It’s complicated…environmental DNA as a predictor of trout and char abundance in streams

Adam Sepulveda; Robert Al-Chokhachy; Matthew Laramie; Kyle Crapster; Ladd Knotek; Brian T. Miller; Alexander V. Zale; David S. Pilliod

doi:10.1139/cjfas-2020-0182

USGS · 70219104

It’s complicated…environmental DNA as a predictor of trout and char abundance in streams

Adam Sepulveda·Robert Al-Chokhachy·Matthew Laramie·Kyle Crapster·Ladd Knotek·Brian T. Miller·Alexander V. Zale·David S. Pilliod

View original source ↗Export metadata ↓

Abstract

The potential to provide inferences about fish abundance from environmental (e)DNA samples has generated great interest. However, the accuracy of these abundance estimates is often low and variable across species and space. A plausible refinement is the use of common aquatic habitat monitoring data to account for attributes that influence eDNA dynamics. We therefore evaluated the relationships between eDNA concentration and abundance of bull trout ( Salvelinus confluentus ), westslope cutthroat trout ( Oncorhynchus clarkii lewisi ) and rainbow trout ( Oncorhynchus mykiss ) at 42 stream sites in the Intermountain West (USA and Canada) and tested whether accounting for site-specific habitat attributes improved the accuracy of fish abundance estimates. eDNA concentrations were positively associated with fish abundance, but these relationships varied by species and site, and there was still considerable variation unaccounted for. Random site-level differences explained much of this variation, but specific habitat attributes of those sites explained relatively small amounts of this variation. Our results underscore that either eDNA sampling or environmental characterization will require further refinement before eDNA can be used reliably to estimate fish abundance in streams.

Explore related subjects

Canadian Journal of Fisheries and Aquatic Sciences Article

Source-reported bounding extent: 43.77109381775651° to 49.439556958940855° latitude; -120.4541015625° to -111.4013671875° longitude. This indicates report coverage, not an exact sampling location. View area on OpenStreetMap.

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Adam Sepulveda, Robert Al-Chokhachy, Matthew Laramie, Kyle Crapster, Ladd Knotek, Brian T. Miller, Alexander V. Zale, David S. Pilliod. 2021. It’s complicated…environmental DNA as a predictor of trout and char abundance in streams. https://doi.org/10.1139/cjfas-2020-0182

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related USGS reports

USGS2026

A framework for estimating age and growth using sibship relationships inferred from genomic data

Pedigree reconstruction based on genomic data offers a novel approach for estimating age and growth in wild populations. However, frameworks that use reconstructed pedigrees to parameterize growth models have not been available. We developed a sibship age and growth framework and evaluated the approach using simulation and an empirical application to Sea Lamprey ( Petromyzon marinus ) age and growth analysis. Simulation research revealed that the framework may be widely applicable to semelparous fishes. Applicability to iteroparous fishes was constrained to scenarios in which the percentage of multi-age sibling groups was low. Age assignment using the framework was unbiased for sibling groups first captured at younger ages. Age assignment for sibling groups first captured at older ages (after growth rate had substantially slowed) was biased low due to the hierarchal approach that we adopted to estimate sibling group age-at-first capture. However, this did not result in biased growth parameter estimates. Model output allowed for identification of unreliable age assignments. Finally, the empirical application provided evidence that the framework could address knowledge gaps that have been challenging to address with established age and growth methods.

Canadian Journal of Fisheries and Aquatic Sciences↗

USGS2026

Identifying overlap between native fish movements and a possible seasonal Grass Carp deterrent in the Sandusky River, Ohio, USA

Riverine fishes are vulnerable to habitat fragmentation caused by interrupted access to vital habitats. Fragmentation using artificial structures can be used to limit the spread of invasive fishes by inhibiting movement between critical habitats. Thus, tradeoffs exist between maintaining connectivity for native species and restricting movement of invasive fishes. A nonphysical deterrent has been proposed to prevent invasive Grass Carp ( Ctenopharyngodon idella ) from reaching spawning habitats in the Sandusky River, a tributary to Lake Erie, during late spring–summer. However, this timing overlaps with spawning periods of a suite of native fishes. We used acoustic telemetry and ichthyoplankton surveys to examine movement and spawning activity of multiple native species and to assess potential impacts of deterrent operation on reproduction. All species used the proposed deterrent location during the Grass Carp spawning period, and their movements corresponded with larval fish collections, indicating upstream spawning. These findings suggest the deterrent could unintentionally restrict native species’ access to essential habitats. Balancing habitat connectivity and invasive species control will likely depend on species-specific responses and careful timing of deterrent operation.

Ohio↗

USGS2026

Availability of dark daytime refuge may limit mysid abundance in the Laurentian Great Lakes

The zooplankton Mysis diluviana is a major component of the Laurentian Great Lakes food web and has recently declined in abundance in both lakes Michigan and Huron. Drivers of these declines are not well understood. Here, we explore the hypothesis that recent increases in water clarity have contributed to the decline of M. diluviana (mysids) by limiting the availability of daytime dark refuge from visual predators. Using Secchi depth data from 1996 to 2021, we estimate that dark refuge has decreased substantially in lakes Michigan and Huron where mysids have declined, but dark refuge has remained more stable in lakes Ontario and Superior where mysid populations did not decline. Results from a 2021 uncrewed surface vessel hydroacoustic survey and lake-wide, net-based sampling in lakes Michigan and Huron revealed significantly more mysids in areas with dark refuge, such as Lake Michigan’s northern basin. Conversely, Lake Huron contains sparse dark refuge consistent with low mysid densities in that lake. Higher water clarity leading to increased predation may be a primary driver of mysid declines in the Great Lakes.

Laurentian Great Lakes↗