Environmental DNA from Residual Saliva for Efficient Noninvasive Genetic Monitoring of Brown Bears (Ursus arctos)

Abstract

Noninvasive genetic sampling is an important tool in wildlife ecology and management, typically relying on hair snaring or scat sampling techniques, but hair snaring is labor and cost intensive, and scats yield relatively low quality DNA. New approaches utilizing environmental DNA (eDNA) may provide supplementary, cost-effective tools for noninvasive genetic sampling. We tested whether eDNA from residual saliva on partially-consumed Pacific salmon (Oncorhynchus spp.) carcasses might yield suitable DNA quality for noninvasive monitoring of brown bears (Ursus arctos). We compared the efficiency of monitoring brown bear populations using both fecal DNA and salivary eDNA collected from partially-consumed salmon carcasses in Southeast Alaska. We swabbed a range of tissue types from 156 partially-consumed salmon carcasses from a midseason run of lakeshore-spawning sockeye (O. nerka) and a late season run of stream-spawning chum (O. keta) salmon in 2014. We also swabbed a total of 272 scats from the same locations. Saliva swabs collected from the braincases of salmon had the best amplification rate, followed by swabs taken from individual bite holes. Saliva collected from salmon carcasses identified unique individuals more quickly and required much less labor to locate than scat samples. Salmon carcass swabbing is a promising method to aid in efficient and affordable monitoring of bear populations, and suggests that the swabbing of food remains or consumed baits from other animals may be an additional cost-effective and valuable tool in the study of the ecology and population biology of many elusive and/or wide-ranging species.

Alaskan brown bears (Ursus arctos) aggregate and display fidelity to foraging neighborhoods while preying on Pacific salmon along small streams

“…For example, bear hair could easily be sampled and used for both CMR population estimation and individual monitoring where trail networks facilitate deployment of unbaited, single‐catch snares (Beier et al., ). Localized and noninvasive efforts of this nature (see Wheat, Allen, Miller, Wilmers, & Levi, for another approach using environmental DNA) are likely to be especially useful in cases where bears are difficult to observe directly and deployment of enough GPS collars to make inferences at the population level is intractable.…”

The primacy of bears as seed dispersers in salmon‐bearing ecosystems

“…), as well as recent research demonstrating the efficacy of identifying individual bears using residual saliva on salmon carcasses (Wheat et al. ), we used residual saliva left from browsing bears on the stalks of berry‐producing plants to noninvasively detect the species and sex of bears that consumed devil's club fruit.…”

An eDNA-Based SNP Assay for Ungulate Species and Sex Identification

“…For example, protocols for identifying fish species from eDNA in water have been developed [2][3][4], and DNA from soil has also been used to reflect above-and below-ground species compositions [5,6]. DNA can also be isolated from food items such as browsed twigs [7][8][9] and salmon carcasses [10], allowing for the determination of the species of browsing ungulates [8] or predators [10]. Browsed twig environmental DNA (biteDNA) allows the quantification of species-specific browsing patterns of temperate ungulates using trace amounts of DNA left during foraging [7].…”