Rapid species identification of pygmy rabbits <i>(Brachylagus idahoensis)</i> from faecal pellet DNA

Adams, Jennifer R.; Goldberg, Caren S.; Bosworth, William R.; Rachlow, Janet L.; Waits, Lisette P.

doi:10.1111/j.1755-0998.2011.03020.x

Cited by 19 publications

(39 citation statements)

References 26 publications

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“…However, very few (if any) of these scats are likely to have produced a successful individual identification since all samples that amplified at less than 50% of the loci were removed from analyses, and PCR amplification success rates for carnivore samples older than 2 months were 0–39% (

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= 19%; Piggott , Murphy et al ). Furthermore, DNA degradation rates are greater in wet (Piggott , Murphy et al , Brinkman et al ) and hot environments (Nsubuga et al , DeMay et al ) and less in dry and cold environments (Lucchini et al , Adams et al ).…”

Section: Discussionmentioning

confidence: 99%

Estimating cougar densities in northeast Oregon using conservation detection dogs

et al. 2014

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Estimating densities of cougar (Puma concolor) is important for managing cougars and their prey but remains challenging because of cougar's elusive and solitary behavior. To evaluate a non‐invasive, genetic capture–recapture method to estimate cougar population size and density, we surveyed a 220‐km2 area using conservation detection dogs trained to locate scat over a 4‐week sampling period in northeast Oregon. We collected 272 scat samples and conducted DNA analysis on 249 samples from which we determined individual identification from 73 samples that represented 21 cougars (9 males and 12 females). We evaluated 4 models to estimate cougar densities: Huggins closed population capture–recapture (Huggins), CAPWIRE, multiple detections with Poisson (MDP), and spatially explicit capture–recapture (SECR). Population estimates for cougars using our study area were 26 (95% CI = 22–35, 9 males and 17 females) from Huggins models, 24 (95% CI = 21–30, 9 males and 15 females) from CAPWIRE, and 27 (95% CI = 24–42, 9 males and 18 females) from the MDP model. We accounted for the edge effect in density estimates caused by individuals whose home ranges included only a portion of the survey grid by buffering the study area using the mean home range radius of 8 cougars equipped with global positioning system collars on or near the study area. We estimated densities of 4.6 cougars/100 km2 (95% CI = 3.8–8.3) for the Huggins model, 4.8 cougars/100 km2 (95% CI = 4.2–7.8) for the MDP model, 4.2 cougars/100 km2 (95% CI = 3.3–5.3) for the CAPWIRE model, and 5.0 cougars/100 km2 (95% CI = 3.2–7.7) for the SECR model. Our results suggested estimating cougar densities using scat detection dogs could be feasible at a broader scale with less effort than other methods currently being used. © 2014 The Wildlife Society.

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Section: Discussionmentioning

confidence: 99%

Estimating cougar densities in northeast Oregon using conservation detection dogs

et al. 2014

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“…Adams et al . () developed the mtDNA species ID test used in this study and found 72% PCR success for nonwinter pygmy rabbit pellet samples of unknown age (Adams et al . ).…”

Section: Discussionmentioning

confidence: 99%

“…() developed the mtDNA species ID test used in this study and found 72% PCR success for nonwinter pygmy rabbit pellet samples of unknown age (Adams et al . ). Noninvasive genetic sampling and mtDNA species identification is also an important tool for monitoring the distribution of threatened New England cottontails (Kovach et al .…”

Section: Discussionmentioning

confidence: 99%

“…The PCR concentrations were as published in Adams et al . (), but PCR conditions differed. The PCR profile had an initial denaturation of 95 °C for 10 min, followed by a touchdown of 15 cycles with a 30‐s denaturation at 95 °C, 30‐s annealing step at 63 °C decreasing 0.5 °C each cycle and 60‐s extension at 72 °C.…”

Section: Methodsmentioning

confidence: 99%

“…Pygmy rabbits have previously been surveyed using a species‐specific mtDNA test on faecal pellets (Adams et al . ), and faecal DNA is also being used to monitor the range of the New England cottontail ( Sylvilagus transitionalis ), a rabbit species of conservation concern in the northeastern United States (Kovach et al . ; Litvaitis et al .…”

Section: Introductionmentioning

confidence: 99%

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Evaluating DNA degradation rates in faecal pellets of the endangered pygmy rabbit

DeMay

Becker

Eidson

et al. 2013

Molecular Ecology Resources

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Noninvasive genetic sampling of faecal pellets can be a valuable method for monitoring rare and cryptic wildlife populations, like the pygmy rabbit (Brachylagus idahoensis). To investigate this method's efficiency for pygmy rabbit monitoring, we evaluated the effect of sample age on DNA degradation in faecal pellets under summer field conditions. We placed 275 samples from known individuals in natural field conditions for 1-60 days and assessed DNA quality by amplifying a 294-base-pair (bp) mitochondrial DNA (mtDNA) locus and five nuclear DNA (nDNA) microsatellite loci (111-221 bp). DNA degradation was influenced by sample age, DNA type, locus length and rabbit sex. Both mtDNA and nDNA exhibited high PCR success rates (94.4%) in samples <1 day old. Success rates for microsatellite loci declined rapidly from 80.0% to 42.7% between days 5 and 7, likely due to increased environmental temperature. Success rates for mtDNA amplification remained higher than nDNA over time, with moderate success (66.7%) at 21 days. Allelic dropout rates were relatively high (17.6% at <1 day) and increased to 100% at 60 days. False allele rates ranged from 0 to 30.0% and increased gradually over time. We recommend collecting samples as fresh as possible for individual identification during summer field conditions. Our study suggests that this method can be useful for future monitoring efforts, including occupancy surveys, individual identification, population estimation, parentage analysis and monitoring of genetic diversity both of a re-introduced population in central Washington and across their range.

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DNA mini‐barcoding of leporids using noninvasive fecal DNA samples and its significance for monitoring an invasive species

Rodrigues

Saranholi

Angeloni

et al. 2020

Ecology and Evolution

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Introduced in South America at the end of the 19th century, the European hare population has expanded dramatically and now represents a risk to native Brazilian forest rabbits. Monitoring the invasive Lepus europaeus and its coexistence with native Sylvilagus brasiliensis is a challenge that can be efficiently addressed by the use of molecular tools. This work describes a set of primers useful for amplifying three mini‐barcodes for the molecular identification of both invasive and native leporid species using degraded fecal DNA. In addition, tests in silico indicate that these mini‐barcodes can successfully amplify the DNA sequences of a number of leporids. These mini‐barcodes constitute a powerful tool for the monitoring and management of the invasive L. europaeus and the conservation of native rabbits.

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Rapid species identification of pygmy rabbits (Brachylagus idahoensis) from faecal pellet DNA

Cited by 19 publications

References 26 publications

Estimating cougar densities in northeast Oregon using conservation detection dogs

Estimating cougar densities in northeast Oregon using conservation detection dogs

Evaluating DNA degradation rates in faecal pellets of the endangered pygmy rabbit

DNA mini‐barcoding of leporids using noninvasive fecal DNA samples and its significance for monitoring an invasive species

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