This course will introduce attendees to how genomic and transcriptomic data can be used to detect 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 different types of sex chromosomes and sex determination systems, and hands-on exercises, running analyses, 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.

The course is aimed at graduate students and researchers who are interested in using genomic/transcriptomic data to explore the presence and mode of sex chromosome evolution. Participants should have some basic background in evolutionary biology, genetics/genomics, bioinformatics, or other relevant disciplines. Basic experience in UNIX-based command line and R is recommended. 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.

The course will be delivered fully online over 5 half-day (5 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.

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

Monday– Classes 11-4 pm Berlin time
We will introduce different types of sex determination systems and of sex chromosomes (X0, XY, ZW, UV). We will then discuss different sequencing strategies for the study of sex chromosomes and common approaches and challenges in identifying sex chromosomes.
We will start the practical sessions with processing NGS data and mapping sequencing reads to a reference genome.

Tuesday– Classes 11-4 pm Berlin time
We will discuss the theory on the causes and consequences of recombination suppression on sex chromosomes. We will then explore bioinformatic approaches for identifying homomorphic and heteromorphic sex chromosomes using coverage-based , SNP-based, and reference genome free (i.e.,k-mer based) methods.

Wednesday– Classes 11-4 pm Berlin time
We will analyse the structure (pseudoautosomal versus non-recombining regions; evolutionary strata), gene content, gene density and GC content of sex chromosomes.

Thursday– Classes 11-4 pm Berlin time
We will discuss the relationship between sex chromosome evolution and patterns of sex-biased gene expression, as well as theory on the evolution of dosage compensation. We will use transcriptomics data to analyse gene expression differences between males and females across different tissues, identify patterns of sexualization of gene expression on the sex chromosomes, and perform tests for dosage compensation.

Friday– Classes 11-4 pm Berlin time
We will discuss theory and empirical evidence for the evolutionary drivers of sex chromosome turnover. We will perform comparisons of sex chromosome evolution across species, synteny analysis and infer rates of gene gain and loss in sex-specific regions.
There will be time for finishing up the analyses and time for a general discussion.
Each student will have the opportunity to receive feedback on their datasets and analyses.

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.