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Discovery of 20,000 RAD–SNPs and development of a 52-SNP array for monitoring river otters

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Abstract

Many North American river otter (Lontra canadensis) populations are threatened or recovering but are difficult to study because they occur at low densities, it is difficult to visually identify individuals, and they inhabit aquatic environments that accelerate degradation of biological samples. Single nucleotide polymorphisms (SNPs) can improve our ability to monitor demographic and genetic parameters of difficult to study species. We used restriction site associated DNA (RAD) sequencing to discover 20,772 SNPs present in Montana, USA, river otter populations, including 14,512 loci that were also variable in at least one other population range-wide. After applying careful filtering criteria meant to minimize ascertainment bias and identify high quality, highly heterozygous (H o  = 0.2–0.50) SNPs, we developed and tested 52 independent SNP qPCR genotyping assays, including 41 that performed well with diluted DNA. The 41 loci provided high power for population assignment tests with only 1 misassignment (1.6 %) between closely neighboring populations. Our SNPs showed high power to differentiate individuals and assign them to population of origin, as well as strong concordance of genotypes from high and diluted concentrations of DNA, and between original RAD and the SNP qPCR array.

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References

  • Allendorf FW, Hohenlohe P, Luikart G (2010) Genomics and the future of conservation, invited review. Nat Rev Genet 11:697–709

    Article  CAS  PubMed  Google Scholar 

  • Amish SJ, Hohenlohe PA, Painter S, Leary RF, Muhlfeld C, Allendorf FW, Luikart G (2012) RAD sequencing yields a high success rate for westslope cutthroat and rainbow trout species-diagnostic SNP assays. Mol Ecol Resour 12:653–660

    Article  CAS  PubMed  Google Scholar 

  • Campbell NR, Narum SR (2009) Quantitative PCR assessment of microsatellite and SNP genotyping with variable quality DNA extracts. Conserv Genet. doi:10.1007/s10592-008-9661-7

    Google Scholar 

  • Etter PD, Bassham S, Hohenlohe PA, Johnson EA, Cresko WA (2011) SNP discovery and genotyping for evolutionary genetics using RAD sequencing. In: Orgogozo V, Rockman MV (eds) Molecular methods for evolutionary genetics. Humana Press, New York, pp 157–178

    Google Scholar 

  • Fabbri E, Caniglia R, Mucci N, Thomsen HP, Krag K, Pertoldi C, Loeschcke V, Randi E (2012) Comparison of single nucleotide polymorphisms and microsatellites in non-invasive genetic monitoring of a wolf population. Arch Biol Sci Belgrade 64:321–335

    Article  Google Scholar 

  • Fitak RR, Naidu A, Thompson RW, Culver M (2015) A new panel of SNP markers for the individual identification of North American pumas. J Fish Wildl Manag 7:13–27. doi:10.3996/112014-JFWM-080

    Article  Google Scholar 

  • Helyar SJ, Hemmer-Hansen J, Bekkevold D, Taylor MI, Ogden R, Limborg MT, Cariani A, Maes GE, Diopere E, Carvalho GR, Nielsen EE (2011) Application of SNPs for population genetics of nonmodel organisms: new opportunities and challenges. Mol Ecol Resour 11:123–136

    Article  PubMed  Google Scholar 

  • Melquist W, Hornocker M (1983) Ecology of river otters in west central Idaho. Wildl Monogr 83:3–60

    Google Scholar 

  • Melquist WE, Polechla PJ, Toweill D (2003) River otter: lontra canadensis. In: Feldhamer GA, Thompson BC, Chapman JA (eds) Wild mammals of North America: biology, management, and conservation. Johns Hopkins University Press, Baltimore, pp 708–734

    Google Scholar 

  • Morin PA, McCarthy M (2007) Highly accurate SNP genotyping from historical and low-quality samples. Mol Ecol Notes 7:937–946

    Article  CAS  Google Scholar 

  • Morin PA, Luikart G, Wayne RK (2004) SNPs in ecology, evolution and conservation. Trends Ecol Evol 19:208–216

    Article  Google Scholar 

  • Mowry RA, Gompper ME, Beringer J, Eggert LS (2011) River otter population size estimation using noninvasive latrine surveys. J Wildl Manag 75:1625–1636

    Article  Google Scholar 

  • Newton DE (2012) Northern river otter population assessment and connectivity in western Montana. Thesis, University of Montana, Missoula, MT

  • Paetkau D, Calvert W, Stirling I, Strobeck C (1995) Microsatellite analysis of population structure in Canadian polar bears. Mol Ecol 4:347–354

    Article  CAS  PubMed  Google Scholar 

  • Peakall R, Smouse PE (2006) GENALEX 6, genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 6:288–295

    Article  Google Scholar 

  • Piry S, Alapetite A, Cornuet J-M, Paetkau D, Baudouin L, Estoup A (2004) GENECLASS2: a software for genetic assignment and first-generation migrant detection. J Hered 95:536–539

    Article  CAS  PubMed  Google Scholar 

  • Rannala B, Mountain JL (1997) Detecting immigration by using multilocus genotypes. Proc Natl Acad Sci 94:9197–9201

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Stetz JB, Seitz T, Sawaya MA (2015) Effects of exposure on genotyping success rates of hair samples from grizzly and American black bears. J Fish Wildl Manag 6:191–198

    Article  Google Scholar 

  • Vynne C, Baker MR, Breuer ZL, Wasser SK (2011) Factors influencing degradation of DNA and hormones in maned wolf scat. Anim Conserv 15:194

    Google Scholar 

Download references

Acknowledgments

We are grateful to MPG Ranch for generously funding this research and to the University of Montana for in-kind support, including laboratory facilities, equipment, and protocols. We thank the following for providing river otter tissue samples or source DNA: E. Bunting (Cornell University), C. Brown (Rhode Island Division of Fish and Wildlife), C. Bernier (Vermont Fish & Wildlife Department), J. Cormier and L. Elson (New Brunswick Department of Environment), P. Canac-Marquis (Quebec Ministry of Energy and Natural Resources), J. Gude and N. Anderson (Montana Department of Fish, Wildlife, and Park), C. Nelson (British Columbia Forests, Lands and Natural Resource Operations), J. Harms (Environment Yukon), S. Talbot (U.S. Geological Survey), J. Hayden and Z. Lockyer (Idaho Department of Fish and Game), and K. Pilgrim (U.S. Forest Service Rocky Mountain Research Station).

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Authors and Affiliations

  1. Sinopah Wildlife Research Associates, 127 N. Higgins, Suite 310, Missoula, MT, 59802, USA

    Jeffrey B. Stetz & Michael A. Sawaya

  2. Fish and Wildlife Genomics Group, Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA

    Seth smith, Stephen J. Amish & Gordon Luikart

  3. MPG Ranch, Missoula, MT, 59803, USA

    Alan B. Ramsey

  4. National Genomics Center for Wildlife and Fish Conservation, Rocky Mountain Research Station, United States Forest Service, Missoula, MT, 59801, USA

    Michael K. Schwartz

  5. Flathead Lake Biological Station, University of Montana, Polson, MT, 59860, USA

    Gordon Luikart

Authors
  1. Jeffrey B. Stetz
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  2. Seth smith
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  3. Michael A. Sawaya
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  4. Alan B. Ramsey
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  5. Stephen J. Amish
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  6. Michael K. Schwartz
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  7. Gordon Luikart
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Corresponding author

Correspondence to Jeffrey B. Stetz.

Additional information

Data available from the Dryad Digital Repository: 10.5061/dryad.96m9r].

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Table S1

Allelic diversity and heterozygosity of 52-locus SNP-array for North American river otters identified through RAD sequencing (DOCX 32 kb)

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Stetz, J.B., smith, S., Sawaya, M.A. et al. Discovery of 20,000 RAD–SNPs and development of a 52-SNP array for monitoring river otters. Conservation Genet Resour 8, 299–302 (2016). https://doi.org/10.1007/s12686-016-0558-3

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  • DOI: https://doi.org/10.1007/s12686-016-0558-3

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