B4996 - PALEOGENOMICA

Learning outcomes

At the end of the course the student has basic and applicative technical-scientific skills concerning the use of paleogenomic analysis for the study and enhancement of biological materials from archaeological and paleontological contexts. In particular the course is based on the analysis of DNA extracted from human, animal and plant remains aimed at their characterization and genetic identification and related scientific subjects. The student knows limits and potential of ancient DNA analysis, is able to select and evaluate the samples suitable for paleogenomic analysis, knows the wet lab analysis processes and the main tools and pipelines for bioinformatics analysis of NGS sequencing data.

Course contents

• Ancient DNA: definition, history, potential, and limitations. The main challenges: post-mortem damage and contamination from exogenous DNA. Environmental conditions that favor DNA preservation, temporal limits of conservation. Authentication criteria and guidelines. Ethical implications. Setting up a laboratory for ancient DNA analysis.
• Types of samples for ancient DNA analysis. Sampling. DNA extraction. Creation of genomic libraries. NGS sequencing and comparison with classical methodologies. Shotgun sequencing and enrichment methods.
• Computational processing of high-throughput ancient DNA sequencing data. Understanding NGS data. Overview of paleogenomic analysis pipelines (e.g., Paleomix and Eager). Alignment to a reference genome. Quality and quantity controls. Authentication and assessment of contamination in NGS data from ancient remains. Estimation of endogenous DNA content. Variant calling. Methods for sex determination. Methods for calculating kinship relationships.
• Case studies: the contribution to the reconstruction of human phylogeny and evolutionary history, as well as migration and dispersal dynamics of human populations; reconstruction of the origins and epidemiological history of infectious diseases, identification of pathogens and the study of their evolution and spread; reconstruction of domestication processes; reconstruction and selection of ancient phenotypes; environmental DNA.

The concluding part of the course (1 ECTS) will be dedicated to practical exercises on the use of software/pipelines for the processing of paleogenomic data.

Readings/Bibliography

- Brown T., Brown K.- Biomolecular archaeology. An introduction. Wiley-Blackwell, 2011.

- Richards M.P., Britton K. - Archaeological Science. An introduction. Cambridge University Press 2020.

- Caramelli D. - Antropologia molecolare: manuale di base. Firenze University Press, 2009.

- Ancient DNA, Methods and Protocols. Springer Protocols. Editors: Shapiro, B., Barlow, A., Heintzman, P.D., Hofreiter, M., Paijmans, J.L.A., Soares, A.E.R. (Eds.)

 

Non-attending students.

The program of the course is the same for both attending and non-attending students. The attendance of the lessons is strongly recommended for the achievement of a good profit, however, students who for valid reasons cannot attend are invited to contact the professor and, if necessary, receive recommendations for supplementary reading.

Teaching methods

The presentations shown during the lectures, as well as scientific articles and reviews that may be useful for further exploring some of the topics covered in the course, will be shared with students through specific applications (e.g., Virtuale). On Virtuale, a list of the pages from various texts to be studied for the program will also be uploaded.

5 ECTS will be delivered through lectures.

1 ECTS will be delivered through computer exercises related to the main paleogenomic data analysis methodologies presented during the course.

Assessment methods

The assessment of learning consists of an oral exam. The first part will consist of an exposition of a case study, preferably through a PowerPoint presentation, in which the student will illustrate a scientific article, which can be chosen among the various case studies presented in class or among others that have captured the student's interest. The topic must be agreed with the professor and the presentation must be sent at least one week before the exam. The second part of the exam will concern the verification of the preparation on the topics of the program.

In order to pass the exam, the student must prove to have acquired adequate knowledge, both general and systematic, on the various topics in the program and to have mastered the scientific and methodological tools of the discipline.

For assessment purposes, the use of AI is prohibited. Any use constitutes a violation of academic integrity.

For the purposes of the final grade of the test will be evaluated:

• the degree of scientific and methodological depth of the topics covered;

• the ability to support a critical and reasoned discussion on the topics in the program and to perform the necessary logical-deductive links;

• the ability to make interdisciplinary connections;

• the property of language and the quality of the exhibition.

Evaluation of the exam

The exam includes an assessment of the level of learning of the topics in the program with a grade expressed in thirtieths.

Graduation of the final grade:

• Very in-depth knowledge of the topics together with high critical analysis skills, connection and safe mastery of specific terminology: grade 30-30L;

• In-depth knowledge of the topics together with good analytical and critical skills and possession of an adequate mastery of specific terminology: grade 27-29;

• Technically adequate preparation and sufficient analytical skills, even if not particularly articulated, expressed in a correct language: grade 23-26;

• Sufficient preparation and analytical skills, expressed in a barely formally correct language: grade 18-22.

Teaching tools

The teaching materials, including the lecture slides and the scientific papers discussed during the course, will be made available on the Virtuale platform. Additional seminar sessions may be organized to explore specific topics and case studies in greater depth and may, where appropriate, be delivered by invited specialists.

Students with a specific learning profile or with a temporary or permanent disability are encouraged to contact the University Disability and Specific Learning Disabilities (SLD) Office as soon as possible (https://site.unibo.it/studenti-con-disabilita-e-dsa/en/for-students ). The Office will provide support in identifying the solutions and accommodations best suited to their individual needs.

 

Office hours

See the website of Donata Luiselli