Open AccessEnvironmental DNA Marker Development with Sparse Biological Information: A Case Study on Opossum Shrimp (Mysis diluviana)
Author(s) -
Kellie J. Carim,
Kyle R. Christianson,
Kevin M. McKelvey,
William M. Pate,
Douglas Silver,
Brett M. Johnson,
Benjamin Thomas. Galloway,
Michael K. Young,
Michael K. Schwartz
Publication year - 2016
Publication title -
plos one
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.99
H-Index - 332
ISSN - 1932-6203
DOI - 10.1371/journal.pone.0161664
Subject(s) - environmental dna , biology , sympatric speciation , taxon , annelid , ecology , range (aeronautics) , zoology , biodiversity , materials science , composite material
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.