Estimating the Distribution of Juvenile Chinook Salmon Using Habitat Modeling and Environmental DNA in an Interior Alaska River Basin

Identification and protection of anadromous water bodies in Alaska are critical in light of increasing threats to fish populations, yet challenging given budgetary and logistical limitations. Non-invasive, 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 Chinook Salmon rearing habitats and select sites to sample throughout the Chena River basin for juvenile occupancy using environmental DNA (eDNA). Water samples were collected from 75 tributary sites in 2014 and 2015 and eDNA was extracted from water samples and amplified using quantitative PCR.  The IP model predicted over 900 stream-km in the basin to support high quality (IP > 0.75) rearing habitat. Occupancy estimation based on eDNA samples indicated that 80.2% (± 9.6 SE) of previously unsampled sites classified as high IP were occupied, supporting the utility of this model framework. The probability of detection of Chinook Salmon DNA from three replicate water samples was high (0.74 ± 0.05 SE) but varied with tributary area. Our results will provide tools for managers to rapidly and efficiently map critical rearing habitats and prioritize sampling efforts to expand the known distribution of juvenile salmon in interior Alaska streams.