Evaluating the reliability of field identification and morphometric classifications for carnivore scats confirmed with genetic analysis

Lonsinger, Robert C.; Gese, Eric M.; Waits, Lisette P.

doi:10.1002/wsb.549

Cited by 32 publications

(73 citation statements)

References 47 publications

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“…Protocols restricted movement of supplies, equipment, and people from the historical to noninvasive laboratories, and from the noninvasive to postamplification laboratories (Waits & Paetkau, 2005). For contemporary samples, DNA storage, extraction, amplification, and scoring methods are detailed in Lonsinger, Gese, and Waits (). We determined species identification of contemporary samples using a mitochondrial DNA fragment analysis test (De Barba et al, ).…”

Section: Methodsmentioning

confidence: 99%

Evaluating effective population size and genetic diversity of a declining kit fox population using contemporary and historical specimens

Lonsinger

Adams

Waits

2018

Ecology and Evolution

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Loss of genetic diversity has serious conservation consequences (e.g., loss of adaptive potential, reduced population viability), but is difficult to evaluate without developing long‐term, multigenerational datasets. Alternatively, historical samples can provide insights into changes in genetic diversity and effective population size (N e). Kit foxes (Vulpes macrotis) are a species of conservation concern across much of their range. In western Utah, kit fox abundance has declined precipitously from historical levels, causing concern about population persistence. We analyzed genetic samples from museum specimens and contemporary scats to evaluate temporal changes in (a) genetic diversity and (b) N e for kit foxes in western Utah, and (c) discuss our findings with respect to population risk and conservation. The N e of kit foxes in western Utah has decreased substantially. When compared to established conservation thresholds for N e (e.g., the 50/500 rule), observed levels suggest the population may be at risk of inbreeding depression and local extinction. In contrast, we found no significant decrease in genetic diversity associated with declining N e. We detected evidence of low levels of immigration into the population and suspect genetic diversity may have been maintained by this previously undescribed gene flow from adjacent populations. Low or intermittent immigration may serve to temper the potential short‐term negative consequences of low N e. We recommend that kit fox conservation efforts focus on evaluating and maintaining landscape connectivity. We demonstrate how historical specimens can provide a baseline of comparison for contemporary populations, highlighting the importance of natural history collections to conservation during a period of declining funding and support.

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Section: Methodsmentioning

confidence: 99%

Evaluating effective population size and genetic diversity of a declining kit fox population using contemporary and historical specimens

Lonsinger

Adams

Waits

2018

Ecology and Evolution

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“…1). The locations of removal plots were selected to avoid overlap with transects being surveyed concurrently for native canids (Lonsinger et al 2015b). This was important to avoid introducing scats from captive animals and minimize behavioral responses of native canids along sites being monitored with noninvasive genetic sampling, and to ensure a balanced design among strata.…”

Section: Scat Removal Experimentsmentioning

confidence: 99%

“…When a carnivore scat was detected, we collected ∼0.7 ml of fecal material into 1.4 ml of DETS buffer (20% DMSO, 0.25 M EDTA, 100 mM Tris, pH 7.5 and NaCl to saturation; Seutin et al 1991). We measured each scat diameter, length and number of segments (Lonsinger et al 2015b) and recorded the location and position (median, track or shoulder), before removing remaining portions. We identified scats to species using mitochondrial DNA (mtDNA; De Barba et al 2014) following DNA storage, extraction, amplification, and scoring methods detailed in Lonsinger et al (2015a).…”

Section: Relative Abundance Field Surveysmentioning

confidence: 99%

Quantifying and correcting for scat removal in noninvasive carnivore scat surveys

Lonsinger¹,

Gese

Knight

et al. 2016

Wildlife Biology

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Scat surveys are commonly used to monitor wildlife populations. For carnivores, surveys are typically conducted along roads and trails. Scats available for detection may not relect scats deposited and variation in disappearance may bias results. Previous research has investigated natural decay and deterioration, but scats deposited along roads or trails are likely inluenced to a greater degree by anthropogenic disturbance in some systems. We used experimental plots to evaluate variation in scat removal for two model carnivores, coyote Canis latrans and kit fox Vulpes macrotis, along roads in the Great Basin Desert, USA. Using parametric survival regression, we predicted scat survival and developed persistence-rate correction factors, which were applied to results from relative abundance scat surveys conducted along 15 transects. Kit fox scats disappeared more rapidly than coyote scats, with 3.3% and 10.6%, respectively, persisting through 42 days. At 14 days, 90.8-41.7% of scats had been removed across road types. Survival models indicated species, road type, scat position and daily traic were important predictors of scat persistence. Applying persistence-rate correction factors to scat survey results altered the inferred relative abundances. Across seasons, mean corrected:uncorrected relative abundance ratios ranged from 1.0-91.2 for coyotes and 1.3-139.3 for kit foxes, with higher mean ratios being inluenced by high corrected relative abundances on roads with high traic volumes. Understanding scat removal rates and patterns can improve inferences from surveys. Persistence-rate correction factors can be used to reduce bias in indices of abundance, but caution should be used when removal rates are high. Knowledge of spatial variation in persistence can elucidate concerns of false-positives and false-negatives in occupancy and capture-recapture studies. Considering the disparity in scat removal between species and among road types and positions, we recommend practitioners quantify and consider variation in removal when interpreting scat survey results.

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“…1). During the final occasion of summer 2014, we only collected scats identified as fox based on size (Lonsinger et al 2015b).…”

Section: Study Site and Sample Collectionmentioning

confidence: 99%

Empirical comparisons of abundance estimators for two sympatric carnivores using noninvasive genetic sampling

et al. 2019

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Abundance estimators are often evaluated with simulations, or by comparing estimates to populations of known size. Advances in noninvasive genetic sampling have fueled an increase in the use of noninvasive genetic sampling‐based capture–recapture. However, when working with free‐ranging populations of unknown size, managers often lack data necessary to select the appropriate estimator. This leads to uncertainty regarding how choice of estimator or sampling design influence estimates, and managers may select estimators based on funding or logistical constraints. Alternatively, comparing estimates from multiple estimators can provide managers with greater confidence in estimates, or highlight potential differences. We used noninvasive genetic sampling to estimate the abundance of free‐ranging kit foxes Vulpes macrotis and coyotes Canis latrans. We generated estimates of abundance with two non‐spatial likelihood‐based estimators: 1) robust design Huggins capture–recapture models and 2) single‐occasion capture with replacement (CAPWIRE) models. We compared these with recently published estimates derived from spatially explicit capture–recapture (SECR) models. For both species, estimates from Huggins models were generally lower than those from SECR. Abundance estimates from CAPWIRE, which was developed specifically for noninvasive genetic sampling and generates estimates from a single sampling occasion, tended to be biased low with high precision. Our results suggest that choice of estimator and sampling design can significantly influence estimates, and that the relationship between estimators varied between species. Our results further suggest that single‐occasion sampling often employed with CAPWIRE abundance estimation may produce biased results and be inappropriate for species requiring dispersed sampling strategies.

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Evaluating the reliability of field identification and morphometric classifications for carnivore scats confirmed with genetic analysis

Cited by 32 publications

References 47 publications

Evaluating effective population size and genetic diversity of a declining kit fox population using contemporary and historical specimens

Evaluating effective population size and genetic diversity of a declining kit fox population using contemporary and historical specimens

Quantifying and correcting for scat removal in noninvasive carnivore scat surveys

Empirical comparisons of abundance estimators for two sympatric carnivores using noninvasive genetic sampling

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