Advertisement

Conservation Genetics Resources

, Volume 8, Issue 3, pp 259–261 | Cite as

An environmental DNA marker for detecting nonnative brown trout (Salmo trutta)

  • K. J. CarimEmail author
  • T. M. Wilcox
  • M. Anderson
  • D. J. Lawrence
  • M. K. Young
  • K. S. McKelvey
  • M. K. Schwartz
Technical Note

Abstract

Brown trout (Salmo trutta) are widely introduced in western North America where their presence has led to declines of several native species. To assist conservation efforts aimed at early detection and eradication of this species, we developed a quantitative PCR marker to detect the presence of brown trout DNA in environmental samples. The marker strongly amplified brown trout eDNA, and produced no amplification of eDNA from 17 other species commonly found in western North America. We field tested this marker and demonstrated positive detections in field samples where brown trout presence was known.

Keywords

Salmonids eDNA Invasive species qPCR 

Supplementary material

12686_2016_548_MOESM1_ESM.docx (24 kb)
Supplementary material 1 (DOCX 24 kb)

References

  1. Biggs JN, Ewald A, Valentini C, Gaboriaud T, Dejean RA, Griffiths J, Foster JW, Wilkinson A, Arnell P, Brotherton P, Williams P, Dunn F (2015) Using eDNA to develop a national citizen science based monitoring programme for the great crested newt (Triturus cristatus). Biol Conserv 183:19–28. doi: 10.1016/j.biocon.2014.11.029 CrossRefGoogle Scholar
  2. Carim KJ, Padgett TM, Wilcox TM, Young MK, Schwartz MK, McKelvey K (2015) Protocol for collecting eDNA samples from streams. USDA Forest Service- Rocky Mountain Research Station, Missoula, Montana.http://www.fs.fed.us/research/genomics-center/docs/edna/edna-protocol.pdf
  3. Dejean T, Valentini A, Miquel C, Taberlet P, Bellemain E, Miaud C (2012) Improved detection of an alien invasive species through environmental DNA barcoding: the example of the American bullfrog Lithobates catesbeianus. J Appl Ecol 49:953–959. doi: 10.1111/j.1365-2664.2012.02171.x CrossRefGoogle Scholar
  4. Goldberg CS, Pilliod DS, Arkle RS, Waits LP (2011) Molecular detection of vertebrates in stream water: a demonstration using Rocky Mountain tailed frogs and Idaho giant salamanders. PLoS ONE 6:e22746. doi: 10.1371/journal.pone.0022746 CrossRefPubMedPubMedCentralGoogle Scholar
  5. Gustavson MS, Collings PC, Finarelli JA, Egan D, Conchuir RO, Wightman GD, King JJ, Gauther DT, Whelan K, Carlsson JEL, Carlsson J (2015) An eDNA marker for Irish Petromyzon mariunis and Salmo trutta and field validation in running water. J Fish Biol. doi: 10.1111/jfb.12781 PubMedGoogle Scholar
  6. MacCrimmon HR, Marshall TL (1968) World distribution of brown trout, Salmo trutta. J Fish Res Board Canada 1968(25):2527–2548CrossRefGoogle Scholar
  7. McHugh P, Budy P (2005) Experimental effects of nonnative brown trout on the individual- and populations-level performance of native Bonneville cutthroat trout. Trans Am Fish Soc 135:1441–1455. doi: 10.1577/T05-309.1 CrossRefGoogle Scholar
  8. McKelvey KS, Young MK, Knotek EL, Wilcox TM, Carim KJ, Padgett TM, Schwartz MK (2016) Sampling large geographic areas for rare species using environmental DNA (eDNA): a study of bull trout Salvelinus confluentus occupancy in western Montana. J Fish Biol 88:1215–1222 CrossRefPubMedGoogle Scholar
  9. R Core Team (2014) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. http://www.R-project.org/
  10. Rees H, Bishop K, Middleditch DJ, Parmore JR, Maddison BC, Gough KC (2014) The application of eDNA for monitoring of the great crested new in the U.K. Ecol Evol 4:4023–4032. doi: 10.1002/ece3.1272 CrossRefPubMedPubMedCentralGoogle Scholar
  11. Siggsgaard AA, Carl H, Moller P, Thomsen PF (2015) Monitoring near-extinct of European weather loach in Denmark based on enviornmental DNA from water samples. Biol Conserv 183:46–52. doi: 10.1016/j.biocon.2014.11.023 CrossRefGoogle Scholar
  12. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739. doi: 10.1093/molbev/msr121 CrossRefPubMedPubMedCentralGoogle Scholar
  13. U.S. Fish and Wildlife Service (2009) Apache trout recovery plan, second revision. Albuquerque, New MexicoGoogle Scholar
  14. Wilcox TM, Carim KJ, McKelvey KS, Young MK, Schwartz MK (2015) The dual challenges of generality and specificity with developing environmental DNA markers for species and subspecies of Oncorhynchus. PLoS ONE. doi: 10.1371/journal.pone.0142008 Google Scholar
  15. Wilcox TM, McKelvey KS, Young MK, Sepulveda AJ, Shepard BB, Jane SF, Whiteley AR, Lowe WH, Schwartz MK (2016) Understanding environmental DNA detection probabilities: a case study using a stream dwelling char Salvelinus fontinalis. Biol Conserv 194:209–216CrossRefGoogle Scholar
  16. Wright ES, Yilmaz LS, Ram S, Gasser JM, Harrington GW, Noguera DR (2013) Exploiting extension bias in polymerase chain reaction to improve primer specificity in ensembles of nearly identical DNA templates. Environ Microbiol 16:1354–1365. doi: 10.1111/1462-2920.12259 CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht (outside the USA) 2016

Authors and Affiliations

  • K. J. Carim
    • 1
    Email author
  • T. M. Wilcox
    • 1
    • 2
  • M. Anderson
    • 3
  • D. J. Lawrence
    • 4
  • M. K. Young
    • 1
  • K. S. McKelvey
    • 1
  • M. K. Schwartz
    • 1
  1. 1.Rocky Mountain Research Station, United States Department of Agriculture, Forest ServiceNational Genomics Center for Wildlife and Fish ConservationMissoulaUSA
  2. 2.Division of Biological SciencesUniversity of MontanaMissoulaUSA
  3. 3.Arizona Department of Game and FishPhoenixUSA
  4. 4.National Fish and Wildlife FoundationWashingtonUSA

Personalised recommendations