diversification rate Shift (ClaDS) model for estimating branch-specific diversification rates
- Introduction to Julia
- Running and interpreting ClaDS using jPANDA
Session 4 (Julien Clavel & Hélène Morlon):
- Introduction to trait evolution models and their use for testing hypotheses on the mode and tempo of trait evolution
- Introduction to environment-dependent trait evolution models for testing if and how past environmental changes influenced rates of trait evolution
- Running and interpreting environment-dependent trait evolution models
Session 5 (Jonathan Drury & Hélène Morlon):
- Introduction to the trait matching competition model and its use for testing hypotheses on the role of competition in shaping trait evolution
- Running and interpreting the matching competition model
- Introduction to the matching competition birth-death model
Session 6 (Benoit Perez-Lamarque & Hélène Morlon):
- Introduction to the BipartiteEvol model for modeling the eco-evolutionary emergence of bipartite interaction networks.
- Running simulations with BipartiteEvol
- Testing for phylogenetic signal in species interactions
- Introduction to non-parametric analyses of phylogenetric trees (spectral density profiles) and their utility
- Running and interpreting spectral density analyses