ONLINE COURSE -Introduction to eco-phylogenetics and comparative analyses using R (ECPH01) This course will be delivered live
7th February 2022 - 11th February 2022£500.00
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).
This course is aimed at anyone who wishes to introduce into phylogenetic ecology and comparative analyses.
Venue – Delivered remotely
Availability – 30 places
Duration – 5 days
Contact hours – Approx. 35 hours
ECT’s – Equal to 3 ECT’s
Language – English
PLEASE READ – CANCELLATION POLICY: Cancellations are accepted up to 28 days before the course start date subject to a 25% cancellation fee. Cancellations later than this may be considered, contact email@example.com. Failure to attend will result in the full cost of the course being charged.
Dr Rafael Molina Venegas
Teaches – Phylogenetic comparative methods (PGCM01)
Rafael Molina Venegas is an evolutionary plant ecologist interested in the ecological and evolutionary mechanisms that jointly shape assemblages at the community and macroecological scales. He uses phylogenetic methods along with functional trait information to get insight on such processes, and further explores bridges between fundamental biodiversity research and conservation planning in species-rich biomes such as the Mediterranean and the tropics. He is also interested in understanding the links between plant biodiversity and human well-being, with a particular focus on the role that evolution pays in this relationship.Personal web: http://rafmolven.wixsite.com/rafmolven
Dr Ignacio Morales Castilla
Teaches – Phylogenetic comparative methods (PGCM01)
Ignacio Morales Castilla is an evolutionary ecologist interested in disentangling the eco-evolutionary drivers of community structure, understanding how different aspects of the species’ niches are evolutionarily conserved and integrating phylogenetic, functional and geographic information to enhance models of biotic interactions and species distributions. Ultimately, he aims at predicting species and ecosystem vulnerability to global change.Personal web: https://moralescastilla.github.io
The course will be hands-on and workshop based. Throughout each day, there will be some introductory remarks for each new topic, introducing and explaining key concepts.
The course will take place online using Zoom. On each day, the live video broadcasts will
occur between (UK local time) at:
All sessions will be video recorded and made available to all attendees.
Attendees in different time zones will be able to join into some of these live broadcasts, even if all of them are not convenient times.
By joining any live sessions that are possible, this will allow attendees to benefit Fromm asking questions and having discussions, rather than just watching prerecorded sessions. All the sessions will be video recorded, and made available immediately on a private video hosting website. Any materials, such as slides, data sets, etc., will be shared with the attendees.
Assumed quantitative knowledge
We will assume general familiarity with the very basics of statistics (e.g. summary statistics, distributions). As this is an introductory course, no phylogenetic background is required.
Assumed computer background
We will assume general familiarity with R elementary operations (e.g. package sourcing, data importing and exporting, object indexing) and some familiarity with programming in R (writing code).
Equipment and software requirements
Attendees of the course must use a computer with R/RStudio installed, as well as the necessary additional R packages. Instructions on how to install the software will be provided before the start of the course. R and RStudio are supported by both PC and MAC and can be downloaded for free by following these links.
UNSURE ABOUT SUITABLILITY THEN PLEASE ASK firstname.lastname@example.org
Monday 7th – Classes from 08:00 to 16:30
• 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.
Tuesday 8th – Classes from 08:00 to 16:30
• 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.
Wednesday 9th – Classes from 08:00 to 16:30
• 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.
Thursday 10th from 08:00 to 16:30
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.
Friday 11th – Classes from 08:00 to 16:30
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.