Introduction to eco-phylogenetics and comparative analyses using R (ECPH01R)
7th February 2025
£400.00
Course Format
Pre Recorded
About This Course
In this five day course, we provide an introduction to eco-phylogenetics and comparative analyses using R. We begin by providing an overview on the use of phylogenies as a tool for evolutionary biologists and modern techniques to deal with large phylogenies and to incorporate phylogenetic uncertainty in the analyses (day 1). We then cover some of the most relevant eco-phylogenetic analyses and provide examples from the community to themacro-ecological scale (day 2-3). Finally, we introduce a diversity of classic and modern phylogenetic comparative methods to consider the historical relationship of lineages in eco-evolutionary research, including models of trait evolution, analysis of clade diversification and the use of phylogenies in spatial distribution models among others (day 4-5).
Intended Audiences
Course Details
Duration – Approx. 30 hours
ECT’s – Equal to 3ECT’s
Language – English
Teaching Format
The course will take place online using Zoom. On each day, the live video broadcasts will
occur between (UK local time) at:
• 8:00am-10:00am
• 11:00pm-13:00pm
• 14:30pm-16:30pm
All sessions will be video recorded and made available to all attendees.
Assumed quantative knowledge
Assumed computer background
Equipment and software requirements
A laptop computer with a working version of R or RStudio is required. R and RStudio are both available as free and open source software for PCs, Macs, and Linux computers. R may be downloaded by following the links here https://www.r-project.org/. RStudio may be downloaded by following the links here: https://www.rstudio.com/.
All the R packages that we will use in this course will be possible to download and install during the workshop itself as and when they are needed, and a full list of required packages will be made available to all attendees prior to the course.
A working webcam is desirable for enhanced interactivity during the live sessions, we encourage attendees to keep their cameras on during live zoom sessions.
Although not strictly required, using a large monitor or preferably even a second monitor will improve he learning experience
PLEASE READ – CANCELLATION POLICY
Cancellations/refunds are accepted as long as the course materials have not been accessed,.
There is a 20% cancellation fee to cover administration and possible bank fess.
If you need to discuss cancelling please contact oliverhooker@prstatistics.com.
If you are unsure about course suitability, please get in touch by email to find out more oliverhooker@prstatistics.com
COURSE PROGRAMME
Day 1
• Introduction and a brief phylogenetic primer. Basic terminology for non- phylogeneticists, phylogenetic inference (quick overview), phylogenies aevolutionary hypotheses.
• Working with phylogenies. Newick format and structure of the R phylo object. Elementary operations on phylogenies (pruning, resolving polytomies, sticking species). Visualizing large phylogenies.
• Building purpose-specific mega-trees from extant trees and incorporating phylogenetic uncertainty. Software phylocom, V.PhyloMaker, SUNPLIN and randtip R package.
Day 2
• Introduction to the eco-phylogenetic framework, classical conception and posterior modifications.
• Phylogenetic alpha diversity (how much? how different? how regular?). Community data matrices, null models, applications to biodiversity conservation.
• Phylogenetic beta diversity. The turnover and nestedness component of beta diversity.
Day 3
• Incorporating the exact branching pattern of phylogenies into eco-phylogenetic analyses.
• Spatial phylogenetics. RPD, RPE and CANEPE analysis.
• Overview of functional trait ecology. Functional richness, evenness and divergence.Community weighted means.
• Phylogenetic imputation of trait datasets. Bounding prediction uncertainty using evolutionary models. Phylogenies as a null model in ecology
Day 4
- The phylogenetic comparative method, from independent contrasts to sophisticated modelling.
- Analyses of phylogenetic signal and models of evolution: rationale, common- practice, and new trends.
- Correlated evolution and ancestral trait reconstruction.
- Analyses of diversification, speciation and extinction rates in a geographic context.
Day 5
- The need to account for phylogenetic relationships in models.
- Most common phylogenetic modelling approaches: PGLS, PGLMM, BayesianPMM.
- Putting phylogenies in the geography: how to combine phylogenies with species distribution models.
Course Instructor
Rafael Molina Venegas
Works at: Universidad Autónoma de Madrid
Teaches: Introduction to eco-phylogenetics and comparative analyses using R
The scientific career of Rafael Molina Venegas revolves around three research lines pertaining to (1) the ecological and evolutionary mechanisms that jointly shape species assemblages at the community and macroecological scales, (2) the development, improvement, and assessment of phylogenetic methods, and (3) the links between biodiversity and human well-being. While these lines represent clearly differentiated research interests, phylogenetics is a cross-cutting background for all of them. Considering that plants are his true passion in science, he defines himself as a Phylogenetic Plant Ecologist.