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Advanced Courses in Life Sciences

1st Edition

Model-Based Statistical Inference in Ecological and Evolutionary Biogeography

November 28th-December 2nd, 2016, Barcelona (Spain)

Model-Based Statistical Inference in Ecological and Evolutionary Biogeography

This course will cover the theory and practice of widely used methods in evolutionary and ecological biogeography, namely ecological niche modelling / species distribution modelling, and ancestral range estimation on phylogenies.

The course will cover both the practical challenges to using these techniques (the basics of R, obtaining and processing geographical occurrence data from GBIF, setting up and using the models), and the assumptions that various models and methods make.

The instructors will also cover the statistical fundamentals behind model-based inference (likelihood, AIC, Bayesian techniques). R packages we will use include rgbif, dismo, ENMTools, and BioGeoBEARS.

Finally, this course will introduce several new approaches being developed by the instructors for linking ecological and evolutionary models.

We take the view that evolutionary models will be improved by including ecology (for example, perhaps the probability of a dispersal event on a phylogeny is likely to be correlated with the environmental distance between regions), and that ecological models are likely to be improved by integrating phylogenetic information into models of species distributions.

We will discuss why the integration of evolutionary information is fundamental to the further development of ecological biogeography, discuss a number of ways in which this might be done, and demonstrate the use of new R packages to implement some of these analyses.

LOCATION

Centre de Restauració i Interpretació Paleontològica

C/ Mestre J. Lladós, 1
08781 Els Hostalets de Pierola, Barcelona.

How to get there

LANGUAGE

English

COURSE LENGTH & ECTS

40 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 25 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

Dan Warren instructor for Transmitting Science

Dr. Dan Warren
Macquarie University
Australia

Nick Matzke instructor for Transmitting Science

Dr. Nick Matzke
ANU College of Medicine, Biology and Environment
Australia

Coordinator

Soledad De Esteban-Trivigno instructor at Transmitting Science

Dr. Soledad De Esteban-Trivigno
Transmitting Science
Spain

Requirements

Training in the biological sciences, preferably some aspect of ecology or evolutionary biology. Participants must bring a laptop. Participants should have some knowledge of R, or must participate in the introduction to R offered the first day of the course.

Program

Monday, November 28th, 2016 (Optional**).

  • Organisation and Intro R.
  • Introductions and discuss optional participant research projects.
  • Introduction to the R statistical programming environment.
  • R Studio.
  • Interacting with the console.
  • Working with variables.
  • Control flow.
  • Writing functions.
  • Writing and reading scripts.
  • Basic graphics.

Tuesday, November 29th, 2016.

  • Spatial data in R.
  • Point data, vector data, and raster data.
  • GBIF, the Global Biodiversity Information Facility.
  • Interacting with Google Maps.
  • Working with raster and vector data.
  • Simulating species occurrence data.

Wednesday, November 30th, 2016.

  • Ecological biogeography.
  • ENM / SDM concepts and assumptions.
  • Dismo.
  • Testing ecological hypotheses via Monte Carlo methods.
  • ENMTools R package.
  • Ecospat.
  • Conceptual issues with ecological inferences from distribution data.
  • Questions of taxonomic scale.
  • New methods for incorporating niche conservatism into the modelling process.

Thursday, December 1st, 2016.

  • Phylogenetic biogeography.
  • How to read and use phylogenies.
  • Short history of historical biogeography methods and assumptions.
  • Likelihood-based statistical model choice.
  • New probabilistic models for historical biogeography in BioGeoBEARS.
  • Using BioGeoBEARS and interpreting results.
  • Including geographical and environmental distance in models.
  • PhyloSDM: joint estimation of modern niches and niche evolution models using R and JAGS.

Friday, December 2nd, 2016.

  • Student projects.
  • Help session for student projects.
  • Optional student presentations.
  • Wrap-up.


** Participants that are familiar with R and have chosen the all-inclusive option could take this day off.

Previous editions of this course

 

1st Editon, November 28th-December 2nd, 2016

Course Model-Based Statistical Inference in Ecological and Evolutionary Biogeography - 1st Editon, November 28th-December 2nd, 2016Twenty-three people belonging to the following countries and institutions participated in this edition:

  • Czech Republic: National Museum, Charles University, Institute of Vertebrate Biology.
  • Denmark: University of Copenhagen.
  • Italy: University of Ferrara, University of Roma Tre.
  • Austria: University of Innsbruck.
  • United Kingdom: Natural History Museum London, Cardiff Unversity.
  • Spain: Universidad Complutense de Madrid, Instituto de Biología Evolutiva – CSIC, Estación Biológica de Doñana – CSIC, University of Oviedo, Universitat de Barcelona, Universidad Rey Juan Carlos, Institut de Recerca y Tecnologia Agroalimentàries.
  • Canada: Canadian Museum of Nature.
  • USA: Elon University.
  • Germany: University of Göttingen.
  • Brazil: Universidade Estadual de Campinas.
  • France: Centre national de la recherche scientifique (CNRS).

Fees

  • Course Fee
  • Early bird (until May 15th, 2016):
  • 515
  • Regular (after May 15th, 2016):
  • 720
  • This includes course material, coffee breaks and lunches.
    (VAT included)
  • Accommodation Package
  • Early bird (until May 15th, 2016):
  • 360
  • Regular (after May 15th, 2016):
  • 360
  • This includes local transportation, lodging, breakfasts, dinners and social (tourist) activities.
    (VAT included)
  • Course Fee + Accommodation Package
  • Early bird (until May 15th, 2016):
  • 875
  • Regular (after May 15th, 2016):
  • 1,080
  • This includes course material, coffee breaks, local transportation, lodging, breakfasts, lunches, dinners and social (tourist) activities.
    (VAT included)

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

If you take the Accommodation Package you will be hosted in the Youth Hostel Can Roviralta, in shared 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 indicate so in the “Comments” field of the Registration form (see below).

A supplemental charge will be added if you prefer to stay in a single room with private bathroom. The number of rooms is limited and if you prefer to have a single room, let us know it as soon as possible. If you want more information on this please contact the course coordinator.

Please be aware that from the centre of Barcelona city it takes about one hour by car and one hour and a half by public transport to arrive to Els Hostalets de Pierola. Course participants will find that staying in Els Hostalets de Pierola is more convenient.

If you do not want the Accommodation Package, accommodation is available in places other than Els Hostalets de Pierola. You may stay in Barcelona city, Martorell or Igualada. You will find information about Hotels in Martorell here, and information about Hotels in Igualada here.

How to get to Els Hostalets de Pierola from Barcelona city, Martorell and Igualada.

Youth Hostel Can Roviralta (Els Hostalets de Pierola, Barcelona, Spain)

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 coordinator. 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.

Schedule

Course ScheduleCourse + Accommodation Package Schedule
Sunday, November 27th, 201619:00 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 Youth Hostel.
20:30 Dinner.
Monday, November 28th through Friday, December 2nd, 20169:30 to 13:30 Lessons.
13:30 to 15:00 Lunch.
15:00 to 19:00 Lessons.

There will be two coffee breaks each day, halfway through each lesson session.

8:00 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, December 3rd, 20168:00 to 9:00 Breakfast.
9:15 Meeting point in the Youth Hostel to take the bus to visit a wine cellar.
10:00 Arrival at the wine cellar.
11:30 Bus to Barcelona city.
13:00 Arrival at 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.

Organizers

Transmitting Science Logo
Centre de Restauració i Interpretació Paleontològica (CRIP) Logo
Institut Català de Paleontologia Miquel Crusafont (ICP) Logo

Collaborators

Colegio Oficial de Biólogos de Castilla y León Logo
Colegio Oficial de Biólogos de Euskadi Logo
Colexio Oficial de Biólogos de Galicia Logo
Col·legi Oficial de Biòlegs de la Comunitat Valenciana Logo
Distributed European School of Taxonomy (DEST) Logo
European Association of Vertebrate Palaeontologists (EAVP) Logo
Sociedade Brasileira de Paleontologia (SBP) Logo

Registration