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ECPHPR

Introduction to eco-phylogenetics and comparative analyses using R

Ideal for researchers studying trait evolution, biodiversity patterns, and community structure.

  • Duration: 30 hours
  • Format: Recorded ‘on-demand’ Format

£450Registration Fee

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5.0

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  • Overview
  • Instructors
  • Schedule

Course Description

This 30 hour course provides an introduction to eco-phylogenetics andcomparative 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. We then cover some of the most relevant eco-phylogenetic analyses and provide examples from the community to themacro-ecological scale. 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.

What You’ll Learn

During the course will cover the following:

  • Explain the basic principles of phylogenetics, including terminology, inference methods, and the interpretation of phylogenies as evolutionary hypotheses.
  • Work with phylogenetic data in R, including importing Newick files, manipulating phylo objects, pruning and modifying trees, and visualising large phylogenies.
  • Construct customised mega-trees using available software and R packages (e.g. phylocom, V.PhyloMaker, SUNPLIN, randtip), and incorporate phylogenetic uncertainty into analyses.
  • Apply the eco-phylogenetic framework to explore community assembly processes, and calculate measures of phylogenetic alpha and beta diversity, including null models for biodiversity conservation.
  • Incorporate branching patterns into eco-phylogenetic analyses, and apply spatial phylogenetic approaches such as RPD, RPE, and CANEPE.
  • Integrate functional trait data with phylogenies, including analyses of functional diversity, community weighted means, and trait imputation while accounting for evolutionary uncertainty.

    • <li Use phylogenetic comparative methods (from independent contrasts to advanced modelling) to assess phylogenetic signal, models of evolution, and correlated trait evolution, including ancestral state reconstruction.

  • Analyse diversification processes, including speciation and extinction rates in ecological and geographic contexts, and interpret their implications for biodiversity patterns.

Course Format

Flexible Learning Structure

Learn through a carefully structured mix of lecture recordings and guided exercises that you can pause, revisit, and complete at your own pace—ideal for busy professionals or those balancing multiple commitments.

Access Anytime, Anywhere

All course content is available on-demand, making it accessible across all time zones without the need to attend live sessions or adjust your schedule.

Independent Exploration with Support

Engage deeply with course topics through self-directed study, with the option to reach out to instructors via email for clarification or deeper discussion.

Comprehensive Learning Resources

Gain full access to the same high-quality materials provided in live sessions, including code, datasets, and presentation slides—all available to download and keep. Please note recordings can only be streamed.

Work With Your Own Data, On Your Terms

Apply what you learn directly to your own data projects as you go, allowing for a personalized and immediately practical learning experience.

Continued Guidance and Resource Access

Receive 30 days of post-enrolment email support and unrestricted access to all session recordings during that time, so you can review and reinforce your learning as needed.

Who Should Attend / Intended Audiences

This course is aimed at anyone wishing to gain an introduction to phylogenetic ecology and comparative analyses. No prior background in phylogenetics is required, and only a general familiarity with basic statistics (e.g. summary statistics, distributions) is assumed. Participants should also be comfortable with elementary R operations such as sourcing packages, importing and exporting data, and indexing objects, as well as having some basic experience with writing R code.

Equipment and Software requirements

A laptop or desktop computer with a functioning installation of R and RStudio is required. Both R and RStudio are free, open-source programs compatible with Windows, macOS, and Linux systems.

While not essential, using a large monitor—or ideally a dual-monitor setup—can significantly enhance your learning experience by allowing you to view course materials and work in R simultaneously.

All necessary R packages will be introduced and installed during the workshop.

Download R Download RStudio Download Zoom

Dr. Ignacio Morales-Castilla

Dr. Ignacio Morales-Castilla

Ignacio is a biogeographer and macroecologist whose research focuses on the spatial and temporal distribution of biodiversity. His work integrates ecological, evolutionary, and biogeographical perspectives to better understand how species assemble into communities and how biodiversity patterns emerge across scales. His research program aims to: (1) disentangle the relative roles of evolution and ecology as drivers of community structure, (2) investigate how different aspects of species’ niches are evolutionarily conserved, and (3) improve models of biotic interactions and species distributions by incorporating phylogenetic, functional, and geographic information.

 

Education & Career
• PhD in Ecology from the University of Alcalá (Universidad de Alcalá), Alcalá de Henares, Spain.
• Affiliated with the the GloCEE – Global Change Ecology and Evolution Group, in the Department of Life Sciences at the Universidad de Alcalá, Alcalá de Henares, Spain, where hue is a is currently a Beatriz Galindo Fellow.

 

Research Focus
Ignacio’s work centres on:
• Disentangling ecological and evolutionary processes that shape community structure
• Niche evolution and the degree of evolutionary conservatism across traits and taxa
• Integrating phylogenetic and functional data into species distribution models
• Advancing models of biotic interactions and biodiversity under global change

 

Current Projects
• Developing integrative models of species distributions that account for evolutionary history and functional traits
• Exploring the role of evolutionary constraints in shaping biodiversity patterns across large spatial and temporal scales
• Assessing biodiversity responses to global change by linking ecology, evolution, and biogeography

 

Professional Consultancy & Teaching
Ignacio contributes expertise in macroecology, biodiversity modelling, and biogeography to interdisciplinary projects. He trains students and researchers in phylogenetic and functional approaches to ecology, and is engaged in advancing reproducible, open science practices within biodiversity research.

 

Links
• ResearchGate
• ORCID
• University Profile
• Personal Site
• GitHub

Dr. Rafael Molina Venegas

Dr. Rafael Molina Venegas

Rafael is a phylogenetic plant ecologist whose research sits at the intersection of community ecology, macroecology, phylogenetics, and human well-being. His scientific career revolves around three interconnected themes: (1) understanding the ecological and evolutionary mechanisms that jointly shape species assemblages at both community and macroecological scales, (2) the development, improvement, and critical assessment of phylogenetic methods, and (3) exploring the links between biodiversity and human well-being. While diverse, these research lines are unified by a strong phylogenetic perspective, with plants as his primary passion and study system.

 

Education & Career
• PhD in Integrative Biology from the Department of Plant Biology and Ecology, Universidad de Sevilla, Spain.
• Affiliated with the GloCEE – Global Change Ecology and Evolution Group, within the Department of Life Sciences at the Universidad de Alcalá, Alcalá de Henares, Spain. Additionally, he holds a position as a researcher at the Estación Biológica de Doñana (CSIC), indicated through institutional listings and Google Scholar affiliation.

 

Research Focus
Rafael’s work centres on:
• Ecological and evolutionary drivers of species assemblages at multiple spatial scales
• Development and refinement of phylogenetic methods for ecology and biodiversity research
• Exploring how biodiversity underpins ecosystem services and human well-being
• Plant phylogenetics as a cross-cutting framework for ecological and evolutionary research

 

Current Projects
• Investigating community assembly and macroecological biodiversity patterns in plants
• Testing and improving methods in comparative phylogenetics and eco-phylogenetics
• Assessing the role of biodiversity and phylogenetic diversity in supporting human well-being and ecosystem services

 

Professional Consultancy & Teaching
Rafael contributes his expertise in phylogenetic ecology and comparative analyses to academic and applied research projects. He also supervises and trains postgraduate students in biodiversity science, macroecology, and phylogenetic methods, and regularly contributes to collaborative, interdisciplinary projects at the interface of ecology, evolution, and conservation.

 

Links
• ResearchGate
• Google Scholar
• University Profile
• Personal Site

Session 1 – 02:20:00 – Introduction and a brief phylogenetic primer.
Basic terminology for non- phylogeneticists, phylogenetic inference (quick overview), phylogenies aevolutionary hypotheses.

Session 2 – 02:20:00 – Working with phylogenies.
Newick format and structure of the R phylo object. Elementary operations on phylogenies (pruning, resolving polytomies, sticking species). Visualizing large phylogenies.

Session 3 – 02:20:00 – Building purpose-specific mega-trees from extant trees and incorporating phylogenetic uncertainty. Software phylocom, V.PhyloMaker, SUNPLIN and randtip R package.

Session 4 – 02:20:00 – Introduction to the eco-phylogenetic framework.
Introduction to the eco-phylogenetic framework classical conception and posterior modifications.

Session 5 – 02:20:00 – Phylogenetic alpha diversity.
How much? How different? How regular?). Community data matrices, null models, applications to biodiversity conservation.

Session 6 – 02:20:00 – Phylogenetic beta diversity.
The turnover and nestedness component of beta diversity.

Session 7 – 01:45:00 – Incorporating the branching patterns.
Incorporating the exact branching pattern of phylogenies into eco-phylogenetic analyses.

Session 8 – 01:45:00 – Spatial phylogenetics.
RPD, RPE and CANEPE analysis.

Session 9 – 01:45:00 – Overview of functional trait ecology.
Functional richness, evenness and divergence.Community weighted means.

Session 10 – 01:45:00 – Phylogenetic imputation of trait datasets.
Bounding prediction uncertainty using evolutionary models. Phylogenies as a null model in ecology

Session 11 – 01:45:00 – The phylogenetic comparative method.
From independent contrasts to sophisticated modelling.

Session 12 – 01:45:00 – Analyses of phylogenetic signal and models of evolution.
Rationale, common practice, and new trends.

Session 13 – 01:45:00 – Correlated evolution.
Ancestral trait reconstruction.

Session 14 – 01:45:00 – Analyses of diversification.
Diversificartion, speciation and extinction rates in a geographic context.

Session 15 – 02:20:00 – Why do we need to account for phylogenetic relationships?
The need to account for phylogenetic relationships in models.

Session 16 – 02:20:00 – Most common phylogenetic modelling approaches.
PGLS, PGLMM, BayesianPMM.

Session 17 – 02:20:00 – Putting phylogenies in the geography.
How to combine phylogenies with species distribution models.

Testimonials

PRStats offers a great lineup of courses on statistical and analytical methods that are super relevant for ecologists and biologists. My lab and I have taken several of their courses—like Bayesian mixing models, time series analysis, and machine/deep learning—and we've found them very informative and directly useful for our work. I often recommend PRStats to my students and colleagues as a great way to brush up on or learn new R-based statistical skills.

Rolando O. Santos

PhD Assistant Professor, Florida International University

Courses attended

SIMM05, IMDL03, ITSA02, GEEE01 and MOVE07

Testimonials

PRStats offers a great lineup of courses on statistical and analytical methods that are super relevant for ecologists and biologists. My lab and I have taken several of their courses—like Bayesian mixing models, time series analysis, and machine/deep learning—and we've found them very informative and directly useful for our work. I often recommend PRStats to my students and colleagues as a great way to brush up on or learn new R-based statistical skills.

Rolando O. Santos

PhD Assistant Professor, Florida International University

Courses attended

SIMM05, IMDL03, ITSA02, GEEE01 and MOVE07

Testimonials

PRStats offers a great lineup of courses on statistical and analytical methods that are super relevant for ecologists and biologists. My lab and I have taken several of their courses—like Bayesian mixing models, time series analysis, and machine/deep learning—and we've found them very informative and directly useful for our work. I often recommend PRStats to my students and colleagues as a great way to brush up on or learn new R-based statistical skills.

Rolando O. Santos

PhD Assistant Professor, Florida International University

Courses attended

SIMM05, IMDL03, ITSA02, GEEE01 and MOVE07

Frequently asked questions

Everything you need to know about the product and billing.

When will I receive instructions on how to join?

You’ll receive an email on the Friday before the course begins, with full instructions on how to join via Zoom. Please ensure you have Zoom installed in advance.

Do I need administrator rights on my computer?

Yes — administrator access is recommended, as you may need to install software during the course. If you don’t have admin rights, please contact us before the course begins and we’ll provide a list of software to install manually.

I’m attending the course live — will I also get access to the session recordings?

Yes. All participants will receive access to the recordings for 30 days after the course ends.

I can’t attend every live session — can I join some sessions live and catch up on others later?

Absolutely. You’re welcome to join the live sessions you can and use the recordings for those you miss. We do encourage attending live if possible, as it gives you the chance to ask questions and interact with the instructor. You’re also welcome to send questions by email after the sessions.

I’m in a different time zone and plan to follow the course via recordings. When will these be available?

We aim to upload recordings on the same day, but occasionally they may be available the following day.

I can’t attend live — how can I ask questions?

You can email the instructor with any questions. For more complex topics, we’re happy to arrange a short Zoom call at a time that works for both of you.

Will I receive a certificate?

Yes. All participants receive a digital certificate of attendance, which includes the course title, number of hours, course dates, and the instructor’s name.

When will I receive instructions on how to join?

You’ll receive an email on the Friday before the course begins, with full instructions on how to join via Zoom. Please ensure you have Zoom installed in advance.

Do I need administrator rights on my computer?

Yes — administrator access is recommended, as you may need to install software during the course. If you don’t have admin rights, please contact us before the course begins and we’ll provide a list of software to install manually.

I’m attending the course live — will I also get access to the session recordings?

Yes. All participants will receive access to the recordings for 30 days after the course ends.

I can’t attend every live session — can I join some sessions live and catch up on others later?

Absolutely. You’re welcome to join the live sessions you can and use the recordings for those you miss. We do encourage attending live if possible, as it gives you the chance to ask questions and interact with the instructor. You’re also welcome to send questions by email after the sessions.

I’m in a different time zone and plan to follow the course via recordings. When will these be available?

We aim to upload recordings on the same day, but occasionally they may be available the following day.

I can’t attend live — how can I ask questions?

You can email the instructor with any questions. For more complex topics, we’re happy to arrange a short Zoom call at a time that works for both of you.

Will I receive a certificate?

Yes. All participants receive a digital certificate of attendance, which includes the course title, number of hours, course dates, and the instructor’s name.

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£450.00
14th July 2035
Recorded, United Kingdom
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