Phylogenetic Analysis Using R
October 14-18, 2019 (Spain)
Evolution
Course Overview
The course provides a comprehensive overview of the state-of-the-art methods in mapping phenotypic trait evolution and will provide participants with a springboard to using these methods to answering their own research questions.
We focus on analyses that use a phylogenetic tree and observed trait information from tip taxa (extant and/or extinct) to describe how traits have changed along the branches of a phylogeny. The course covers methods that estimate and test patterns related to changes in mean, covariation, and rate. Applications for continuous and categorical, and univariate and multivariate research designs are discussed.
At the end of this course, participants will have developed an understanding of:
(1) Brownian motion and Ornstein-Uhlenbeck models of evolution.
(2) How these models can be applied to estimate and test patterns of trait evolution.
(3) What the advantages and disadvantages are of different models/methods.
(4) How to recognize which model/method is most appropriate given a particular dataset and research question.
We provide several data sets that will be used to exemplify the application of these methods. We do, however, encourage participants to bring their own data so as to get direct experience with analysing precisely what they expect to analyse.
Methods from the following R packages will be discussed: ape, geiger, phytools, evomap, l1ou, bayou, surface, OUwie, mvMORPH, geomorph (this list may change as new packages become available).
Important note: Please bear in mind that this course is not about reconstructing (building) phylogenetic trees, the methods we cover in this course assume that a phylogeny is known.
DATE
June 3rd-7th, 2019
LANGUAGE
English
COURSE LENGTH & ECTS
35 hours on-site.
This course is equivalent to 2 ECTS (European Credit Transfer System) at the Life Science Zurich Graduate School.
The recognition of ECTS by other institutions depends on each university or school.
PLACES
Places are limited to 20 participants and will be occupied by strict registration order.
Participants who have completed the course will receive a certificate at the end of it.
Instructors
Dr. Jeroen B. Smaers
Stony Brook University
United States of America
Carrie S. Mongle
Stony Brook University
United States of America
Coordinators
Dr. Soledad De Esteban-Trivigno
Transmitting Science
Spain
Dr. Ana Rosa Gómez-Cano
Transmitting Science
Spain
Requirements
Graduate or postgraduate degree in any Biosciences discipline. Knowledge of multivariate statistics.
A reminder of R-skills that are of particular relevance when applying phylogenetic comparative methods will be given the first day, though a medium level of R knowledge is needed for following the course (i.e. knowledge on how to load and save data, manipulate data frames, use basic plotting functions, and use functions to analyse data).
All participants must bring their own personal laptop (Windows, Macintosh, Linux).
Program
Monday, June 3rd, 2019. (R packages: ape, Geiger).
- Morning: Phylogenetic data.
- What is the basic structure of phylogenetic data?
- How to visualize and manipulate phylogenetic data?
- Afternoon: Models of evolution.
- What are models of evolution?
- What are the assumptions of the different models of evolution?
- How are models of evolution utilized?
Tuesday, June 4th, 2019. (R packages: ape, nlme, caper, evomap).
- Morning: Phylogenetic regression.
- Assumptions, properties, and applications of the phylogenetic regression.
- Afternoon: Phylogenetic ancova.
- Testing for grade shifts using the phylogenetic regression.
Wednesday, June 5th, 2019. (R packages: phytools, motmot, geiger, ape, evomap, BayesTraits).
- Morning: Ancestral estimation.
- Using models of evolution to estimate values of ancestral nodes.
- Afternoon: Analysis of rates of evolution.
- Estimation of rates of evolution.
- Testing hypothesis about rates of evolution.
Thursday, June 6th, 2019. (R packages: bayou, phylolm, surface, OUwie, mvMORPH).
- Morning: Inferring the structure of a macroevolutionary landscape.
- Using Ornstein-Uhlenbeck models to map macroevolutionary patterns.
- Afternoon: Testing the structure of a macroevolutionary landscape.
- Applications and assumptions of OU models.
- Using OU models to test macroevolutionary hypotheses.
Friday, June 7th, 2019. (R packages: geomorph).
- Morning: Modularity and integration.
- What is ‘phylogenetic’ modularity and integration?
- Applications and assumptions.
- Afternoon: Case study.
Fees
- Course Fee
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- Early bird (until March 31st, 2019):
- 535 € *
- Regular (after March 31st, 2019):
- 675 € *
- This includes course material, coffee breaks and lunches (VAT included).
* Participants from companies/industry will have an extra charge of 100 €.
- Course Fee + Accommodation Package
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- Early bird (until March 31st, 2019):
- 535 € * + 330 € = 865 €
- Regular (after March 31st, 2019):
- 675 € * + 330 € = 1,005 €
- This includes course material, coffee breaks, transportation from and to Barcelona city, accommodation from Sunday to Friday, breakfasts, lunches and dinners (VAT included).
* Participants from companies/industry will have an extra charge of 100 €.
We offer the possibility of paying in two instalments (contact the course coordinator). Discounts (see Funding below) are not cumulative and apply only on the fee, not to Accommodation Package or other options.
Accommodation
Accommodation Package
If you take the Accommodation Package you will be hosted in the Rural House Can Carol, in single-sex shared dormitories (2 – 4 people) with bathroom en-suite.
If the number of participants exceeds the available rooms at Can Carol, some of them could be accommodated in the Hotel Tall del Conill, by registration order. The hotel is at 10 minutes walking, although transport will be provided in the morning and after dinner. Lunches and dinners will be with the whole group.
A supplemental charge will be added if you prefer to stay in a single room.
Accommodation is included from Sunday (check-in) to Friday (check-out). Breakfast, lunch and dinner are also provided during the week, starting from the dinner of Sunday to lunch of Friday (included).
Other accommodation options
If you do not want the Accommodation Package, accommodation is available in places other than Can Carol: Where to stay near the Venue.
Rural House Can Carol
Rural House Can Carol
Rural House Can Carol
Schedule
Course Schedule
- Monday to Friday:
- 9:30 to 13:30 Lessons.
- 13:30 to 14:30 Lunch (included).
- 15:00 to 18:30 Lessons.
Accommodation Package Schedule
- Sunday:
- 19:00 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 get there.
- 20:00 Registration in the Hotel.
- 20:30 Dinner.
- Monday to Thursday:
- 8:00 to 9:00 Breakfast.
- 20:30 Dinner.
- Friday:
- 8:00 to 9:00 Breakfast.
- 18:30 Meeting point in the Hotel to take the bus to Barcelona city.
- 20:00 Arrival to Plaza Catalunya (Barcelona).
The schedule is approximate; it is possible that the content of one day may run into the next and a working day may be longer than advertised.
Funding
Former participants will have a 5 % discount on the Course Fee.
Unfortunately there are no scholarships available for this course. However a 20 % discount on the Course Fee is offered for members of some organizations (Organizations with discount). If you want to apply to this discount please indicate it in the Registration form (proof will be asked later).
Spanish unemployed scientists, as well as Spanish PhD students without any grant or scholarship to develop their PhD, could benefit from a 40 % discount on the Course Fee. If you want to ask for this discount, please contact the course coordinators. That would apply for a maximum of 2 places and they will be covered by strict inscription order.
Discounts are not cumulative and apply only on the fee, not to Accommodation Package or other options.
1st Edition, June 5th-9th, 2017
Twenty people belonging to the following countries and institutions participated in this edition:
- United Kingdom: University of Manchester, Royal Botanic Gardens – Kew, Liverpool John Moores University, University of St Andrews, University of Cambridge.
- Switzerland: University of Zurich, Swiss Federal Institute of Aquatic Science and Technology – Eawag.
- Portugal: Instituto de Ciências e Tecnologias Agroambiente da Universidade do Porto, Centro de Investigação em Biodiversidade e Recursos Genéticos – CIBIO-InBIO.
- Austria: University of Innsbruck, Institute of Science and Technology, University of Vienna.
- Spain: Universitat de Barcelona, Universidad Rey Juan Carlos, Estación Biológica de Doñana – CSIC, University of Santiago de Compostela.
- United States of America: The Ohio State University, University of Maine.
- France: French National Research Institute for Sustainable Development.
Organizers
Collaborators
Registration
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Transmitting Science started in 2012 to manage specialized courses and workshops we were already organizing within our own Partnerships. Up to date, we have already run more than 120 advanced courses in different topics related to Life Sciences.
All the courses are self-financed with participant’s fees and we strive to keep the fees to the minimum necessary for running them.
Our courses cover a wide range of research methods and are aimed at postgraduate students, postdoctoral researchers and established academics from all over the world.
All the courses are self-financed with participant’s fees and we strive to keep the fees to the minimum necessary for running them.
Our courses cover a wide range of research methods and are aimed at postgraduate students, postdoctoral researchers and established academics from all over the world.