Conservation Genetics Resources

, Volume 6, Issue 1, pp 17–19 | Cite as

Development and application of a molecular sexing protocol in the climate change-sensitive American pika

  • Clayton T. Lamb
  • Kelsey M. Robson
  • Michael A. Russello
Technical Note


Non-invasive sampling paired with molecular sexing provides a valuable tool for the study of elusive mammals, yet species-specific assays are required to ensure accurate identifications. The American pika (Ochotona princeps) is one example, having emerged as a focal mammalian species for studies of metapopulation dynamics and extinction risk in the face of climate change. Despite extensive study, knowledge of sex-specific patterns has been limited to small sample sizes given the need for live-trapping and field-based sexing. Here we describe a molecular sexing protocol designed to reliably determine sex from non-invasively collected hair. Our polymerase chain reaction-based method co-amplifies a male-specific sex-determining gene Y fragment and a species-specific autosomal microsatellite, the accuracy of which was validated on 15 internally-sexed individuals. Subsequent application to 157 hair samples demonstrated high rates of amplification success (96.0 %) and unambiguous sex determination (94.7 %), revealing a strong male-bias in the sample and one instance of inaccurate, field-based sex identification.


SRY Ochotona princeps Non-invasive Conservation genetics 



Joanna Varner, Cheryl Blair and Karl Larsen provided samples of known sex. Funding was provided by an NSERC Discovery Grant #341711–07 (MR) and UBC Okanagan in the form of an Undergraduate Research Award from the Barber School of Arts and Sciences (CL), and an University Graduate Fellowship (KR).


  1. Banks SC, Hoyle SD, Horsup A, Sunnucks P, Taylor AC (2003) Demographic monitoring of an entire species (the northern hairy-nosed wombat, Lasiorhinus krefftii) by genetic analysis of non-invasively collected material. Anim Conserv 6:101–107CrossRefGoogle Scholar
  2. Brownstein MJ, Carpten JD, Smith JR (1996) Modulation of non-templated nucleotide addition by Taq DNA polymerase: primer modifications that facilitate genotyping. Biotechniques 20:1004–1010PubMedGoogle Scholar
  3. Duke K (1951) The external genitalia of the pika, Ochotona princeps. J Mammal 32:169–173CrossRefGoogle Scholar
  4. Fontanesi L, Tazzoli M, Pecchioli E, Hauffe HC, Robinson TJ, Russo V (2008) Sexing European rabbits (Oryctolagus cuniculus), European brown hares (Lepus europaeus) and mountain hares (Lepus timidus) with ZFX and ZFY loci. Mol Ecol Resour 8:1294–1296PubMedCrossRefGoogle Scholar
  5. Henry P, Russello M (2011) Obtaining high-quality DNA from elusive small mammals using low-tech hair snares. Eur J Wildl Res 57:429–435CrossRefGoogle Scholar
  6. MacArthur R, Wang L (1974) Physiology of thermoregulation in the pika, Ochotona princeps. Can J Zool 51:11–16CrossRefGoogle Scholar
  7. Morin P, Wallis J, Moore J, Chakraborty R, Woodruff D (1993) Non-invasive sampling and DNA amplification for paternity exclusion, community structure, and phylogeography in wild chimpanzees. Primates 34:347–356CrossRefGoogle Scholar
  8. Palsbøll P, Vader A (1992) Determination of gender in cetaceans by the polymerase chain reaction. Can J Zool 70:2166–2170CrossRefGoogle Scholar
  9. Piggott MP, Taylor AC (2003) Remote collection of animal DNA and its applications in conservation management and understanding the population biology of rare and cryptic species. Wildl Res 30:1CrossRefGoogle Scholar
  10. Robson KM (2013) American pika population genetic structure, demographic history, and behavior in an atypical environment. MSc Thesis, The University of British Columbia.
  11. Schuelke M (2000) An economic method for the fluorescent labeling of PCR fragments. Nat Biotechnol 18:1–2CrossRefGoogle Scholar
  12. Smith A (1974) The distribution and dispersal of pikas: consequences of insular population structure. Ecology 55:1112–1119Google Scholar
  13. Smith AT, Weidong L, Hik DS (2004) Pikas as harbingers of global warming. Species 41:4–5Google Scholar
  14. Taberlet P, Luikart G (1999) Non-invasive genetic sampling and individual identification. Biol J Linn Soc 68:41–55Google Scholar
  15. Taberlet P, Griffin S, Goossens B, Questiau S, Manceau V, Escaravage N, Waits LP, Bouvet J (1996) Reliable genotyping of samples with very low DNA quantities using PCR. Nucleic Acids Res 24:3189–3194PubMedCentralPubMedGoogle Scholar
  16. Vanpé C, Salmona J, Pais I, Kun-Rodrigues C, Pichon C, Meyler SV, Rabarivola C, Lewis RJ, Ibouroi MT, Chikhi L (2013) Noninvasive molecular sexing: an evaluation and validation of the SRY- and amelogenin-based method in three new lemur species. Am J Phys Anthropol 150:492–503PubMedGoogle Scholar
  17. Wielgus R, Bunnell F (1994) Dynamics of a small, hunted brown bear Ursus arctos population in Southwestern Alberta, Canada. Biol Conserv 67:161–166Google Scholar
  18. Williams C, Breck S, Baker B (2004) Genetic methods improve accuracy of gender determination in beavers. J Mammal 85:1145–1148Google Scholar
  19. Zgurski JM, Hik DS (2012) Polygynandry and even-sexed dispersal in a population of collared pikas, Ochotona collaris. Anim Behav 83:1075–1082Google Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  • Clayton T. Lamb
    • 1
  • Kelsey M. Robson
    • 1
  • Michael A. Russello
    • 1
  1. 1.Department of BiologyUniversity of British ColumbiaKelownaCanada

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