Short courses > SC4 - Sedimentary ancient DNA: theory and practices

Organisers

1.     Charline Giguet-Covex (EDYTEM, CNRS, Université Savoie Mont-Blanc, France)

2.     Stanislav Jelavić (Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, IRD, Université Gustave Eiffel, ISTerre, Grenoble, France)

3.     Lise Alonzo (EDYTEM, CNRS, Université Savoie Mont-Blanc, France)

4.     Lina Fabre (CNRS, UMR 5023 - LEHNA, Lyon et EDYTEM, CNRS, Université Savoie Mont-Blanc, France)

Description

The aim of this full-day course is to provide some key knowledge to perform sedaDNA analyses from the DNA extraction protocols to the data interpretation. Four courses will be organised around two main themes which should allow you to better design and implement a sedaDNA study. This course that will be a mix between presentations and practical works is more dedicated to beginners. 

Theme 1. sedaDNA as a geobiological tool 

In recent years, the sedaDNA scientific community has greatly improved its knowledge of taphonomic processes affecting this tool and how they can bias our ecological reconstructions. There is still much to be understood in the future, but it is this state of the art that we want to share with you, to give you some keys to better choose a site and a protocol according to your scientific question.

1. Mineral-DNA interactions and influence on DNA preservation (Stanislav Jelavić, 1h45)

2. General DNA taphonomic processes and influence on selections of extraction protocols (Charline Giguet-Covex, 1h45)

These courses will aim to give you an overview of the taphonomic processes (DNA sources, transfer and deposition) that drive the sedaDNA signals, in function of the group of organisms you are interested in and in function of the DNA fraction you are looking at (extracellular or total DNA), which depends on the extraction protocol selection.

Theme 2. from the sample to the production of a sedaDNA dataset

3. Virtual sampling Lab visit (30 min)

The idea, here, is to show the equipment used for this step of the analytical process and to demonstrate the protocol set up at the EDYTEM laboratory.

4. Practical works for bioinformatic treatment of metabarcoding data on microbial communities (Lise Alonso et Lina Fabre, 4h)

This course will be a mixture of theoretical presentations and practical work. The theory will cover existing bioinformatics tools and descriptive statistics used to describe community diversity. Then, you will perform a bioinformatics analysis from raw sequencing data to obtain a table of abundance, using pipelines implemented in FROGS (i.e. a suite for metabarcoding analysis).

In this aim, you will need to create an account on the Galaxy platform. All the necessary information will be provided once you have registered.

Limited to 30 applicants.