Queen's University Environmental DNA Workshop 2023

Stylized image of DNA

Where: Queen's University Biological Station - Opinicon Campus

When: Arriving Sunday, July 23rd to Friday, July 28th 2023

Target audience: professional biologists in governmental or consulting sectors, NGO personnel, senior undergraduates and grad students seeking additional skills

Registration: Meals & accommodations included.

Students $850, General Public/Professionals $1100

Transportation to/from Kingston and the Biological Station is included (from Queen's University main campus or Kingston bus or train stations)

Participants will receive a Queen's University micro-credential.

Synopsis: Environmental DNA (eDNA) is becoming a mainstay of non-invasive, reliable, and cost-effective surveys of at-risk and invasive species, pathogen detection, and biodiversity assessment. These approaches rely on the fact that organisms leave their DNA in the environment, making it possible to detect their presence without capture or even direct observation. Reliable eDNA data depend on field and lab rigorous technique because significant biases can occur through the process from the sampling to the data processing, and they greatly influence species detection results.

Drone shot of water sampling
Water sampling on the St. Lawrence. Photo. Allen Tian

This eDNA workshop will provide a broad overview of the approaches used in eDNA studies for both single-species and multi-species detections. This five-day course will benefit those interested in undertaking or overseeing eDNA studies, or evaluating research proposals and research, especially in management and monitoring applications. The workshop includes lectures, field and lab demonstrations, and hands-on training in analysis and interpretation of data, but does not require detailed knowledge of genetics or molecular biology. We offer a background on sources and fates of eDNA  in the environment, methods and applications with emphasis on design, implementation, analysis and interpretation of species-specific and multi-species eDNA approaches. We will cover advantages and limitations of each , as well as the precautions needed through the whole process to get robust data. We will provide a manual that includes method overviews, field and lab protocols, links to key web resources, and useful literature.

Instructors (click on names for bios): Dr. Steve Lougheed, Allen Tian, Stafford Maracle

Consultants: Dr. Yuxiang Wang, Dr. Orianne Tournayre

Guest speakers: Dr. Robert Hanner (University of Guelph) on Monday, July 24th 7-8 PM, and Dr. Chris Wilson (MNRF) on Wednesday, July 26th 7-8 PM 

Timetable for 2023 workshop.

Sunday Late afternoon Arrival at QUBS
  5:30-6:30 PM Dinner
  7:00-8:00 PM Welcome to QUBS - Introductions
Monday 7:30-8:30 AM Breakfast
  9:00-10:15 AM Presentation: Overview of eDNA (Lougheed)
  10:15-10:30 AM Break
  10:30AM-noon Presentation: Introduction to eDNA study design, qPCR, ddPCR (Tian)
  12:00-1:00 PM Lunch
  1:00-2:15 PM Presentation: Overview of fieldwork, sampling, filtration, transport, storage, extraction (Tian)
  2:15-2:30 PM Break
  2:30-5:30 PM Field practicum: Sampling water, sediment, and soil + metadata collection + water filtration (Tian & Maracle)
  5:30-6:30 PM Dinner
  7:00-8:00 PM Guest Speaker: Dr. Robert Hanner (Guelph University). 
Tuesday 7:30-8:30 AM Breakfast
  9:00-10:15AM Practicum: DNA extraction of samples collected the day before - (QIAGEN Powerwater kit, QIAGEN Powersoil kit) part 1
  10:15-10:30AM Break
  10:30-12:00 Practicum: DNA extraction of samples collected the day before - (QIAGEN Powerwater kit, QIAGEN Powersoil kit) part 2
  12:00-1:00PM Lunch
  1:00-3:15PM Practicum: Bio-RAD qPCR demo: qPCR. While the qPCR runs, presentation on capabilities of qPCR and dPCR.
  3:15-3:30PM Break
  3:30-5:30PM Lecture: Bio-RAD. Interpretation of qPCR results. Second part of session. Primer design for qPCR (and for ddPCR).
  5:30-6:30PM Dinner
  7:00-8:00 PM Lecture: Data analysis and interpretation of qPCR results, with a case study (Tian)
Wednesday 7:30-8:00 AM Breakfast
  8:00 - 9:40 Lecture: Overview of metabarcoding and high throughput sequencing platforms. (Maracle)
  9:40-9:45 AM Break
  9:45-noon Lab practicum: Polymerase chain reaction: Prepare mix and run PCR (Tian & Maracle)
  noon-1PM Lunch
  1-3:30 PM Lecture: Presentation: Library prep and DNA quantification (Tian)
  3:30-4:00 PM Break
  4:00-5:00 PM Practicum: Loading & Running agarose gels. Estimating insert size. Qubit + Nanodrop.
  5:30-6:30 PM Dinner
  7:00-8:00 PM QUBS weekly seminar. Dr. Chris Wilson
Thursday 7:30-8:30 AM Breakfast
  8:30 - 9:30 AM Lecture: General introduction to command line interface
  9:30 -10:00 AM Break
  10:00 - 11:30 Practicum: Practicum: Command line troubleshooting (Tian & Maracle)
  11:30- 12:30 Lecture: Bioinformatics data interpretation
  12:30 -1:30 PM Lunch
  1:30-3:00 PM Practicum: Bioinformatics analysis & interpretation of metabarcoding results. Part 1 (Maracle)
  3:00-3:30 PM Break
  3:30-5:30 PM Practicum: Bioinformatics analysis & interpretation of metabarcoding results. Part 2 (Maracle)
  5:30-6:30 PM Dinner
  7:00-8:30 PM Quiz
Friday 7:30-8:30 AM Breakfast
  9:00 AM-noon  Quiz results and debrief. Depart