eDNA reveals spatial differences in species composition of protected rockfishes

Abstract

Rare species are difficult and time-consuming to detect, but environmental DNA (eDNA) methods can be used to increase data availability for monitoring and management. Here, we use the diverse rockfish species flock (genus Sebastes) to demonstrate the utility of eDNA as a tool for detecting rare and difficult to observe species in the marine environment. We describe the identification of a phylogenetically informative gene region for eDNA metabarcoding which uniquely identifies 93 of the 109 Sebastes species currently described. We then use this assay to differentiate rockfish communities in field samples collected from two sub-basins within Puget Sound in Washington, USA. Across three field sampling platforms, we found that sample collection location (distance from seafloor) has substantial impacts on rates of detection and on the diversity of species detected, likely reflecting the habitat preferences of the target species. This metabarcoding region provides an important tool for rockfish monitoring, both within Puget Sound and across the North Pacific. More generally, this work speaks to the usefulness of eDNA data as a tool for the conservation and management of rare and difficult-to-distinguish species.

Fig 1. Geographic locations sampled in this study.

Shapes represent the sampling platforms used at each location. Site names denote whether each site was a Hood Canal environment (HC) or Admiralty Inlet environment (AI), as shown in Fig 3. Inset shows the sampling map location relative to the west coast of North America. Seattle, WA is annotated for reference. Bathymetry and topography are sourced from the ETOPO 2022 global relief model from NOAA National Centers for Environmental Information. Bathymetry and topography data are freely available through the Creative Commons Zero 1.0 Universal Public Domain Dedication.

Fig 2. Neighbor-joining tree of Sebastes species occurring in Puget Sound and the greater Salish Sea.

Species with Distinct Population Segments (DPS) in Puget Sound listed under the Endangered Species Act as Threatened or Endangered are highlighted in orange and red, respectively. Species of special concern in Washington State are highlighted in blue. The UPGMA tree was visualized based on MAFFT alignment. Scale bar represents genetic distance.

Fig 3. Range of near-bottom environments experienced at each sampling location, for temperature (top row), salinity (middle row), and oxygen (bottom row), across the 2024 calendar year.

Environmental ranges at each sampling location were used to classify sampling sites as Hood Canal-like or Admiralty Inlet-like. Raincloud plots show the density of modeled values across the full environmental range for each station; boxplots extend from the lower quantile to the upper quantile, and whiskers indicate the total range excluding outliers. See Fig 1 for the geographic location of each site.

Fig 4. Detection of each of the seven Sebastes species observed by metabarcoding of eDNA samples.

Ticks along the x-axis represent discrete biological samples collected in the field. Each sample indicates a unique biological replicate, including water filtered by any method, from any depth, at any station, within the two basins. Heatmap colors denote presence and absence of species in each sample. Samples collected from Admiralty Inlet and Hood Canal are shown in separate panels, following the basins denoted in Fig 2. Species names are colored by their conservation status: red = threatened (DPS); blue = special concern (WA state).

Fig 5. The number of Sebastes species observed in each biological sample decreases with distance from the seafloor.

Each biological sample is shown by a partly opaque circle, colors indicate sampling platform. Points are jittered vertically for visibility; all species counts are integers. Shaded region indicates the 95% credible interval. All Smith Root samples were collected as surface grabs, across locations with different bottom depths.