A validated and optimized environmental DNA and RNA assay to detect Arctic grayling (Thymallus arcticus)

Abstract

Arctic grayling (Thymallus arcticus) is a salmonid fish of significant conservation value. However, conservation efforts are hindered by a lack of fundamental information regarding details such as current population distribution, migratory patterns, and natal habitats. In the current study, we designed, optimized, and field- and laboratory-validated an environmental DNA (eDNA) and environmental RNA (eRNA) assay for Arctic grayling biomonitoring. Using an in silico approach, a robust species-specific eDNA assay was generated, and filtering and extraction protocols were optimized for maximal eDNA yield. A Preserve, Precipitate, Lyse, Precipitate, and Purify (PPLPP) extraction method generated 70-fold higher eDNA yields than a column-based approach. Species-specificity relative to co-occurring salmonid fish was validated, and no significant amplification was noted for rainbow trout, brook trout, or mountain whitefish. Shedding rates of eDNA were around eight to nine times higher than those of eRNA, although the two types of nucleic acids decayed at similar rates. Shedding and decay rates were subsequently used to build detection probability models that account for pool size and water exchange rates. These data indicate that eDNA and eRNA are detectable in pools up to 32,500 m3 in volume and with water flow of less than 0.5 m3s−1 when an Arctic grayling is present. This knowledge can be implemented when designing field sampling strategies. Finally, the assay successfully amplified Arctic grayling eDNA from field-collected samples, with signal strength indicating preferred Arctic grayling habitat or conditions that favored the concentration and retention of eDNA.