Introduction to eco-phylogenetics and comparative analyses using R (ECPH01

oliver-hookerOliver Hooker
  • 29 Jul

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

22 September 2021 - 28 September 2021

TIME ZONE – UK local time (GMT+0) – however all sessions will be recorded and made available allowing attendees from different time
zones to follow a day behind with an additional 1/2 days support after the official course finish date (please email for full details or to discuss how we can accommodate you).

Course Overview:

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).


Dr. Rafael Molina Venegas
Dr. Ignacio Morales Castilla

Course Programme

Wednesday 22nd – 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.

Thursday 23rd – 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.

Friday 24th – 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.

Monday 27th 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.

Tuesday 28th – 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.


Missing Data Analytics (MDAR01)
8 September 2021 - 10 September 2021

Functional ecology from organism to ecosystem: theory and computation (FEER02)
13 September 2021 - 17 September 2021

Meta-analysis in ecology, evolution and environmental sciences (METR02)
13 September 2021 - 17 September 2021

Species Distribution Modeling using R (SDMR04)
21 September 2021 - 30 September 2021

Phylogenetic comparative methods (PGCM01)
22 September 2021 - 28 September 2021

Multivariate analysis of ecological communities in R with the VEGAN package (VGNR03)
4 October 2021 - 8 October

Introduction to Data Wrangling and Data Visualization using R (DWDV01)
4 October 2021 - 8 October 2021

Introduction to Bayesian modelling with INLA (BMIN02)
4 October 2021 - 8 October 2021

Landscape genetic data analysis using R (LNDG05)
18 October 2021 - 27 October 2021

Species distribution modelling with Bayesian statistics in R (SDMB03)
6 December 2021 - 10 December 2021

Time Series Data Analysis (TSDA01)
14 December 2021 - 17 December 2021

Bayesian Data Analysis (BADA01)
10th January 2022 - 14th January 2022

Stable Isotope Mixing Models using SIBER, SIAR, MixSIAR (SIMM08)
1st February 2022 - 4th February 2022