Lead by Isabel Sanmartin (Royal Botanical Garden, CSIC, Madrid)

Maximum of 20 participants.

About the workshop: Alfred Russell Wallace and Charles Darwin founded the field of phylogenetic biogeography on the concept that the branching order of lineages in a phylogeny contain information about their geographic origins. Biogeography is the study of organism diversity and distributions through space and geological time. It spans such disciplines as systematics, paleontology, geology, ecology and evolution. In my introductory lecture, I will cover central concepts in the development of phylogenetic biogeography, from cladistic and parsimony-based approaches such as dispersal-vicariance analysis, to parametric, probabilistic approaches based on Markov chain processes that allow integrating temporal information and geological scenarios of area connectivity through time.

The workshop will also provide an introduction to the open software RevBayes, an R-like interactive environment based on graphic model concepts for the modeling of evolutionary problems. There is no need of previous knowledge on programming or R. The student will learn the basics of how to set up a simple biogeographic analysis using the program, ad then proceed to set up more complex biogeographic models, stepping-stone, directional dispersal models and time-stratified models, based on the popular Dispersal-Extinction-Cladogenesis (DEC) model. I will also introduce geographic-dependent diversification models (GeoSSE), in which speciation and extinction rates are tied to the species geographic range and the rate of dispersal.

Objectives: The student would understand the basic concepts of phylogenetic biogeography, including the processes of dispersal, vicariance, duplication and extinction, why parsimony is limited to tree topology and the meaning of branch lengths in biogeography. The student will learn how Bayesian inference works and the rudiments of Markov chain Monte Carlo. Finally, the student will learn how to set up a biogeographic problem in RevBayes, starting from area definition, to introducing area connectivity and distance-dependence, etc.

The workshop will consist on lectures in the morning and hands-on, computer sessions in the afternoon. Lectures and computer sessions will be tightly linked.

Day One

Morning: L, Background, terms, concepts; Limitations of parsimony-based biogeography: Dispersal-Vicariance Analysis.

Introduction to Parametric, probabilistic biogeography. The Dispersal-Extinction-Cladogenesis Model.

Afternoon: L, P, Installing and using RevBayes. Setting up a simple DEC biogeographic analysis in RevBayes. Setting up more complex, time-stratified DEC models integrating geological information, distance, etc.

Day Two

Morning: L, Biogeographic diversification models that tie speciation and extinction rates to range evolution or paleoenvironmental variables.

Afternoon: P, Setting up a biogeographic-dependent diversification model in RevBayes (GeoSSE). Setting up a paleoenvironmental diversification model.