Characterization, optimization, and validation of environmental DNA (eDNA) markers to detect an endangered aquatic mammal

Ma, Hui; Stewart, Kathryn A.; Lougheed, Stephen C.; Zheng, Jinsong; Wang, Yuxiang; Zhao, Jianfu

doi:10.1007/s12686-016-0597-9

Cited by 43 publications

(55 citation statements)

References 41 publications

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“…This characteristic may increase the efficiency of eDNA collection. To reduce the clogging of filters during filtration, some studies performed prefiltration using a filter with a large pore size, such as a coffee filter or gauze, as a preprocessing collection step (Ma et al, 2016;Takahara, Minamoto, & Doi, 2013;Wilson et al, 2014). Such prefiltration can increase the processable water volume, but the optimal pore size of prefilters is unknown.…”

Section: Filtration Methodsmentioning

confidence: 99%

The detection of aquatic macroorganisms using environmental DNA analysis—A review of methods for collection, extraction, and detection

et al. 2019

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The field of environmental DNA (eDNA) analysis has rapidly developed over the past decade and the technique has become widely used for detecting aquatic macroorganisms in a variety of habitats. However, a variety of measurement protocols have been individually developed for different eDNA studies and this may lead to confusion for others who wish to incorporate eDNA analysis in their research. It is important therefore to synthesize the current status of—and future challenges to—the methodology of eDNA analysis. We here synthesized the protocols from total 438 published eDNA studies detecting aquatic macroorganisms were used to calculate the frequency of using each method in eDNA analysis steps. We found that the frequency of methods used converged to one or two methods for any analysis step. Furthermore, although the procedure with highest frequency is not always the best, it was shown that the eDNA collection by filtration and subsequent extraction/purification using a DNeasy Blood and Tissue DNA extraction kit (Qiagen, Hilden, Germany) or PowerWater DNA Extraction Kit (Qiagen) is the most common procedure. An understanding of the characteristics of commonly used methods can help those newly engaged in eDNA studies to understand the basic outline of eDNA analysis. Our review will be useful for the future improvement and development of analytical eDNA techniques of eDNA by sharing the recognition of methodological characteristic including advantages and disadvantages in major analytical techniques.

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Section: Filtration Methodsmentioning

confidence: 99%

The detection of aquatic macroorganisms using environmental DNA analysis—A review of methods for collection, extraction, and detection

et al. 2019

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“…In previous research (Ma et al. ), we used conventional PCR to design species‐specific primer pairs for YFP in Tian e‐Zhou and found they accurately detected the presence of YFP DNA in silico (bioinformatically), in vitro (blood samples), and in situ within aquaria at the Wuhan Baiji Dolphinarium (Institute of Hydrobiology, Chinese Academy of Sciences, located in Wuhan, China) and in nature (Tian e‐Zhou). Quantitative PCR approaches, however, have prominent advantages over conventional PCR for eDNA surveys, including increased sensitivity to low concentrations of nucleic acids within environmental samples and broad dynamic ranges for calculations (Perez ).…”

Section: Introductionmentioning

confidence: 99%

Using environmental DNA to assess population‐wide spatiotemporal reserve use

Stewart

Zheng

et al. 2017

Conservation Biology

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Scientists increasingly rely on protected areas to assist in biodiversity conservation, yet the efficacy of these areas is rarely systematically assessed, often because of underfunding. Still, adaptive management strategies to maximize conservation success often rely on understanding the temporal and spatial dynamism of populations therein. Examination of environmental DNA (eDNA) is a time and cost-effective way to monitor species' distribution, and quantitative polymerase chain reaction (qPCR) provides information on organismal abundance. To date, however, such techniques remain underused for population assessments in protected areas. We determined eDNA concentration of the critically endangered Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis) to describe its occurrence, range, and use of the Tian e-Zhou National Nature Reserve in Hubei, China, across seasons and hydrological depths. Despite the observation that total eDNA concentrations were highest in surface waters in summer, finless porpoise eDNA concentrations were significantly higher in deeper waters than in surface waters in summer. During the breeding season (spring), eDNA signals were site specific and restricted to the core area of the reserve. However, postbreeding eDNA concentrations were widespread across the reserve, encompassing sites previously thought to be unfrequented by the species. Our results suggest spatiotemporal idiosyncrasies in site, depth, and seasonal use of the reserve and a propensity for postbreeding population dispersal. With eDNA and qPCR we were able to assess an entire population's use of a protected area. Illuminating nuances in habitat use via eDNA could be valuable to set pragmatic conservation goals for this, and other, species.

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“…Although the majority of eDNA studies in aquatic systems have been carried out in marine or lake environments, an increasing number of studies demonstrates that eDNA may be used to identify the presence of species in fluvial environments, such as rivers (Deiner et al ., ; Ma et al ., ) and river‐floodplain lakes (Tessler et al ., ). For example, sequencing of CoxI (i.e.…”

Section: New Molecular Methods For Assessing Present‐day and Past Biotamentioning

confidence: 97%

“…Parducci et al, 2015;Deiner et al, 2016), soils (Hebsgaard et al, 2009), silt (Fortin et al, 2004), sand (Lakay et al, 2007), peatbogs (Dedysh et al, 2006), ice , cave deposits , permafrost (Parducci et al, 2012;Bellemain et al, 2013) and coprorlites (Wood et al, 2012). Although the majority of eDNA studies in aquatic systems have been carried out in marine or lake environments, an increasing number of studies demonstrates that eDNA may be used to identify the presence of species in fluvial environments, such as rivers Ma et al, 2016) and riverfloodplain lakes (Tessler et al, 2017). For example, sequencing of CoxI (i.e.…”

Section: New Molecular Methods For Assessing Present-day and Past Biotamentioning

confidence: 99%

Biotic drivers of river and floodplain geomorphology – New molecular methods for assessing present‐day and past biota

Larsen

Alvarez

Sperisen

et al. 2017

Earth Surf Processes Landf

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Geomorphology has increasingly considered the role of biotic factors as controls upon geomorphic processes across a wide range of spatial and temporal scales. Where timescales are long (centennial and longer), it has been possible to quantify relationships between geomorphic processes and vegetation using, for example, the pollen record. However, where the biotic agents are fauna, longer term reconstruction of the impacts of biological activity upon geomorphic processes is more challenging. Here, we review the prospect of using environmental DNA as a molecular proxy to decipher the presence and nature of faunal influences on geomorphic processes in both present and ancient deposits. When used appropriately, this method has the potential to improve our understanding of biotic drivers of geomorphic processes, notably fauna, over long timescales and so to reconstruct how such drivers might explain the landscape as we see it today. Copyright © 2017 John Wiley & Sons, Ltd.

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Characterization, optimization, and validation of environmental DNA (eDNA) markers to detect an endangered aquatic mammal

Abstract: 1demonstrates no significant amplicon size effects on primer sensitivity or longevity. We summarize the impact primer design may have on eDNA applications in general and suggest future considerations for conservation efforts with the Yangtze finless porpoise.

Cited by 43 publications

References 41 publications

The detection of aquatic macroorganisms using environmental DNA analysis—A review of methods for collection, extraction, and detection

The detection of aquatic macroorganisms using environmental DNA analysis—A review of methods for collection, extraction, and detection

Using environmental DNA to assess population‐wide spatiotemporal reserve use

Biotic drivers of river and floodplain geomorphology – New molecular methods for assessing present‐day and past biota

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