Canadian Freshwater Fish Detectionwith Genetics
Standing
Undergraduate
Type of Proposal
Oral Research Presentation
Challenges Theme
Open Challenge
Faculty Sponsor
Daniel Heath
Proposal
Environmental DNA (eDNA) sampling is now routinely utilized to detect aquatic species of conservation concern. Due to the high sensitivity of eDNA assays, DNA sampling can be very effective even when target DNA occurs in low concentrations. However, genetic sequences can be almost identically shared by closely related fish species, constraining the taxonomic resolution of eDNA assays that depend on base pair mismatches to differentiate between taxa. Commonly used metabarcoding assays target sequences approximately 100-150 base pairs in length. To improve taxonomic resolution, we designed two novel universal eDNA metabarcoding (12S) primers that target sequence fragments with significantly greater lengths (250 and 320 base pairs). To validate the amplification of each primer set, we created a list of 21 species from a variety of Canadian freshwater fish taxonomic groups, including, but not limited to, lamprey, sturgeon, and major teleost (bony) fish groups. Overall, the assays successfully amplified all selected species, but Lamprey exhibited limited amplification. To further assess marker performance, we conduct a full-factorial experiment in which DNA from artificial communities is spiked into environmental DNA samples. Mock communities will vary in i) the number of species present (7 or 15 species); and (ii) the distribution of DNA concentrations across species (a few ‘common’/mostly ‘rare,’ even distribution, a few ‘rare’/’mostly’ common). Detecting endangered and rare fish species and monitoring their environments is essential for wildlife conservation and management. The metabarcoding assays designed herein will improve the capacity to locate species of conservation concern and facilitate the detection of invasive species.
Grand Challenges
Viable, Healthy and Safe Communities
Canadian Freshwater Fish Detectionwith Genetics
Environmental DNA (eDNA) sampling is now routinely utilized to detect aquatic species of conservation concern. Due to the high sensitivity of eDNA assays, DNA sampling can be very effective even when target DNA occurs in low concentrations. However, genetic sequences can be almost identically shared by closely related fish species, constraining the taxonomic resolution of eDNA assays that depend on base pair mismatches to differentiate between taxa. Commonly used metabarcoding assays target sequences approximately 100-150 base pairs in length. To improve taxonomic resolution, we designed two novel universal eDNA metabarcoding (12S) primers that target sequence fragments with significantly greater lengths (250 and 320 base pairs). To validate the amplification of each primer set, we created a list of 21 species from a variety of Canadian freshwater fish taxonomic groups, including, but not limited to, lamprey, sturgeon, and major teleost (bony) fish groups. Overall, the assays successfully amplified all selected species, but Lamprey exhibited limited amplification. To further assess marker performance, we conduct a full-factorial experiment in which DNA from artificial communities is spiked into environmental DNA samples. Mock communities will vary in i) the number of species present (7 or 15 species); and (ii) the distribution of DNA concentrations across species (a few ‘common’/mostly ‘rare,’ even distribution, a few ‘rare’/’mostly’ common). Detecting endangered and rare fish species and monitoring their environments is essential for wildlife conservation and management. The metabarcoding assays designed herein will improve the capacity to locate species of conservation concern and facilitate the detection of invasive species.