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

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.

State-of-the-art of data analyses in environmental DNA approaches towards its applicability to sustainable fisheries management

“…Occupancy modelling can be applied to eDNA metabarcoding (i.e. Doi et al, 2019;McClenaghan et al, 2020, Valdivia-Carrillo et al, 2021, and in targeted eDNA approach (Dorazio andErickson, 2018, Fukaya et al, 2021;Buxton et al, 2022). Appropriate data for fitting an Occupancy Site model consist of a series of samples obtained from S sampling sites, with K replicate samples obtained per site (Dorazio and Erickson, 2018).…”

“…Thus, the occupancy modelling framework can be also applied to study the optimal conditions for sampling and laboratory stages (Doi et al, 2019). Modelling is frequently performed by Bayesian inference, and modeled parameters can include environmental and experimental covariates (Guillera-Arroita et al, 2017;McClenaghan et al, 2020;Burian et al, 2021;Buxton et al, 2022).…”

Illustrated keys and a DNA barcode reference library of the amphibians and terrestrial reptiles (Amphibia, Reptilia) of São Tomé and Príncipe (Gulf of Guinea, West Africa)

“…More recently, environmental DNA approaches have been employed to contribute to the survey of vertebrate species, including amphibians and reptiles ( Ficetola et al 2019 ; Buxton et al 2022 ; Moss et al 2022 ; Nordstrom et al 2022 ). These approaches can, theoretically, be faster and less dependent on taxonomic expertise ( Ruppert et al 2019 ) and have been used to try to document the presence of rare and ecologically cryptic and difficult to observe taxa ( Rojahn et al 2021 ), as well as invasive taxa ( Mahon and Jerde 2016 ).…”

“…These approaches can, theoretically, be faster and less dependent on taxonomic expertise ( Ruppert et al 2019 ) and have been used to try to document the presence of rare and ecologically cryptic and difficult to observe taxa ( Rojahn et al 2021 ), as well as invasive taxa ( Mahon and Jerde 2016 ). The effectiveness of environmental DNA approaches to survey amphibians and reptiles in the wild is not generalized across the different taxonomic and functional groups, being much more effective for the case of strictly aquatic amphibians ( Buxton et al 2022 ; Moss et al 2022 ) but tends to be less complete for the case of more terrestrial amphibians and reptiles ( Kyle et al 2022 ; Nordstrom et al 2022 ; pers. obs.).…”

A revised system for interpreting great crested newt habitat suitability indices

“…Presence was assigned to any site where the eDNA sample showed amplification of at least one qPCR replicate. This threshold is commonly used in assigning occupancy of eDNA samples to increase sensitivity, however there is a risk that a low qPCR replication threshold may exacerbate false positive error (Buxton et al, 2021b;Buxton et al, 2022). We removed 359 records where an HSI score could not be calculated due to missing information, we further removed 188 records that gave an inconclusive eDNA result so could not be assigned to either species presence or absence, which left a total sample size of 5318.…”