Practices in Environmental DNA

Course Description:

The Introduction to eDNA course provides participants with a comprehensive understanding of environmental DNA (eDNA) and its applications in environmental sciences. Participants will learn about the origins of eDNA, how it enters the environment, and its significance in measuring biodiversity. The advantages and disadvantages of using eDNA as a tool will be explored. The course begins with an overview of eDNA, including its definition and different ecosystems where it can be studied. Participants will gain insights into the historical development of eDNA and its current applications. They will also learn about the differences between barcoding and metabarcoding techniques.

Practical application of eDNA is a key focus of the course. Participants will engage in paper discussions, searching for relevant papers and generating ideas for potential eDNA applications. They will explore the advantages and disadvantages of eDNA compared to traditional sampling methods. Graphical materials will be provided to illustrate the concept of eDNA and its application examples. Sampling methods and designs will be explored in detail. Participants will discuss the strengths and weaknesses of different sampling designs and learn about biological replicates and the behavior of eDNA in the environment. Practical exercises, including a virtual landscape exercise and a field sampling excursion, will provide hands-on experience in selecting optimal sampling points and using sampling equipment.

The laboratory analysis module will introduce participants to the necessary laboratory steps involved in eDNA analysis. They will learn about clean lab requirements, contamination prevention, and the use of technical replicates and controls. Detailed instructions will be provided for DNA extraction and target amplification in different environments such as freshwater, marine water, and soil. Bioinformatics analysis of eDNA data will be a key focus of the course. Participants will learn about the importance of data storage, data cleaning, and sources of errors. They will gain insights into the bioinformatics workflow, including filtering, clustering, and taxonomic assignment of DNA sequences. Practical exercises will allow participants to apply bioinformatics tools and analyze eDNA data.

The course concludes with a module on ecological interpretation, where participants will learn how to interpret signals and analyze sequencing depth and PCR/sample numbers. Different types of data analysis, such as computing metrics for functional diversity, will be explored. Participants will have the opportunity to work on case studies and perform data analysis using provided datasets and R codes. The final module focuses on decision-making in eDNA projects. Participants will learn how to draft their own eDNA project proposals and critically reflect on potential problems and solutions. Stakeholders will share their perspectives on how eDNA can help them, providing real-world insights into the practical applications of eDNA.

Throughout the course, a combination of videos, textual resources, and interactive activities will facilitate learning and knowledge application. Participants will have opportunities for peer review and evaluation to enhance their understanding and skill development in the field of eDNA.