25 hours of online live lessons
Ancient DNA (aDNA) research, defined as the retrieval and analysis of DNA sequences from various degraded biological materials, has been evolving as a research field for four decades. Through advances in DNA isolation and amplification techniques, sequencing technologies and data analysis pipelines, the field has revolutionized and transitioned to what we now know as palaeogenomics. DNA extracted from archaeological samples, and museum specimens has proven useful to study species and life on earth from the genomic perspective. It has made it possible to measure changes in genetic diversity through time, test hypotheses about the association of environmental phenomena and genetic changes in natural populations, and to resolve long-standing questions about the evolutionary relationships between species.
In a combination of interactive lectures and hands-on practical sessions, this course will provide a theoretical overview of molecular biology laboratory techniques for the retrieval of aDNA from ancient samples from different species and an introduction to the bioinformatic pipelines for the analysis of palaeogenomic data. Students will be introduced to the standard bioinformatic methods often used in palaeogenomic projects for the analysis of aDNA data from human and non-human samples. We will also review the history and developments of the field to understand how it came to be what it is today, and consider and discuss the practical problems of ancient DNA recovery, the theoretical problems associated with the interpretation of palaeogenomic data, and the ethical implications embedded in this type of research.
At the end of the course, students will have gained a general understanding of common key methods and tools used in palaeogenomics projects: from the basics in the field to the interpretation of the results, as well as ethical and responsibility aspects and implications of aDNA research.
Graduate or postgraduate degree in Life sciences discipline. Basic knowledge and experience on linux command line and bash scripting.
All participants must have a personal laptop and access to a stable internet connection.
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- Introduction to ancient DNA and palaeogenomics – History and development of the field. Contamination and degradation of DNA. Best practices and sampling strategies. Ethical implications of aDNA research
- Laboratory methods – DNA extraction. Library preparation methods (ds, ss, BEST, BEMT, SC). Sequencing strategies. Best practices.
- Data preprocessing, particularities of ancient DNA data and basic data quality statistics.
- Standard and alternative mapping strategies. Overview of palaeogenomics analysis pipelines (e.g. paleomix and eager). Selection of reference genome. Reference bias and strategies to overcome it.
- aDNA authentication. Damage, error rates and contamination analysis.
- Analysis of low coverage data using Angsd (potential strategies using genotype likelihoods and pseudo-haploid data)
- Broad ancestry estimation using NGS tools. Clustering strategies (PCA, Admixture). Phylogenomics (Treemix)
- Introduction to F-statistics (D-statistics, F3) and Admixture graphs.
- Course Fee
- Early bird (until April 30th, 2021):
- 485 €
(388 € for Ambassador Institutions)
- Regular (after April 30th, 2021):
- 585 €
(468 € for Ambassador Institutions)
- This includes course material (VAT included).
After registration you will receive confirmation of your acceptance in the course. Payment is not required during registration.