THE ARCHAEOGENOMICS OF DOMESTIC ANIMALS
(The course will take place in a classroom context)
Diachronic genetic studies are required in order to infer the origins and evolutionary trajectories of domestic animals. Data spanning long time scales from zooarchaeological specimens allow the investigation of genomic variation within populations over time. Analysis of ancient DNA opens a direct window into the past for reconstruction of the genetic history of animal populations.
The objective of this course is to provide an overview of the most recent Archaeogenomics findings on the origin and evolution of domestic animals. It will also cover some of the recommended bioinformatics tools and methods for the study of ancient DNA genomics data. There will be hands-on sessions, including bioinformatics on how to filter, infer damage patterns and authenticate next-generation-sequencing data obtained from archaeological specimens, as well as on population genomics. One invited speaker in Archaeogenomics will also contribute to the course.
At the end of the course students should understand the importance of including genomic data concerning past populations to make evolutionary inferences, as well as get familiar with the challenges and peculiarities of ancient DNA analysis.
Topics that will be discussed:
- Animal evolution and population dynamics
- Phylochronological studies
- Domestication events
- Livestock improvement
- Zooarchaeology: radiocarbon dating, isotope analysis and osteometry
- Population Genomics
- Ancient DNA data analysis
PROGRAMME:
November 14
10:00-10:30 – Course Introduction
10:30-11:30 – Zooarchaeology of domestic animals | S Davis & C Detry
12:00-13:00 – Hands-on Zooarchaeology | S Davis & C Detry
14:15-16:00 – Hands-on Zooarchaeology | S Davis & C Detry
16:30-17:30 – The origin and subsequent evolution of the dog | AE Pires
17:30-18:00 – Art & Science: Digital animation – "The Muge dog – a pre-historic friend” | AE Pires
November 15
09:30-11:30 – Recap (30 min). Archaeobotany of domesticated plants | J Tereso
12:00-13:00 - Hands-on Archaeobotany | J Tereso
14:15-16:00 – Genomic studies on aurochs and their domestic counterparts | C Ginja
16:30-17:30 – Hands-on Population Genomics (some practical examples on cattle) | S Guimarães & C Ginja & C Sarmento (to be confirmed)
November 16
09:30-11:30 -
Recap (30 min). Demography and Approximate Bayesian
Simulation | R Tournebize & L Chikhi
12:00-13:00 - Hands-on Population demography | R Tournebize & L Chikhi
14:15-16:00 - Hands-on Population demography | R Tournebize & L Chikhi
Coffee break
16:30-17:30 - Hands-on Population demography | R Tournebize & L Chikhi
November 17
09:30-11:30 - Recap (30 min). Bayesian phylogenetic inference of ancient mitogenomes using BEAST | R Rasteiro
12:00-13:00 - Hands-on Archaeogenomics data analysis | C Ottoni
14:15-16:00 - Hands-on Archaeogenomics data analysis | C Ottoni
16:30-17:30 - Hands-on Archaeogenomics data analysis | C Ottoni
November 18
09:30-11:30 - Recap (30 min). Hands-on Archaeogenomics data analysis | C Ottoni
12:00-13:00 – Analysis and Discussion of the BEAST output | R Rasteiro
14:15-15:15 – Concluding session and evaluation. General conclusions.
15:30-16:30 - Senior seminar in Biodiversity & Evolution (open to the scientific community) - Oral microbiomes from the past: reconstructing health, diet and lifestyles through dental calculus analysis - C Ottoni
Total: 28 hour
REQUIREMENTS
Participants are advised to bring their own laptop
All sessions will be in English
COURSE INSTRUCTORS
Catarina Ginja (coordinator) | BIOPOLIS/CIBIO-InBIO | ARCHGEN
Ana Elisabete Pires | BIOPOLIS/CIBIO-InBIO | ARCHGEN
Claudio Ottoni | University of Rome
Cleia Detry | UNIARQ-FLUL
João Tereso | CIBIO-InBIO-BIOPOLIS/ENVARCH
Lounés Chikhi | Instituto Gulbenkian de Ciência
Rémi Tournebize | Instituto Gulbenkian de Ciência
Rita Rasteiro | University of Bristol
Sílvia Guimarães | BIOPOLIS/CIBIO-InBIO | ARCHGEN
Simon Davis | LARC-DGPC & BIOPOLIS/CIBIO-InBIO | ENVARCH & ARCHGEN
INTENDED AUDIENCE
The course will be open to a maximum number of 20 participants.
SELECTION CRITERIA
75% of available student slots are reserved for BIODIV students.
Priority will be given to:
• 1st year and other PhD students attending the BIODIV Doctoral Program;
• PhD students attending other courses;
• Other post-graduate students and researchers.
REGISTRATION
Participation is free of charge for BIODIV students | 95€ (students) | 200€ (other participants). CIBIO-InBIO members will have an additional discount of 20%.
Please note the rules apply for all BIODIV students
APPLICATIONS OPEN
Registration deadline: October 6, 2022
All applicants will be notified about whether they are accepted until October 12, 2022
Fill out the application form and confirm if you receive a copy in your email confirming the application.