Integrating multiple genetic detection methods to estimate population density of social and territorial carnivores

Murphy, Sean M.; Augustine, Ben C.; Adams, Jennifer R.; Waits, Lisette P.; Cox, John J.

doi:10.1002/ecs2.2479

Cited by 13 publications

(24 citation statements)

References 62 publications

(137 reference statements)

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“…Rub tree estimates alone were lower than hair-snag estimates and the joint use of rub tree and hair-snag data increased overall population estimate precision. Similarly, integrating hair rub pads and scat transect data improved population density estimate precision using SECR methods for coyotes Canis latrans in Louisiana (Murphy et al 2018). Combining techniques comes with challenges of required resources, but could be a way to address estimate precision issues when monitoring small populations and low-density areas.…”

Section: Discussionmentioning

confidence: 99%

Comparison of grizzly bear hair‐snag and scat sampling along roads to inform wildlife population monitoring

Phoebus¹,

Boulanger²,

Eiken

et al. 2020

Wildlife Biology

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Section: Discussionmentioning

confidence: 99%

Comparison of grizzly bear hair‐snag and scat sampling along roads to inform wildlife population monitoring

Phoebus¹,

Boulanger²,

Eiken

et al. 2020

Wildlife Biology

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Section: Methodsmentioning

confidence: 99%

“…The probability of identity for siblings ( P ID(sibs) ) for nine nDNA microsatellite loci was calculated for those 70 samples by Murphy et al. () using GenAlEx v6.5 (Peakall & Smouse, ); five loci were required to differentiate between individuals ( P ID(sibs) = 0.0082), so samples were considered as originating from the same individual if they matched at more than five loci. A matching analysis identified 32 individuals from those 70 scat and hair samples (Murphy et al., ).…”

Section: Methodsmentioning

confidence: 99%

“…We used 54 scat and 16 hair samples that were collected noninvasively from individual canids in southwestern Louisiana during December 2015 to February 2016 via systematic scat transects and hair rub pads in a capture-recapture framework (Murphy, Augustine, Adams, Waits, & Cox, 2018b). The probability of identity for siblings (P ID(sibs) ) for nine nDNA microsatellite loci was calculated for those 70 samples by Murphy et al (2018b) using GenAlEx v6.5 (Peakall & Smouse, 2012); five loci were required to differentiate between individuals (P ID(sibs) = 0.0082), so samples were considered as originating from the same individual if they matched at more than five loci. A matching analysis identified 32 individuals from those 70 scat and hair samples (Murphy et al, 2018b).…”

Section: Sample Collectionmentioning

confidence: 99%

“…The probability of identity for siblings (P ID(sibs) ) for nine nDNA microsatellite loci was calculated for those 70 samples by Murphy et al (2018b) using GenAlEx v6.5 (Peakall & Smouse, 2012); five loci were required to differentiate between individuals (P ID(sibs) = 0.0082), so samples were considered as originating from the same individual if they matched at more than five loci. A matching analysis identified 32 individuals from those 70 scat and hair samples (Murphy et al, 2018b). We augmented that data set with tissue samples collected from six dead canids (killed in vehicle collisions or by government biologists as part of coyote control efforts [Leblanc et al, 2016]) in southwestern Louisiana during the same time period.…”

Section: Sample Collectionmentioning

confidence: 99%

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Substantial red wolf genetic ancestry persists in wild canids of southwestern Louisiana

Murphy

Adams

Cox

et al. 2018

CONSERVATION LETTERS

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Concerns over red wolf (Canis rufus) extinction caused by hybridization with coyotes (C. latrans) led to the capture and removal of remnant wild wolves from southwestern Louisiana and southeastern Texas, United States, during the 1970s. Here we show that despite decades of unmitigated hybridization, and declaration of endangered red wolves as functionally extinct in the wild, red wolf mitochondrial or nuclear DNA ancestry persists in ∼55% of contemporary wild canids sampled in southwestern Louisiana. Surprisingly, one individual had 78–100% red wolf ancestry, which is within the range for 75% red wolf, red wolf backcross, or putative red wolf, depending on estimation method. Our findings bolster support for designation of red wolves as a distinct species, demonstrate a critical need for the United States Government to consider adopting an existing but unimplemented hybrid policy, and suggest that immediate reassessment of canid management and taxonomic designation in southwestern Louisiana may be warranted.

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Evaluating and integrating spatial capture–recapture models with data of variable individual identifiability

Ruprecht

Eriksson

Forrester

et al. 2021

Ecological Applications

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Spatial capture-recapture (SCR) models have become the preferred tool for estimating densities of carnivores. Within this family of models are variants requiring identification of all individuals in each encounter (SCR), a subset of individuals only (generalized spatial mark-resight, gSMR), or no individual identification (spatial count or spatial presence-absence). Although each technique has been shown through simulation to yield unbiased results, the consistency and relative precision of estimates across methods in real-world settings are seldom considered. We tested a suite of models ranging from those only requiring detections of unmarked individuals to others that integrate remote camera, physical capture, genetic, and global positioning system (GPS) data into a 'hybrid' model, to estimate population densities of black bears, bobcats, cougars, and coyotes. For each species we genotyped fecal DNA collected with detection dogs during a 20-day period. A subset of individuals from each species was affixed with GPS collars bearing unique markings and resighted by remote cameras over 140 days contemporaneous with scat collection. Camera-based gSMR models produced density estimates that differed by less than 10% from genetic SCR for bears, cougars, and coyotes once important sources of variation (sex or behavioral status) were controlled for. For bobcats, SCR estimates were 33% higher than gSMR. The cause of the discrepancies in estimates was likely attributable to challenges designing a study compatible for species with disparate home range sizes and the difficulty of collecting sufficient data in a timeframe in which demographic closure could be assumed. Unmarked models estimated densities that varied greatly from SCR, but estimates became more consistent in models wherein more individuals were identifiable. Hybrid models containing all data sources exhibited the most precise estimates for all species. For studies in which only sparse data can be obtained and the strictest model assumptions are unlikely to be met, we suggest researchers use caution making inference from models lacking individual identity. For best results, we further recommend the use of methods requiring at least a subset of the population is marked and that multiple datasets are incorporated when possible.

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Integrating multiple genetic detection methods to estimate population density of social and territorial carnivores

Abstract: Spatial capture-recapture models can produce unbiased estimates of population density, but

Cited by 13 publications

References 62 publications

Comparison of grizzly bear hair‐snag and scat sampling along roads to inform wildlife population monitoring

Comparison of grizzly bear hair‐snag and scat sampling along roads to inform wildlife population monitoring

Substantial red wolf genetic ancestry persists in wild canids of southwestern Louisiana

Evaluating and integrating spatial capture–recapture models with data of variable individual identifiability

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