title: Development of species-specific primers with potential for amplifying eDNA from imperilled freshwater unionid mussels.
abstract: Environmental DNA (eDNA) is emerging as a potentially powerful tool for inferring species' presence, and hence occupancy, from DNA that is shed into environmental samples such as water. Although eDNA screening has been used to detect DNA from a variety of taxonomic groups, it has not yet been used to identify DNA from species with numerous potentially sympatric confamilial species, a situation that may preclude the development of species-specific markers. There are 41 native freshwater mussel species (Unionidae) in Ontario, Canada. Many of these are potentially sympatric, and 14 species have been formally assessed as endangered, threatened, or special concern. We investigated whether there was sufficient variation within the cytochrome oxidase region (COI) to develop species-specific eDNA markers for at-risk unionids. We developed 32 COI markers for eight unionid species, and tested each of these on the target species plus 29 potentially sympatric unionid taxa. Six of these markers amplified DNA only from the intended target species. We then extracted and amplified mussel eDNA from rearing-tank water samples. We conclude that despite high species diversity, it should be possible to develop eDNA COI markers and screen water samples for habitat occupancy by unionid mussels.
authors.affiliation: a Department of Biology, Trent University, Peterborough, ON, Canada.
authors.forename: Anna
authors.initials: A
authors.lastname: Cho
authors.affiliation: b Department of Fisheries and Oceans, Canada Centre for Inland Waters, Burlington, ON, Canada.
authors.forename: Todd
authors.initials: T
authors.lastname: Morris
authors.affiliation: c Ontario Ministry of Resources and Forestry, Trent University, Peterborough, ON, Canada.
authors.forename: Chris
authors.initials: C
authors.lastname: Wilson
authors.affiliation: a Department of Biology, Trent University, Peterborough, ON, Canada.
authors.forename: Joanna
authors.initials: J
authors.lastname: Freeland
mesh_terms: D000818:Animals; D002170:Canada; D058893:DNA Barcoding, Taxonomic / Q000379:methods; D017931:DNA Primers; D004272:DNA, Mitochondrial; D003576:Electron Transport Complex IV / Q000235:genetics; D005618:Fresh Water; D049876:Unionidae / Q000145:classification* / Q000235:genetics*
chemical_list: D017931:DNA Primers; D004272:DNA, Mitochondrial; D003576:Electron Transport Complex IV
keywords: ADNe; ADNmt; cytochrome oxidase I; cytochrome oxydase I; eDNA; freshwater mussels; moules d’eau douce; mtDNA; unionidae; unionidés