Scat DNA provides important data for effective monitoring of mammal and bird biodiversity

Heyde, Mieke van der; Bateman, Philip W.; Bunce, Michael; Wardell‐Johnson, Grant; White, Nicole E.; Nevill, Paul

doi:10.1007/s10531-021-02264-x

Cited by 16 publications

(12 citation statements)

References 70 publications

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“…This review illustrates that eDNA can be used successfully with reptiles, although it is clear that success has been difficult to achieve in the past (Baker et al, 2020 ; van der Heyde et al, 2021 ). It is important to note that cases where eDNA has been unsuccessful are less likely to be published (Beng & Corlett, 2020 ), and there is likely a publication bias toward reptile eDNA studies that have had some level of success.…”

Section: Discussionmentioning

confidence: 99%

“…Detecting reptile DNA from environmental samples is reputedly difficult to achieve (Adams et al, 2019 ; Baker et al, 2020 ; Kucherenko et al, 2018 ; van der Heyde et al, 2021 ), especially when compared to other animal taxa such as fish or amphibians (Adams, Hoekstra, et al, 2019 ; Raemy & Ursenbacher, 2018 ). Here, we review literature on eDNA studies of reptiles and summarize the utility of eDNA in reptile conservation and management.…”

Section: Introductionmentioning

confidence: 99%

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A review of applications of environmental DNA for reptile conservation and management

Nordstrom

Mitchell

Byrne

et al. 2022

Ecology and Evolution

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Reptile populations are in decline globally, with total reptile abundance halving in the past half century, and approximately a fifth of species currently threatened with extinction. Research on reptile distributions, population trends, and trophic interactions can greatly improve the accuracy of conservation listings and planning for species recovery, but data deficiency is an impediment for many species. Environmental DNA (eDNA) can detect species and measure community diversity at diverse spatio‐temporal scales, and is especially useful for detection of elusive, cryptic, or rare species, making it potentially very valuable in herpetology. We aim to summarize the utility of eDNA as a tool for informing reptile conservation and management and discuss the benefits and limitations of this approach. A literature review was conducted to collect all studies that used eDNA and focus on reptile ecology, conservation, or management. Results of the literature search are summarized into key discussion points, and the review also draws on eDNA studies from other taxa to highlight methodological challenges and to identify future research directions. eDNA has had limited application to reptiles, relative to other vertebrate groups, and little use in regions with high species richness. eDNA techniques have been more successfully applied to aquatic reptiles than to terrestrial reptiles, and most (64%) of studies focused on aquatic habitats. Two of the four reptilian orders dominate the existing eDNA studies (56% Testudines, 49% Squamata, 5% Crocodilia, 0% Rhynchocephalia). Our review provides direction for the application of eDNA as an emerging tool in reptile ecology and conservation, especially when it can be paired with traditional monitoring approaches. Technologies associated with eDNA are rapidly advancing, and as techniques become more sensitive and accessible, we expect eDNA will be increasingly valuable for addressing key knowledge gaps for reptiles.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

A review of applications of environmental DNA for reptile conservation and management

Nordstrom

Mitchell

Byrne

et al. 2022

Ecology and Evolution

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“…DNA metabarcoding is continuously being refined for more detailed multispecies detection (Creer et al, 2016), but we consider the aquatic eDNA metabarcoding method ready for large-scale monitoring of fish in European freshwater habitats. More terrestrial mammals might have been detected if eDNA from soil, dung or air samples had been included as well (Leempoel et al, 2020; Sales et al, 2020; Lynggaard et al, 2021; van der Heyde et al, 2021).…”

Section: Discussionmentioning

confidence: 99%

Holistic monitoring of freshwater and terrestrial vertebrates by camera trapping and environmental DNA

Holm

Knudsen²,

Maansson

et al. 2022

Preprint

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The anthropogenic impact on the worlds ecosystems is severe and the need for non-invasive, cost-effective tools for monitoring and understanding those impacts are therefore urgent. Here we combine two such methods in a comprehensive multi-year study; camera trapping (CT) and analysis of environmental DNA (eDNA), in river marginal zones of a temperate, wetland Nature Park in Denmark. CT was performed from 2015 to 2019 for a total of 8,778 camera trap days and yielded 24,376 animal observations. The CT observations covered 87 taxa, of which 78 were identified to species level, and 73 were wild native species. For eDNA metabarcoding, a total of 114 freshwater samples were collected from eight sites in all four seasons from 2017 to 2018. The eDNA results yielded a total detection of 80 taxa, of which 74 were identified to species level, and 65 were wild native species. While the number of taxa detected with the two methods were comparable, the species overlap was only 20 %. In combination, CT and eDNA monitoring thus yielded a total of 115 wild species (20 fishes, four amphibians, one snake, 23 mammals and 67 birds), representing half of the species found via conventional surveys over the last ca. 20 years (83% of fishes, 68 % of mammals, 67 % of amphibians, 41 % of birds and 20 % of reptiles). Our study demonstrates that a holistic approach combining two non-invasive methods, CT and eDNA metabarcoding, has great potential as a cost-effective biomonitoring tool for vertebrates.

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“…The DNA metabarcoding approach has important applications for biomonitoring of species in diverse communities [ 25 ], and is particularly applied to restoration monitoring [ 24 ]. Additionally, recent practices in environmental DNA (eDNA) barcoding (i.e., simultaneous identification of species from multiple taxa within one environmental sample, using a specific fragment of DNA) demonstrated the advantage of using environmental bulk DNA extracts over DNA barcoding of individual organisms [ 26 , 27 , 28 ]. Following these recent advances, in this study, for the first time, we apply a “bulk” extraction of DNA from multiple nymphal individuals of L. delicatula .…”

Section: Introductionmentioning

confidence: 99%

Diverse Host Plants of the First Instars of the Invasive Lycorma delicatula: Insights from eDNA Metabarcoding

McPherson

Avanesyan

Lamp

2022

Insects

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Identification of host plants of the invasive spotted lanternfly, Lycorma delicatula (Hemiptera: Fulgoridae), has been the focus of many studies. While the adults and late nymphs are relatively easy to observe on plants and to use for molecular gut-content analysis, studying the early instars is more challenging. This study is the continuation of our ongoing efforts to determine the host range for each developmental stage of L. delicatula. In the present study, we focused exclusively on the first nymphal instars, and we used a novel approach, utilizing “bulk” DNA extracts for DNA metabarcoding of nymphal gut contents, to identify all the detectable plants that the nymphs had ingested prior to being collected. We were able to obtain high-quality amplicons (up to 406 bp) of a portion of the rbcL gene and detect 27 unique ingested plant species belonging to 17 families. Both native and introduced plants with the prevalence of trees and grasses were present among the ingested plants. We also identified 13 novel host plants that have not been previously reported for L. delicatula on the U.S. territory. The results from our study have important applications for developing effective programs on early monitoring of invasive L. delicatula.

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Scat DNA provides important data for effective monitoring of mammal and bird biodiversity

Cited by 16 publications

References 70 publications

A review of applications of environmental DNA for reptile conservation and management

A review of applications of environmental DNA for reptile conservation and management

Holistic monitoring of freshwater and terrestrial vertebrates by camera trapping and environmental DNA

Diverse Host Plants of the First Instars of the Invasive Lycorma delicatula: Insights from eDNA Metabarcoding

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