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Quantitative PCR assays for detection of five arctic fish species: Lota lota, Cottus cognatus, Salvelinus alpinus, Salvelinus malma, and Thymallus arcticus from environmental DNA

Abstract

The North Slope of Alaska contains arctic fish populations that are important for subsistence of local human populations, and are under threat from natural resource extraction and climate change. We designed and evaluated four quantitative PCR assays for the detection of environmental DNA from five Alaskan fish species present on the North Slope of Alaska: burbot (Lota lota), arctic char (Salvelinus alpinus), Dolly Varden (Salvelinus malma), arctic grayling (Thymallus arcticus), and slimy sculpin (Cottus cognatus). All assays were designed and tested for species specificity and sensitivity, and all assays detected target species from filtered water samples collected from the field. These assays will enable efficient and economical detection and monitoring of these species in lakes and rivers. This in turn will provide managers with improved knowledge of current distributions and future range shifts associated with climate and development threats, enabling more timely management.

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Acknowledgements

We would like to thank Greta Burkart and the USFWS Arctic National Wildlife Refuge and Alaska Refuges Inventory and Monitoring Program for management direction and funding. We would also like to thank Andres Lopes and the University of Alaska Museum for providing tissue specimens for sequencing, and Matthew Whitman and Phaedra Budy for providing tissue specimens and eDNA samples. This work was funded by NASA Biodiversity and Ecological Forecasting program Grant NNX14AC40G.

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Correspondence to Torrey W. Rodgers.

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Rodgers, T.W., Olson, J.R., Klobucar, S.L. et al. Quantitative PCR assays for detection of five arctic fish species: Lota lota, Cottus cognatus, Salvelinus alpinus, Salvelinus malma, and Thymallus arcticus from environmental DNA. Conservation Genet Resour 10, 859–865 (2018). https://doi.org/10.1007/s12686-017-0883-1

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Keywords

  • Alaska North Slope
  • eDNA
  • Species detection