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ONLINE COURSE – An Introduction to Spatial Eco-Phylogenetics and Comparative Methods (SECM01) This course will be delivered live
19 March 2024 - 22 March 2024
£350.00
Event Date
Tuesday, March 19th, 2024
COURSE FORMAT
This is a ‘LIVE COURSE’ – the instructor will be delivering lectures and coaching attendees through the accompanying computer practical’s via video link, a good internet connection is essential.
COURSE PROGRAM
TIME ZONE – CET (Central European Time) – however all sessions will be recorded and made available allowing attendees from different time zones to follow.
Please email oliverhooker@prstatistics.com for full details or to discuss how we can accommodate you).
About This Course
In this course we introduce phylogenetic analyses in a spatial context. Phylogenetic analyses often imply a high number of species for which phylogenetic information is unavailable, hence we begin by providing an overview on modern techniques to incorporate phylogenetic uncertainty in the analyses (day 1). We then cover the most popular analyses in the spatial phylogenetics discipline (day 2), with particular focus on the canonical analysis of neo- and paleo-endemism (CANAPE). The second part of the course will be devoted to integrating phylogenetic information into models of geographic distribution of species (day 3), followed by an overview of recent advances to improve ecological forecasts using phylogenetic mixed models in a Bayesian framework (day 4).
By the end of the course, participants should:
- Know how to expand incomplete phylogenies based on taxonomic information and customizing simulation parameters for optimal expansion.
- Understand the metrics and concepts used in spatial phylogenetics (i.e. phylogenetic alpha and beta diversity, phylogenetic endemism), interpret them critically, and assess pros and cons of analytical techniques.
- Calculate phylogenetic predictors that can be included as covariates in Species Distribution or Niche Models.
- Understand and implement the phylogenetic mixed model (PMM) and translate its predictions into a spatial context.
Intended Audiences
This course is aimed at anyone who wishes to introduce into spatial phylogenetics and comparative analyses (in general and within a spatial context in particular)
Course Details
Venue – Delivered remotely
Availability – 30 places
Duration – 5 days
Contact hours – Approx. 35 hours
ECT’s – Equal to 3 ECT’s
Language – English
Teaching Format
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.
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 quantative 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
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.
Participants should be able to install additional software on their own computer during the course (please make sure you have administration rights to your computer).
A large monitor and a second screen, although not absolutely necessary, could improve the learning experience. Participants are also encouraged to keep their webcam active to increase the interaction with the instructor and other students.
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 oliverhooker@prstatistics.com. Failure to attend will result in the full cost of the course being charged. In the unfortunate event that a course is cancelled due to unforeseen circumstances a full refund of the course fees will be credited.
If you are unsure about course suitability, please get in touch by email to find out more 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
Tuesday 19th
Classes from 8:00 to 13:00 CET
DAY 1
Expansion of molecular trees using taxonomic information and fundamental metrics of phylogenetic structure
- Software for tree expansion exercises; randtip, PhyloMaker
- An overview of the fundamental metrics of phylogenetic structure. Null models.
Wednesday 20th
Classes from 8:00 to 13:00 CET
DAY 2
Spatial Phylogenetics
- Canonical analysis of neo- and paleo- endemism. Metrics, rationale, workflow, and implementation.
Thursday 21st
Classes from 8:00 to 13:00 CET
DAY 3
Phylogenetic Species Distribution Models
- Putting phylogenies in the geography: the imprints of evolutionary relationships in distribution models.
- Combining phylogenies with co-occurrence to infer spatial phylogenetic predictors.
- Fitting, evaluating and interpreting Phylogenetic-SDMs.
Friday 22nd
Classes from 8:00 to 13:00 CET
DAY 4
Beyond PGLS – Bayes and more
- Most common phylogenetic modelling approaches: PGLS
- PGLMM
- The phylogenetic mixed model (PMM) in a Bayesian framework
Course Instructor
Dr. Rafael Molina Venegas
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. I personal page can be found here
Course Instructor
Dr. Morales Castilla Ignacio
Dr. Morales-Castilla is a biogeographer and macroecologist interested in the spatial-temporal distribution of biodiversity. His research program aims to: (1) disentangle the relative roles of evolution and ecology as drivers of community structure, (2) understand how different aspects of the species’ niches are evolutionarily conserved and, (3) enhance models of biotic interactions and/or species distributions by integrating phylogenetic, functional and geographic information. You can check his publication record at the links provided above. You can find hiss homepage here