Surveys of environmental DNA (eDNA): a new approach to estimate occurrence in Vulnerable manatee populations

Hunter, Margaret E.; Meigs‐Friend, Gaia; Ferrante, Jason A.; Kamla, Aristide Takoukam; Dorazio, Robert M.; Diagne, L; Luna, Fábia de Oliveira; Lanyon, Janet M.; Reid, James P.

doi:10.3354/esr00880

Cited by 56 publications

(42 citation statements)

References 39 publications

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“…The use of ddPCR™ for single species detections is gaining popularity in eDNA research due to its unparalleled ability to detect minute quantities of target DNA amongst high concentrations of non-target DNA and in the presence of natural inhibitors found in water samples (Evans et al 2017; Hunter et al 2018). DdPCR™ assays developed for species such as the Bull Shark, Carcharhinus leucas (Schweiss et al In Press) and Killer Whale, Orcinus orca (Baker et al 2018), have found this platform to be capable of detecting less than 0.5 pg of target DNA in a reaction.…”

Section: Discussionmentioning

confidence: 99%

“…DdPCR™ assays developed for species such as the Bull Shark, Carcharhinus leucas (Schweiss et al In Press) and Killer Whale, Orcinus orca (Baker et al 2018), have found this platform to be capable of detecting less than 0.5 pg of target DNA in a reaction. Such highly sensitive assays are especially critical in eDNA surveys targeting Critically Endangered or Endangered species, where there can be substantial conservation outcomes based on the results of such surveys (Hunter et al 2018; Poulakis and Grubbs 2019). For instance, the use of ddPCR™ could reduce the risk of false negatives (i.e., where target DNA is present but not detected) stemming from the use of a less sensitive PCR platform such as conventional or qRT-PCR, which are unlikely to detect such minute quantities of target DNA (Doi et al 2015).…”

Section: Discussionmentioning

confidence: 99%

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An environmental DNA tool for monitoring the status of the Critically Endangered Smalltooth Sawfish, Pristis pectinata, in the Western Atlantic

Lehman

Poulakis

Scharer

et al. 2019

Preprint

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AbstractThe Critically Endangered Smalltooth Sawfish, Pristis pectinata, was once widespread in the tropical and subtropical waters of the Atlantic Ocean, but following substantial declines over the past century, the core population is currently confined to southwest Florida in the U.S. and the Bahamas. Recent research and verified public encounter reports suggests that this core population may be stabilizing and, potentially, expanding into formerly occupied areas of their historic range in the Western Atlantic; however, the status of this species in non-core waters is not well understood. Environmental DNA (eDNA) methods provide a relatively cost effective and rapid assessment tool for monitoring species occurrence in aquatic habitats. Here, we have developed an eDNA tool: a species-specific Droplet Digital™ PCR (ddPCR™) assay targeting a 100-base pair portion of the mitochondrial NADH dehydrogenase subunit 2 gene in P. pectinata, with the ability to reliably detect as little as 0.25 pg of target DNA. The assay was validated by collecting and analyzing a water sample from known P. pectinata nursery habitat in Florida, which was found to contain an average of 11.54 copies of target DNA/µL (SE = 0.72) in the reaction. The assay was then further tested by placing a juvenile sawfish in an ex situ tank and analyzing water samples collected at time intervals. The implementation of this eDNA tool into field surveys will provide additional, reliable data to assess species recovery and aid in prioritizing localities beyond the core range in which to focus research and education initiatives.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

An environmental DNA tool for monitoring the status of the Critically Endangered Smalltooth Sawfish, Pristis pectinata, in the Western Atlantic

Lehman

Poulakis

Scharer

et al. 2019

Preprint

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“…Although occupancy modelling is widely used in wildlife studies, applications of occupancy models to eDNA studies have been limited. However, an increasing number of studies have recently applied occupancy modelling successfully to detection/non-detection data obtained through eDNA analyses (Ficetola et al, 2015;Hunter et al, 2018;Pilliod, Goldberg, Arkle, & Waits, 2013;Schmelzle & Kinziger, 2016;Schmidt, Kery, Ursenbacher, Hyman, & Collins, 2013;Wineland et al, 2019). Based on these first eDNA occupancy studies Dorazio and Erickson (2018) recently developed an R package ednaoccupancy, which makes use of a multi-scale occupancy framework (Nichols et al, 2008), and accounts for the varying detection probabilities at different hierarchical levels (i.e.…”

Section: Introductionmentioning

confidence: 99%

Shifting up a gear with iDNA: From mammal detection events to standardised surveys

Abrams

Hörig

Brozovic

et al. 2019

Journal of Applied Ecology

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1. Invertebrate-derived DNA (iDNA), in combination with high throughput sequencing, has been proposed as a cost-efficient and powerful tool to survey vertebrate species. Previous studies, however, have only provided evidence that vertebrates can be detected using iDNA, but have not taken the next step of placing these detection events within a statistical framework that allows for robust biodiversity assessments.2. Here, we compare concurrent iDNA and camera-trap surveys. Leeches were repeatedly collected in close vicinity to 64 camera-trap stations in Sabah, Malaysian Borneo. We analyse iDNA-derived mammalian detection events in a modern occupancy model that accounts for imperfect detection and compare the results with those from occupancy models parameterised with camera-trap-derived detection events. We also combine leech-iDNA and camera-trap data in a single occupancy model.3. We found consistent estimates of occupancy probabilities produced by our cameratrap and leech datasets. This indicates that the metabarcoding of leech-iDNA method provides reasonable estimates of occupancy and may be a suitable method for studying and monitoring mammal species in tropical rainforests. However, we also show that a more extensive collection of leeches would be needed to assess mammal biodiversity with a robustness similar to that of camera traps. As certain taxa were only detected in leeches, we see great potential in complementing camera-trap studies with the iDNA approach, as long as the collection of leeches follows a robust and standardised sampling scheme. Synthesis and applications.Here, we describe an approach to analyse detection records of mammals derived from leech samples using an occupancy framework that accounts for leech-specific factors influencing the detection probability.We further combined camera trap and leech data, which lead to increased confidence in occupancy estimates. Our approach is not restricted to the processing of leech samples, but can be used for the analysis of other invertebrate DNA and | 1641Journal of Applied Ecology ABRAMS et Al.

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“…The strategy has the potential to help researchers identify the geographic ranges of vulnerable species. Hunter and her team also designed primers for amplifying a region of manatee DNA from water samples (8). Earlier this year, in a proof-ofconcept study, they reported that this eDNA test for three species of manatee offered a higher probability of detecting the animals than did traditional aerial surveys (8).…”

Section: Protecting Threatened Speciesmentioning

confidence: 99%

Environmental DNA helps researchers track pythons and other stealthy creatures

Beans¹

2018

Proc. Natl. Acad. Sci. U.S.A.

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It's no secret that Florida has a snake problem. The Burmese python, which can reach up to 200 pounds and stretch to more than 20 feet, first became common in the Everglades in the late 1990s, likely as escaped pets. The snake quickly settled into its new home, breeding and taking down rabbits, bobcats, and other native animals in its path. Wildlife managers in Florida turned to expert snake hunters, electronic tracking devices, and search dogs to wrangle the pet-turned-ecosystem-wrecker and had little success. The snakes, although massive, are hard to find in the south Florida habitat. "They're well camouflaged, secretive, and often slow moving," says geneticist Margaret Hunter of the US Geological Survey, Wetland and Aquatic Research Center. Biologists thought the Arthur R. Marshall Loxahatchee National Wildlife Refuge was one place that was safe. Pythons have on rare occasion been spotted there, but only in areas easily accessible to humans, suggesting that the snakes were likely released pets rather than a growing population. But from 2014 through 2016, Hunter combed the waters in and around the refuge for environmental DNA (eDNA)-the trail of DNA left behind by an organism in sources such as feces, mucus, gametes, and shed skin or hair. The results suggested that the python's DNA was, in fact, widespread throughout the refuge. Hunter is one of a growing group of researchers who are using eDNA to track invasive species that they'd like to remove and vulnerable species they'd like to protect. Hunter also developed an eDNA test for manatees that's more sensitive than traditional aerial surveys. But challenges remain before eDNA can become a widely used tool for conservation biology. The technique carries the risk of false negatives and false positives. And it's not always clear how to make eDNA results translate into putting eyes, and hands, on the actual animals that managers are after. Burmese pythons are well camouflaged in the Everglades, but the trail of DNA they leave behind helps researchers track their presence. Image courtesy of USGS/Emma Hanslowe.

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Surveys of environmental DNA (eDNA): a new approach to estimate occurrence in Vulnerable manatee populations

Cited by 56 publications

References 39 publications

An environmental DNA tool for monitoring the status of the Critically Endangered Smalltooth Sawfish, Pristis pectinata, in the Western Atlantic

An environmental DNA tool for monitoring the status of the Critically Endangered Smalltooth Sawfish, Pristis pectinata, in the Western Atlantic

Shifting up a gear with iDNA: From mammal detection events to standardised surveys

Environmental DNA helps researchers track pythons and other stealthy creatures

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