9-13  November 2020

University of California, Santa Cruz 

Molecular biodiversity assessment technologies based on the analysis of environmental DNA are revolutionizing the way we sample and monitor natural ecosystems. Metabarcoding techniques can be used to objectively and accurately assess biodiversity of natural communities. Their potential applications include (but are not limited to) water quality assessment, soil diversity studies, trophic analyses of digestive contents, impact assessment of fisheries, early detection of non-indigenous species, inventories of elusive megafauna, analysis of global ecological patterns or biomonitoring of anthropogenic impacts. This workshop gives an overview of the ecology of environmental DNA and the metabarcoding procedures used to analyze it. Emphasis is placed on practical problem-solving and hands-on work using analysis pipelines on real datasets. After completing the workshop, students should be in a position to (1) understand the potential and capabilities of environmental DNA analysis through metabarcoding, (2) run complete analysis pipelines and obtain diversity inventories and ecologically interpretable data from raw next-generation sequence data and (3) design their own metabarcoding projects, using bespoke primer sets and custom reference databases. 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 mainly aimed at researchers and technical workers with a background in ecology, biodiversity or community biology who want to use molecular tools for biodiversity assessment and at researchers in other areas of bioinformatics who want to learn ecological applications for biodiversity analysis. In general, it is suitable for every researcher who wants to join the growing community of metabarcoders worldwide. This workshop will mostly review techniques and software useful for eukaryotic metabarcoding. Another workshop focused on procedures currently used in microbial metabarcoding is available from Physalia-courses.

The workshop is delivered over ten half-day sessions (see the detailed curriculum below). Each session consists of roughly a one hour lecture followed by two hours of practical exercises, with breaks at the organizer’s discretion.

No programming or scripting experience is necessary, but some previous expertise using the Linux console and/or R will be most welcome. All examples will be run in a Linux remote server where all the needed software will be installed. Either a Linux or MacOSX PC or a virtual box running Linux under Windows environment will be needed to access this server. The syllabus has been planned for people which have some previous experience running simple commands in Linux and using the R environment (preferently RStudio) for performing basic plots and statistical procedures. If in doubt, take a look at the detailed session content below or e-mail Owen S. Wangensteen (owenwangensteen@gmail.com).

Monday – Classes from 09:30 to 17:30

Session 1. Introduction to environmental DNA. The ecology of eDNA.

First, we will introduce the course and explain its format. We will talk about the ecology of environmental DNA, discussing the different forms in which DNA can be present in the environment. We will discuss the different kinds of information that can be obtained from community-DNA samples and trace-DNA samples, and implications for quantitative value of different methods based on eDNA. We will introduce single-species methods based on quantitative PCR, and multi-species methods based on metabarcoding and metagenomics.

Core concepts introduced: environmental DNA, community DNA, trace DNA, metabarcoding, qPCR, stochasticity and reproducibility, quantitative value.

Session 2. Introduction to metabarcoding procedures. The metabarcoding pipeline.

In this session participants will be introduced to the key concepts of metabarcoding and the different high-throughput sequencing platforms currently available for implementing this technology. Some examples of results that can be obtained from metabarcoding projects are explained. We will outline the different steps of a typical metabarcoding pipeline. In the practical session, we will check that the computing infrastructure for the rest of the course is in place and all the needed software is installed.

Core concepts introduced: high-throughput sequencing, multiplexing, NGS library, metabarcoding pipeline, metabarcoding marker, clustering algorithms, molecular operational taxonomic unit (MOTU), taxonomic assignment

Registration deadline: 2nd October of 2020