Sex chromosome evolution


23-27 January 2023

Due to the COVID-19 outbreak, this course will be held online


This course will introduce attendees to how genomic and transcriptomic data can be used to detect homomorphic/heteromorphic sex chromosomes and inform the cause and consequences of sex chromosome differentiation. The instructors will guide students through study design, genomic/transcriptomic data collection methods, handling of raw genomic/transcriptomic data, and methods to identify sex chromosomes. Then, we will work through a suite of analyses looking at the molecular evolution of sex chromosomes, particularly the timing and patterns of recombination suppression, gene gain/loss, gene expression differentiation, and genome divergence. We will provide background on the theory and hands-on exercises, running analysis, and interpreting results. After completing the course, the participants should be able to manipulate, visualize and interpret genomic data and patterns of sex chromosome evolution.

Target audience and assumed background

The course is aimed at graduate students and researchers who are interested in using genomic/transcriptomic data to explore the mode of sex chromosome evolution. Participants should have some basic background in evolutionary biology, genetics, bioinformatics, or other relevant disciplines. Basic experience in UNIX-based command line and R is an advantage. Hands-on exercises will be run in a Linux environment on remote servers and data analysis and visualization will be run in R using RStudio.

Teaching format

The course will be delivered fully online over 5 half-day (6 hours) sessions, with a combination of lectures and practical exercises that will be live (synchronous). Discussions among participants and with the instructors on concepts and data analysis will be possible through video conferencing and a dedicated Slack workspace.




Learning outcomes

1. Conduct computational analysis to detect homo/heteromorphic sex chromosomes.
2. Searching for signals of early stages of sex chromosome differentiation.
4. Detect the timing and patterns of recombination suppression.
5. Conduct computational analysis to detect sex chromosome gene expression differentiation and genome divergence.
6. Study of dosage compensation.
7. Interpret these in the light of evolution.



Monday. 2 -8 pm Berlin time


We will introduce different sex determination systems and explore types of sex chromosomes (X0, XY, ZW, UV). We will then discuss the typical workflows from study design, sample collection, through NGS data to sex chromosome identification.
We will start the practical sessions with an introduction to Unix, manipulation of the NGS data, mapping sequencing reads to reference genomes, and finally, we will use coverage-based methods to identify sex-linked genomic regions.





Dr. Aline Muyle (CNRS, France)





Dr. Agnieszka Lipinska (Max Planck Institute, Germany)



COst overview

Package 1


480 €

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.