This course introduces students and professionals with a background in evolutionary biology and/or genomics to museomics, the generation and analysis of genomic data from natural history collections. The course will combine lectures and hands-on exercises, covering essential bioinformatics workflows and analytical methods.

Participants must have a basic understanding of evolutionary genomics and population genetics.

By completing this course, participants will gain theoretical and practical experience in:

- Processing museum-derived genomic data (data generation, mapping, filtering, quality control).
- Extracting genomic metrics (diversity, allele frequencies, population structure, relatedness).
- Applying museomics in molecular ecology and conservation genomics using case studies:
- Local adaptation through time (molecular ecology).
- Genetic diversity loss through time (conservation genomics).

Teaching time : 9:00 AM - 2:00 PM Berlin time
 
Monday– Classes from 9:00 AM to 2:00 PM Berlin time - Data generation and processing
Topic: How can we generate museum-derived genomic data, and what are the main challenges?

Lecture : Introduction to Museomics – Historical and technological perspectives.
Lecture : Museum Sample Processing and data generation– DNA extraction, library preparation, enrichment techniques, sequencing strategies.
Lecture : Data processing and quality control – Cleaning, mapping, filtering, assessing DNA damage, error rates, and contamination.
Practical: Mapping reads to a reference genome & assessing damage patterns.

Tuesday–Classes from 9:00 AM to 2:00 PM Berlin time- Exploratory analyses
Topic: How do we evaluate the quality and usability of museum-derived genomic datasets?

Lecture : Understanding Dataset Power – Coverage depth, callable sites, biases.
Lecture : Exploratory Analyses – Principal Component Analysis (PCA), admixture analysis, relatedness.
Practical: Running PCA, admixture and relatedness analysis on a historical genomic dataset.

Wednesday– Classes from 9:00 AM to 2:00 PM Berlin time - Population genetics
Topic: What can we infer about population history from museum-derived genomic data?

Lecture : Genome-Wide Diversity & Demographic Inference – Allelic frequencies, heterozygosity, inbreeding.
Lecture : Population Structure & Connectivity Over Time.
Practical: Estimating genetic diversity and inbreeding using historical genomic data.

Thursday– Classes from 9:00 AM to 2:00 PM Berlin time - Local adaptation
Topic: How can historical genomic data be used to study local adaptation to environmental change?

Lecture : Detecting Local Adaptation Over Time – Overview of selection scans, allele frequency shifts, and genomic vulnerability to climate change.
Practical:Analyzing temporal allele frequency shifts using SNP datasets.
Practical:  Running selection scans to identify loci under natural selection.

Friday– Classes from 9:00 AM to 2:00 PM Berlin time - Conservation genomics
Topic: How can historical genomic data be used to study genetic diversity loss?

Lecture 10: Genomic Erosion and Drift Debt
Lecture 11: Case Study: Genomic Erosion through time in endangered species
Practical:Estimating genetic diversity and inbreeding over time using genomic data.
Practical: Exploring genetic load accumulation using mutation impact predictions.

Should you have any further questions, please send an email to info@physalia-courses.org