Instructors Organising committee Requirements Language Site Program	Course length Schedule Number of places Fees Accommodation Grants	Contact Organisers Collaborators Registration Form

 

Course Poster

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.



Instructors:

 

Dr. Alejandro González-Voyer (Estación Biológica de Doñana – CSIC, Spain).

Dr. Achaz von Hardenberg (Alpine Wildlife Research Centre, Parco Nazionale Gran Paradiso, Italy).

Organising committee:

 

Dr. Soledad De Esteban-Trivigno (Transmitting Science, Spain).

Dr. Jesús Marugán-Lobón (Universidad Autónoma de Madrid, Spain).

Requirements:

Graduate or postgraduate degree in Biological Sciences, basic knowledge in 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.

Language:

English.

Site:

Els Hostalets de Pierola, Barcelona (Spain). How to arrive.

Program:

1st Day (Optional). - 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.

Course length:

- Five day course (including optional first day of introduction to R): 40 hours on-site.

- Four day course: 32 hours on-site.

Schedule:

Sunday: 18:00: Meeting point in Plaza Catalunya (Barcelona) to take the bus to Els Hostalets de Pierola. If you are planning to arrive later, you can find more information in How to arrive. 19:00: Registration in the Youth Hostel. 20:00: Welcome party at the council. Monday to Friday: 8:30 to 9:00: Breakfast 9:30 to 13:30: Lessons. 13:30 to 15:00: Lunch. 15:00 to 19:00: Lessons. 20:30: Dinner. There will be two coffee breaks each day, halfway through each lesson session.

Saturday: 8:30 to 9:00: Breakfast. 9:30: Meeting point in the Youth Hostel to take the bus to Barcelona city. 13:00: Arrival at Plaza Catalunya (Barcelona).

Number of places:

Places are limited to 20 participants and will be occupied by strict registration order.

Fees:

Accommodation:

The course will take place in the town of Els Hostalets de Pierola, Barcelona (Spain).

- All Inclusive option:
To make it affordable, you will be hosted in four-bed dormitories (common bathrooms), although you will only share rooms with other classmates. The possibility exists that the dormitories will be mixed. Therefore, if this is an inconvenience for you, and you require staying in a dormitory with only women, or only men, please state it in the “Comments” field of the Registration Form (see below).
There are no Hotels in Els Hostalets de Pierola. However, if you do not want to share rooms with other participants, the council offers the possibility of renting a house (no kitchen available). If you want more information regarding this option, please contact us at courses@transmittingscience.org.
How to arrive to Els Hostalets de Pierola.

- Only Lunches Included option (no accommodation, no dinners):
In that case there are different options for accommodation, all of them in places other than Els Hostalets de Pierola. You may stay in: Barcelona city, Martorell or Igualada. Information about Hotels in Martorell here. Information about Hotels in Igualada here.
How to arrive to Els Hostalets de Pierola from Barcelona city, Martorell and Igualada.

Grants:

Unfortunately there are no internal grants available for this course. For information on External Financial Support, please check the link.

Contact:

For further information contact: courses@transmittingscience.org.

Organisers:

Collaborators: