A Confidence Scoring Procedure for eDNA Metabarcoding Records and Its Application to a Global Marine Fish Dataset

Environmental DNA, Journal Year: 2025, Volume and Issue: 7(2)

Published: March 1, 2025

ABSTRACT Environmental DNA (eDNA) metabarcoding is changing the way biodiversity surveyed in many types of ecosystems. eDNA surveys are now commonly performed and integrated into monitoring programs public databases. Although it widely recognized that records require interpretation light taxonomy biogeography, there remains a range perceptions about how thoroughly should be evaluated which ones reported. Here, we present modular procedure, available as an R script, uses set five steps to assess confidence species‐level by assigning them score from 0 5. This procedure includes evaluations known geographic distribution each taxon, taxonomic resolution marker used, regional completeness reference database, diversification rate, map taxon. We tested on large‐scale marine fish dataset (572 samples) covering 15 ecoregions worldwide, poles tropics, using teleo mitochondrial 12S ribosomal gene. Our analysis revealed broad variation average among regions, with highest scores occurring along European Eastern Atlantic coasts. Generalized linear models applied record covariates highlighted significant influences latitude species richness low (< 2.5). The polar regions notably displayed high proportions scores, probably due limited databases marker. conclude only (> 2.5) medium (2.5) relatively low‐confidence correspond further investigation may after inspection ensure high‐quality records.

Language: Английский

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Global patterns and gaps in the study of terrestrial birds and mammals' use of freshwater sources: a mapping review

Wildlife Biology, Journal Year: 2025, Volume and Issue: unknown

Published: March 26, 2025

Water availability strongly influences the ecology of terrestrial birds and mammals. It will likely play an increasing role as a limiting factor climate change human demand make water scarcer. However, we lack knowledge synthesis describing our current understanding use sources, particularly for wildlife hydration. To provide comprehensive overview available research regarding utilization bodies hydration sources by mammals, conducted mapping review based on extensive search papers in Web Science Scopus databases published up to 2022. We compiled 181 that met inclusion criteria. Earlier date back 1965, but stable publication rate was not reached until 2005, there has been significant growth since 2015. The USA, Mexico, Zimbabwe had most papers. Studies were concentrated areas with mean annual precipitation lower than 1000 mm, predominantly deserts xeric shrublands, well tropical subtropical grasslands, savannas, shrublands. heavily focused mammals less frequently included overrepresentation species classified ‘Least concern' both groups. Very few studies canopy, even fewer compared surface versus arboreal sources. Cameras direct observations main methods used document wildlife's use. Attention shows trend; however, given globalized reduction quality, it is urgent widen scope include greater variety habitat types, animal species. Such increase necessary unravel magnitude impacts reductions can have short long term viability.

Language: Английский

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Combining eDNA Metabarcoding, Hydrology‐Based Modeling and Camera Trap Datasets to Assess the Potential of River eDNA in Monitoring Terrestrial Mammals

Environmental DNA, Journal Year: 2025, Volume and Issue: 7(2)

Published: March 1, 2025

ABSTRACT Global efforts aimed at safeguarding and restoring biodiversity require methods to monitor progress towards conservation objectives. Such should provide a systematic robust assessment of for the lowest cost. River environmental DNA (eDNA) metabarcoding has been successfully applied measure in dendritic riverine habitats is increasingly used describe communities terrestrial vertebrates ecosystems that are challenging survey using traditional methods. However, interpreting eDNA surveys requires an understanding influence transport, decay, production on distribution eDNA. To this end, hydrology‐based eDITH (eDNA Integrating Transport Hydrology) model incorporates such factors can recover reliable spatial patterns aquatic taxa, but its potential taxa so far unexplored. Here, we data mammals collected over two mountainous catchments (575 745 km 2 ) British Columbia, Canada. We assessed prediction transferability between neighboring compared predictions with observations from camera trapping. found 9 out 15 detected by both traps, predicted distributions predominantly matched trap surveys, illustrating uncover mammal catchments. While lacking knowledge actual taxon density prevents us determining whether discrepancies stem limitations or complex production‐density relationships, good suggests some semi‐aquatic partly determined habitat preference hydrology. Downstream sampling most across catchment, inclusion upstream samples aid detecting elusive species. This study underscores broader applications river beyond species illustrates use addressing monitoring objectives tailored approaches.

Language: Английский

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A stakeholder empowerment framework to advance eDNA biodiversity monitoring in Africa: Perspectives from Namibia

One Earth, Journal Year: 2025, Volume and Issue: 8(4), P. 101244 - 101244

Published: April 1, 2025

Language: Английский

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Comparison of soil eDNA to camera traps for assessing mammal and bird community composition and site use

Ecology and Evolution, Journal Year: 2024, Volume and Issue: 14(7)

Published: July 1, 2024

Species detections often vary depending on the survey methods employed. Some species may go undetected when using only one approach in community-level inventory and monitoring programs, which has management conservation implications. We conducted a comparative study of terrestrial mammal bird spring summer 2021 by placing camera traps at 30 locations across large military installation northern Michigan, USA testing replicate soil samples from these sites for environmental DNA (eDNA) an established vertebrate metabarcoding assay. detected total 48 taxa both methods: 26 mammalian (excluding humans, 24 to two genus) 22 avian (21 genus). relatively even distribution cameras (17) via eDNA analysis (15), with seven methods. Most medium-to-large carnivores were cameras, whereas semi-fossorial small mammals analysis. higher diversity (18 taxa) compared (eight taxa; four methods), but alone most effective detecting smaller birds that frequently occupy arboreal environments. also used Bayesian spatial occupancy models widely distributed game (white-tailed deer,

Language: Английский

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

Environmental DNA, Journal Year: 2023, Volume and Issue: 5(6), P. 1608 - 1622

Published: Oct. 20, 2023

Abstract The anthropogenic impact on the world's ecosystems is severe and need for non‐invasive, cost‐effective tools monitoring understanding those impacts are therefore urgent. Here, we combine two such methods in a comprehensive multi‐year study; camera trapping (CT) analysis of environmental DNA (eDNA), river marginal zones temperate, wetland Nature Park Denmark. CT was performed from 2015 to 2019 total 8778 trap days yielded 24,376 animal observations. observations covered 87 taxa, which 78 were identified species level, 73 wild native species. For eDNA metabarcoding, 114 freshwater samples collected eight sites all four seasons 2017 2018. results detection 80 74 65 While number taxa detected with comparable, overlap only 20%. In combination, thus 115 (20 fishes, 4 amphibians, one snake, 23 mammals, 67 birds), representing half found via conventional surveys over last ca. 20 years (83% 68% 67% 41% birds, 20% reptiles). Our study demonstrates that holistic approach combining non‐invasive methods, CT, has great potential as biomonitoring tool vertebrates.

Language: Английский

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A hybrid approach to invertebrate biomonitoring using computer vision and DNA metabarcoding

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 3, 2024

Abstract Automated invertebrate classification using computer vision has shown significant potential to improve specimen processing efficiency. However, challenges such as diversity and morphological similarity among taxa can make it difficult infer fine-scale taxonomic classifications vision. As a result, many models are forced at coarser levels, family or order. Here we propose novel framework combine bulk DNA metabarcoding pipelines the accuracy granularity of individual classifications. To accuracy, our uses multimodal fusion that image data with DNA-based assemblage data. refine model’s classifications, cross-references detections from samples. We demonstrated this continental-scale, bycatch dataset collected by National Ecological Observatory Network. The included 17 spanning three phyla (Annelida, Arthropoda, Mollusca), finest starting these being order-level. Using framework, reached 79.6% across real data, 83.6% when was “error-free”, resulting in 2.2% 6.2% increase compared model trained only images. After cross-referencing detections, improved up 72.2% 5.7% reaching species-level. By providing coincident refining greatly expand capabilities biological classifiers. This allows classifiers taxonomically fine-grained would otherwise be impossible due morphologic scarcity. is not limited terrestrial invertebrates could applied any instance where concurrently collected.

Language: Английский

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Analysing the effects of distance, taxon and biomass on vertebrate detections using bulk-collected carrion fly iDNA

Royal Society Open Science, Journal Year: 2024, Volume and Issue: 11(4)

Published: April 1, 2024

Invertebrate-derived DNA (iDNA) metabarcoding from carrion flies is a powerful, non-invasive tool that has value for assessing vertebrate diversity. However, unknowns exist around the factors influence detections, such as spatial limits to iDNA signals or if detections are influenced by taxonomic class estimated biomass of vertebrates interest. Using bulk-collection method, we captured within zoo and along transects extending 4 km away this location. From 920 flies, detected 28 species. Of species, identified 9 species kept at zoo, 8 mammals 1 bird, but no reptiles. were highly geographically localized, only few animals outside setting. due low number in our dataset, found group on their detectability. Our data suggest bulk-collected least urban settings Australia, predominantly determined geographic proximity sampling This study presents an important step understanding how techniques can be used biodiversity monitoring.

Language: Английский

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Environmental DNA and wildlife camera traps uncover complimentary vertebrate visitation patterns at freshwater granite rock-holes

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 3, 2024

Abstract Freshwater ecosystems are in decline globally. In Australia, threatening processes include invasive species, increasing drought frequency, climate change and changes to land use, all of which have been associated with declining vertebrate diversity, particularly Australia’s arid interior. Efficient monitoring tools required effectively monitor conserve freshwater their communities. Environmental DNA (eDNA) metabarcoding is one tool that shows promise for these systems, but knowledge how eDNA data compares more established ecological assessment techniques limited. To address this gap, we sampled from seven water bodies proposed conservation importance the Australian arid-lands, at three timepoints measure visitation compare our findings camera trapping same locations. Using detected 19 species vertebrates, including native (such as macropods, wombats emus) feral goats, cats foxes). contrast, traps 32 was much successful detecting bird than eDNA. These communities varied both spatially between rock-holes, temporally, summer collection periods being distinct winter-spring. Our results demonstrate success a arid-lands complementary traditional survey methods such wildlife trapping. Finally, provide recommendations discuss efficacy resources environments.

Language: Английский

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Constructing ecological indices for urban environments using species distribution models

Urban Ecosystems, Journal Year: 2022, Volume and Issue: 25(6), P. 1745 - 1764

Published: July 16, 2022

Abstract In an increasingly urbanized world, there is a need to study urban areas as their own class of ecosystems well assess the impacts anthropogenic on biodiversity. However, collecting sufficient number species observations estimate patterns biodiversity in city can be costly. Here we investigated use community science-based data occurrences, combined with distribution models (SDMs), built using MaxEnt and remotely-sensed measures environment, predict across environment Los Angeles. By selecting most accurate SDMs, then summarizing these by class, were able produce two richness (SRMs) for Aves Magnoliopsida how they respond variety natural environmental gradients. We found that considered native Angeles tend have significantly more SDMs than non-native counterparts. For all this variables describing activities, such housing density alterations land cover, influential factors, terrain proximity freshwater, shaping SDMs. Using random forest model our SRMs could account approximately 54% 62% predicted variation classes respectively. used roles factors them.

Language: Английский

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