Environmental DNA for tracking waterhole visitation in savanna ecosystems

AbstractThe analysis of waterborne environmental DNA (eDNA) is effective for detecting invasive species and conducting large-scale biodiversity assessments, making it a potentially powerful tool for documenting diversity at sites where large numbers of species aggregate. We explore the utility of eDNA from waterholes for describing local mammal communities, quantifying patterns of species co-occurrences, and monitoring of rare or threatened species. In savanna ecosystems water can be a scarce resource during dry seasons and in periods of drought, promoting the aggregation of medium to large mammals. To explore the reliability of eDNA as a biodiversity indicator in these arid and semi-arid environments, we compare eDNA metabarcoding and camera traps for documenting waterhole use by mammals in the Kruger National Park, South Africa. We find that eDNA metabarcoding can recover the majority of mammal species detected in camera traps, but the DNA signatures of mammal visitation are temporally limited. Detection rates varied across sites, sampling time, species, and choice of reference library, with the best performance for water-dependent large bodied mammals visiting within two days of sampling, and matched to a curated system-specific reference library. Our results demonstrate that eDNA-based approaches can be used to track mammals of conservation concern, and reflect patterns of recent waterhole use and co-occurrence across water-dependent species, but also highlight limitations including the lack of long-term eDNA persistence in small and highly utilized waterholes and variability in detection rates among species. Sequencing of eDNA is a valuable tool for next-generation biodiversity sampling and has many exciting applications, but it is not sufficient to capture long-term waterhole visitation patterns or reliably detect rare and small-bodied species.

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eDNA sampled from stream networks correlates with camera trap detection rates of terrestrial mammals

Scientific Reports ◽

10.1038/s41598-021-90598-5 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Arnaud Lyet ◽

Loïc Pellissier ◽

Alice Valentini ◽

Tony Dejean ◽

Abigail Hehmeyer ◽

...

Keyword(s):

Large Scale ◽

Stream Water ◽

Spatial Scales ◽

Environmental Dna ◽

Camera Trap ◽

Camera Traps ◽

Sufficient Information ◽

Multiple Time ◽

Detection Rates ◽

Terrestrial Mammals

AbstractBiodiversity monitoring delivers vital information to those making conservation decisions. Comprehensively measuring terrestrial biodiversity usually requires costly methods that can rarely be deployed at large spatial scales over multiple time periods, limiting conservation efficiency. Here we investigated the capacity of environmental DNA (eDNA) from stream water samples to survey terrestrial mammal diversity at multiple spatial scales within a large catchment. We compared biodiversity information recovered using an eDNA metabarcoding approach with data from a dense camera trap survey, as well as the sampling costs of both methods. Via the sampling of large volumes of water from the two largest streams that drained the study area, eDNA metabarcoding provided information on the presence and detection probabilities of 35 mammal taxa, 25% more than camera traps and for half the cost. While eDNA metabarcoding had limited capacity to detect felid species and provide individual-level demographic information, it is a cost-efficient method for large-scale monitoring of terrestrial mammals that can offer sufficient information to solve many conservation problems.

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Long-term monitoring of margays (Leopardus wiedii): Implications for understanding low detection rates

PLoS ONE ◽

10.1371/journal.pone.0247536 ◽

2021 ◽

Vol 16 (3) ◽

pp. e0247536

Author(s):

Bart J. Harmsen ◽

Nicola Saville ◽

Rebecca J. Foster

Keyword(s):

Detection Rate ◽

Camera Trap ◽

Wide Distribution ◽

Camera Traps ◽

Detection Rates ◽

Terrestrial Mammals ◽

Exclusive Territories ◽

Carnivore Species ◽

Density Population

Population assessments of wide-ranging, cryptic, terrestrial mammals rely on camera trap surveys. While camera trapping is a powerful method of detecting presence, it is difficult distinguishing rarity from low detection rate. The margay (Leopardus wiedii) is an example of a species considered rare based on its low detection rates across its range. Although margays have a wide distribution, detection rates with camera traps are universally low; consequently, the species is listed as Near Threatened. Our 12-year camera trap study of margays in protected broadleaf forest in Belize suggests that while margays have low detection rate, they do not seem to be rare, rather that they are difficult to detect with camera traps. We detected a maximum of 187 individuals, all with few or no recaptures over the years (mean = 2.0 captures/individual ± SD 2.1), with two-thirds of individuals detected only once. The few individuals that were recaptured across years exhibited long tenures up to 9 years and were at least 10 years old at their final detection. We detected multiple individuals of both sexes at the same locations during the same survey, suggesting overlapping ranges with non-exclusive territories, providing further evidence of a high-density population. By studying the sparse annual datasets across multiple years, we found evidence of an abundant margay population in the forest of the Cockscomb Basin, which might have been deemed low density and rare, if studied in the short term. We encourage more long-term camera trap studies to assess population status of semi-arboreal carnivore species that have hitherto been considered rare based on low detection rates.

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The effect of camera-trap viewshed obstruction on wildlife detection: implications for inference

Wildlife Research ◽

10.1071/wr19004 ◽

2020 ◽

Vol 47 (2) ◽

pp. 158 ◽

Cited By ~ 1

Author(s):

Remington J. Moll ◽

Waldemar Ortiz-Calo ◽

Jonathon D. Cepek ◽

Patrick D. Lorch ◽

Patricia M. Dennis ◽

...

Keyword(s):

Image Data ◽

Camera Trap ◽

Camera Traps ◽

Mammal Species ◽

Ecological Processes ◽

Detection Rates ◽

Management Application ◽

Efficiency And Effectiveness ◽

Steep Slopes ◽

Wildlife Detection

Abstract ContextCamera traps are one of the most popular tools used to study wildlife worldwide. Numerous recent studies have evaluated the efficiency and effectiveness of camera traps as a research tool. Nonetheless, important aspects of camera-trap methodology remain in need of critical investigation. One such issue relates to camera-trap viewshed visibility, which is often compromised in the field by physical obstructions (e.g. trees) or topography (e.g. steep slopes). The loss of visibility due to these obstructions could affect wildlife detection rates, with associated implications for study inference and management application. AimsWe aimed to determine the effect of camera-trap viewshed obstruction on wildlife detection rates for a suite of eight North American species that vary in terms of ecology, commonness and body size. MethodsWe deployed camera traps at 204 sites throughout an extensive semi-urban park system in Cleveland, Ohio, USA, from June to September 2016. At each site, we quantified camera-trap viewshed obstruction by using a cover-board design. We then modelled the effects of obstruction on wildlife detection rates for the eight focal species. Key resultsWe found that detection rates significantly decreased with an increasing viewshed obstruction for five of the eight species, including both larger and smaller mammal species (white-tailed deer, Odocoileus virginianus, and squirrels, Sciurus sp., respectively). The number of detections per week per camera decreased two- to three-fold as visibility at a camera site decreased from completely free of obstruction to mostly obstructed. ConclusionsThese results imply that wildlife detection rates are influenced by site-level viewshed obstruction for a variety of species, and sometimes considerably so. ImplicationsResearchers using camera traps should address the potential for this effect to ensure robust inference from wildlife image data. Accounting for viewshed obstruction is critical when interpreting detection rates as indices of abundance or habitat use because variation in detection rate could be an artefact of site-level viewshed obstruction rather than due to underlying ecological processes.

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Improving herpetological surveys in eastern North America using the environmental DNA method

Genome ◽

10.1139/gen-2015-0218 ◽

2016 ◽

Vol 59 (11) ◽

pp. 991-1007 ◽

Cited By ~ 35

Author(s):

Anaïs Lacoursière-Roussel ◽

Yohann Dubois ◽

Eric Normandeau ◽

Louis Bernatchez

Keyword(s):

Large Scale ◽

Habitat Type ◽

Environmental Dna ◽

Conservation Strategies ◽

Natural Environments ◽

Detection Rates ◽

Survey Tool ◽

Declining Species ◽

Species Specific ◽

Wood Turtle

Among vertebrates, herpetofauna has the highest proportion of declining species. Detection of environmental DNA (eDNA) is a promising method towards significantly increasing large-scale herpetological conservation efforts. However, the integration of eDNA results within a management framework requires an evaluation of the efficiency of the method in large natural environments and the calibration of eDNA surveys with the quantitative monitoring tools currently used by conservation biologists. Towards this end, we first developed species-specific primers to detect the wood turtle (Glyptemys insculpta) a species at risk in Canada, by quantitative PCR (qPCR). The rate of eDNA detection obtained by qPCR was also compared to the relative abundance of this species in nine rivers obtained by standardized visual surveys in the Province of Québec (Canada). Second, we developed multi-species primers to detect North American amphibian and reptile species using eDNA metabarcoding analysis. An occurrence index based on the distribution range and habitat type was compared with the eDNA metabarcoding dataset from samples collected in seven lakes and five rivers. Our results empirically support the effectiveness of eDNA metabarcoding to characterize herpetological species distributions. Moreover, detection rates provided similar results to standardized visual surveys currently used to develop conservation strategies for the wood turtle. We conclude that eDNA detection rates may provide an effective semiquantitative survey tool, provided that assay calibration and standardization is performed.

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The effectiveness and cost of camera traps for surveying small reptiles and critical weight range mammals: a comparison with labour-intensive complementary methods

Wildlife Research ◽

10.1071/wr15054 ◽

2015 ◽

Vol 42 (5) ◽

pp. 414 ◽

Cited By ~ 35

Author(s):

Dustin J. Welbourne ◽

Christopher MacGregor ◽

David Paull ◽

David B. Lindenmayer

Keyword(s):

Monitoring Program ◽

Camera Traps ◽

Camera Trapping ◽

Mammal Species ◽

Critical Weight ◽

Complementary Methods ◽

Incidence Data ◽

Trapping Method ◽

The Difference

Context Biodiversity studies often require wildlife researchers to survey multiple species across taxonomic classes. To detect terrestrial squamate and mammal species, often multiple labour-intensive survey techniques are required. Camera traps appear to be more effective and cost-efficient than labour-intensive methods for detecting some mammal species. Recent developments have seen camera traps used for detecting terrestrial squamates. However, the performance of camera traps to survey terrestrial squamate and mammal species simultaneously has not been evaluated. Aim We compared the effectiveness and financial cost of a camera trapping method capable of detecting small squamates and mammals with a set of labour-intensive complementary methods, which have been used in a long-term monitoring program. Methods We compared two survey protocols: one employed labour-intensive complementary methods consisting of cage traps, Elliott traps and artificial refuges; the second utilised camera traps. Comparisons were made of the total number of species detected, species detectability, and cost of executing each type of survey. Key results Camera traps detected significantly more target species per transect than the complementary methods used. Although camera traps detected more species of reptile per transect, the difference was not significant. For the initial survey, camera traps were more expensive than the complementary methods employed, but for realistic cost scenarios camera traps were less expensive in the long term. Conclusions Camera traps are more effective and less expensive than the complementary methods used for acquiring incidence data on terrestrial squamate and mammal species. Implications The camera trapping method presented does not require customised equipment; thus, wildlife managers can use existing camera trapping equipment to detect cryptic mammal and squamate species simultaneously.

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Late Quaternary dynamics of Arctic biota from ancient environmental genomics

Nature ◽

10.1038/s41586-021-04016-x ◽

2021 ◽

Author(s):

Yucheng Wang ◽

Mikkel Winther Pedersen ◽

Inger Greve Alsos ◽

Bianca De Sanctis ◽

Fernando Racimo ◽

...

Keyword(s):

Large Scale ◽

Late Quaternary ◽

Environmental Dna ◽

Plant Genome ◽

The Arctic ◽

Last Glacial ◽

Animal Diversity ◽

Arctic Biota ◽

The Last Glacial

AbstractDuring the last glacial–interglacial cycle, Arctic biotas experienced substantial climatic changes, yet the nature, extent and rate of their responses are not fully understood1–8. Here we report a large-scale environmental DNA metagenomic study of ancient plant and mammal communities, analysing 535 permafrost and lake sediment samples from across the Arctic spanning the past 50,000 years. Furthermore, we present 1,541 contemporary plant genome assemblies that were generated as reference sequences. Our study provides several insights into the long-term dynamics of the Arctic biota at the circumpolar and regional scales. Our key findings include: (1) a relatively homogeneous steppe–tundra flora dominated the Arctic during the Last Glacial Maximum, followed by regional divergence of vegetation during the Holocene epoch; (2) certain grazing animals consistently co-occurred in space and time; (3) humans appear to have been a minor factor in driving animal distributions; (4) higher effective precipitation, as well as an increase in the proportion of wetland plants, show negative effects on animal diversity; (5) the persistence of the steppe–tundra vegetation in northern Siberia enabled the late survival of several now-extinct megafauna species, including the woolly mammoth until 3.9 ± 0.2 thousand years ago (ka) and the woolly rhinoceros until 9.8 ± 0.2 ka; and (6) phylogenetic analysis of mammoth environmental DNA reveals a previously unsampled mitochondrial lineage. Our findings highlight the power of ancient environmental metagenomics analyses to advance understanding of population histories and long-term ecological dynamics.

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Visual lures increase camera-trap detection of the southern cassowary (Casuarius casuarius johnsonii)

Wildlife Research ◽

10.1071/wr16025 ◽

2017 ◽

Vol 44 (3) ◽

pp. 230 ◽

Cited By ~ 4

Author(s):

Wren R. McLean ◽

Ross L. Goldingay ◽

David A. Westcott

Keyword(s):

Endangered Species ◽

Camera Traps ◽

Population Surveys ◽

Monitoring Methods ◽

Detection Rates ◽

Mobile Species ◽

Population Sizes ◽

Cost Efficient ◽

A Site

Context Monitoring is a key component in managing wildlife populations and is critical for revealing long-term population trends of endangered species. Cryptic or highly mobile species that occur in low densities and in remote terrain require the development of specific monitoring methods. The southern cassowary is an Australian endangered species that poses many challenges for conducting population surveys. Aims The aims of the present study were to determine the effectiveness of camera traps in detecting cassowaries at a site, to determine whether visual lures increased detection rates, and to explore the potential of camera traps in population surveys. Methods Coloured lures (mimicking large blue and red fruit) were placed in front of a set of camera traps and compared with controls (no lures) at 29 survey sites on the Daintree coast, northern Queensland, Australia. Key results Camera traps with lures (1) detected more birds, (2) had a shorter detection latency, (3) had a marginally greater number of captures, (4) experienced a longer capture duration, (5) were more likely to have the cassowary stop in front of the camera, and (6) achieved a 95% probability of detecting cassowaries in 12 trap days, compared with 28 trap days without lures. Conclusions An increase in the number of cassowaries detected, the reduction in camera latency times and the ability to identify the birds enables a more efficient approach to estimating population sizes over existing methods. This is the first published study to use visual lures to conduct camera trapping of birds. Implications The use of camera traps with lures is a practical and cost-efficient technique for the rapid detection of cassowaries at a site and lends itself to studies of population structure, size and trends.

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Shifting up a gear with iDNA: from mammal detection events to standardized surveys

10.1101/449165 ◽

2018 ◽

Cited By ~ 2

Author(s):

Jesse F Abrams ◽

Lisa Hoerig ◽

Robert Brozovic ◽

Jan Axtner ◽

Alex Crampton-Platt ◽

...

Keyword(s):

High Throughput Sequencing ◽

Ad Hoc ◽

Environmental Dna ◽

Camera Trap ◽

Camera Traps ◽

Occupancy Models ◽

Imperfect Detection ◽

Mammal Species ◽

Occupancy Model ◽

Cost Efficient

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. 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 analyze iDNA-derived mammalian detection events in a modern occupancy model that accounts for imperfect detection and compare the results with those from occupancy models parameterized with camera-trap-derived detection events. We also combine leech-iDNA and camera-trap data in a single occupancy model. We found consistent estimates of occupancy probabilities produced by our camera-trap and leech datasets. This indicates that the metabarcoding of leech-iDNA method provides reasonable estimates of occupancy and can 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 similar robustness as with 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 similar robust and standardized sampling scheme. Synthesis and applications: The approach we describe here is not restricted to the processing of leech samples, but can be used for the analysis of other iDNA and environmental DNA (eDNA) data. Our study is the first step to shift the application of e/iDNA studies from opportunistic ad-hoc collections to systematic surveys required for long-term wildlife populations and biodiversity monitoring programs.

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Generating and testing ecological hypotheses at the pondscape with environmental DNA metabarcoding: a case study on a threatened amphibian

10.1101/278309 ◽

2018 ◽

Cited By ~ 3

Author(s):

Lynsey R. Harper ◽

Lori Lawson Handley ◽

Christoph Hahn ◽

Neil Boonham ◽

Helen C. Rees ◽

...

Keyword(s):

Species Richness ◽

Large Scale ◽

Gasterosteus Aculeatus ◽

Abiotic Factors ◽

Environmental Dna ◽

Hypothesis Generation ◽

Vertebrate Species ◽

Mammal Species ◽

Negatively Associated ◽

Fulica Atra

AbstractEnvironmental DNA (eDNA) metabarcoding is revolutionising biodiversity monitoring, but has unrealised potential for ecological hypothesis generation and testing. Here, we validate this potential in a large-scale analysis of vertebrate community data generated by eDNA metabarcoding of 532 UK ponds. We test biotic associations between the threatened great crested newt (Triturus cristatus) and other vertebrates as well as abiotic factors influencing T. cristatus detection at the pondscape. Furthermore, we test the status of T. cristatus as an umbrella species for pond conservation by assessing whether vertebrate species richness is greater in ponds with T. cristatus and higher T. cristatus Habitat Suitability Index (HSI) scores. T. cristatus detection was positively correlated with amphibian and waterfowl species richness. Specifically, T. cristatus was positively associated with smooth newt (Lissotriton vulgaris), common coot (Fulica atra), and common moorhen (Gallinula chloropus), but negatively associated with common toad (Bufo bufo). T. cristatus detection did not significantly decrease as fish species richness increased, but negative associations with common carp (Cyprinus carpio), three-spined stickleback (Gasterosteus aculeatus) and ninespine stickleback (Pungitius pungitius) were identified. T. cristatus detection was negatively correlated with mammal species richness, and T. cristatus was negatively associated with grey squirrel (Sciurus carolinensis). T. cristatus detection was negatively correlated with larger pond area, presence of inflow, and higher percentage of shading, but positively correlated with HSI score, supporting its application to T. cristatus survey. Vertebrate species richness was significantly higher in T. cristatus ponds and broadly increased as T. cristatus HSI scores increased. We reaffirm reported associations (e.g. T. cristatus preference for smaller ponds) but also provide novel insights, including a negative effect of pond inflow on T. cristatus. Our findings demonstrate the prospects of eDNA metabarcoding for ecological hypothesis generation and testing at landscape scale, and dramatic enhancement of freshwater conservation, management, monitoring and research.

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Antarctic biodiversity predictions through substrate qualities and environmental DNA

10.1101/2021.08.18.456862 ◽

2021 ◽

Author(s):

Paul Czechowski ◽

Michel de Lange ◽

Michael Knapp ◽

Aleks Terauds ◽

Mark Stevens

Keyword(s):

Large Scale ◽

Sequence Data ◽

Spatial Scales ◽

Environmental Dna ◽

Distribution Modelling ◽

Remote Areas ◽

Long Term Effect ◽

Substrate Properties ◽

Substrate Ph

Antarctic conservation science is important to enhance Antarctic policy and to understand alterations of terrestrial Antarctic biodiversity. Antarctic conservation will have limited long-term effect in the absence of large-scale biodiversity data, but if such data were available, it is likely to improve environmental protection regimes. To enable Antarctic biodiversity prediction across continental spatial scales through proxy variables, in the absence of baseline surveys, we link Antarctic substrate-derived environmental DNA (eDNA) sequence data from the remote Antarctic Prince Charles Mountains to a selected range of concomitantly collected measurements of substrate properties. We achieve this using a statistical method commonly used in machine learning. We find neutral substrate pH, low conductivity, and some substrate minerals to be important predictors of presence for basidiomycetes, chlorophytes, ciliophorans, nematodes, or tardigrades. Our bootstrapped regression reveals how variations of the identified substrate parameters influence probabilities of detecting eukaryote phyla across vast and remote areas of Antarctica. We believe that our work may improve future taxon distribution modelling and aid targeting logistically challenging biodiversity surveys.

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