Sciences and Teaching of Natural Systems

LAURA PARDUCCI
LAURA PARDUCCI

The course consists of two parts:
1. Ancient DNA - theory and study, discussion and oral presentation of recent case studies.
2. Ancient DNA - practice with visits to modern DNA laboratories in Sapienza and virtual visits to ancient DNA laboratories in Italy and other European countries.
OBJECTIVES and LEARNING OUTCOMES of the COURSE.
After completing the first part, students are expected to be able to:
- explain the peculiarities of ancient DNA and its importance in reconstructions of the past
- provide an overview of laboratory and genetic analysis methodologies used in the study of ancient material
- present basic theoretical knowledge of the evolutionary and ecological processes that occurred during the last ice age
- explain how environments have changed over the past 2.6 million years
- relate chronologically the events that occurred during the last 2.6 million years
- provide an overview of the processes that have changed environments over the past 2.6 million years
- contextualize the evolutionary processes that have occurred in plants and animals through a synthesis of knowledge from the different areas of research covered in the course.
After completing the second part, students are expected to be able to:
- explain how to extract DNA from ancient fossil specimens and sediments and perform analyses on ancient DNA
- explain the peculiarities of an ancient DNA laboratory versus a modern one and how to work in this environment.

By the end of the course, students will be able to explain the characteristics of ancient DNA and its importance in reconstructing past environments, providing an overview of the laboratory methods and genetic analyses used in the study of ancient material. They will be able to present the basic theoretical knowledge of evolutionary and ecological processes that occurred during the last glacial period and explain how environments have changed over the past 2.6 million years, establishing a chronological framework of major events and providing an overview of the processes that have shaped these environments over time.

Students will also be able to contextualize the evolutionary processes affecting plants and animals by synthesizing knowledge from the various research areas covered in the course. Finally, they will be able to explain how DNA is extracted from fossil and sedimentary remains and perform analyses on ancient DNA, understanding the specific characteristics of an ancient DNA laboratory compared to a modern one and the operational procedures required to work safely in this environment.

Basic knowledge in Archaeology, Geography, Geology, Genetics, and Biology is required for enrollment in the course.

This course aims to provide the latest knowledge on how DNA extracted from fossil remains and ancient sediments is used to study the processes that have shaped the evolution and distribution of plant and animal species over the last 2.6 million years. These processes include both climate and sea level changes and biological changes such as speciation and species extinction. The course analyzes recent case studies such as the reconstruction of palaeoenvironments, hybridization between human species, migration, demographic expansions after the glaciations and the extinction of plant and animal species. An overview of other biomolecular methods currently used on ancient remains will also be provided. The course has a practical component in which students will visit laboratories and watch videos shot in ancient DNA laboratories and will learn how DNA is extracted and analyzed from fossil remains and how to use computational tools to analyze the resulting sequence data.

The course consists of two parts:
1. Ancient DNA – theory and study, discussion and oral presentation of recent case studies.
2. Ancient DNA – practice with visits to modern DNA laboratories in Sapienza and virtual visits to ancient DNA laboratories in Italy and other European countries.

Course Materials:
Most of the course materials will be made available through the Moodle e-learning platform.

Recommended Textbooks:

Lindqvist, Charlotte, and Om P. Rajora (eds.). Paleogenomics: Genome-Scale Analysis of Ancient DNA. Springer, 2019. ISBN 978-3-030-04753-5. Also available as an e-book at Stockholm University.

Capo, Eric, Cecilia Barouillet, and John Smol (eds.). Tracking Environmental Change Using Lake Sediments. Springer, 2024. Also available as an e-book

The course consists of approximately 32 hours of lectures, divided into 16–18 theoretical sessions and around 24 hours of practical exercises, including seminars with oral presentations conducted in the classroom and hands-on laboratory work. Laboratory activities related to ancient DNA, where direct access is restricted due to the high risk of contamination, will be conducted virtually.

The lessons and the practical part of the course provide an overview of the main topics. Attendance at lessons is not compulsory but it is desirable: frequent absences result in a lesser ability to answer exam questions.

The assessment includes an intermediate project, consisting of a 15-minute oral presentation on a selected topic, carried out during the course as a seminar or individual presentation (25% of the final grade), and a final oral exam (75%), which evaluates the student’s overall understanding of the course topics.

Explain the main characteristics of ancient DNA and discuss its role in studying the environmental and evolutionary changes that occurred during the Quaternary.
Describe the main steps of DNA extraction from ancient sediments. What specific precautions must be taken in an ancient DNA laboratory compared to a modern laboratory?
Choose a period within the last 130,000 years and reconstruct a possible evolutionary scenario for vegetation present in southern Italy, integrating genetic, paleoenvironmental, and paleontological data.

• Topic 1, week 1
  • Books: xx


• Topic 2, week 2
  • Books: xx