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ONLINE COURSE -Introduction to eco-phylogenetics and comparative analyses using R (ECPH01) This course will be delivered live
7 February 2022 - 11 February 2022
Wednesday, April 13th, 2022
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).
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
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 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
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.
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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 email@example.com.
If you are unsure about course suitability, please get in touch by email to find out more firstname.lastname@example.org
Classes from 8:00 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.
• 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.
• 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
- 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.
- 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.