Improving herpetological surveys in eastern North America using the environmental DNA method

Abstract

Among vertebrates, herpetofauna has the highest proportion of declining species. Detection of environmental DNA (eDNA) is a promising method towards significantly increasing large-scale herpetological conservation efforts. However, the integration of eDNA results within a management framework requires an evaluation of the efficiency of the method in large natural environments and the calibration of eDNA surveys with the quantitative monitoring tools currently used by conservation biologists. Towards this end, we first developed species-specific primers to detect the wood turtle (Glyptemys insculpta) a species at risk in Canada, by quantitative PCR (qPCR). The rate of eDNA detection obtained by qPCR was also compared to the relative abundance of this species in nine rivers obtained by standardized visual surveys in the Province of Québec (Canada). Second, we developed multi-species primers to detect North American amphibian and reptile species using eDNA metabarcoding analysis. An occurrence index based on the distribution range and habitat type was compared with the eDNA metabarcoding dataset from samples collected in seven lakes and five rivers. Our results empirically support the effectiveness of eDNA metabarcoding to characterize herpetological species distributions. Moreover, detection rates provided similar results to standardized visual surveys currently used to develop conservation strategies for the wood turtle. We conclude that eDNA detection rates may provide an effective semiquantitative survey tool, provided that assay calibration and standardization is performed.

Needle in a haystack? A comparison of eDNA metabarcoding and targeted qPCR for detection of the great crested newt (Triturus cristatus)

“…We have demonstrated eDNA metabarcoding is a highly sensitive tool for monitoring T. cristatus alongside the wider biological community, corroborating other comparisons of eDNA metabarcoding and qPCR for single‐species monitoring (Lacoursière‐Roussel et al., ; Schneider et al., ). Despite reduction in single‐species detection, eDNA metabarcoding revealed a wealth of biodiversity information and could enable more effective freshwater monitoring networks and better understanding of community structure and ecosystem function alongside T. cristatus monitoring (Biggs, von Fumetti, & Kelly‐Quinn, ).…”

“…Conversely, the passive approach uses conserved primers (i.e., primers with binding sites that are shared across multiple taxa, and flank a region of highly variable DNA sequence that enables discrimination between these taxa) and PCR to sequence whole communities with high‐throughput sequencing (HTS), termed eDNA metabarcoding (Deiner et al., ; Shaw, Weyrich, et al., ; Taberlet, Coissac, Pompanon, Brochmann, & Willerslev, ; Valentini et al., ). Passive eDNA monitoring is particularly attractive to ecologists for biodiversity assessment as a means to detect entire species assemblages alongside rare or invasive species (Blackman et al., ; Lacoursière‐Roussel, Dubois, Normandeau, & Bernatchez, ). However, this gain in community understanding may come at the cost of accuracy and sensitivity.…”

“…The sensitivity of eDNA metabarcoding has been evaluated against conventional biodiversity monitoring methods in freshwater ecosystems (Bálint et al., ; Civade et al., ; Evans, Li, et al., ; Hänfling et al., ; Lopes et al., ; Shaw, Clarke, et al., ; Valentini et al., ), yet specific investigations comparing the sensitivity of eDNA metabarcoding and targeted qPCR are sparse. Similarly, comparisons of qPCR and conventional survey for species monitoring have included cost projections (Biggs, Ewald, Valentini, Gaboriaud, & Griffiths, ; Davy et al., ; Evans, Shirey, et al., ; Smart et al., ), but cost has not been thoroughly assessed in qPCR and eDNA metabarcoding comparisons (Lacoursière‐Roussel et al., ; Schneider et al., ). Schneider et al.…”

From Barcodes to Biomes: Special Issues from the 6th International Barcode of Life Conference

“…Lee et al (2016) compare multiple methods of surveying tropical forest mammals in two reserves in Malaysia, revealing that sequencing blowfly-derived mammal DNA using HTS is a promising tool. Applying both metabarcoding via HTS and quantitative PCR (qPCR), Lacoursière-Roussel et al (2016) develop methods for the detection of amphibians and reptiles using aquatic environmental DNA (eDNA). With these groups being particularly threatened, it is important to be able to study their distributions and population health efficiently.…”

Water sampling for environmental DNA surveys by using an unmanned aerial vehicle

“…Extracellular DNA fragments from the genomes of various micro‐ and macroorganisms (Hoffmann et al ) are found in nature and referred to as “environmental DNA (eDNA).” Techniques using eDNA to investigate the distribution and abundance/biomass of organisms have recently been developed for species inhabiting various habitats (Goldberg et al ; Thomsen and Willerslev ), including freshwater lentic (Ficetola et al ; Jerde et al ; Takahara et al ; Doi et al ; Dougherty et al ; Hänfling et al ) and lotic (Pilliod et al ; Fukumoto et al ; Deiner et al ; Ikeda et al ; Shaw et al ; Yamanaka and Minamoto ) systems and marine systems (Thomsen et al ; Miya et al ; Lacoursière‐Roussel et al ; Yamamoto et al ; Yamamoto et al ). The eDNA technique is likely to become a revolutionary tool used to increase both spatial and temporal scales for species‐distribution monitoring (Thomsen and Willerslev ).…”