Adaptation Genomics


24-28 June 2024


To foster international participation, this course will be held online



Course Overview

This course provides an introduction to the study of the genomic basis of adaptation using population genomics approaches applied to the analysis of both sequence and structural genetic variation. The instructors will guide the participants from the handling of raw genomic data and data exploration (e.g., summary statistics and population structure) up to more advanced methods, including the detection of candidate genomics regions involved in local adaptation using genotype-phenotype or genotype-environment association studies based on both sequence and structural variants. Through hands-on exercises, the course will teach basic bioinformatics skills and how to manipulate, visualize, and interpret genomic data patterns. Thanks to the combination of theoretical and conceptual lectures, the students should end the course with a good understanding of the possibilities and challenges to study the genomics of adaptation using population genomic approaches, as well as the confidence to apply similar methods to their own research.


target audience and assumed background

The course is aimed at graduate students and researchers who are interested in using genomic tools to investigate the genomic basis of adaptation. Participants should have some basic background in evolution and population genetics. Previous experience in UNIX-based command line and R is an advantage, and a short tutorial may be provided prior to the course for participants without previous experience. Hands-on exercises will be run in a Linux environment on remote servers and data analysis and visualisation will be run in R using RStudio.



teaching format

The course will focus on the analysis of high-coverage whole genome and long-read data. In 2024, this course will be delivered online over 5 days with a combination of lectures (live) and practical exercises (flexible schedule; see details below). The course will be held 14h30 to 20h30 CET to allow participation from different time zones. Discussions among participants and with the instructors on concepts and data analysis will be possible through video conferencing and a dedicated Google group.


Learning Outcomes

1.    Handling genomic data from raw reads to genetic variants
2.    Calculating basic population genetic statistics
3.    Visualizing genetic population structure
4.    Detecting genomic regions linked to adaptive divergence or local adaptation
5.    Detecting signatures of selection in the genome
6.    Detecting putative structural variants of adaptive significance
7.    Understanding the potential and the limitations of different methods to study the genomic basis of adaptation



Monday - Introduction to adaptation genomics -2.30-8.30 pm Berlin time
Lectures: Population genomic approaches
Practical: Basic handling of genomic data - from raw data to variant calling

Tuesday - Population structure and other confounding factors -2.30-8.30 pm Berlin time
Lectures: Factors affecting genomic differentiation - population structure, recombination, and others.
Practical: Summary statistics (π, FST) and methods to investigate population structure (PCA, Admixture)

Wednesday - Detection of putative adaptive loci and signatures of selection- 2.30-8.30 pm Berlin time
Lectures: Strength and weaknesses of outlier detection, phenotype-genotype and phenotype-environment association methods
Practical: outlier detection, phenotype-genotype and phenotype-environment association methods

Thursday - Accounting for structural variation - 2.30-8.30 pm Berlin time
Lectures: The role of structural variants (e.g., inversions, copy-number variants [CNVs], transposable elements) in adaptation and the implications of the presence of structural variation in a genomic dataset
Practical: Direct and indirect detection of SVs and their analysis

Friday - Follow-up studies, other methods & troubleshooting - 2.30-8.30 pm Berlin time
Lectures: The richness of approaches to study adaptation and validate candidate loci
Practical: Functional annotation of candidate loci for adaptation + final discussion


Cost overview

Package 1


530 €

Cancellation Policy:




> 30  days before the start date = 30% cancellation fee


< 30 days before the start date= No Refund.




Physalia-courses cannot be held responsible for any travel fees, accommodation or other expenses incurred to you as a result of the cancellation.