Next week is the registration deadline for the course on Landscape Genomics and we have the last 3 spots available.
6-10 November 2017
Dr. Stéphane Joost and Oliver Salmoni, MSc ( Laboratory of Geographic Information System (LASIG), Swiss Federal Institute of Technology of Lausanne (EPFL))
Landscape genomics is an emerging research field that studies how genetic diversity distributes across space and how environmental features can modify this structure through local adaptation. In this workshop, students will learn the basics of this approach and train using state of the art methods. The course will provide an overview of the type of dataset that can be used for a landscape genomics analysis. Firstly, students will learn how to obtain environmental data from publicly available databases, how to process it with Geographic Information Systems (GIS) and how to use the latter to produce indicators able to describe the characteristics of the landscape. Next, the course will discuss the different approaches to obtain genetic data and subsequently show how to study genetic variation and population structure across space in the R environment. Students will be given an overview of the different statistical approaches to study local adaptation, and will be trained in using two of them, Sambada and LFMM. The course will also cover the critical task of the interpretation and validation of the results. Finally, the workshop will consider the crucial aspects and good habits to account for when planning a landscape genomics experiment (e.g. sampling design).
Targeted Audience & Assumed Background
This workshop is aimed at all biologists, ecologists, geneticists, veterinarians that want to implement the landscape genomics approach in their own studies of evolutionary biology and conservation. Even though the course is not intended for a specialized audience, basic knowledge in evolutionary biology and population genetics would help. Students will learn how to use GIS, but basic computer skills are desirable (e.g. in the R environment). A basic understanding of statistics is also necessary.
The course is organized in ten learning sessions. During the first two sessions, the course will provide a contextualization of the research field. Then, students will be guided through a landscape genomics experiment with sessions that couple brief theoretical introductions with practical work.
Monday 6th - Classes from 09:30 to 17:30
- Overview of the course program
- Introduction on Landscape Genomics
Session 2 - Dataset
- The environmental data
- The genetic data
Tuesday 7th - Classes from 09:30 to 17:30
Session 3-Environmental Data 1
- GIS basics
- Main environmental databases
- Derived environmental variables
Session 4- Environmental Data 2
- Environmental characterization of the samples
- Point versus surface
- Analysis of environmental diversity of samples
Wednesday 8th - Classes from 09:30 to 17:30
Session 5- Genetic Data 1
- Sequencing strategies
- Data filtering
Session 6- Genetic Data 2
- Spatial genetic variation
- Population structure
Thursday 9th - Classes from 09:30 to 17:30
Session 7-Statistical Analysis
- Overview of statistical methods (univariate, multivariate, w/wo population structure)
- samβada: logistic regression
Session 8-Interpreting Results
- Spatial autocorrleation
- Process samβada output in R
- Validation of results
Friday 10th - Classes from 09:30 to 17:30
Session 9- Planning a Landscape Genomics Experiment
- Scale and Resolution
- Sampling Design
- Take home messages
- Question time
Application deadline is: October 6th, 2017.
The cost is 480 euros (VAT included) including course material and refreshments. We also offer an all-inclusive package at 745 euros (VAT included), which includes course material, refreshments, accommodation and meals.