Evaluating the predictive power of field variables for species and individual molecular identification on wolf noninvasive samples

Nakamura, Mónia; Godinho, Raquel; Rio-Maior, Helena; Roque, Sara; Kaliontzopoulou, Antigoni; Bernardo, J.; Castro, Diana; Lopes, Susana; Petrucci-Fonseca, Francisco; Álvares, Francisco

doi:10.1007/s10344-017-1112-7

Cited by 20 publications

(14 citation statements)

References 68 publications

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“…Concerning climate conditions during sample collection, similar studies investigating DNA quality of scats originating from various animal species and regions concluded that either dry and/or very cold climatic conditions preserve the DNA in the field best (Piggott 2004;Murphy et al 2007;Brinkman et al 2010;Demay et al 2013;Agetsuma-Yanagihara et al 2017;Nakamura et al 2017;Klütsch and Thomas 2018). With otter scats deposited in the night before collection, our results indicated that ambient temperature seemed to have no impact on DNA quality, whereas the probability of a sample resulting in a positive genotype decreased with increasing humidity.…”

Section: Discussionsupporting

confidence: 51%

Factors influencing genotyping success and genotyping error rate of Eurasian otter (Lutra lutra) faeces collected in temperate Central Europe

et al. 2020

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The use of non-invasively collected DNA source material for genetic and genomic applications is usually characterized by low target DNA concentration and quality, genotyping errors and cost-intensive lab procedures. However, for otters (Lutrinae) as elusive species of conservation concern, genetic non-invasive sampling has become an important tool to study their ecology and demography. To increase cost-efficiency of monitoring programmes and to promote the expansion of genomic approaches to non-invasive samples, we aimed to refine sample collection and preparation. Therefore, we examined the effects of intrinsic sample characteristics (including diet), environmental conditions in the field and sample treatment in the molecular laboratory on the success of genotyping and allelic dropout (ADO) rates using microsatellite markers in 1970 fresh Eurasian otter (Lutra lutra) scats. Using fresh samples only, we probably eliminated one of the most important impediments of genotyping DNA from otter faecal samples beforehand. But, we observed higher genotyping success and lower ADO rates for anal glad secretions and faecal samples containing high proportions of mucus. Moist conditions during sample collection may promote DNA degradation and PCR inhibition, leading to decreased genotyping success rates. ADO was further affected by the type of extraction kit. However, a high proportion of variance remaining unexplained by our models implied that additional parameters were acting (amount of PCR inhibitors, non-uniform distribution of intestinal cells, efficiency of PCRs, specific microclimate at marking sites). We summarized influential factors maximizing genotyping quality of otter scats and give recommendations for sample collection, storage and DNA extraction based on our results and current literature.

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Section: Discussionsupporting

confidence: 51%

Factors influencing genotyping success and genotyping error rate of Eurasian otter (Lutra lutra) faeces collected in temperate Central Europe

et al. 2020

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“…Multiple factors can influence the success rate of genotyping and individual identification, such as the age of the wolf scat (related to the presence of odour) 51 . Nevertheless, the success rate observed in this study was similar to other values reported in studies using non-invasive DNA 51 . Estimated allelic dropout across loci was ADO = 0.033, and estimated false alleles were FA = 0.005 49 .…”

Section: Methodsmentioning

confidence: 99%

Toward reliable population estimates of wolves by combining spatial capture-recapture models and non-invasive DNA monitoring

López‐Bao

Godinho

Pacheco

et al. 2018

Sci Rep

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Decision-makers in wildlife policy require reliable population size estimates to justify interventions, to build acceptance and support in their decisions and, ultimately, to build trust in managing authorities. Traditional capture-recapture approaches present two main shortcomings, namely, the uncertainty in defining the effective sampling area, and the spatially-induced heterogeneity in encounter probabilities. These limitations are overcome using spatially explicit capture-recapture approaches (SCR). Using wolves as case study, and non-invasive DNA monitoring (faeces), we implemented a SCR with a Poisson observation model in a single survey to estimate wolf density and population size, and identify the locations of individual activity centres, in NW Iberia over 4,378 km 2 . During the breeding period, posterior mean wolf density was 2.55 wolves/100 km 2 (95%BCI = 1.87-3.51), and the posterior mean population size was 111.6 ± 18.8 wolves (95%BCI = 81.8-153.6). From simulation studies, addressing different scenarios of non-independence and spatial aggregation of individuals, we only found a slight underestimation in population size estimates, supporting the reliability of SCR for social species. The strategy used here (DNA monitoring combined with SCR) may be a cost-effective way to generate reliable population estimates for large carnivores at regional scales, especially for endangered species or populations under game management.Estimating the abundance of species is one of the most contentious issues in conservation and applied ecology 1,2 . Decision-makers in wildlife policy require reliable population size and density estimates to adopt and justify interventions. Reliability is essential to build acceptance and support in management decisions and, ultimately, trust in managing authorities. Otherwise, speculation and distrust can emerge after decisions are made, and may undermine entire management or conservation strategies 1,3 . Incorrect population estimates may lead to misinterpretations of the status of populations, the impact of interventions (e.g., hunting quotas or culling programs), or the degree to which conservation goals have been achieved.The management of large carnivores is controversial due to the multiple political, socio-economic and conservation interests involved. Information on population size or the impact of interventions is in constant demand, not only by managers, researchers and conservationists, but also by other interest groups. This is exemplified by recurrent debates around large carnivore numbers, particularly centred on endangered and charismatic species, such as in the case of tigers (Panthera tigris), lions (Panthera leo) or wolves (Canis lupus) [4][5][6][7][8] . Clear population targets are often established by managing authorities, and have become political issues, with reliable assessments of changes in large carnivore ranges and population size required to justify actions 9 .Wolves are a good example of a species whose estimates of population size and range are systemati...

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“…Human studies suggest that more salivary DNA can be collected from a hard, nonporous surface than from porous one, with the most effective transfer occurring when the saliva is collected by rubbing the nonporous surface with a porous material, analogous to swabbing (Goray et al ). The considerably greater success of the Collar swabs over Remains swabs may also have been due to predator epithelial cells captured on Remains swabs being swamped by hare cells sloughing off the carcass; for example, Nakamura et al () found that wolf ( Canis lupus ) saliva had larger amplification rates from hair alone in comparison with hair and skin, bone, or muscle. Although this information could help future studies target carcass‐swabbing efforts, the effect of carcass substrate likely varies by prey species; snowshoe hare fur is fine and difficult to unwrap from a swab after sample collection without risking the loss of predator cells.…”

Section: Discussionmentioning

confidence: 99%

Identifying predators from saliva at kill sites with limited remains

et al. 2019

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Kill-site investigations can yield valuable data about elusive predators and predator-prey interactions, provided the predator species can be definitively identified as the one responsible for the predation event. The traditional method of visually analyzing prey remains to identify predators is prone to observer bias and may be particularly challenging when few remains are present or in systems with congeneric predators. Other potential evidence left by predators, such as scat, may be difficult to reliably link to the responsible predator, whereas tracking requires adequate substrate conditions. Swabbing for predator DNA from saliva is an objective yet underutilized alternative that has primarily been applied to larger carcasses. We demonstrate the usefulness of a saliva-swabbing method for smaller prey with minimal surface area, including kill sites with almost no prey remains or even just a radiocollar left behind. This study is also the first to compare saliva-swabbing success by sample type (carcass remains vs. radiocollar). From 2010 to 2014, in the Loomis State Forest and Okanogan National Forest, Washington, USA, we employed forensic techniques to increase certainty about predator species identification at snowshoe hare (Lepus americanus) kill sites for the ultimate purpose of elucidating predator-prey interactions. Predator saliva was sampled from remains and radiocollars with foam buccal swabs, stored in lysis buffer for shelfstable preservation, and tested for mitochondrial DNA using polymerase chain reaction and species-specific primers. This saliva-swabbing protocol yielded definitive and objective predator species identification for a majority (58.5%) of sampled kill sites (n kill sites = 31/53). Not only were minimal remains often able to yield predator DNA, but swabs from radiocollars provided significantly more predator identifications. Saliva swabbing also provided identifications at 65.5% of kill sites lacking identifiable predator sign and contributed significantly more predator identifications throughout the year when compared with snow-tracking methods. Expanding saliva-swabbing methods to smaller prey, radiocollars, and limited remains should allow for more definitive predator identifications at kill sites than have been possible with commonly employed methods, thus augmenting the potential to understand and manage for predators and prey.

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Evaluating the predictive power of field variables for species and individual molecular identification on wolf noninvasive samples

Cited by 20 publications

References 68 publications

Factors influencing genotyping success and genotyping error rate of Eurasian otter (Lutra lutra) faeces collected in temperate Central Europe

Factors influencing genotyping success and genotyping error rate of Eurasian otter (Lutra lutra) faeces collected in temperate Central Europe

Toward reliable population estimates of wolves by combining spatial capture-recapture models and non-invasive DNA monitoring

Identifying predators from saliva at kill sites with limited remains

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