“Sight-unseen” detection of rare aquatic species using environmental DNA

Jerde, Christopher L.; Mahon, Andrew R.; Chadderton, W. Lindsay; Lodge, David M.

doi:10.1111/j.1755-263x.2010.00158.x

Cited by 1,029 publications

(1,196 citation statements)

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“…Yet, it was not until 2008, that French researchers first applied eDNA methods to confirm the presence of an aquatic invasive species (Rana catesbiana) from water samples in a natural lotic system (Ficetola et al, 2008). In North America, Jerde, Mahon, Chadderton & Lodge (2011) demonstrated the efficacy of eDNA as a detection tool for invasive species in freshwater systems. This study focused on the detection of silver and bighead Asian carp (Hypophthalmichthys molitrix and H. nobilis).…”

Section: History Of Ednamentioning

confidence: 99%

History, applications, methodological issues and perspectives for the use environmental DNA (eDNA) in marine and freshwater environments

Díaz-Ferguson

Moyer

2014

RBT

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Genetic material (short DNA fragments) left behind by species in nonliving components of the environment (e.g. soil, sediment, or water) is defined as environmental DNA (eDNA). This DNA has been previously described as particulate DNA and has been used to detect and describe microbial communities in marine sediments since the mid-1980's and phytoplankton communities in the water column since the early-1990's. More recently, eDNA has been used to monitor invasive or endangered vertebrate and invertebrate species. While there is a steady increase in the applicability of eDNA as a monitoring tool, a variety of eDNA applications are emerging in fields such as forensics, population and community ecology, and taxonomy. This review provides scientist with an understanding of the methods underlying eDNA detection as well as applications, key methodological considerations, and emerging areas of interest for its use in ecology and conservation of freshwater and marine environments. Rev. Biol. Trop. 62 (4): 1273-1284. Epub 2014 December 01.Key words: environmental DNA (eDNA), detection probability, occupancy models, persistence, metabarcode, minibarcode.In order to understand distributions, patterns, and abundances for populations or species, the collection (detection) and identification of individuals from their physical origins must be undertaken. Thus, species detection is fundamental to scientific disciplines such as phylogenetics, conservation biology, and ecology. However, species detection is sometimes extremely difficult especially in marine and aquatic environments where organisms have complex life cycles, and direct observation of early development stages is almost impossible (Ficetola, Miaud, Pompanon, & Taberlet, 2008). Species detection in these environments has been conducted using traditional direct observation methods (visual or acoustic) (Thomsen et al., 2012a). Nonetheless, traditional detection methods can have logistic limitations, be time consuming, expensive, and in some cases, harmful to the environment (e.g., marine bottom trawls, electrofishing and rotenone poisoning) (Thomsen et al., 2012b). The advent of novel molecular and forensic methods have provided innovative tools for detecting marine and aquatic organisms that may circumvent the aforementioned limitations (Darling & Blum, 2007;valentini, Pompano, & Taberlet, 2009;Lodge et al., 2012).One such tool is the detection of an organism's environmental DNA (eDNA). Defined as short DNA fragments that an organism leaves behind in non-living components of the ecosystem (i.e., water, air or sediments), eDNA is derived from either cellular DNA present in epithelial cells released by organisms to the environment through skin, urine, feces or mucus or extracellular DNA that is the DNA in the environment resulting from cell death and subsequent destruction of cell structure (Foote, Thomsen, Sveegaard, Wahlberg, Kielgast, Kyhn, Salling, Galatius, Orlando, & Gilbert, 2012;Taberlet, Coissac, Hajibabaei, & Rieseberg, 2012a). Methodologically, eDNA d...

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Section: History Of Ednamentioning

confidence: 99%

History, applications, methodological issues and perspectives for the use environmental DNA (eDNA) in marine and freshwater environments

Díaz-Ferguson

Moyer

2014

RBT

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“…However, no single approach has so far been able to accomplish this goal for fish (Evans & Lamberti, 2018; Harvey, Qureshi, & MacIsaac, 2009; Jerde, Mahon, Chadderton, & Lodge, 2011). Nevertheless, surveying for fish using the DNA they release (environmental DNA or “eDNA”) has become a method of choice because of the sensitivity and specificity of the technique, and the ease with which water can be collected (Bylemans et al., 2017; Ficetola, Miaud, Pompanon, & Taberlet, 2008; Jerde et al., 2011; Lacoursière‐Roussel, Rosabal, & Bernatchez, 2016; Minamoto et al., 2017; Taberlet, Coissac, Hajibabaei, & Rieseberg, 2012; Takahara, Minamoto, Yamanaka, Doi, & Kawabata, 2012; Thomsen & Willerslev, 2015). However, the utility of measuring eDNA is presently limited by the fact that many basic tenants of the ecology of eDNA are not well understood (Barnes & Turner, 2016; Evans & Lamberti, 2018).…”

Section: Introductionmentioning

confidence: 99%

Attracting Common Carp to a bait site with food reveals strong positive relationships between fish density, feeding activity, environmental DNA, and sex pheromone release that could be used in invasive fish management

Ghosal

Eichmiller

Witthuhn

et al. 2018

Ecology and Evolution

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Measurement of environmental DNA (eDNA) is becoming a common technique to survey for rare and invasive fish due to its sensitivity and specificity. However, its utility is limited by an incomplete understanding of factors governing its sources and fates. Failure to detect eDNA is especially difficult to interpret so surveillance techniques often collect large numbers of samples across broad regions. If, however, fish could be reliably attracted to a single location where their eDNA could be easily measured that would be useful. We conducted a proof‐of‐concept study of this idea using invasive Common Carp. We monitored the distribution of radio‐tagged Carp and their eDNA across a 67 ha lake focusing at the bait site while a pheromone (Prostaglandin F2α; PGF 2α) was also measured to determine their reproductive condition. Prior to baiting, Carp were patchily distributed and while eDNA was occasionally detectable, it was patchy and only loosely associated with moderately dense groups of fish. Further, neither Carp, nor their eDNA were consistently measurable at the bait site and surrounding region, and the pheromone was not measurable at all. However, once baiting commenced, Carp started visiting the bait site and feeding, especially at night, where eDNA levels increased 500‐fold as fish densities doubled and PGF 2α became detectable. Fish presence, eDNA and pheromone concentrations peaked at night after 6 days, strongly suggesting feeding activity was the main driver. While the presence of eDNA precisely coincided with this aggregation, levels had dropped dramatically within 5 m. PGF 2α levels dropped less rapidly and demonstrated the presence of live mature fish. We suggest that food could be used to train fish to come to locations where they otherwise are too scarce to be reliably measured, increasing their eDNA release, making them measurable, and their reproductive condition also discernable by measuring pheromones.

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“…Freshwater lotic bodies can provide important information due to their longitudinal downstream dynamics, such as, (i) eDNA persistence in the environment Wilcox et al, 2016), (ii) residence time of eDNA , and (iii) the ecology of eDNA (Barnes and Turner, 2016). In case of newly introduced IAS, measures of low abundances present another limitation (Jerde et al, 2011) which is highly important when discerning between presence and absence records. Some of the reported examples are applied to non-invasive species, but the reason why we focus on IAS is that time, i.e., rapid response, is key to management, so that an identified IAS can be eradicated/controlled before any negative ecosystem impact occurs.…”

Section: Current Limitationsmentioning

confidence: 99%

“…An increased eDNA sampling effort based on a temporary scale would provide a more accurate proportion of positive (negative) detections and should be replaced by research proposed on a single sampling events (Simmons et al, 2015;Fujiwara et al, 2016;Hänfling et al, 2016). Independent observations would need to become a necessary procedure especially when dealing with estimations of newly introduced species (Jerde et al, 2011) or dealing with the estimations of successful eradication measures (Dunker et al, 2016). To avoid bias due to inconsistent use of eDNA tools a minimum information based on field and laboratory procedures should always be reported and presented in a consistent manner as presented by (Goldberg et al, 2016).…”

Section: Current Limitationsmentioning

confidence: 99%

Using Environmental DNA to Improve Species Distribution Models for Freshwater Invaders

et al. 2017

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Species Distribution Models (SDMs) have been reported as a useful tool for the risk assessment and modeling of the pathways of dispersal of freshwater invasive alien species (IAS). Environmental DNA (eDNA) is a novel tool that can help detect IAS at their early stage of introduction and additionally improve the data available for a more efficient management. SDMs rely on presence and absence of the species in the study area to infer the predictors affecting species distributions. Presence is verified once a species is detected, but confirmation of absence can be problematic because this depends both on the detectability of the species and the sampling strategy. eDNA is a technique that presents higher detectability and accuracy in comparison to conventional sampling techniques, and can effectively differentiate between presence or absence of specific species or entire communities by using a barcoding or metabarcoding approach. However, a number of potential bias can be introduced during (i) sampling, (ii) amplification, (iii) sequencing, or (iv) through the usage of bioinformatics pipelines. Therefore, it is important to report and conduct the field and laboratory procedures in a consistent way, by (i) introducing eDNA independent observations, (ii) amplifying and sequencing control samples, (iii) achieving quality sequence reads by appropriate clean-up steps, (iv) controlling primer amplification preferences, (v) introducing PCR-free sequence capturing, (vi) estimating primer detection capabilities through controlled experiments and/or (vii) post-hoc introduction of "site occupancy-detection models." With eDNA methodology becoming increasingly routine, its use is strongly recommended to retrieve species distributional data for SDMs.

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“Sight-unseen” detection of rare aquatic species using environmental DNA

Cited by 1,029 publications

References 20 publications

History, applications, methodological issues and perspectives for the use environmental DNA (eDNA) in marine and freshwater environments

History, applications, methodological issues and perspectives for the use environmental DNA (eDNA) in marine and freshwater environments

Attracting Common Carp to a bait site with food reveals strong positive relationships between fish density, feeding activity, environmental DNA, and sex pheromone release that could be used in invasive fish management

Using Environmental DNA to Improve Species Distribution Models for Freshwater Invaders

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