The speckled dace (Rhinichthys osculus) is a small freshwater minnow listed as Endangered under Canada’s Species at Risk Act. In Canada, the species is restricted to the Kettle River watershed in south-central British Columbia and is geographically isolated from populations in the United States by Cascade Falls. Threats to speckled dace include low water flow conditions, habitat degradation, climate change, and threats posed by aquatic invasive species (AIS). Critical habitat for speckled dace is delineated as 2.4 km sections of the West Kettle, Kettle, and Granby rivers, starting at the species’ northernmost documented occurrence and extending downstream; however, evidence suggests this does not accurately reflect the species’ distribution. We used 16S environmental DNA (eDNA) metabarcoding with species assignments using a custom reference DNA sequence database to assess the distribution of speckled dace in the Kettle River above Cascade Falls. eDNA detection of speckled dace was consistently strong across filter replicates and markers at sites of known occupancy and was observed at two sites north of its currently described range. We also detected three invasive fish species with little or no records of occurrence in the sampled region, which warrant further investigation to confirm or refute. Overall, findings suggest that speckled dace occupy habitat beyond the existing upper boundary of their documented range in the Kettle River and co-occur with multiple AIS.
[This dataset was processed using the GBIF Metabarcoding Data Toolkit.]
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samples were collected at ten sampling sites in, or immediately adjacent to the Kettle River in British Columbia, Canada.","boundingBox":{"minLatitude":49.1102,"maxLatitude":50.1207,"minLongitude":-118.9795,"maxLongitude":-118.4069,"globalCoverage":false}}],"temporalCoverages":[{"@type":"range","start":"2023-07-07T00:00:00.000+00:00","end":"2023-07-08T00:00:00.000+00:00"}],"keywordCollections":[{"thesaurus":"N/A","keywords":["metabarcoding","eDNA metabarcoding","DNA","species at risk","Freshwater fish","Critical Habitat","MDT","Kettle River"]}],"project":{"title":"Distribution of endangered Speckled Dace (Rhinichthys osculus) in British Columbia, Canada, based on environmental DNA metabarcoding","funding":"This research was made possible by financial support from Genome BC (Project #SIP26-06) and DFO’s Species at Risk Program.","awards":[],"studyAreaDescription":"Shore-based eDNA sampling occurred July 7-8, 2023, at 10 sampling sites in, or immediately adjacent to, the Kettle River in British Columbia, Canada. This timing was chosen because: (1) water levels are relatively low, which has been shown to increase eDNA detectability due to lower dilution effect and are safer for field personnel; and (2) fish are active at this time of year, which should increase eDNA availability. Sites were selected based on public accessibility and occurred along a gradient from known occupancy in the south (sites 1-3) to beyond the northern extent of their critical habitat (sites 4-10), which is currently defined as the northernmost extent of their range.","relatedProjects":[]},"samplingDescription":{"studyExtent":"Shore-based eDNA sampling occurred July 7-8, 2023, at 10 sampling sites in, or immediately adjacent to, the Kettle River in British Columbia, Canada.","sampling":"Water sampling and filtration were done using an eDNA Backpack Sampler with 5 µm self-preserving filters (both from Smith-Root, Inc.), and multiple cleaning steps were implemented before sampling at each site to minimize contamination. One field blank was collected per site before taking field samples; this was done by opening a 1.0 L bottle of Millipore water for approximately one minute and then filtering it. Six field samples were taken with a target water volume of 3 L per sample; a total of 60 field samples were collected across sites. The average volume of water filtered for field samples (i.e. excluding controls) was 2.98 L; the range was 1.09-4.07 L, with the anomalies being one filter that clogged after only 1.09 L and another that filtered 4.07 L due to a machine malfunction. Filtered water samples were stored at room temperature, following the manufacturer’s recommendations, for approximately 45 days before eDNA extraction.","methodSteps":["Study Area and eDNA sampling","eDNA extraction and PCR amplification","Library construction and sequencing","Bioinformatics","Taxonomy assignment and data analysis","The potentially invasive Phoxinus sp. ASVs detected were originally classified as Alburnus alburnus using the Midori2 database. However, mitogenome phylogenies show the Alburnus alburnus mitogenome reference sequence (MT410946) in the Midori database is more similar to species in the genus Phoxinus (Cheng et al. 2022), and the 12S ASV detected in our study is an identical match to a reference sequence generated from a vouchered specimen of Phoxinus sp. from Switzerland (Blackman et al. 2022).","Literature Cited: Blackman, R. C., Walser, J.-C., Rüber, L., Brantschen, J., Villalba, S., Brodersen, J., Seehausen, O., & Altermatt, F. (2023). General principles for assignments of communities from eDNA: Open versus closed taxonomic databases. Environmental DNA, 5, 326–342. https://doi.org/10.1002/edn3.382 Cheng L, Wang E, Li W, Yu X, Liao X. The Complete Mitochondrial Genome of Eurasian Minnow (Phoxinus cf. Phoxinus) from the Heilongjiang River, and Its Phylogenetic Implications. Animals (Basel). 2022 Oct 27;12(21):2960. doi: 10.3390/ani12212960. PMID: 36359084; PMCID: PMC9658870."]},"countryCoverage":[],"collections":[],"dataDescriptions":[],"dataLanguage":"eng","pubDate":"2026-04-01T00:00:00.000+00:00","maintenanceUpdateFrequency":"UNKOWN","maintenanceDescription":"","license":"http://creativecommons.org/licenses/by/4.0/legalcode","dwca":{"coreType":"http://rs.tdwg.org/dwc/terms/Occurrence","extensions":["http://rs.iobis.org/obis/terms/ExtendedMeasurementOrFact","http://rs.gbif.org/terms/1.0/DNADerivedData"],"modified":"2026-10-12T01:51:53.303+00:00"},"category":["eDNA"],"approximateCounts":{"occurrenceCount":1810}}