29th June- 3rd July 2020
Freie Universität Berlin, 14195 Berlin
Environmental DNA (eDNA) is fast becoming a, non-invasive, reliable and readily used methodological tool for assessing eukaryotic population and community dynamics, with widespread applications in both academic and applied research. Environmental DNA can be isolated from a vast range of environmental samples(e.g. water, soil, gut contents, feces, pollen etc.) making the analysis of eDNA pertinent for marine, freshwater and terrestrial research. Furthermore, eDNA can be adapted to study virtually any species or community of interest making it highly versatile. However, given the wide range of possible applications for eDNA combined with the immense diversity of sampling,DNA extraction, and analytical approaches, it can be quite daunting to initiate an eDNA based project. Here we offer an introduction into eDNA based science with key emphasis on how to design, implement and analyze 1) species specific (targeted) eDNA using qPCR and 2) community based analyses using metabarcoding and high throughput sequencing.
After completing the workshop, students should be in a position to (1) Design their own eDNA study based on their research needs (2) understand the principles of qPCR, including in-silico primer development and experimental setup (3) analyse high throughput sequencing eDNA metabarcoding data (4) Perform preliminary analyses of both qPCR and metabarcoding data and (5) Create publication quality figures. All course materials (including copies of presentations, practical exercises, data files, and example scripts prepared by the instructing team) will be provided electronically to participants.
This workshop is aimed at researchers and technical workers with a background in ecology, biodiversity or community biology who want to use molecular tools for biodiversity research. The course is intentionally broad with an aim of providing a general overview of the current state-of-the-art in eDNA research as well as equipping practical researchers with some basic tools to begin their own research projects.
This workshop focuses on the use of eDNA to detect eukaryotic species from environmental samples. Practical information and knowledge into microbial metabarcoding, metagenomics and metatranscriptomics are provided in other Physalia courses.
No programming or scripting experience is necessary and we will assume no prior knowledge of command line programming, but those with previous expertise using the Linux console or R are most welcome, and we aim to provide something new for everyone. The practical sessions will be run using Amazon Web Services (AWS) linux servers, so participants must bring their own computer system. Instructions for pre-installing software will be provided.
The workshop is delivered over 5 days (see the detailed curriculum below). The lectures are interactive with active discussion where asking questions is strongly encouraged.
Monday - 9:30 - 17:30
-Participant and instructor introductions, housekeeping and course overview
-Hands-on introduction to UNIX and command line computing
-The history and ecology of eDNA. Overview of applications across disciplines
-Hands-on introduction to R
COURSE + REFRESHMENTS
COURSE + Lunch + REFRESHMENTS +Accommodation
Registration deadline: 30th May 2020
> 30 days before the start date = 30% cancellation fee
< 30 days before the start date= No Refund.
Physalia-courses cannot be held responsible for any travel fees, accommodation or other expenses incurred to you as a result of the cancellation.