ednaoccupancy: An r package for multiscale occupancy modelling of environmental DNA data

Molecular Ecology Resources, Journal Year: 2017, Volume and Issue: 18(2), P. 368 - 380

Published: Nov. 9, 2017

In this article, we describe ednaoccupancy, an r package for fitting Bayesian, multiscale occupancy models. These models are appropriate surveys that include three nested levels of sampling: primary sample units within a study area, secondary collected from each unit and replicates unit. This design is commonly used in environmental DNA (eDNA). ednaoccupancy allows users to specify fit with or without covariates, estimate posterior summaries occurrence detection probabilities, compare different using Bayesian model-selection criteria. We illustrate these features by analysing two published data sets: eDNA fungal pathogen amphibians endangered fish species.

Language: Английский

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Genetic and Manual Survey Methods Yield Different and Complementary Views of an Ecosystem

Frontiers in Marine Science, Journal Year: 2017, Volume and Issue: 3

Published: Jan. 8, 2017

Given the rapid rise of environmental DNA (eDNA) surveys in ecology and science, it is important to be able compare results these traditional methods measuring biodiversity. Here we samples from a method (a manual tow-net) companion eDNA sequenced at three different genetic loci. We find only partial taxonomic overlap among resulting datasets, with each reflecting portion larger suite taxa present sampled nearshore marine environment. In context sequencing surveys, our suggest that primer amplification bias drives much detection, baseline probability detecting any given taxon broad-spectrum set likely low. Whether catching fish nets or using PCR sets, multiple data types can provide complementary views common ecosystem. However, remains difficult cross-validate techniques field, either for presence/absence abundance, particularly sets target very wide ranges. Finally, highlight breadth diversity single habitat, although does capture richer sample community than sampling, large number focusing on subsets biota would necessary survey ecological reasonably comprehensive way.

Language: Английский

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Detection limits of quantitative and digital PCR assays and their influence in presence–absence surveys of environmental DNA

Molecular Ecology Resources, Journal Year: 2016, Volume and Issue: 17(2), P. 221 - 229

Published: Oct. 21, 2016

A set of universal guidelines is needed to determine the limit detection (LOD) in PCR-based analyses low-concentration DNA. In particular, environmental DNA (eDNA) studies require sensitive and reliable methods detect rare cryptic species through shed genetic material samples. Current strategies for assessing limits eDNA are either too stringent or subjective, possibly resulting biased estimates species' presence. Here, a conservative LOD analysis grounded analytical chemistry proposed correct overestimated concentrations predominantly caused by concentration plateau, nonlinear relationship between expected measured concentrations. We have used statistical criteria establish formal mathematical models both quantitative droplet digital PCR. To assess method, new Grass Carp (Ctenopharyngodon idella) TaqMan assay was developed tested on PCR platforms using water The adjustment reduced occupancy while increasing uncertainty-indicating that caution needs be applied data without correction. Compared PCR, had higher occurrence due increased sensitivity dilution inhibitors at low Without accurate correction, probabilities based prone source bias cannot an increase sample size replicates. Other applications also could benefit from standardized such as GMO food forensic clinical diagnostics.

Language: Английский

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Assessing the cost‐efficiency of environmental DNA sampling

Methods in Ecology and Evolution, Journal Year: 2016, Volume and Issue: 7(11), P. 1291 - 1298

Published: May 30, 2016

Summary Environmental DNA ( eDNA ) sampling can be a highly sensitive method for detecting aquatic taxa; however, the cost‐efficiency of this technique relative to traditional methods has not been rigorously assessed. We show how that account imperfect and stochastic detection used (i) determine optimal allocation survey effort with fixed budget (i.e. identify combination water samples vs. site visits), (ii) assess techniques. illustrate approach by comparing bottle‐trapping an exotic newt species Lissotriton v. vulgaris recently detected in Melbourne, Australia. Bottle traps produced much lower rates than sampling, but two similar because is cheaper per sample. The was available budget, costs primer/probe development sample processing number positive quantitative PCR assays qPCR s) designate as . more cost‐efficient small intermediate budgets when were low, 1/4 or 2/4 s label However, bottle generally high, regardless threshold budget. Traditional may achieve probabilities compared totality make less efficient techniques some circumstances. Our provides framework determining many visits are required maximize calculate any method.

Language: Английский

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Dealing with false‐positive and false‐negative errors about species occurrence at multiple levels

Methods in Ecology and Evolution, Journal Year: 2017, Volume and Issue: 8(9), P. 1081 - 1091

Published: Jan. 28, 2017

Summary Accurate knowledge of species occurrence is fundamental to a wide variety ecological, evolutionary and conservation applications. Assessing the presence or absence at sites often complicated by imperfect detection, with different mechanisms potentially contributing false‐negative and/or false‐positive errors sampling stages. Ambiguities in data mean that estimation relevant parameters might be confounded unless additional information available resolve those uncertainties. Here, we consider analysis detection multiple levels. We develop examine two‐stage occupancy‐detection model for this purpose. use profile likelihoods identifiability estimation, study types required reliable estimation. test simulated data, then analyse from environmental DNA ( eDNA ) surveys four Australian frog species. In our case study, false positives may arise due contamination water sample quantitative PCR ‐sample levels, whereas negatives not being captured field sample, sensitivity laboratory tests. augment survey aural calibration experiments. demonstrate identifiable if only prone are available. At least two sources extra (e.g. records method unambiguous detections, experiment). Alternatively, can achieved setting plausible bounds on rates as prior Bayesian setting. The results matched simulations respect requirements, revealed greater than zero all provide statistical modelling tools account uncertainties when could occur Such needed support management policy decisions. Dealing these traditional methods, but also promising new techniques, such sampling.

Language: Английский

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