Certain detection of uncertain taxa: eDNA detection of a cryptic mountain sucker ( Pantosteus jordani ) in the Upper Missouri River, USA

Abstract A lineage of the Mountain Sucker species complex (Pantosteus jordani) exists as a genetically and morphologically distinct taxon restricted to the Missouri River basin. This species is thought to be declining throughout its range and is assumed to be extirpated from the southern portion of its distribution. We developed a quantitative PCR‐based environmental DNA assay for P. jordani to help define and monitor its current range. The assay is both specific to P. jordani and sensitive to low amounts of DNA, with a detection limit of 10 DNA copies per reaction. In vitro experiments involved testing DNA from twenty tissue samples, collected from the Missouri River basin in Montana and Wyoming. The assay efficiently detected DNA of all P. jordani samples and did not amplify DNA of any closely related nontarget species. Additionally, 29 environmental DNA samples were taken in 19 waterbodies within P. jordani range and its presence or absence was determined prior to sampling at six of 29 sites. All sites where P. jordani was known absent produced negative results, and all sites where it was known present were confirmed with environmental DNA detections. The new assay was able to detect P. jordani at ten sites which were not previously known to contain individuals, demonstrating that this tool has the potential to rapidly expand the current understanding of this taxon's distribution.