Course: Speciation Genomics
When: 2-6 September
Where: Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval Québec (Québec), Canada
Instructors: Dr. Mark Ravinet (CEES, Univeristy of Oslo, Norway) and Dr. Joana I. Meier (University of Cambridge, UK).
This course will provide a thorough introduction to the growing field of speciation genomics. The course aims to take students from the initial steps required for handling raw sequencing data to demographic modelling and inference of genome-wide signatures of selection and introgression. Through a combination of lectures covering key theoretical and conceptual topics, alongside hands-on exercises, participants will learn the most important computational approaches used in speciation genomics. This will include a heavy emphasis on data visualization and intepretation. After completing of the course, the participants should be able to begin using NGS data to shed light on the genomic aspects of speciation in their study system of choice.
This course is designed for researchers and graduate students with strong interests in applying novel high-throughput DNA sequencing technologies to study the population genomic basis of speciation. The course will mainly focus on the analysis of NGS data for study systems for which a reference genome is available. We will provide theoretical lectures and hands-on exercises drawing on examples of whole-genome resequenced and RAD-sequencing data. Participants will make use of the UNIX command line, R and Python throughout the course.
The participants should have some basic background in evolution and genomics. No programming or scripting expertise is required. Previous experience in UNIX-based command line and R is an advantage but a standard introduction will be provided. All hands-on exercises will be run in a Linux environment on remote servers. Statistical analyses will be run in R using RStudio.
Handling NGS data from raw reads to genetic variants
Applying basic population genetic statistics
Visualizing the genetic structure
Inferring demographic history
Identifying regions under divergent selection or barriers to gene flow
Understanding the potential and limitations of different methods to detect regions under selection
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