Environmental DNA marker development with sparse biological information: A case study on opossum shrimp (Mysis diluviana)Author(s): K. J. Carim; K. R. Christianson; Kevin McKelvey; W. M. Pate; D. B. Silver; B. M. Johnson; B. T. Galloway; Michael Young; Michael Schwartz
Source: PLoS ONE. 11: e0161664.
Publication Series: Scientific Journal (JRNL)
Station: Rocky Mountain Research Station
Download Publication (252.0 KB)
The spread of Mysis diluviana, a small glacial relict crustacean, outside its native range has led to unintended shifts in the composition of native fish communities throughout western North America. As a result, biologists seek accurate methods of determining the presence of M. diluviana, especially at low densities or during the initial stages of an invasion. Environmental DNA (eDNA) provides one solution for detecting M. diluviana, but building eDNA markers that are both sensitive and species-specific is challenging when the distribution and taxonomy of closely related non-target taxa are poorly understood, published genetic data are sparse, and tissue samples are difficult to obtain. To address these issues, we developed a pair of independent eDNA markers to increase the likelihood of a positive detection of M. diluviana when present and reduce the probability of false positive detections from closely related non-target species. Because tissue samples of closely-related and possibly sympatric, non-target taxa could not be obtained, we used synthetic DNA sequences of closely related non-target species to test the specificity of eDNA markers. Both eDNA markers yielded positive detections from five waterbodies where M. diluviana was known to be present, and no detections in five others where this species was thought to be absent. Daytime samples from varying depths in one waterbody occupied by M. diluviana demonstrated that samples near the lake bottom produced 5 to more than 300 times as many eDNA copies as samples taken at other depths, but all samples tested positive regardless of depth.
- You may send email to firstname.lastname@example.org to request a hard copy of this publication.
- (Please specify exactly which publication you are requesting and your mailing address.)
- We recommend that you also print this page and attach it to the printout of the article, to retain the full citation information.
- This article was written and prepared by U.S. Government employees on official time, and is therefore in the public domain.
CitationCarim, K. J.; Christianson, K. R.; McKelvey, K. S.; Pate, W. M.; Silver, D. B.; Johnson, B. M.; Galloway, B. T.; Young, M. K.; Schwartz, M. K. 2016. Environmental DNA marker development with sparse biological information: A case study on opossum shrimp (Mysis diluviana). PLoS ONE. 11: e0161664.
Keywordsenvironmental DNA marker, eDNA, opossum shrimp, Mysis diluviana
- A blocking primer increases specificity in environmental DNA detection of bull trout (Salvelinus confluentus)
- Using environmental DNA sampling to monitor the invasion of nonnative Esox lucius (northern pike) in the Columbia River basin, USA
- An environmental DNA marker for detecting nonnative brown trout (Salmo trutta)
XML: View XML