Lahontan Cutthroat Trout (Oncorhynchus clarkii henshawi) and Paiute Cutthroat Trout (Oncorhynchus clarkii seleniris) Detection from Environmental DNA Samples: A Dual-Purpose Assay

Lahontan cutthroat trout (Oncorhynchus clarkii henshawi) and Paiute cutthroat trout (Oncorhynchus clarkii seleniris) are rare taxa of conservation concern. Their generally low population densities and remote distribution make traditional sampling difficult, but they primarily exist in small streams, a habitat type where environmental DNA (eDNA) sampling has proven extremely effective. We developed a single eDNA assay that allows sensitive detection of both taxa, which occur separate from each other in different regions of the Lahontan Basin. Performance of the assay was evaluated using most lineages of Lahontan cutthroat trout and Paiute cutthroat trout as well as tissues of other cutthroat trout and rainbow trout that have been introduced within the Lahontan Basin. The assay amplified DNA only from the target taxa, and only from eDNA samples collected where those taxa were known to be present. This assay should enhance the ability of managers to more precisely and efficiently describe the distribution of these taxa.