Assessing the potential of environmental DNA metabarcoding for monitoring Neotropical mammals: a case study in the Amazon and Atlantic Forest, Brazil

Sales, Naiara Guimarães; Kaizer, Mariane da Cruz; Coscia, Ilaria; Perkins, J. Clint; Highlands, Andrew; Boubli, Jean P.; Magnusson, William E.; Silva, Maria Nazareth Ferreira da; Benvenuto, Chiara; McDevitt, Allan D.

doi:10.1111/mam.12183

Cited by 51 publications

(52 citation statements)

References 18 publications

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“…At present, we would recommend the use of eDNA metabarcoding alongside other non‐invasive surveying methods (e.g. camera traps) when monitoring invasive species or species of conservation concern to maximize monitoring efforts (Abrams et al, ; Sales, Kaizer, et al, ).…”

Section: Discussionmentioning

confidence: 99%

“…What has become apparent from studies in lentic systems (ponds and lakes) is that semi‐aquatic and terrestrial mammals can also be detected (Hänfling et al, ; Harper et al, ). As a result, there has been an increasing focus on the use of both vertebrate (Harper et al, ) and mammal‐specific primer sets (Leempoel, Herbert, & Hadly, ; Sales, Kaizer, et al, ; Ushio et al, ) for detecting mammalian communities using eDNA metabarcoding.…”

Section: Introductionmentioning

confidence: 99%

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Fishing for mammals: Landscape‐level monitoring of terrestrial and semi‐aquatic communities using eDNA from riverine systems

Sales

McKenzie

Drake

et al. 2020

Journal of Applied Ecology

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101

143

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Environmental DNA (eDNA) metabarcoding has revolutionized biomonitoring in both marine and freshwater ecosystems. However, for semi‐aquatic and terrestrial animals, the application of this technique remains relatively untested. We first assess the efficiency of eDNA metabarcoding in detecting semi‐aquatic and terrestrial mammals in natural lotic ecosystems in the UK by comparing sequence data recovered from water and sediment samples to the mammalian communities expected from historical data. Secondly, using occupancy modelling we compared the detection efficiency of eDNA metabarcoding to multiple conventional non‐invasive survey methods (latrine surveys and camera trapping). eDNA metabarcoding detected a large proportion of the expected mammalian community within each area. Common species in the areas were detected at the majority of sites. Several key species of conservation concern in the UK were detected by eDNA sampling in areas where authenticated records do not currently exist, but potential false positives were also identified. Water‐based eDNA metabarcoding provided comparable results to conventional survey methods in per unit of survey effort for three species (water vole, field vole and red deer) using occupancy models. The comparison between survey ‘effort’ to reach a detection probability of ≥.95 revealed that 3–6 water replicates would be equivalent to 3–5 latrine surveys and 5–30 weeks of single camera deployment, depending on the species. Synthesis and applications. eDNA metabarcoding can be used to generate an initial ‘distribution map’ of mammalian diversity at the landscape level. If conducted during times of peak abundance, carefully chosen sampling points along multiple river courses provide a reliable snapshot of the species that are present in a catchment area. In order to fully capture solitary, rare and invasive species, we would currently recommend the use of eDNA metabarcoding alongside other non‐invasive surveying methods (i.e. camera traps) to maximize monitoring efforts.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Fishing for mammals: Landscape‐level monitoring of terrestrial and semi‐aquatic communities using eDNA from riverine systems

Sales

McKenzie

Drake

et al. 2020

Journal of Applied Ecology

Self Cite

101

143

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“…To validate the possible detection of terrestrial mammals from eDNA in their habitats, Ushio et al (2017) developed a universal primer pair (MiMammal, a modified version of MiFish primers) for metabarcoding mammalian eDNA and then tested its performance using water samples from zoo cages and natural water samples from forest ponds. Using MiMammal primers, these authors successfully detected mammals reared in the zoo and representative mammals in the forest from those samples, and subsequent studies demonstrated that MiMammal primers were useful for detecting tropical forest mammals from a natural saltlick (Ishige et al 2017), Neotropical mammals from the Amazon and Atlantic Forest in Brazil (Sales et al 2020a), forest mammals from Jasper Ridge Biological Preserve, California (Leempoel et al 2020), and mammal species in snow tracks during winter in Kyoto, Japan (Kinoshita et al 2019). To the best of our knowledge, MiMammal primers have not been used to detect marine mammals, partly because most of the species identified by the marine mammal visual surveys have been detected with MiFish primers (Closek et al 2019), and Closek et al (2019) stated that MiMammal primers can be used in future studies.…”

Section: Application Of Mifish Edna Metabarcoding To Other Organismsmentioning

confidence: 99%

MiFish metabarcoding: a high-throughput approach for simultaneous detection of multiple fish species from environmental DNA and other samples

2020

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We reviewed the current methodology and practices of the DNA metabarcoding approach using a universal PCR primer pair MiFish, which co-amplifies a short fragment of fish DNA (approx. 170 bp from the mitochondrial 12S rRNA gene) across a wide variety of taxa. This method has mostly been applied to biodiversity monitoring using environmental DNA (eDNA) shed from fish and, coupled with next-generation sequencing technologies, has enabled massively parallel sequencing of several hundred eDNA samples simultaneously. Since the publication of its technical outline in 2015, this method has been widely used in various aquatic environments in and around the six continents, and MiFish primers have demonstrably outperformed other competing primers. Here, we outline the technical progress in this method over the last 5 years and highlight some case studies on marine, freshwater, and estuarine fish communities. Additionally, we discuss various applications of MiFish metabarcoding to non-fish organisms, single-species detection systems, quantitative biodiversity monitoring, and bulk DNA samples other than eDNA. By recognizing the MiFish eDNA metabarcoding strengths and limitations, we argue that this method is useful for ecosystem conservation strategies and the sustainable use of fishery resources in “ecosystem-based fishery management” through continuous biodiversity monitoring at multiple sites.

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“…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%

“…It is therefore essential that specialised eDNA laboratory facilities (akin to working with ancient DNA) are used (Zinger et al ). 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%

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

2020

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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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Assessing the potential of environmental DNA metabarcoding for monitoring Neotropical mammals: a case study in the Amazon and Atlantic Forest, Brazil

Cited by 51 publications

References 18 publications

Fishing for mammals: Landscape‐level monitoring of terrestrial and semi‐aquatic communities using eDNA from riverine systems

Fishing for mammals: Landscape‐level monitoring of terrestrial and semi‐aquatic communities using eDNA from riverine systems

MiFish metabarcoding: a high-throughput approach for simultaneous detection of multiple fish species from environmental DNA and other samples

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

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