• Advanced Courses in Life Sciences

    Header of Genetics and Genomics at Transmitting Science

Live Online Course – 4th Edition

Introduction to Palaeogenomics

May 9th-15th, 2024

Live sessions will be recorded

Course Introduction to Palaeogenomics – concepts, methods and applications of ancient human and non-human DNA data

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Course Overview & Programme

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 been 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.

This course covers concepts, methods and applications of ancient human and non-human DNA data.

In a combination of interactive lectures and hands-on practical sessions, the 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. 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.

  1. 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
  2. Laboratory methods – DNA extraction. Library preparation methods (ds, ss, BEST, BEMT, SC). Sequencing strategies. Best practices.
  3. Data preprocessing, particularities of ancient DNA data and basic data quality statistics.
  4. 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.
  5. aDNA authentication. Damage, error rates and contamination analysis.
  6. Analysis of low coverage data using Angsd (potential strategies using genotype likelihoods and pseudo-haploid data)
  7. Broad ancestry estimation using NGS tools. Clustering strategies (PCA, Admixture). Phylogenomics (Treemix)
  8. Introduction to F-statistics (D-statistics, F3) and Admixture graphs.

Graduate or postgraduate degree in a Life Sciences discipline.

Basic knowledge and experience in linux command line and bash scripting is required.

All participants must have a personal computer and access to a good internet connection.

Instructors

Marcela Sandoval Velasco instructor for Transmitting Science

Dr. Marcela Sandoval Velasco
Smithsonian Institution, Museum of Natural History
United States of America

Jazmín Ramos-Madrigal instructor for Transmitting Science

Dr. Jazmín Ramos-Madrigal
University of Copenhagen
Denmark

Dates & Schedule

May 9th-15th, 2024

16:00-20:30 (Madrid time zone)

Online live sessions on 9th, 10th, 13th, 14th, 15th of May

Total course hours: 26 

22.5 hours of live online lectures, plus 3.5 hours of participants working on their own.

This course is equivalent to 1 ECTS (European Credit Transfer System) at the Life Science Zurich Graduate School.

The recognition of ECTS by other institutions depends on each university or school.

Language

English

This course will be delivered live online

The course will be taught using a combination of live (synchronous) sessions on Zoom and Slack.
Live sessions will be recorded. Recordings will be made available to participants for a limited period of time. However, attendance to the live sessions is required.

Places

Places are limited to 16 participants and will be occupied by strict registration order.

Participants who have completed the course will receive a certificate at the end.

Haris Saslis instructor for Transmitting Science

Dr. Haris Saslis

Transmitting Science
Greece

Fees & Discounts

  • Course Fee
  • Early bird (until April 30th, 2024):
  • 548 €
    (438.80 € for Ambassador Institutions)
  • Regular (after April 30th, 2024):
  • 638 €
    (510.40 € for Ambassador Institutions)
  • Prices include VAT.
    After registration you will receive confirmation of your acceptance on the course.
    Payment is not required during registration.

We offer discounts on the Course Fee.

Discounts are not cumulative. Participants receive the highest appropriate discount.

We also offer the possibility of paying in two instalments. Please contact us to request this.

Former participants of Transmitting Science courses receive a 5% discount on the Course Fee.

20% discount on the Course Fee is offered to members of certain organisations (Ambassador Institutions). If you wish to apply for this discount, please indicate it in the Registration form (proof will be asked later). If you would like your institution to become a Transmitting Science Ambassador Institution, please contact us at communication@transmittingscience.com

Unemployed scientists, as well as PhD students without any grant or scholarship to develop their PhD, can benefit from a 40% discount on the Course Fee. This applies only to participants based in Spain. If you wish to ask for this discount, please contact us. The discount may apply for a maximum of 2 places, which will be covered by strict registration order.