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Header of the course Disentangling Evolutionary Relationships with Phylogenetic Comparative Methods - 3rd Edition


Organising committee









PLEASE NOTE: Next edition for this course will be held in 2016. If you want to receive information once the registration is open, please subscribe without any obligation by selecting the topic Evolution.


Disentangling Evolutionary Relationships with Phylogenetic Comparative Methods
This course will provide an introduction to phylogenetic comparative methods (PCM) focusing on Phylogenetic Generalized Least Squares (PGLS) and introducing Phylogenetic Path Analysis methods. PCMs provide a means of incorporating information about the evolutionary relationships of organisms (phylogeny) in statistical analyses. Phylogenetic generalized least squares (PGLS) is a generalized case of the more widely known Independent Contrasts (IC) method. It offers some important advantages over IC, including: Greater flexibility with respect to the model of evolution; traits being able to be modelled as evolving via a Brownian motion model or an Ornstein Uhlenbeck model; the ability to incorporate discrete traits in analyses; and the fact that the intercept is not forced to be 0. Phylogenetic Path Analysis allows researchers to analyse indirect relationships between traits and the directionality of linear relationships between traits accounting for non-independence of data due to phylogenetic relatedness. To enhance the practical approach of the course, participants are encouraged to bring their own data to conduct analyses and discuss the results.


Dr. Alejandro González-Voyer instructor at Transmitting Science
Dr. Alejandro González-Voyer

(Estación Biológica de Doñana – CSIC, Spain).
Dr. Achaz von Hardenberg instructor at Transmitting Science
Dr. Achaz von Hardenberg
(Alpine Wildlife Research Centre, Parco Nazionale Gran Paradiso, Italy).

Organising committee:

Dr. Soledad De Esteban-Trivigno course coordinator at Transmitting Science
Dr. Soledad De Esteban-Trivigno

(Transmitting Science, Spain).
Dr. Jesús Marugán-Lobón course coordinator at Transmitting Science
Jesús Marugán-Lobón

(Universidad Autónoma de Madrid, Spain).


Graduate or postgraduate degree in Biological Sciences, basic knowledge of statistics and personal computers. All participants must bring their own personal laptop (Windows, Macintosh, Linux). Good knowledge of R, or mandatory participation in the one-day introduction to R offered the first day of the course.




1st Day (Optional).

0. Introduction to R.

    • What is R and where to start with R.
    • R Packages.
    • Basics of the R language.
    • How to load data into R.
    • Handling data in dataframes.
    • Introduction to graphics in R.
    • Simple Regression models.
    • Regression models with correlated errors (GLS).
    • Using scripts and writing your own functions.





 2nd Day.

- Morning:

1. Introduction: What are Phylogenetic Comparative Methods (PCMs)?

    • Brief introduction to PCMs, overview of different approaches, and questions that can be addressed.
    • Phylogenetic relationships and non-independence of data points.
    • Data for comparative analyses: Bias and error.
    • Evolution of phenotypic traits: The Brownian motion and Ornstein-Uhlenbeck models models.
    • Phylogenetic independent contrasts (PIC).
    • Assumptions and tests of assumptions.

- Afternoon:

2. Introduction to phylogenetic comparative analyses in R and APE (Analyses of Phylogenetics and Evolution).

    • Reading phylogenies with APE.
    • Plotting trees.
    • Associating species data to the phylogeny.
    • Cropping phylogenies.
    • Phylogenetic independent contrasts (PIC).
    • Testing the assumptions.
    • Analyses with PIC.

3rd Day.

- Morning:

3. Phylogenetic Generalized Least Squares (PGLS).

    • PGLS method.
    • PIC vs. PGLS.
    • Continuous data and categorical traits.
    • Advantages of PGLS over PIC.
    • Models of trait evolution (Brownian motion and Ornstein-Uhlenbeck model).
    • Measurement error and phylogenetic signal.
    • The seven deadly sins of comparative analyses.
    • Examples.

- Afternoon:

4. PGLS in R.

    • PGLS.
    • Models of evolution and covariance matrices.
    • Phylogenetic signal in linear models.
    • Assumptions of PGLS.
    • Interpretation of the results.


4th Day.

- Morning:

5. Phylogenetic confirmatory Path Analysis (PPA).

    • Correlation and Causation.
    • Classical Path Analysis.
    • Directed Acyclic Graphs (DAGs).
    • The d-sep test method.
    • Phylogenetic confirmatory Path Analysis (PPA).
    • Model selection.
    • Examples.

- Afternoon:

6. PPA in practice using R.

    • Integrating the d-sep test with PGLS.
    • The six steps of the d-sep method.
    • Fisher’s C statistic.
    • The C statistic Information Criterion (CIC).
    • Model selection and model averaging in practice.


 5th Day.

Supervised practical session with students’ data or an exercise provided by the teachers.


You will find below some testimonials from former participants to previous editions of this course:

Roi Maor former participant at Transmitting Science“I really feel that apart from being fun and funny the course was very helpful. I gained essential knowledge, understanding and skills that will surely serve my studies in the future, as well as great new ideas that the course has given me.”
Roi Maor, Tel Aviv University, Israel (2nd Edition).


Diego Gil former participant at Transmitting Science“Extremely useful introduction to PGLS in the R environment, and hugely enjoyable course as far as atmosphere, organisation and food are concerned!”
Diego Gil, Museo Nacional de Ciencias Naturales – CSIC, Spain (2nd Edition).



Transmitting Science Avatar“It was overall a great course! Thanks a lot!”
Participants’ comment in the course evaluation (2nd Edition).



Transmitting Science Avatar“I enjoyed the course a lot, thanks.”
Participants’ comment in the course evaluation (2nd Edition).



Dr. H. Christoph Liedtke former participant at Transmitting Science“I attended the course in March 2012 and I couldn’t recommend it more! This was my first course in comparative methods and it has really kick-started my enthusiasm for R, phylogenetics and studying trait evolution. The course was well planned and the material covered was clearly presented and very current. The size and organisation of the course meant that Alejandro González-Voyer, the course instructor, could really provide a very personal experience.”
Dr. H. Christoph Liedtke, University of Basel, Switzerland (1st Edition).

Transmitting Science Avatar“Everything was fine, I think is the best course I have ever taken (and I have taken many). Probably, one of the reasons was the teacher, who was really clear and had a fantastic balance between theory and practice. The group of people was also very nice, and organisation was really efficient.”
Participants’ comment in the course evaluation (1st Edition).


Transmitting Science Avatar“I really liked the course and it was totally worth for me to attend.”
Participants’ comment in the course evaluation (1st Edition)



More Testimonials.


For further information contact: courses@transmittingscience.org.


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