School of BioSciences - Research Publications
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ItemAccounting for false positive detections in occupancy studies based on environmental DNA: A case study of a threatened freshwater fish (Galaxiella pusilla)(Wiley, 2021-03-01)Abstract Environmental DNA (eDNA) sampling is a promising method for surveying aquatic fauna. Recent eDNA studies have investigated the likelihood of false negative errors in the laboratory and in the field, but the likelihood of false positives remains poorly studied. We investigated the likelihood of both types of errors in eDNA surveys of an Australian threatened freshwater fish (Galaxiella pusilla) using laboratory experiments, field surveys, and recent advances in hierarchical site occupancy‐detection modeling. Laboratory experiments revealed high primer/probe specificity; absence of sample contamination in extraction and qPCR blanks; and rapid accumulation and deterioration of eDNA in aquaria. Hierarchical site occupancy‐detection models fitted to pilot data collected at 13 wetlands revealed that two water samples, each with two qPCRs, would be required to achieve a cumulative detection probability >.95. A more comprehensive survey, in which we simultaneously used dip netting and eDNA sampling at 29 wetlands, revealed similar mean detection probabilities of the two sampling methods (trapping: 0.74 vs. eDNA: 0.68), and low probabilities of false positive errors at the water sample level (0.0080) and at the qPCR level (0.0039) for eDNA sampling. Collectively, our results illustrate that eDNA sampling can be a sensitive and specific method for monitoring the occurrence of freshwater fauna. Detection probabilities of eDNA sampling were comparable to those of a traditional sampling method, and probabilities of laboratory‐induced false positives were low. Future studies employing eDNA sampling should estimate, and properly account for, false positive errors in addition to false negatives.
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ItemMultispecies models reveal that eDNA metabarcoding is more sensitive than backpack electrofishing for conducting fish surveys in freshwater streams(WILEY, 2021-07)Environmental DNA (eDNA) sampling can provide accurate, cost-effective, landscape-level data on species distributions. Previous studies have compared the sensitivity of eDNA sampling to traditional sampling methods for single species, but similar comparative studies on multispecies eDNA metabarcoding are rare. Using hierarchical site occupancy detection models, we examined whether key choices associated with eDNA metabarcoding (primer selection, low-abundance read filtering and the number of positive water samples used to classify a species as present at a site) affect the sensitivity of metabarcoding, relative to backpack electrofishing for fish in freshwater streams. Under all scenarios (teleostei and vertebrate primers; 0%, 0.1% and 1% read filtering thresholds; one or two positive samples required to classify species as present), we found that eDNA metabarcoding is, on average, more sensitive than electrofishing. Combining vertebrate and teleostei markers resulted in higher detection probabilities relative to the use of either marker in isolation. Increasing the threshold used to filter low-abundance reads decreased species detection probabilities but did not change our overall finding that eDNA metabarcoding was more sensitive than electrofishing. Using a threshold of two positive water samples (out of five) to classify a species as present typically had negligible effects on detection probabilities compared to using one positive water sample. Our findings demonstrate that eDNA metabarcoding is generally more sensitive than electrofishing for conducting fish surveys in freshwater streams, and that this outcome is not sensitive to methodological decisions associated with metabarcoding.
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ItemDealing with false-positive and false-negative errors about species occurrence at multiple levels(Wiley, 2017-09-01)Summary 1. Accurate knowledge of species occurrence is fundamental to a wide variety of ecological, evolutionary and conservation applications. Assessing the presence or absence of species at sites is often complicated by imperfect detection, with different mechanisms potentially contributing to false‐negative and/or false‐positive errors at different sampling stages. Ambiguities in the data mean that estimation of relevant parameters might be confounded unless additional information is available to resolve those uncertainties. 2. Here, we consider the analysis of species detection data with false‐positive and false‐negative errors at multiple levels. We develop and examine a two‐stage occupancy‐detection model for this purpose. We use profile likelihoods for identifiability analysis and estimation, and study the types of additional data required for reliable estimation. We test the model with simulated data, and then analyse data from environmental DNA (eDNA) surveys of four Australian frog species. In our case study, we consider that false positives may arise due to contamination at the water sample and quantitative PCR‐sample levels, whereas false negatives may arise due to eDNA not being captured in a field sample, or due to the sensitivity of laboratory tests. We augment our eDNA survey data with data from aural surveys and laboratory calibration experiments. 3. We demonstrate that the two‐stage model with false‐positive and false‐negative errors is not identifiable if only survey data prone to false positives are available. At least two sources of extra information are required for reliable estimation (e.g. records from a survey method with unambiguous detections, and a calibration experiment). Alternatively, identifiability can be achieved by setting plausible bounds on false detection rates as prior information in a Bayesian setting. The results of our case study matched our simulations with respect to data requirements, and revealed false‐positive rates greater than zero for all species. 4. We provide statistical modelling tools to account for uncertainties in species occurrence survey data when false negatives and false positives could occur at multiple sampling stages. Such data are often needed to support management and policy decisions. Dealing with these uncertainties is relevant for traditional survey methods, but also for promising new techniques, such as eDNA sampling.
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ItemAssessing the cost-efficiency of environmental DNA sampling(WILEY, 2016-11)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 methods that account for imperfect and stochastic detection can be used to (i) determine the optimal allocation of survey effort with eDNA sampling for a fixed budget (i.e. identify the optimal combination of water samples vs. site visits), and (ii) assess the cost‐efficiency of eDNA sampling relative to traditional survey techniques. We illustrate this approach by comparing eDNA sampling and bottle‐trapping for an exotic newt species (Lissotriton v. vulgaris) recently detected in Melbourne, Australia. Bottle traps produced much lower detection rates than eDNA sampling, but the cost‐efficiency of the two methods can be similar because bottle‐trapping is cheaper per sample. The relative cost‐efficiency of the two sampling methods was sensitive to the available survey budget, the costs of eDNA primer/probe development and sample processing and the number of positive quantitative PCR assays (qPCRs) used to designate a water sample as positive for newt DNA. Environmental DNA sampling was more cost‐efficient than bottle‐trapping for small to intermediate budgets when primer/probe development and sample processing costs were low, and 1/4 or 2/4 positive qPCRs were used to label a water sample as positive for newt eDNA. However, bottle traps were generally more cost‐efficient than eDNA sampling when primer/probe development and sample processing costs were high, regardless of qPCR threshold or survey budget. Traditional sampling methods may achieve lower detection probabilities compared to eDNA sampling, but the totality of costs can make eDNA sampling less efficient than traditional techniques in some circumstances. Our approach provides a quantitative framework for determining how many water samples and site visits are required to maximize detection probabilities with eDNA sampling, and can calculate the cost‐efficiency of any sampling method.