Advertisement

Development of two quantitative PCR assays for detection of several Cottus species from environmental DNA in Pacific coast watersheds of North America

  • Marshal S. HoyEmail author
  • Carl O. Ostberg
Technical Note

Abstract

We developed two quantitative PCR assays for use with environmental DNA (eDNA) to detect numerous species in the genus Cottus that are indigenous to the Pacific coast watersheds of North America. We conducted in vitro assay validations on ten Cottus species and 32 potentially co-occurring non-Cottus species. We demonstrate the efficacy of these assays by field testing eDNA samples collected from streams inhabited by Cottus. These assays will be particularly useful for detecting Cottus in habitats where one (or more) of several Cottus species could be present.

Keywords

Cottus eDNA qPCR Pacific coast 

Notes

Acknowledgements

Funding for this work was provided by Seattle City Light agreement #18WNTAAYD00SCL. Cottus samples were obtained from the University of Washington Burke Museum Fish Collection. Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government.

Supplementary material

12686_2019_1118_MOESM1_ESM.docx (19 kb)
Supplementary material 1 (DOCX 18 kb)

References

  1. April J, Mayden RL, Hanner RH, Bernatchez L (2011) Genetic calibration of species diversity among North America’s freshwater fishes. Proc Natl Acad Sci USA 108:10602–10607CrossRefGoogle Scholar
  2. Armbruster DA, Pry T (2008) Limit of blank, limit of detection and limit of quantitation. Clin Biochem Rev 29(Suppl 1):49–52Google Scholar
  3. Beauchamp DA (1990) Seasonal and diel food habits of rainbow trout as juveniles in Lake Washington. Trans Am Fish Soc 119:475–482CrossRefGoogle Scholar
  4. Connolly PJ, Brenkman SJ (2008) Fish assemblage, density and growth in lateral habitats within natural and regulated sections of Washington’s Elwha River prior to dam removal. Northwest Sci 82(special issue):107–118.  https://doi.org/10.3955/0029-344X-82.S.I.107 CrossRefGoogle Scholar
  5. Cyterski M, Barber C (2006) Identification and prediction of fish assemblages in streams of the Mid-Atlantic Highlands, USA. Trans Am Fish Soc 135:40–48CrossRefGoogle Scholar
  6. Freeman MC, Crawford MK, Barrett JC et al (1988) Fish Assemblage stability in a southern Appalachian Stream. Can J Fish Aquat Sci 45:1949–1958CrossRefGoogle Scholar
  7. Hudy M, Shiflet J (2009) Movement and recolonization of Potomac sculpin in Virginia stream. N Am J Fish Manag 29:196–207CrossRefGoogle Scholar
  8. Kinziger AP, Wood RM, Neely DA (2005) Molecular systematics of the genus Cottus (Scorpaeniformes:Cottidae). Copeia 2:303–311CrossRefGoogle Scholar
  9. Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874CrossRefGoogle Scholar
  10. McPhail JD (2007) The freshwater fishes of British Columbia. University of Alberta Press, EdmontonGoogle Scholar
  11. Morley SA, Hall JE, Chamberlin J, Hanson KM (2013) Thornton Creek restoration: baseline project effectiveness monitoring, 2012-2013. Report of the National Marine Fisheries Service to the City of Seattle Department of Public Utilities, Seattle, WAGoogle Scholar
  12. Pess GR, Liermann MC, McHenry ML, Peters RJ, Bennett TR (2012) Juvenile salmon response to the placement of engineered log jams (ELJS) in the Elwha River, Washington State, USA. River Res Appl 28:872–881CrossRefGoogle Scholar
  13. Petty JT, Grossman GD (2007) Size-dependent territoriality of mottled sculpin in a southern Appalachian Stream. Trans Am Fish Soc 136:1750–1761CrossRefGoogle Scholar
  14. Poe TP, Hansel HC, Vigg S, Palmer DE, Prendergast LA (1991) Feeding of predaceous fishes on out-migrating juvenile salmonids on John Day Reservoir, Columbia River, USA. Trans Am Fish Soc 120:405–420CrossRefGoogle Scholar
  15. Tillotson MD, Kelly RP, Duda JJ, Hoy MS, Kralj J, Quinn TP (2018) Concentrations of environmental DNA eDNA reflect spawning salmon abundance at fine spatial and temporal scales. Biol Concerv 220:1–11CrossRefGoogle Scholar
  16. Wydoski RS, Whitney RR (2003) Inland fishes of Washington, 2nd edn. American Fisheries Society and University of Washington Press, BethesdaGoogle Scholar

Copyright information

© This is a U.S. government work and its text is not subject to copyright protection in the United States; however, its text may be subject to foreign copyright protection 2019

Authors and Affiliations

  1. 1.Western Fisheries Research Center, USGSSeattleUSA

Personalised recommendations