An eDNA approach to detect eastern hellbenders (Cryptobranchus a. alleganiensis) using samples of water

Abstract

Context Environmental DNA, or eDNA, methods are a novel application of non-invasive genetic sampling in which DNA from organisms is detected via sampling of water or soil, typically for the purposes of determining the presence or absence of an organism. eDNA methods have the potential to revolutionise the study of rare or endangered taxa. Aims We evaluated the efficacy of eDNA sampling to detect populations of an amphibian of conservation concern, the eastern hellbender (Cryptobranchus a. alleganiensis), indirectly from their aquatic environments. Methods We developed species-specific primers, validated their specificity and sensitivity, and assessed the utility of our methods in silico and in laboratory trials. In the field, we collected water samples from three sites with known densities of hellbenders, and from one site where hellbenders do not occur. We filtered water samples, extracted DNA from filters, and assayed the extraction products for hellbender DNA by using polymerase chain reaction (PCR) and gel electrophoresis. Key results Our methods detected hellbenders at densities approaching the lowest of reported natural densities. The low-density site (0.16 hellbenders per 100 m2) yielded two positive amplifications, the medium-density site (0.38 hellbenders per 100 m2) yielded eight positive amplifications, and the high-density site (0.88 hellbenders per 100 m2) yielded 10 positive amplifications. The apparent relationship between density and detection was obfuscated when river discharge was considered. There was no amplification in any negative control. Conclusion eDNA methods may represent a cost-effective means by which to establish broad-scale patterns of occupancy for hellbenders. Implications eDNA can be considered a valuable tool for detecting many species that are otherwise difficult to study.

Utility of environmental DNA for monitoring rare and indicator macroinvertebrate species

“…Comparisons of conventional and eDNA surveillance methods already have been made (e.g., Goldberg et al 2011, Jerde et al 2011, Thomsen et al 2011, Olson et al 2012, but methods were rarely applied simultaneously or were focused on 1 species only , Pilliod et al 2013. We found that the taxon-specific match of the 2 methods was moderate to high (Fig.…”

iDNA at Sea: Recovery of Whale Shark (Rhincodon typus) Mitochondrial DNA Sequences from the Whale Shark Copepod (Pandarus rhincodonicus) Confirms Global Population Structure

“…We found iDNA sequences from multiple copepods sampled from the same whale shark host to be identical, suggesting copepods have a persistent, long-term association with their host shark, which contrasts with the more generalist and mobile host associations of other invertebrate ectoparasites in terrestrial and aquatic ecosystems, such as leeches, blow flies, and mosquitoes (Calvignac-Spencer et al, 2013). However, these findings should be treated with some degree of caution and a multi-locus approach using microsatellite Frontiers in Marine Science | www.frontiersin.org markers (Olson et al, 2012) might offer a more powerful means to validate these findings. As reported by Vignaud et al (2014), our estimates of genetic structure across the Indian, Pacific, and Atlantic oceans indicated the presence of two distinct populations, one in the Indo-Pacific and the other in the Atlantic Ocean.…”

Modelling the transport of environmental DNA through a porous substrate using continuous flow-through column experiments

“…While recent studies have demonstrated that eDNA is a powerful tool for detecting target species in aquatic ecosystems [11], the majority of studies to date focus on detection from water in mesocosms [2,[12][13][14][15][16] or experimental/ natural ponds [1,[7][8][9]11,12,16]. A few studies have used eDNA survey methods in stream or river water samples for detection of amphibians [9,15,17], molluscs [18], fish [6,9,13,19] and invertebrates [20].…”