Improved genotyping and sequencing success rates for North American river otter (Lontra canadensis)

  • C. F. C. Klütsch
  • P. J. Thomas
Methods Paper


Genetic analysis of non-invasively collected fecal samples has become an important monitoring tool in wildlife management and population and conservation genetics. However, these samples are often difficult to obtain for bioindicator species such as river otters (Lontra canadensis). Moreover, DNA extraction and genotyping success rates have often been low in this species. In this technical note, alternate means of collecting fecal DNA samples at river otter latrine sites are described. Using a modified fecal swabbing protocol and a DNA lysis buffer solution, we were able to increase genotyping success rates to ≥ 69% at 9/11 loci. The increased success rate now renders this protocol a more cost-efficient and reliable method for generating population level data in this species.


Fecal DNA Lontra canadensis Microsatellites Mitochondrial DNA Monitoring Non-invasive River otter 



We would like to thank Justin O’Reilly and Marina Kerr for the technical support. Domenico Santomauro, Chris Perra, and Emilie Brien (Great Bear Environmental Consulting Ltd.) provided assistance with field collections. We are extremely grateful to Reed Gauthier and E. Stephen Price, two Alberta trappers who provided access, guiding services, and logistical support for this program. We are thankful to Riverview Park and Zoo (Steve Thexton/ Sarah Law) as well as Carrie Sadowski and Dr. Jeff Bowman (Ontario Ministry of Natural Resources and Forestry) for providing swabbed fecal samples from river otters for testing purposes.

Funding information

Funding was provided by the Joint Oil Sands Monitoring program (JOSM), the Government of Alberta, and Environment and Climate Change Canada.

Supplementary material

10344_2018_1177_MOESM1_ESM.docx (34 kb)
ESM 1 (DOCX 34.2 kb)


  1. Arrendal J, Vilà C, Björklund M (2007) Reliability of noninvasive genetic census of otters compared to field censuses. Conserv Genet 8:1097–1107. CrossRefGoogle Scholar
  2. Beheler AS, Fike JA, Murfitt LM, Rhodes OE Jr, Serfass TS (2004) Development of polymorphic microsatellite loci for North American river otters (Lontra canadensis) and amplification in related mustelids. Mol Ecol Notes 4:56–58. CrossRefGoogle Scholar
  3. Beheler AS, Fike JA, Dharmarajan G, Rhodes OE Jr, Serfass TL (2005) Ten new polymorphic microsatellite loci for North American river otters (Lontra canadensis) and their utility in related mustelids. Mol Ecol Notes 5:602–604. CrossRefGoogle Scholar
  4. Beja-Pereira A, Oliveira R, Alves PC, Schwartz MK, Luikart G (2009) Advancing ecological understandings through technological transformations in noninvasive genetics. Mol Ecol Resour 9:1279–1301. CrossRefPubMedGoogle Scholar
  5. Dallas JF, Coxon KE, Sykes T, Chanin PR, Marshall F, Carss DN, Bacon PJ, Piertney SB, Racey PA (2003) Similar estimates of population genetic composition and sex ratio derived from carcasses and faeces of Eurasian otter Lutra lutra. Mol Ecol 12:275–282. CrossRefPubMedGoogle Scholar
  6. Elliott JE, Guertin DA, Balke JME (2008) Chlorinated hydrocarbon contaminants in feces of river otters from the southern Pacific coast of Canada, 1998–2004. Sci Tot Environ 397:58–71. CrossRefGoogle Scholar
  7. Galpern P, Manseau M, Hettinga P, Smith K, Wilson P (2012) Allelematch: an R package for identifying unique multilocus genotypes where genotyping error and missing data may be present. Mol Ecol Resour 12:771–778. CrossRefPubMedGoogle Scholar
  8. Gaydos JK, Miller WA, Gilardi KVK, Melli A, Schwantje H, Engelstoft C, Fritz H, Conrad PA (2007) Cryptosporidium and Giardia in marine-foraging river otters (Lontra canadesis) from the Puget Sound Georgia Basin Esosystem. J Parasitol 93(1):198–202. CrossRefPubMedGoogle Scholar
  9. Godwin BL, Albeke SE, Bergman HL, Walters A, Ben-David M (2015) Density of river otters (Lontra canadensis) in relation to energy development in the Green River Basin, Wyoming. Sci Total Environ 532:780–790. CrossRefPubMedGoogle Scholar
  10. Guertin DA, Harestad AS, Ben-David M, Drouillard KG, Elliott JE (2010) Fecal genotyping and contaminant analyses reveal variation in individual river otter exposure to localized persistent contaminants. Environ Toxicol Chem 29:275–284. CrossRefPubMedGoogle Scholar
  11. Hájková P, Zemanová B, Bryja J, Hájek B, Roche K, Tkadlec E, Zima J (2006) Factors affecting success of PCR amplification of microsatellite loci from otter faeces. Mol Ecol Notes 6:559–562. CrossRefGoogle Scholar
  12. Hájková P, Zemanová B, Roche K, Hájek B (2009) An evaluation of field and noninvasive genetic methods for estimating Eurasian otter population size. Conserv Genet 10:1667–1681. CrossRefGoogle Scholar
  13. Harms V, Nowak C, Carl S, Muñoz-Fuentes V (2015) Experimental evaluation of genetic predator identification from saliva traces on wildlife kills. J Mammal 96:138–143. CrossRefGoogle Scholar
  14. Hung CM, Li SH, Lee LL (2004) Faecal DNA typing to determine the abundance and spatial organization of otters (Lutra lutra) along two stream systems in Kinmen. Anim Conserv 7:301–311. CrossRefGoogle Scholar
  15. Janssens X, Fontaine MC, Michaux JR, Libois R, de Kermabon J, Defourny P, Baret PV (2008) Genetic pattern of the recent recovery of European otters in southern France. Ecography 31:176–186. CrossRefGoogle Scholar
  16. Johnson CJ, Hodder DP, Crowley S (2013) Assessing noninvasive hair and fecal sampling for monitoring the distribution and abundance of river otter. Ecol Res 28:881–892. CrossRefGoogle Scholar
  17. Kersey DC, Dehnhard M (2014) The use of noninvasive and minimally invasive methods in endocrinology for threatened mammalian conservation. Gen Comp Endocrinol 203:296–306. CrossRefPubMedGoogle Scholar
  18. Klütsch CFC, Manseau M, Wilson PJ (2012) Phylogeographical analysis of mtDNA data indicates postglacial expansion from multiple glacial refugia in woodland caribou (Rangifer tarandus caribou). PLoS One 7:e52661. CrossRefPubMedPubMedCentralGoogle Scholar
  19. Lonsinger RC, Waits LP (2015) ConGenR: rapid determination of consensus genotypes and estimates of genotyping errors from replicated genetic samples. Conserv Genet Resour 7(4):841–843. CrossRefGoogle Scholar
  20. Mowry RA, Gompper ME, Beringer J, Eggert LS (2011) River otter population size estimation using noninvasive latrine surveys. J Wildl Manag 75:1625–1636. CrossRefGoogle Scholar
  21. Ramón-Laca A, Soriano L, Gleeson D, Godoy JA (2015) A simple and effective method for obtaining mammal DNA from feces. Wildl Biol 21:195–203. CrossRefGoogle Scholar
  22. Rousset F (2008) GENEPOP '007: a complete reimplementation of the GENEPOP software for Windows and Linux. Mol Ecol Resour 8:103–106. CrossRefPubMedGoogle Scholar
  23. Rutledge LY, Holloway JJ, Patterson BR, White BN (2009) An improved field method to obtain DNA for individual identification from wolf scat. J Wildl Manag 73:1430–1435. CrossRefGoogle Scholar
  24. Sorenson MD, Fleischer RC (1996) Multiple independent transpositions of mitochondrial DNA control region sequences to the nucleus. PNAS 93:15239–15243CrossRefPubMedPubMedCentralGoogle Scholar
  25. van Oosterhout C, Hutchinson WF, Wills DPM, Shipley P (2004) Micro-Checker: software for identifying and correcting genotyping errors in microsatellite data. Mol Ecol Resour 4:535–538. CrossRefGoogle Scholar

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Biology DepartmentTrent UniversityPeterboroughCanada
  2. 2.Environment and Climate Change Canada, Science and Technology Branch, National Wildlife Research CenterCarleton UniversityOttawaCanada

Personalised recommendations