qPCR-based eDNA workflow for humic-rich lake sediments: Combined use of sedimentary DNA (sedDNA) and Indigenous Knowledge in reconstructing historical fish records

dc.contributor.authorLopez, Mark Louie D.
dc.contributor.authorBonderud, Matthew
dc.contributor.authorAllison, Michael J.
dc.contributor.authorMacDermid, Findlay
dc.contributor.authorUssery, Erin J.
dc.contributor.authorMcMaster, Mark E.
dc.contributor.authorDersch, Ave
dc.contributor.authorStaniszewska, Kasia J.
dc.contributor.authorCooke, Colin A.
dc.contributor.authorDrevnik, Paul
dc.contributor.authorHelbing, Caren C.
dc.description.abstractLake sediment serves as a natural archive of historical biological information. The use of sedimentary DNA (sedDNA), a form of environmental DNA (eDNA) shed by aquatic organisms and preserved in sediment, has been instrumental in reconstructing past faunal composition in aquatic communities. However, the low abundance of fish sedDNA and the often humic-rich nature of lake sediments create methodological challenges for the accurate detection of target sedDNA using quantitative polymerase chain reaction (qPCR)-based approaches. Herein, we present a consolidated qPCR-based eDNA workflow to reconstruct past and current fish fauna in Cowpar Lake located in the Oil Sands region in Alberta (Canada), which were then validated using Indigenous Knowledge from Chipewyan Prairie First Nation community members. The present study highlights the importance of combining column- and precipitation-based PCR inhibitor clean-up, nucleic acid concentration, incorporating endogenous chloroplast DNA as a sample integrity control. Robust qPCR-based eDNA assays were also useful in preventing the false-negative detection of low copies of target fish DNA. The presence of Northern pike (1905 to 2019) and Cisco (1919 to 1942) in Cowpar Lake was confirmed based on detected sedDNA from sediment core. The reconstructed fish records from sedDNA-inferred data aligned with the Indigenous accounts of natural and human-mediated changes in land use around the lake. Overall, the present study addresses common methodological concerns in processing lake sediment samples for fish eDNA detection and demonstrates the great potential of combined eDNA-inferred data and Indigenous Knowledge in reconstructing historical fish records in aquatic communities.en_US
dc.description.sponsorshipThis work was funded under the Oil Sands Monitoring program workplan (W-LTM-S-5-2122: Indigenous Community-based Monitoring Projects Integrated with Core Aquatic Ecosystem Health Monitoring) but does not necessarily reflect the position of the Program or its participants. MLDL is supported by a Liber Ero postdoctoral fellowship and Genome Canada, Genome British Columbia, and Genome Québec largescale applied research project #312ITD awarded to CCH. The funders had no role in study design; in the collection, analysis, and interpretation of data; in the writing of the report; and in the decision to submit the article for publication.en_US
dc.identifier.citationLopez, M. L. D., Bonderud, M., Allison, M. J., MacDermid, F., Ussery, E. J., McMaster, M. E., ... Helbing, C. C. (2023). qPCR-based eDNA workflow for humic-rich lake sediments: Combined use of sedimentary DNA (sedDNA) and Indigenous Knowledge in reconstructing historical fish records. Ecological Indicators, 155, 111014. https://doi.org/10.1016/j.ecolind.2023.111014en_US
dc.publisherEcological Indicatorsen_US
dc.subjecteDNA assayen_US
dc.subjectenvironmental DNAen_US
dc.subjectPCR inhibitorsen_US
dc.subjectFirst Nations knowledgeen_US
dc.subjectfish faunaen_US
dc.subjecthistorical biodiversity reconstructionen_US
dc.titleqPCR-based eDNA workflow for humic-rich lake sediments: Combined use of sedimentary DNA (sedDNA) and Indigenous Knowledge in reconstructing historical fish recordsen_US


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