The Ancient Environmental Genomics Course is an intensive six-day PhD-level program introducing participants to the study of ancient environmental DNA (eDNA). This genetic material is preserved outside of bones and teeth, often embedded in sediments, ice, or other natural archives. Damaged and fragmentary, it provides unique windows into past ecosystems, revealing information about species that once persisted, interacted, and some disappeared.
The course will discuss the diverse materials that can yield ancient eDNA, such as permafrost soils, lake sediments, ice cores, cave deposits, artifacts, dental calculus, and coprolites. Each archive type offers distinct preservation conditions and scientific opportunities, and you will gain hands-on experience in how to approach and work with this complex type of data..
Our goal is to introduce you to the skills to analyze complex mixtures of ancient DNA and reconstruct past biodiversity. You will learn how to identify microbes, plants, animals, and humans through taxonomic profiling, organelle-based methods, and nuclear DNA analyses. The course will also emphasize best practices for documenting, reporting, and communicating your results, preparing you to contribute confidently to the growing field of ancient environmental genomics.
Mikkel Winther Pedersen, mail: [email protected], phone/whatsapp: +45 2927 5342
Sunday, September 21st
- Natural History Museum of Denmark, Oester Voldgade 5-7. Main auditorium. (13-17) direction
Monday, September 22nd
- CSS 22.0.19 (9-13) and CSS 7.0.01 (13-17) direction
Tusday, September 23rd
- CSS 2.0.30 (9-13) and CSS 7.0.01 (13-17) direction
Wednesday, September 24th
- CSS 35.3.20 - Faculty Lounge direction
Thursday, September 25th
- CSS 35.3.20 - Faculty Lounge. (9-17) direction
Friday, September 26th
- CSS 35.3.20 - Faculty Lounge. (9-16) direction
Sunday September 21st, 17-19, Ice breaker drinks and snacks at the Natural History Museum of Denmark.
Note: The days will contain alternations between ‘talks’ and tutorials, these will be interwoven in-between each other and it is therefore not outlined here.
- Day 1 – 1pm-5pm (21st September): Welcome, intro to the ancient environmental DNA summer course, computational cloud setup, github + github classroom introduction, 2-min introduction to student's projects/datasets (Pete Heintzman & Mikkel W. Pedersen).
- Day 2 - 9am-5pm (22nd September): Continued intro to ancient environmental DNA, sources of ancient eDNA, data generation, mineral-DNA binding, DNA and microfossils, tour de labs, pros and cons of automation, sequencing facility. (Mikkel WP and guest talk by Karina Sand).
- Day 3 - 9am-5pm (23rd September): Lecture on structuring ancient environmental DNA studies and introduction to basics in data analysis, command line, workflow, pipelines, and proper analysis documentation GitHub and version control etc. standards and data submission. Setting up and instructions on how to access the course server. (Thorfinn Korneliussen, Mikkel WP and Antonio FG).
- Day 4 - 9am-5pm (24th September): Lecture on Eukaryotic profiling, ancient DNA estimation, extraction of ‘ancient/damages) reads, consensus genome generation, phylogenetic placement and analysis, and measure of the split time. Practicals: mapping, LCA, damage, Environmental Genome Assembly, PanGenomeGraphs, Phylogenetic placement, database building and choice, Data wrangling and documentation. Hands-on Eukaryotic ancient eDNA data. Lecture on hominin DNA from ancient sediments and hands-on (Mikkel WP & Benjamin Vernot).
- Day 5 - 9am-5pm (25th September): Introduction to Prokaryotic analysis from marine, lakes, caves, Ice etc. Ancient vs living communities. Unknowns, MAGs, Databases, Function, Binning, Hands-on exercises (Mateu Menendez-Serra).
- Day 7 - 9am-5pm (26th September): Diseases, viruses and bacterial pathogens, how best to catch’em. Hand-on exercises (Martin Sikora). Lectures on guide and explain standards and best practices for documenting and reporting analysis and results, and eventually making these publicly available. Evaluation and summarising (Mikkel WP, Martin Sikora).