A Rapid‐Assessment Method to Estimate the Distribution of Juvenile Chinook Salmon in Tributary Habitats UsingeDNAand Occupancy Estimation

Abstract

Identification and protection of water bodies used by anadromous species are critical in light of increasing threats to fish populations, yet often challenging given budgetary and logistical limitations. Noninvasive, rapid-assessment, sampling techniques may reduce costs and effort while increasing species detection efficiencies. We used an intrinsic potential (IP) habitat model to identify high-quality rearing habitats for Chinook Salmon Oncorhynchus tshawytscha and select sites to sample throughout the Chena River basin, Alaska, for juvenile occupancy using an environmental DNA (eDNA) approach. Water samples were collected from 75 tributary sites in 2014 and 2015. The presence of Chinook Salmon DNA in water samples was assessed using a species-specific quantitative PCR (qPCR) assay. The IP model predicted over 900 stream kilometers in the basin to support high-quality (IP ≥ 0.75) rearing habitat. Occupancy estimation based on eDNA samples indicated that 80% and 56% of previously unsampled sites classified as high or low IP (IP < 0.75), respectively, were occupied. The probability of detection (p) of Chinook Salmon DNA from three replicate water samples was high (p = 0.76) but varied with drainage area (km 2 ). A power analysis indicated high power to detect proportional changes in occupancy based on parameter values estimated from eDNA occupancy models, although power curves were not symmetrical around zero, indicating greater power to detect positive than negative proportional changes in occupancy. Overall, the combination of IP habitat modeling and occupancy estimation provided a useful, rapid-assessment method to predict and subsequently quantify the distribution of juvenile salmon in previously unsampled tributary habitats. Additionally, these methods are flexible and can be modified for application to other species and in other locations, which may contribute towards improved population monitoring and management.

Environmental DNA is an effective tool to track recolonizing migratory fish following large‐scale dam removal

“…Our study is among a growing body of literature demonstrating that eDNA can be used to monitor the presence, occurrence, and spatial extent of fish populations (Laramie, Pilliod, & Goldberg., 2015; Matter, Falke, López, & Savereide, 2018; Ostberg et al., 2019; Rees et al., 2014; Wilcox et al., 2013) and to assess river connectivity for migratory fishes (Yamanaka & Minamoto, 2016). In the case of the Elwha River, we used eDNA to assess the presence of fish in upstream areas of the watershed that were previously inaccessible due to the presence of the dams, which provides evidence that key objectives for the dam removal project (i.e., fish passage, restoring connectivity) are being met for several focal species (Peters et al., 2014).…”

Applications of environmental DNA (eDNA) in ecology and conservation: opportunities, challenges and prospects

“…Although there is increasing global concern about declines in populations of wildlife (Jia et al 2018;Saha et al 2018;Sekercioglu et al 2019), monitoring the population dynamics of some species remains a challenge, partly due to large uncertainties in their geographic distributions, limited understanding of their lifestyles, the complexity of their life histories, and methodological constraints (Riggio et al 2018;Srinivasan 2019;Wineland et al 2019). eDNA analyses have enhanced the monitoring of wildlife species distribution and abundance over large spatial and temporal scales using efficient, sensitive and standardized methods (Matter et al 2018;Hobbs et al 2019;Itakura et al 2019).…”

“…Cases where eDNA is detected in the environment in the absence of target organisms (false positives, (Ficetola et al 2015;Ficetola et al 2016;Lahoz-Monfort et al 2016;Stoeckle et al 2016;Guillera-Arroita et al 2017)) or where eDNA is not detected but the target organism is present (false negatives, (Morin et al 2001;Ficetola et al 2008;Schmidt et al 2013;Ficetola et al 2015;Willoughby et al 2016;Doi et al 2019)) are common. Although site occupancy models have been proposed as a way to account for imperfect detection, they largely depend on the number of replicate samples per site and on the number of replicate amplifications per DNA sample (PCR), which vary considerably across taxa (Schmidt et al 2013;Matter et al 2018;Chen & Ficetola 2019;Doi et al 2019;Strickland & Roberts 2019). Causes of false detections include…”

Vulnerability of Pacific salmon to invasion of northern pike (Esox lucius) in Southcentral Alaska

“…This method allows for characterization of fish habitat quality at the stream reach scale (100-1000 m), over large portions of the landscape. Intrinsic potential models have been used to predict the distribution of salmonid habitat in the Pacific Northwest region of the conterminous U.S. and Alaska [34][35][36]. Generally, IP models use static, reachscale, geomorphic attributes to assign a suitability value for a species [34].…”