A software tool for environmental DNA survey design and data analysis - ON-185

Preferred Disciplines: Statistics, Software (Masters or PhD)
Company: Precision Biomonitoring Inc.
Project Length: 6 months (1 unit)
Desired start date: As soon as possible
Location: Guelph, ON
No. of Positions: 1
Preferences: Southern Ontario

About the Company: 

Precision Biomonitoring Inc. (PBI) is a pioneer and a leader in environmental DNA (eDNA) survey services. Our primary customers are environmental consulting firms that need to carry out assessment of sites for the presence of endangered or invasive species. Our advanced approach offers clients end-to-end cost-effective solutions that incorporate ground-breaking innovations in biomonitoring.  

Project Description:

Dozens of species can be detected from a single environmental sample using modern molecular techniques such as qPCR. A factor limiting the efficiency of eDNA survey methods, however, is the lack of a software tool to design a survey that answers a specific purpose and integrates the multiple variables that influence the outcome of the survey. As of now, survey strategies are designed empirically and do not integrate optimally all the variables pertaining to a specific site targeted for assessment. This lack of customization impacts the outcome of the survey. There is an acute need for a software tool that will generate survey designs customized for a specific site.

The goal of this project is to build a flexible statistical tool in R that can generate an eDNA survey design based on environmental data and perform species occupancy analysis (probability of presence/absence) using eDNA analytical results from appropriately collected samples.

Research Objectives:

  1. This software tool will generate survey and sampling designs tailored to the individual study sites and produce actionable results by ensuring that the research output is standardized, transparent, clearly understandable, and useful for the company.
  2. The proprietary tool is structured to operate only with the company’s proprietary workflow, and accessible only to the company.
  3. Automated tools for study design and data analysis will increase service efficiency, keeping costs competitive and maximizing the quality of deliverables.

Methodology:

  1. Reviewing the latest literature and consult with the company to infer the current best practices for eDNA survey design. This will also involve identifying those variables most important to consider when designing eDNA surveys.
  2. Based on the outcomes of that research, code in R a tool that will take input variables (e.g., target species ecology, site data, a map of the intended study area, environmental factors known to affect eDNA dispersion and degradation etc.…) and use these variables to populate a map of points indicating an eDNA survey design with specified numbers of samples, volume of samples, sampling locations, sampling depth etc.…
  3. Then, working with the species eDNA detection data, create a data analysis module tailored to the survey design that will output maps of species occupancy probability. Data product outputs will be standardized to lend themselves effectively to reporting requirements.

Expertise and Skills Needed:

  • Statistics
  • Coding in R an other software
  • Algorithms

For more info or to apply to this applied research position, please

  1. Check your eligibility and find more information about open projects
  2. Interested students need to get the approval from their supervisor and send their CV along with a link to their supervisor’s university webpage by applying through the webform.
Program: