Browsed twig environmental DNA: diagnostic PCR to identify ungulate species

Authors

  • RUTH V. NICHOLS,

    1. Molecular Ecology Research Group, Department of Wildlife, Fish and Environmental Studies, Swedish University of Agricultural Sciences, Skogsmarksgränd, SE 90183 Umeå, Sweden
    Search for more papers by this author
  • HELENA KÖNIGSSON,

    1. Molecular Ecology Research Group, Department of Wildlife, Fish and Environmental Studies, Swedish University of Agricultural Sciences, Skogsmarksgränd, SE 90183 Umeå, Sweden
    Search for more papers by this author
  • KJELL DANELL,

    1. Molecular Ecology Research Group, Department of Wildlife, Fish and Environmental Studies, Swedish University of Agricultural Sciences, Skogsmarksgränd, SE 90183 Umeå, Sweden
    Search for more papers by this author
  • GÖRAN SPONG

    1. Molecular Ecology Research Group, Department of Wildlife, Fish and Environmental Studies, Swedish University of Agricultural Sciences, Skogsmarksgränd, SE 90183 Umeå, Sweden
    Search for more papers by this author

Ruth V. Nichols, Fax: +46-90-786-8162; E-mail: ruth.nichols@slu.se

Abstract

Ungulate browsing can have a strong effect on ecological processes by affecting plant community structure and composition, with cascading effects on nutrient cycling and animal communities. However, in the absence of direct observations of foraging, species-specific foraging behaviours are difficult to quantify. We therefore know relatively little about foraging competition and species-specific browsing patterns in systems with several browsers. However, during browsing, a small amount of saliva containing buccal cells is deposited at the bite site, providing a source of environmental DNA (eDNA) that can be used for species identification. Here, we describe extraction and PCR protocols for a browser species diagnostic kit. Species-specific primers for mitochondrial DNA were optimized and validated using twigs browsed by captive animals. A time series showed that about 50% of the samples will amplify up to 12 weeks after the browsing event and that some samples amplify up to 24 weeks after browsing (12.5%). Applied to samples of natural browsing from an area where moose (Alces alces), roe deer (Capreolus capreolus), fallow deer (Cervus dama) and red deer (Cervus elaphus) are sympatric, amplification success reached 75%. This method promises to greatly improve our understanding of multispecies browsing systems without the need for direct observations.

Ancillary