Reliability of environmental DNA surveys to detect pond occupancy by newts at a national scale

Andrew Buxton,Jim Griffin,Alex Diana,Eleni Matechou,Richard A Griffiths

doi:10.1038/s41598-022-05442-1

Andrew Buxton, Jim Griffin + Show 3 more

Open Access

https://doi.org/10.1038/s41598-022-05442-1

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Abstract

The distribution assessment and monitoring of species is key to reliable environmental impact assessments and conservation interventions. Considerable effort is directed towards survey and monitoring of great crested newts (Triturus cristatus) in England. Surveys are increasingly undertaken using indirect methodologies, such as environmental DNA (eDNA). We used a large data set to estimate national pond occupancy rate, as well as false negative and false positive error rates, for commercial eDNA protocols. Additionally, we explored a range of habitat, landscape and climatic variables as predictors of pond occupancy. In England, 20% of ponds were estimated to be occupied by great crested newts. Pond sample collection error rates were estimated as 5.2% false negative and 1.5% false positive. Laboratory error indicated a negligible false negative rate when 12 qPCR replicates were used. Laboratory false positive error was estimated at 2% per qPCR replicate and is therefore exaggerated by high levels of laboratory replication. Including simple habitat suitability variables into the model revealed the importance of fish, plants and shading as predictors of newt presence. However, variables traditionally considered as important for newt presence may need more precise and consistent measurement if they are to be employed as reliable predictors in modelling exercises.

Highlights

When undertaking any assessment of species distribution, it is imperative to understand the limitations of the survey methods used
An observed pond occupancy rate of 0.30 (1496 occupied sites) was obtained for the data based on a threshold of a single qPCR replicate amplifying
Various estimates for great crested newt pond occupancy rates have been published with most relating to site or regional scale assessments

Summary

Introduction

When undertaking any assessment of species distribution, it is imperative to understand the limitations of the survey methods used. Failure to fully consider sampling efficiency, sampling bias or other methodological limitations can lead to erroneous conclusions Within nature conservation, these may result in inadequate assessments of impact, and inappropriate conservation target setting, leading to poor conservation o utcomes[1,2,3]. Standard occupancy models assume that false positive observations do not occur This assumption is not always met, in cases where a species may be misidentified[20] or in cases of indirect survey methods where the species is inferred to be present through biological products (e.g. tracks, faeces, hair). EDNA false positive error may not be negligible in surveys[7] and—as with all methods—needs to be accounted for when assessing site occupancy. Models have been developed that allow for multiscale occupancy models to be applied, which account for both positive and negative error[21] at both stages

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