Environmental DNA (eDNA) metabarcoding of pond water as a tool to survey conservation and management priority mammals

Harper, Lynsey R.; Handley, Lori Lawson; Carpenter, Angus I.; Ghazālī, Muḥammad; Muri, Cristina Di; Macgregor, Callum J.; Logan, Thomas W.; Law, Alan; Breithaupt, Thomas; Read, Daniel S.; McDevitt, Allan D.; Hänfling, Bernd

doi:10.1101/546218

Cited by 25 publications

(54 citation statements)

References 47 publications

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“…Metabarcoding relies on the occurrence of relatively intact DNA for PCR amplification, and the use of degenerate primers to cover multiple species may bias the results (Taberlet, Bonin, Zinger, & Coissac, ). Metabarcoding of terrestrial animals from eDNA has been performed using environmental sample material of animals in captivity (Harper et al, ; Rodgers & Mock, ), and to a lesser extent, also in the wild (Egeter et al, ; Ushio, Fukuda, et al, ). Under natural conditions, however, this approach is typically hampered by the presumably low amount of target DNA in any given environmental substrate compared to the high amount of background DNA.…”

Section: Discussionmentioning

confidence: 99%

Terrestrial mammal surveillance using hybridization capture of environmental DNA from African waterholes

Seeber

McEwen

Löber

et al. 2019

Molecular Ecology Resources

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Determining species distributions can be extremely challenging but is crucial to ecological and conservation research. Environmental DNA (eDNA) approaches have shown particular promise in aquatic systems for several vertebrate and invertebrate species. For terrestrial animals, however, eDNA‐based surveys are considerably more difficult due to the lack of or difficulty in obtaining appropriate sampling substrate. In water‐limited ecosystem where terrestrial mammals are often forced to congregate at waterholes, water and sediment from shared water sources may be a suitable substrate for noninvasive eDNA approaches. We characterized mitochondrial DNA sequences from a broad range of terrestrial mammal species in two different African ecosystems (in Namibia and Tanzania) using eDNA isolated from native water, sediment and water filtered through glass fibre filters. A hybridization capture enrichment with RNA probes targeting the mitochondrial genomes of 38 mammal species representing the genera/families expected at the respective ecosystems was employed, and 16 species were identified, with a maximum mitogenome coverage of 99.8%. Conventional genus‐specific PCRs were tested on environmental samples for two genera producing fewer positive results than hybridization capture enrichment. An experiment with mock samples using DNA from non‐African mammals showed that baits covering 30% of nontarget mitogenomes produced 91% mitogenome coverage after capture. In the mock samples, over‐representation of DNA of one species still allowed for the detection of DNA of other species that was at a 100‐fold lower concentration. Hybridization capture enrichment of eDNA is therefore an effective method for monitoring terrestrial mammal species from shared water sources.

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Section: Discussionmentioning

confidence: 99%

Terrestrial mammal surveillance using hybridization capture of environmental DNA from African waterholes

Seeber

McEwen

Löber

et al. 2019

Molecular Ecology Resources

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“…Organisms leave genetic material behind in the surrounding environment (e.g. in water bodies and soil) via excretions and secretions (Harper et al ); this is referred to as environmental DNA ( eDNA ). Single‐species detection from eDNA is possible using PCR, qPCR or droplet digital PCR ( ddPCR ).…”

Section: Detection and Monitoringmentioning

confidence: 99%

“…DNA metabarcoding from environmental samples has the potential to be used as an early warning system for the detection of invasive non‐native species, can be used for continuous monitoring programmes, and has been extensively applied for tracking biological invasions in aquatic ecosystems (Deiner et al ). eDNA metabarcoding studies targeting mammalian communities were relatively rare in comparison with other taxonomic groups (Sales et al ), but this may change now that there are established metabarcoding protocols for detecting and monitoring whole communities using vertebrate (Harper et al ) or mammal‐specific primer sets (Ushio et al , Sales et al , b).…”

Section: Detection and Monitoringmentioning

confidence: 99%

“…For example, mammals with larger home ranges (e.g. invasive carnivores) have lower probabilities of detection than more abundant group‐living mammals (Harper et al , Sales et al ). Due to the high sensitivity of metabarcoding, contamination is a concern (Sales et al ).…”

Section: Detection and Monitoringmentioning

confidence: 99%

“…Another consideration is the existence of gaps in customised or online reference databases for identifying sequences to the appropriate species level in under‐studied geographic regions (Sales et al ). However, with a carefully planned experimental design and the appropriate field and laboratory controls (Zinger et al ), eDNA metabarcoding has the potential to be applied for early detection and ongoing surveillance of invasive mammals (Harper et al , Sales et al ).…”

Section: Detection and Monitoringmentioning

confidence: 99%

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Genetic tools in the management of invasive mammals: recent trends and future perspectives

2020

Self Cite

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Invasive non‐native species are now considered to be one of the greatest threats to biodiversity worldwide. Therefore, efficient and cost‐effective management of species invasions requires robust knowledge of their demography, ecology and impacts, and genetic‐based techniques are becoming more widely adopted in acquiring such knowledge. We focus on the use of genetic tools in the applied management of mammalian invasions globally, as well as on their inherent advantages and disadvantages. We cover tools that are used in: 1) detecting and monitoring mammalian invaders; 2) identifying origins and invasive pathways; 3) assessing and quantifying the negative impacts of invaders; and 4) population management and potential eradication of invasive mammals. We highlight changes in sequencing technologies, including how the use of techniques such as Sanger sequencing and microsatellite genotyping, for monitoring and tracing invasive pathways respectively, are now giving way to the use of high‐throughput sequencing methods. These include the emergence of environmental DNA (eDNA) metabarcoding for the early detection of invasive mammals, and single nucleotide polymorphisms or whole genomes to trace the sources of invasive populations. We are now moving towards trials of genome‐editing techniques and gene drives to control or eradicate invasive rodents. Genetic tools can provide vital information that may not be accessible with non‐genetic methods, for the implementation of conservation policies (e.g. early detection using systematic eDNA surveillance, the identification of novel pathogens). However, the lack of clear communication of novel genetic methods and results (including transparency and reproducibility) to relevant stakeholders can be prohibitive in translating these findings to appropriate management actions. Geneticists should engage early with stakeholders to co‐design experiments in relation to management goals for invasive mammals.

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Environmental DNA metabarcoding as a useful tool for evaluating terrestrial mammal diversity in tropical forests

Mena¹,

Yagui²,

Tejeda

et al. 2021

Ecological Applications

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Innovative techniques, such as environmental DNA (eDNA) metabarcoding, are now promoting broader biodiversity monitoring at unprecedented scales, because of the reduction in time, presumably lower cost, and methodological efficiency. Our goal was to assess the efficiency of established inventory techniques (live‐trapping grids, pitfall traps, camera trapping, mist netting) as well as eDNA for detecting Amazonian mammals. For terrestrial small mammals, we used 32 live‐trapping grids based on Sherman and Tomahawk traps (total effort of 10,368 trap‐nights); in addition to 16 pitfall traps (1,408 trap‐nights). For bats, we used mist nets at 8 sites (4,800 net hours). For medium and large mammals, we used 72 camera trap stations (5,208 camera‐days). We identified vertebrate and mammal taxa based on eDNA analysis (12S region, with V05 and Mamm01 markers) from water samples, including a total of 11 3‐km transects for stagnant water sampling and seven small streams for running water sampling. A total of 106 mammal species were recorded. Building on sample‐based rarefaction and extrapolation curves, both trapping grids and pitfall were successful, recording 91.16% and 82.1% of the expected species for these techniques (~22 and ~9 species), and 16.98% and 6.60% of the total recorded mammal species, respectively. Mist nets recorded 83.2% of the expected bat species (~48), and 34.91% of the total recorded species. Camera trapping recorded 99.2% of the predicted large‐ and medium‐sized species (~31), and 33.02% of the total recorded species. eDNA recorded 75.4% of the expected mammal species for this technique (~68), and 47.0% of the total recorded species. eDNA resulted in a useful tool that saves on effort and reduces sampling costs. This study is among the first to show the large potential of eDNA metabarcoding for assessing Amazonian mammal communities, providing, in combination with conventional techniques, a rapid overview of mammal diversity with broad applications to monitoring, management and conservation. By including appropriate genetic markers and updated reference databases, eDNA metabarcoding method can be extended to the whole vertebrate community.

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Environmental DNA (eDNA) metabarcoding of pond water as a tool to survey conservation and management priority mammals

Cited by 25 publications

References 47 publications

Terrestrial mammal surveillance using hybridization capture of environmental DNA from African waterholes

Terrestrial mammal surveillance using hybridization capture of environmental DNA from African waterholes

Genetic tools in the management of invasive mammals: recent trends and future perspectives

Environmental DNA metabarcoding as a useful tool for evaluating terrestrial mammal diversity in tropical forests

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