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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

ONLINE COURSE -Introduction to eco-phylogenetics and comparative analyses using R (ECPH01) This course will be delivered live
Event Date

Wednesday, April 13th, 2022

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

This course is aimed at anyone who wishes to introduce into phylogenetic ecology and comparative analyses.

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.

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.

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.

Download RStudio



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



Monday 7th

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.


Tuesday 8th

• 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

• 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
  • 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
  • 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


Dr. Mark Andrews

Coming Soon


7 February 2022
11 February 2022
Event Category:


Delivered remotely (United Kingdom)
Western European Time Zone, United Kingdom + Google Map