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Evaluating Noninvasive Genetic Sampling Techniques to Estimate Large Carnivore Abundance

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Evaluating Noninvasive Genetic Sampling Techniques to Estimate Large Carnivore Abundance See discussions, stats, and author profiles for this publication at: https://www.researchgate.net/publication/272515587 Evaluating noninvasive genetic sampling techniques to estimate large carnivore abundance Article in Molecular Ecology Resources · February 2015 DOI: 10.1111/1755-0998.12390 · Source: PubMed CITATIONS READS 8 382 5 authors, including: Matthew A Mumma Todd Fuller University of Northern British Columbia University of Massachusetts Amherst 8 PUBLICATIONS 107 CITATIONS 175 PUBLICATIONS 4,633 CITATIONS SEE PROFILE SEE PROFILE Lisette P Waits University of Idaho 364 PUBLICATIONS 11,284 CITATIONS SEE PROFILE Some of the authors of this publication are also working on these related projects: Project done to obtain PhD degree at University of Massachusetts, Amherst, USA, 2000-2004. View project Migration ecology and conservation of Mongolian wild ungulates View project All content following this page was uploaded by Todd Fuller on 23 March 2015. The user has requested enhancement of the downloaded file. Molecular Ecology Resources (2015) doi: 10.1111/1755-0998.12390 Evaluating noninvasive genetic sampling techniques to estimate large carnivore abundance MATTHEW A. MUMMA,* CHRIS ZIEMINSKI,† TODD K. FULLER,† SHANE P. MAHONEY‡1 and LISETTE P. WAITS* *Department of Fish and Wildlife Sciences, University of Idaho, Moscow, ID 83844, USA, †Department of Environmental Conservation, University of Massachusetts, Amherst, MA 01003, USA, ‡Sustainable Development and Strategic Science, Department of Environment and Conservation, Government of Newfoundland and Labrador, Sir Brian Dunfield Bldg., St. John’s, A1B 4J6 NL, Canada Abstract Monitoring large carnivores is difficult because of intrinsically low densities and can be dangerous if physical cap- ture is required. Noninvasive genetic sampling (NGS) is a safe and cost-effective alternative to physical capture. We evaluated the utility of two NGS methods (scat detection dogs and hair sampling) to obtain genetic samples for abundance estimation of coyotes, black bears and Canada lynx in three areas of Newfoundland, Canada. We calcu- lated abundance estimates using program CAPWIRE, compared sampling costs, and the cost/sample for each method relative to species and study site, and performed simulations to determine the sampling intensity necessary to achieve abundance estimates with coefficients of variation (CV) of <10%. Scat sampling was effective for both coy- otes and bears and hair snags effectively sampled bears in two of three study sites. Rub pads were ineffective in sam- pling coyotes and lynx. The precision of abundance estimates was dependent upon the number of captures/ individual. Our simulations suggested that ~3.4 captures/individual will result in a < 10% CV for abundance estimates when populations are small (23–39), but fewer captures/individual may be sufficient for larger populations. We found scat sampling was more cost-effective for sampling multiple species, but suggest that hair sampling may be less expensive at study sites with limited road access for bears. Given the dependence of sampling scheme on species and study site, the optimal sampling scheme is likely to be study-specific warranting pilot studies in most circumstances. Keywords: Canis latrans, CAPWIRE, hair snags, Newfoundland, scat detection dogs, Ursus americanus Received 2 November 2014; revision received 8 February 2015; accepted 13 February 2015 target species and are often a viable alternative that can Introduction increase sampling success, reduce sampling cost and Large carnivore populations occur intrinsically at low increase animal and handler safety (Waits 2004; MacKay densities (MacKay et al. 2008; Mondol et al. 2009) and et al. 2008; Kelly et al. 2012). have been further reduced by direct and indirect anthro- A myriad of noninvasive techniques are available to pogenic influences (Weaver et al. 1996). Managers are provide researchers with the ability to determine the dis- frequently tasked with monitoring population size and tribution, abundance and population trends of carni- distribution to guide management actions for large carni- vores (Long & Zielinski 2008). Track and scat surveys vores. Traditional methods of large carnivore monitoring have a long history of use in determining carnivore occu- depend on capture and handling, which can be difficult, pancy (MacKay et al. 2008), and species detection has expensive and dangerous for both animals and handlers been improved through the use of scat detection dogs (Gompper et al. 2006). Noninvasive sampling techniques (Smith et al. 2003). Camera trapping has been used for do not require physical capture or direct observation of occupancy and abundance estimation of species with distinct, individual markings (e.g. Mondol et al. 2009). Correspondence: Matthew A. Mumma, With the advent of the polymerase chain reaction (PCR), E-mail: [email protected] species, sex and individual were able to be identified by 1Present address: Conservation Visions LLC St. John’s NL genetic analysis of scat, hair, urine and saliva (Waits & Canada A1E 5Y2 Paetkau 2005) for the purpose of improving occupancy © 2015 John Wiley & Sons Ltd 2 M. A. MUMMA ET AL. surveys (Gompper et al. 2006), evaluating genetic diver- identified to species and individually identified) and the sity and structure (Kohn et al. 1995), estimating species highest number of captures/individual for each species? abundance (Kohn et al. 1999) and identifying diet items Second, how many individually identified samples and (Deagle et al. 2005). captures/individual are necessary to precisely estimate Numerous studies have used NGS methods, and population abundances? And finally, what is the total some have combined multiple sampling methods to esti- cost and the cost/individually identified sample for each mate population parameters (De Barba et al. 2010a; Long method? et al. 2011; Reed 2011), but few have compared the effec- tiveness of multiple NGS techniques to sample multiple Materials and methods carnivore species. De Barba et al. (2010b) found that bai- ted hair snags resulted in more samples and higher Study site amplification success than sampling scat and hair oppor- tunistically or along transects for brown bears (Ursus arc- The island of Newfoundland (111 390 km2) is character- tos); however, opportunistic sampling was less expensive ized by a cool, maritime climate and interspersed conif- than hair snags, while identifying a similar number of erous forest, windswept barrens and peatland unique individuals. Other studies have shown that the (McManus & Wood 1991). Caribou are widely distrib- collection of scats along trails or at bait sites provides a uted and are the only native ungulate on Newfoundland. greater number of samples in comparison to hair collec- Three study sites (La Poile – LP, Middle Ridge – MR and tion and/or saliva collection from prey kill sites (Vine Northern Peninsula – NP) ranging in size from ~500 to et al. 2009; Sugimoto et al. 2012), while Latham et al. 1500 km2 were selected following the delineation via (2012) demonstrated that optimal hair sampling methods telemetry data (Rayl et al. 2014) of four caribou calving may differ between bear species (Ursus spp.). Several grounds (La Poile – LP, Middle Ridge – MR, and the clo- additional studies determined that sampling with scat sely associated Northern Peninsula – NP and St. detection dogs provided the highest capture rates (Was- Anthony’s herds – Fig. 1). ser et al. 2004 – bears), but was also the most costly (Har- rison 2006 – bobcats (Lynx rufus); Long et al. 2007 – black bears (Ursus americanus), fishers (Martes pennanti) and 1 - Island of Newfoundland Study Sites bobcats). Our objective was to evaluate the utility of scat Study sites detection dogs and hair sampling to simultaneously pro- Calving grounds vide viable, genetic samples for estimating the abun- LP Scat sampling dance of three large carnivore species across Newfoundland, Canada. Determining predator abundance in Newfoundland has become a priority because of a declining caribou (Rangifer tarandus) population and a changing predator guild. Numbers of caribou in Newfoundland have declined >66% since 1998, and increased calf predation is Northern peninsula (NP) considered a potential driver (Lewis & Mahoney 2014). Historically, gray wolves (Canis lupus), black bears and Canada lynx (Lynx canadensis) were Newfoundland’s Middle Ridge (MR) apex predators, but gray wolves were extirpated from the island prior to the 1930s (Lewis & Mahoney 2014). La Poile (LP) Beginning in the 1980s, coyotes (Canis latrans) colonized Newfoundland (Lewis & Mahoney 2014) and have become a major caribou calf predator (Mumma et al. 2014). In 2009, we used scat detection dogs and hair sam- pling to collect samples across 3 study sites in New- foundland for the purpose of estimating abundances of coyotes, black bears and Canada lynx. We wanted to 025 50 100 km identify the most efficient means and appropriate sam- pling intensity to simultaneously monitor these popula- Fig. 1 The location of our three study sites and associated calv- tions by answering the following questions. First, which ing grounds. Scat sampling in La Poile (LP) is shown because it method provides the greatest number of samples (both was primarily outside the LP calving ground. © 2015 John Wiley & Sons Ltd NGS METHODS FOR ESTIMATING CARNIVORE ABUNDANCE 3 and increase the probability of capture by selecting Scat detection dog sampling nearby locations containing game trails. Our transects A trained scat detection dog
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