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. 2026 Oct 6;36(7):e70323. doi: 10.1002/eap.70323

Using environmental DNA to identify emerging Pacific salmon habitats and support Indigenous governance

Mark Louie D Lopez 1,✉, Isabel G Ma 1, Samantha Vincent 2, Caren C Helbing 1, Michael H H Price 3,4
PMCID: PMC13639513  PMID: 42834790

Abstract

Northern watersheds are facing rapid hydroclimatic reorganization driven by climate warming, glacier retreat, and intensifying land use. These changes are altering the distribution and accessibility of aquatic habitats, creating both risks and opportunities for cold‐adapted species such as Pacific salmon (Oncorhynchus spp.). Effective responses require monitoring approaches capable of detecting contemporary habitat use, as well as emerging or intermittent occupancy in remote and rapidly changing landscapes where conventional monitoring is constrained. Here, we evaluated a species‐targeted, quantitative polymerase chain reaction‐based, environmental DNA framework using paired water and sediment samples to detect Pacific salmon in frontier habitats within a well‐established salmon system of the Skeena River watershed, northwest British Columbia. Paired samples were collected during aerial surveys in 2023–2024 and analyzed using validated assays and rigorous quality controls. Across sites and species, environmental DNA in water provided consistent detection of contemporary salmon presence, particularly in known‐occupancy systems with high spawning abundance. Sediment environmental DNA detections were more variable but occurred frequently at sites where water samples did not detect fish. In discordant cases, sediment more often detects salmon than water, indicating that sediment integrates biological signals over longer temporal windows and captures emerging or early‐onset, low‐density habitat use missed by water sampling. Together, environmental DNA in water and sediment provide complementary perspectives on salmon occupancy across dynamic, glacier‐influenced flow conditions. Environmental DNA surveys revealed salmon presence in multiple tributaries lacking recent or ancestral observations, demonstrating the capacity of paired‐media monitoring approaches to identify emerging or intermittently used habitats in remote northern watersheds. Paired water‐sediment environmental DNA surveys provide a practical, scalable, and noninvasive framework for detecting salmon habitat use across changing northern river systems. By combining real‐time indicators of presence with longer term signals of intermittent or past use, this approach improves habitat inventories, strengthens cumulative‐effects assessments, and enhances early detection of emerging habitats. Integrating paired‐media environmental DNA into Indigenous‐led monitoring and governance frameworks can help restore critical information flows at a time of declining conventional monitoring capacity, supporting proactive stewardship and informed decision‐making under accelerating climatic and industrial change.

Keywords: fish monitoring, habitat use, Indigenous governance, salmon monitoring, Skeena

INTRODUCTION

Planetary warming is rapidly reshaping ecosystems across the globe. Accelerating temperature rise is driving widespread glacier retreat (Hock et al., 2019; Hugonnet et al., 2021), altering hydrologic regimes (Huss & Hock, 2018), and increasing the frequency of extreme climatic events (IPCC, 2021). These physical changes are transforming freshwater and coastal environments and contributing to accelerating biodiversity loss worldwide (IPBES, 2019; Pimm et al., 2014). Many species are shifting their distributions—moving upslope, poleward, or into newly available habitats—as climate niches reorganize (Chen et al., 2011; Lenoir & Svenning, 2015; Parmesan & Yohe, 2003). Such rapid reorganization highlights the urgent need for tools that can detect where species persist, where they have been lost, and where they may be establishing new populations. In regions undergoing pronounced glacier retreat, newly formed or re‐exposed habitats are expected to be colonized by cold‐adapted taxa tracking suitable thermal niches (Cauvy‐Fraunié & Dangles, 2019; Milner et al., 2017; Sunday et al., 2012), highlighting the importance of early detection.

Environmental DNA (eDNA) has emerged as a powerful method for monitoring biodiversity during periods of rapid environmental change. Because organisms shed genetic material into their surrounding environment, eDNA enables sensitive and noninvasive detection of species, including those that are rare, cryptic, or present at low densities (Deeg et al., 2023; Jerde et al., 2019; Spear et al., 2021). Therefore, eDNA offers a promising approach for assessing species persistence in historically occupied habitats and identifying newly established populations as species shift their ranges (Lacoursière‐Roussel et al., 2016). These strengths make eDNA particularly valuable in dynamic systems experiencing hydrologic reorganization, fragmentation, or the emergence of novel habitats through glacier retreat (Carraro et al., 2018). Because sampling requires minimal equipment and can be performed across broad spatial scales, eDNA also enables expanded community‐based or Indigenous‐led monitoring during periods of rapid ecological change (Deeg et al., 2023).

Pacific salmon (Oncorhynchus spp.) exemplify species for which such monitoring is urgently needed. Salmon are ecologically and culturally foundational, transporting marine‐derived nutrients inland (Schindler et al., 2003), structuring freshwater food webs (Walsh et al., 2020), and supporting Indigenous stewardship and governance systems for millennia (Atlas et al., 2021; Reid et al., 2021). Despite such importance, many salmon populations have declined across the southern portion of their range due to habitat loss, warming rivers, cumulative land‐use pressures, and historical overexploitation (Gustafson et al., 2007; Oke et al., 2020; PSF, 2025; Wilson et al., 2022). At the same time, monitoring of Pacific salmon populations in Canada has declined to historically low levels, particularly in northern and remote watersheds (Price & Moore, 2026). Northern watersheds, long regarded as climate‐resilient strongholds, are now experiencing rapid shifts driven by glacier retreat, rising stream temperatures, and intensifying industrial development (Fellman et al., 2023; Moore et al., 2023; Schnorbus et al., 2014). These transformations are expected to reorganize the distribution and accessibility of critical salmon habitats, including cold‐water refugia, glacial channels, headwater lakes, and estuarine corridors (Moore & Schindler, 2022). Detecting how and when salmon use these emerging habitats is increasingly important for conservation planning and supporting Indigenous Nations as they respond to intensified environmental change across their ancestral territories (SkeenaWild Conservation Trust, 2026).

The Skeena River watershed in northwest British Columbia (BC), Canada's second‐largest salmon ecosystem, supports all five species of Pacific salmon and steelhead trout (O. mykiss) across a diverse network of tributaries, lakes, and estuarine habitats (Gottesfeld et al., 2002). Climate‐driven change, together with cumulative pressures from forestry, mining, agriculture, hydropower development, and urbanization, poses growing challenges for salmon persistence in the region (Price & Daust, 2016). The expanding overlap between fast‐tracked industrial projects (Government of Canada, 2025a) and mining claims in areas projected to become future salmon habitat in northern watersheds, including the Skeena (Moore et al., 2023) emphasizes the need for timely monitoring (Price & Daust, 2020; Price & Berchtold, 2026). Although eDNA is increasingly used to detect the presence of salmon, uncertainties remain regarding how different media perform in flowing river systems. Water samples provide snapshots of eDNA currently in the water column, reflecting recent fish presence and active spawning (Su et al., 2024), while sediment samples integrate eDNA over longer time periods, potentially capturing historical presence and eDNA that has settled from the water column (Lopez, Hicks, et al., 2026; Huston et al., 2023). Water samples may be more sensitive to transient changes in fish presence, whereas sediment samples may provide more stable detection signals that persist through seasonal variation. Here, we use targeted quantitative polymerase chain reaction (qPCR)‐based eDNA assays to compare the effectiveness of water and sediment samples for detecting several Pacific salmon species: coho (O. kisutch), Chinook (O. tshawytscha), and sockeye salmon (O. nerka), across diverse habitats in the Skeena watershed. By evaluating the complementary strengths of these approaches, we aim to improve the detection of emerging habitats for Pacific salmon, refine habitat inventories, and support Indigenous governance and conservation planning during a period of rapid ecological change.

MATERIALS AND METHODS

Upper Widzin Kwa watershed

The Upper Widzin Kwa (commonly known as the Morice watershed) is a glacier‐fed tributary of the Skeena River located within the ancestral territory of the Wet'suwet'en Nation (Figure 1). The watershed is characterized by cold waters, extensive forest cover at lower elevations, and a network of glacier‐ and snowmelt‐influenced tributaries that support important spawning, rearing, and migration habitats for multiple Pacific salmon species (Gottesfeld et al., 2002). At the outlet of Widzin Bin (Morice Lake), summer discharge averages approximately 147 m3/s, and summer surface water temperature averages 14.3°C, reflecting the strong influence of snowmelt‐ and glacier‐fed hydrology. Ongoing glacier retreat and hydrologic change are altering flow, temperature, sediment, and habitat conditions throughout the watershed (Wild et al., 2022), creating opportunities for salmon to expand into previously inaccessible or unsuitable habitats. Several low‐gradient glacier‐fed tributaries in the region lack documented records of salmon occupancy, yet their proximity to existing spawning populations suggests strong potential for contemporary or future colonization. Key physical characteristics of the watershed are summarized in Table 1.

FIGURE 1.

FIGURE 1

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Study area and individual collection sites for eDNA samples in search of target Pacific salmon (Oncorhynchus spp.) from rivers connected to Widzin Bin (Morice Lake) within the Skeena Watershed of British Columbia, Canada.

TABLE 1.

Summary of physical, hydrological, and climatic characteristics of the Upper Widzin Kwa (Morice watershed) study area.

Characteristic Value
Drainage area 4379 km2
Elevation 762 m
Glacier cover 5.96%
Discharge (summer) 147 m3/s
Temperature (summer) 14.3°C
Dominant land cover Forested
Major freshwater lakes Morice, Atna, Nanika, Kid‐Price
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Note: Metrics describe watershed size, elevation, glacier influence, and contemporary flow and temperature conditions relevant to Pacific salmon distribution, and eDNA transport and persistence.

Pacific salmon migration timing in the Widzin Kwa has been closely monitored through fisheries assessment and conservation programs over the last several decades. Adult Chinook typically enter freshwater first (late May to July), followed by sockeye (July to August), and coho (August to October; Gottesfeld et al., 2002). Sampling of eDNA was conducted during periods when one or more focal species were expected to be spawning within the watershed (August to October). Juvenile Chinook, coho, and sockeye generally rear in freshwater for one to three years before ocean migration, contributing to the potential presence of salmon eDNA outside adult spawning periods.

Sample collection

We sampled two of these upstream glacier‐fed tributaries (mean elevation: ~800 m) for the presence of salmon in 2023, and three tributaries (mean elevation: ~780 m) in 2024. Water and sediment samples were collected in triplicate at multiple sites on each river during aerial surveys of spawning salmon as part of a broader research investigation. We also sampled the Nenikëkh (Nanika River, mean elevation: 854 m) as a reference location because it currently hosts coho, Chinook, and large annual concentrations of sockeye salmon, where fish were visually observed spawning at the time of sampling. In all years, 1 L of surface water and approximately 50 g of surface sediment were collected (in triplicate) per site. Water samples were filtered using Nalgene single‐use analytical 0.45‐μm cellulose nitrate filter funnels (Thermo Fisher Scientific, Waltham, MA, USA) connected to a peristaltic pump. Each filter was placed in a coin envelope, sealed in a resealable bag with a tablespoon of silica desiccant beads (Allison et al., 2021), and stored at −20°C. Sediment samples were stored at −20°C until eDNA extraction. All sampling equipment was thoroughly decontaminated between sites using a 3% sodium hypochlorite (NaClO) solution followed by rinsing with copious amounts of deionized water.

eDNA extraction and viability testing

The DNA from filtered water samples was extracted from one‐quarter of each filter membrane using the DNeasy Blood & Tissue Kit in combination with QIAshredder spin columns (QIAGEN Inc., Hilden, Germany), following the manufacturer's protocol. The DNA from sediment (sedDNA) was isolated using 10 g of sediment samples with the Soil DNA Isolation Maxi Kit (Norgen Biotek, Ontario, Canada), with a final elution volume of 3 mL. The resulting sedDNA was further concentrated and purified via a modified ethanol precipitation method and resuspended in 300 μL of TE buffer (10 mM Tris, 1 mM EDTA, pH 8.0) as described by Lopez et al. (2023). DNA integrity and potential PCR inhibition were assessed using the IntegritE‐DNA assay (Veldhoen et al., 2016), which targets chloroplast DNA to verify the presence of amplifiable material. All the recovered eDNA samples had sufficient integrity and were sufficiently free from PCR inhibitors, making them suitable for downstream species‐targeted salmon DNA detection using qPCR‐based assays. All DNA samples were stored at −20°C in a manual defrost freezer until qPCR analysis.

eDNA assay design and validation

All species‐specific eDNA assays used in the present study (Table S1) were developed and validated following the framework described by Langlois et al. (2021), with full assay details reported in Langlois et al. (2025). Primer and probe sets were designed from complete mitochondrial genome sequences using the unikseq pipeline (Allison et al., 2023; Lopez et al., 2025). The unique mitochondrial regions identified by this pipeline were used to design primers and probes in Beacon Designer 8.21 (PREMIER Biosoft, California, USA).

Assay specificity was confirmed using genomic DNA (gDNA) from both target species and closely related sympatric taxa. To assess analytical sensitivity, synthetic DNA fragments (gBlocks, Integrated DNA Technologies) were serially diluted to generate standard curves. Limits of detection (LODs) and quantification (LOQs) were calculated using the eLowQuant tool, which applies a modified binomial‐Poisson model (Lesperance et al., 2021). The continuous limit of detection (LOQcontinuous), the lowest copy number detected in at least 95% of replicates, was also determined following Lesperance et al. (2021). This metric represents the threshold separating quantification using continuous Ct data from binomial detection data. DNA concentrations. PCR efficiency, representing the rate of amplification per cycle, was calculated for each assay (Abbott et al., 2023).

Species‐targeted eDNA analysis

All eDNA samples were analyzed using species‐specific assays designed for three Pacific salmon species: Chinook, coho, and sockeye. Each assay was run with eight technical replicates alongside negative and positive controls. Negative controls consisted of eight technical replicates of 2‐μL Ultrapure distilled water serving as non‐template controls (NTCs), while positive controls included two 2‐μL replicates of synthetic gBlocks DNA (10 copies/μL) corresponding to the appropriate target amplicon. Each qPCR reaction was performed in a total volume of 15 μL, containing 2‐μL DNA template (sample or control Ultrapure water), 3.75‐μL 4X QIAcuity Probe Master Mix (Qiagen, Hilden, Germany), 1.5‐μL 10X primer‐probe mix (final concentrations: 7 μM for each primer and 1 μM for the TaqMan probe; Integrated DNA Technologies), and 7.75‐μL Ultrapure distilled water. The thermocycling conditions were as follows: an initial denaturation at 95°C for 9 min, followed by 50 cycles of 95°C for 15 s, 64°C for 30 s, and 72°C for 30 s. DNA concentrations were calculated (as copies/L for water samples and copies/g for sediment samples) based on previously generated standard curves (continuous Ct data for ≥95% technical replicates producing a signal) or copy number estimates (binomial data where <95% technical replicates produced a signal) (Lesperance et al., 2021). Samples yielding eDNA concentrations above the assay‐specific LOD and LOQ (Lesperance et al., 2021) were selected for Sanger sequencing to confirm that the amplified product matched the intended target species (see Appendix S1). Detection criteria used in this study follow the Canadian Standard Association's standard for performance criteria for the analyses of environmental DNA by targeted quantitative polymerase chain reaction (CSA W219: 23; Abbott et al., 2023).

Statistical analysis

Discordance between media was quantified as the proportion of instances in which water and sediment eDNA yielded differing species detections at the same site and sampling event (i.e., detection in one medium but not the other). Replicate detection scores were consolidated using eDNA concentration data into a single value for each year × location × species × method combination before calculating discordance. Based on the eight technical qPCR reactions run per sample, detection scores were converted to numeric values ranging from 0 (no positive qPCR reactions) to 8 (positive amplification in all eight qPCR reactions). Replicates were collapsed using the maximum observed score within each combination (replicates containing only missing values were assigned NA). The resulting dataset was reshaped to a paired format with one water value and one sediment value for each sampling combination. For each species, we classified a detection as “present” in water or sediment when the score was ≥4. We then restricted analyses to combinations in which at least one medium (water or sediment) had a score ≥4 (i.e., ≥ 1 detection). Using these paired data, we calculated:

P(Water|Sediment)—the probability of detecting fish DNA in water given a detection in sediment

PWater|Sediment=nbothnSediment

P(Sediment|Water)—the probability of detecting fish DNA in sediment given a detection in water

PSediment|Water=nbothnWater

where n both is the number of paired observations where both media scored ≥4.

For both conditional probabilities, we generated 90% credible intervals using a Jeffreys interval (a Bayesian binomial interval with Beta (0.5, 0.5) priors), implemented via the Beta quantile function (Lyles et al., 2020). We also quantified the contribution of each medium to discordant detections, defined as cases where only one medium scored ≥4. For these, we calculated (1) the proportion of discordant cases that were water‐only and (2) the proportion of discordant cases that were sediment‐only. These statistics were computed separately for each species and all species combined. All figures and statistical analyses were done in R (R Core Team, 2025) using tidyverse (v. 1.3.0, Wickham et al., 2019).

RESULTS

All three target Pacific salmon species: coho, Chinook, and sockeye, were detected in both water and sediment samples across the study area, including the Nenikëkh, where the occupancy of salmon is known (Table 2). However, there were media‐specific differences among species. In the Nenikëkh, for example, water consistently detected sockeye salmon with high detection frequency during each sampling week, reflecting the high spawning abundance observed in the river during media collection. While sediment also detected sockeye at this location during all collection events, detection frequency was consistently lower and more variable. Water showed moderate detection strength for coho (6 of 9 samples had scores of ≥4), whereas sediment produced weak or absent detections (all scores <3). Chinook showed contrasting patterns between media in the Nenikëkh: Water detections ranged from strong to weak across sampling events, whereas detection in sediment was either precise or absent. All data follow the FAIReDNA framework (Takahashi et al., 2025) and can be accessed in Lopez, Ma, et al. (2026) at https://doi.org/10.5281/zenodo.21924988.

TABLE 2.

eDNA detection scores for each sample (in triplicate; maximum detection score = 8) collected for target Pacific salmon species in water and sediment during three sampling events in the Nenikëkh (Nanika River), where the occupancy of salmon is known.

Species and sampling week Environmental media
Water Sediment
Chinook
1a 8 8
1b 6 8
1c 3 8
2a 2 0
2b 5 0
2c 4 8
3a 0 0
3b 1 0
3c 0 0
Coho
1a 5 0
1b 2 0
1c 3 1
2a 5 0
2b 2 0
2c 6 0
3a 5 0
3b 6 0
3c 4 2
Sockeye
1a 8 8
1b 8 0
1c 8 8
2a 8 0
2b 8 0
2c 8 8
3a 8 1
3b 8 8
3c 8 8
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Note: Higher scores indicate stronger detection confidence.

Identification of emerging habitats for Pacific salmon

To compare how consistently fish eDNA was detected in water versus sediment, we looked at how often the two media types agreed or disagreed. Across species and sampling locations, we found a higher probability (45%; 90% credible intervals of 24% and 69%) of detecting fish in sediment when also detected in water, and a lower probability (23%; 90% credible intervals of 11% and 40%) of detecting fish in water when also detected in sediment (Figure 2a). This trend was broadly similar for each species, with detection probabilities being highest in sediment compared to water, and highest for Chinook, followed by sockeye and coho (Figure 2b). Additionally, most sediment detections (74%) occurred at locations where water samples failed to detect fish, demonstrating that sediment detected salmon more often than water in discordant cases (Table 2).

FIGURE 2.

FIGURE 2

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Conditional detection probabilities for Pacific salmon eDNA: (A) conditional detection probabilities in sediment given a detection in water (Sediment|Water), and the probability of detecting fish in water given a detection in sediment (Water|Sediment), across target salmon species, sampling locations, and years. Error bars indicate 90% credible intervals; and (B) conditional detection probabilities for each target salmon species in sediment given a detection in water (Sediment|Water), and the probability of detecting each target salmon species in water given a detection in sediment (Water|Sediment), across sampling locations and years. Error bars indicate 90% credible intervals.

Our eDNA sampling analysis detected target salmon species at all locations where historical records show no known occupancy and where no individuals were visually observed during aerial surveys (Figure 3). In the C'eneelee Kwa (upper Atna River), Chinook were detected in sediment, but not water, collected in 2023 and absent in both media in 2024. Both coho and sockeye salmon were consistently detected here in water and sediment in 2023, and water only in 2024. At Cabin Creek, all three species were detected in sediment during 2023, whereas only coho was detected in sediment in 2024. Water samples from 2024 at this location showed positive detections for coho and sockeye salmon. In the 2024 sampling of Pyramid Creek, coho and sockeye were detected in the water, and only coho was detected in the sediment.

FIGURE 3.

FIGURE 3

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Detection of three Pacific salmon species from filtered water and sediment eDNA samples, compared with visual surveys conducted in 2023 and 2024. Figure generated in Biorender: https://BioRender.com/t8lzqi8.

DISCUSSION

The present study demonstrates that species‐targeted eDNA from both water and sediment can reliably detect Pacific salmon across diverse and emerging habitats, but that the two media capture different dimensions of habitat use. By comparing detections across known and suspected habitats, we show that water and sediment eDNA provide complementary information for identifying salmon presence in a rapidly changing, glacier‐influenced system. This paired‐media approach offers new insights into how habitat use varies across species, time, and hydrologic settings, with implications for monitoring in northern watersheds experiencing accelerated climate‐driven change.

In the Nenikëkh, where salmon presence is well documented and sockeye salmon were observed spawning during sampling, water eDNA provided consistently strong and unambiguous detections for all three target species. These maximal scores reflect the high abundance of salmon and the tendency of water eDNA to track contemporary biomass within short temporal windows (Tillotson et al., 2018). Differences in detection probabilities among species likely reflect variation in fish abundance, body size, residency duration, and spawning distribution, consistent with patterns reported in previous studies (Fowler et al., 2024; Su et al., 2024). Chinook generally have the largest individual biomass, whereas sockeye often occur at higher densities, and coho exhibit more dispersed habitat use. These differences can influence eDNA production, transport, and persistence and may contribute to species‐specific variation in detection rates. While sediment also detected all species in this known‐occupancy system, the scores were more variable and generally weaker than those from water for both sockeye and coho. This contrast indicates fundamental differences in how water and sediment integrate biological signals over time.

The pronounced asymmetry in discordant detections further supports these differences in media behavior, detection efficiency, and reliability. Across species and locations, most sediment detections occurred at sites where water samples did not detect fish. This pattern is consistent with known differences in eDNA persistence and transport: Water provides a near‐instantaneous signal that degrades or disperses rapidly—typically within hours to days—yielding high temporal detection frequency but also transient signals (Tillotson et al., 2018). Conversely, sediment acts as a longer term reservoir for genetic material, as particles bind and preserve DNA that can persist for weeks or months, even after fish have left the area (Buxton et al., 2018; Turner et al., 2015). Sediment‐based detections therefore provide evidence of fish present earlier in the season or at low densities that are missed by water sampling, effectively broadening the seasonal window of detection and revealing intermittent or off‐season habitat use (Buxton et al., 2018; Shao et al., 2024). Deposition patterns, sediment composition, and occasional PCR inhibitors such as humic substances (Huston et al., 2023), and bacterial composition affecting DNA degradation rate (Beattie et al., 2023), can further influence sedDNA reliability. Hydrologic conditions also shape detectability: Fast‐moving water can dilute DNA and transport it downstream, whereas fine organic‐rich sediments enhance DNA retention (Civade et al., 2016; Jane et al., 2015; Turner et al., 2015). Despite these contrasts, the two media provide complementary perspectives: water capturing real‐time presence and migration timing, and sediment offering a cumulative record of past or intermittent habitat use (Sakata et al., 2020). Together, these dynamics demonstrate that water and sediment eDNA are not interchangeable indicators of occupancy but instead offer distinct and complementary temporal perspectives on salmon use of riverine habitats.

Tracking salmon habitats with eDNA

Across glacier‐influenced tributaries with no historical records of salmon presence, our eDNA surveys revealed occurrences in multiple locations where visual surveys failed to detect fish. These detections demonstrate the power of eDNA to identify low‐density, cryptic, or transient use in emerging habitats (Su et al., 2024), a pattern consistent with other systems where eDNA has detected the recolonization of restored habitat by salmon that conventional surveys missed (Allan et al., 2023; Duda et al., 2021; Ostberg & Chase, 2022). However, media‐specific detections in these systems support different ecological interpretations. For example, the detection of Chinook in sediment but not water in C'eneelee Kwa suggests past occupancy or intermittent use, either by spawning adults or rearing juveniles, that was not captured in contemporary water sampling. Conversely, coho and sockeye were consistently detected at this location in the water, indicating active habitat use despite no visual evidence. Among other tributaries, media‐specific detections varied by year, illustrating that eDNA can reveal shifting habitat use that may reflect run timing, hydrologic variability, and climate‐linked habitat reorganization.

Beyond identifying emerging habitats, these findings highlight the practical advantages of eDNA for monitoring salmon in remote and rapidly changing river systems. Many glacier‐fed tributaries of the Skeena are difficult to access and often require costly helicopter‐based surveys, whereas portable eDNA sampling provides a scalable, low‐impact alternative capable of detecting salmon presence across broad and logistically challenging areas. As drone‐ and aerial‐based eDNA collection methods continue to advance, these approaches may further expand the ability to track colonization, migration timing, and habitat connectivity in previously unsurveyed waters. Integrating eDNA into Indigenous‐led monitoring frameworks offers additional opportunities for frequent, community‐driven assessments of key habitats in a region undergoing accelerated climate, hydrologic, and land‐use change.

Use of eDNA to inform Indigenous governance in Skeena

The granular biological insights provided by eDNA surveys translate directly into better‐informed decision‐making, particularly for Indigenous governments and comanagement bodies tasked with safeguarding salmon. This need is intensified in northern BC, where cumulative land‐use pressures on salmon habitat are increasing while federal environmental safeguards are being weakened (Price & Berchtold, 2026). Canada's recent passage of the One Canadian Economy Act (Bill C‐5) is enabling the fast‐tracking of industrial projects (Prime Minister of Canada, 2025a), while federal budget cuts are set to remove $544 million over 4 years from Fisheries and Oceans Canada, the agency responsible for monitoring wild salmon populations (Government of Canada, 2025b). With salmon monitoring already at an all‐time low and nearly half of Canada's salmon populations lacking sufficient data for assessment (Price & Moore, 2026), our capacity to evaluate emerging risks is increasingly constrained. At the same time, new industrial‐scale developments, including a proposed oil‐pipeline corridor and the lifting of the oil‐tanker moratorium in northwest BC (Prime Minister of Canada, 2025b), may proceed with reduced environmental oversight despite the region containing some of the country's most valuable and climate‐emerging salmon habitats (Moore et al., 2023). For Indigenous Nations whose governance systems rely on accurate assessments of salmon abundance, habitat condition, and connectivity, the combination of accelerated approvals and diminished monitoring heightens the risk of unrecognized declines and irreversible harm. In this context, eDNA provides a biologically grounded, fine‐scale monitoring tool capable of restoring essential information flows at a time when regulatory systems are becoming less protective.

Although eDNA is not a replacement for conventional fish survey approaches, which remain essential for assessing population health, genetics, and abundance, it greatly expands the monitoring toolkit available to Indigenous governments. Its sensitivity and low logistical cost make it particularly well suited for early detection, broad surveillance across difficult terrain, and identifying salmon presence in habitats overlooked by conventional surveys. These features translate into tangible governance applications: eDNA data can strengthen environmental assessments, support legal challenges by documenting species presence along proposed development corridors, and help identify where development activities may pose the greatest cumulative risk to aquatic species.

For the Wet'suwet'en Nation, eDNA evidence of salmon use in undocumented or previously unrecorded rivers has already informed governance decisions. The present study's discovery of Chinook, coho, and sockeye in glacier‐influenced tributaries of the Upper Widzin Kwa has helped identify a network of emerging habitats likely to expand under climate warming as glaciers retreat and aquatic conditions become more suitable. These findings, combined with observed increases in freshwater productivity of Widzin Bin (Price et al., 2024), motivated the Wet'suwet'en to propose the expansion of existing protected areas by 25% to encompass tributary rivers that hold high potential as future salmon strongholds. By illuminating both contemporary use and long‐term habitat potential, eDNA has strengthened Wet'suwet'en‐led stewardship and provided a scientific foundation for proactive protection in a region facing rapid climatic and industrial transformation. Integrating eDNA with Indigenous governance frameworks, therefore, not only enhances the detection of emerging habitats but also supports sovereign decision‐making aimed at securing salmon resilience for generations to come.

AUTHOR CONTRIBUTIONS

Mark Louie D. Lopez, Caren C. Helbing, Samantha Vincent, and Michael H. H. Price conceived the study. Samantha Vincent and Michael H. H. Price designed and carried out the field sampling. Isabel G. Ma processed samples for eDNA analysis. Mark Louie D. Lopez, Caren C. Helbing, and Michael H. H. Price conducted the data analyses and led manuscript preparation. All authors contributed to manuscript revisions and approved the final version for submission.

CONFLICT OF INTEREST STATEMENT

The authors declare no conflicts of interest.

Supporting information

Appendix S1.

EAP-36-e70323-s001.pdf (322.6KB, pdf)

ACKNOWLEDGMENTS

We thank the Office of the Wet'suwet'en and Wet'suwet'en Fisheries for their technical support, project guidance, and generous sharing of ancestral knowledge. We also thank Graeme Knowles, Inbal Harim, Marin Crane, Haley Kuecks‐Winger, and Sarah Trilesky for their technical support. We acknowledge the Liber Ero Fellowship Program and SkeenaWild Conservation Trust for academic and financial support. This project was partly funded by the British Columbia Salmon Restoration and Innovation Fund provided to the Office of the Wet'suwet'en, and by Genome Canada, Genome British Columbia, and Genome Québec's large‐scale applied research project no. 312ITD awarded to Caren C. Helbing.

Lopez, Mark Louie D. , Ma Isabel G., Vincent Samantha, Helbing Caren C., and Price Michael H. H.. 2026. “Using Environmental DNA to Identify Emerging Pacific Salmon Habitats and Support Indigenous Governance.” Ecological Applications 36(7): e70323. 10.1002/eap.70323

Handling Editor: Matthieu Leray

DATA AVAILABILITY STATEMENT

Data (Lopez, Ma, et al., 2026) are available in Zenodo at https://doi.org/10.5281/zenodo.21924988.

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

Appendix S1.

EAP-36-e70323-s001.pdf (322.6KB, pdf)

Data Availability Statement

Data (Lopez, Ma, et al., 2026) are available in Zenodo at https://doi.org/10.5281/zenodo.21924988.

Articles from Ecological Applications are provided here courtesy of Wiley

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