Environmental DNA in Biodiversity Studies

Capture probe, metabarcoding, or shotgun sequencing: which best reflects local vegetation?

This study compares metabarcoding, shotgun sequencing, and capture probes for detecting plant taxa in lake sediments, finding metabarcoding has the lowest false positive rate and highest detection rate.

A Multi-Taxa Approach to Estuarine Biomonitoring: Assessing Vertebrate Biodiversity and Ecological Continuity using Environmental DNA Metabarcoding in the Rance River (Brittany, France)

The paper uses eDNA metabarcoding to assess vertebrate biodiversity and ecological continuity in the Rance Estuary, finding changes in diversity and functional composition related to a tidal power plant.

A strong relationship between environmental DNA metabarcoding and rank-based abundance of fish

The paper examines the relationship between environmental DNA metabarcoding read counts and rank abundance of fish species in lakes, finding a strong correlation and a negative effect of body mass on eDNA sequence abundance.

Multi-seasonal eDNA metabarcoding highlights a resurgence in fish diversity across a severely impacted estuarine ecosystem

This study uses eDNA metabarcoding to detect a resurgence in fish diversity in a degraded estuary, identifying previously absent species and highlighting seasonal and spatial variations.

Propagule and Juvenile-derived Foraminiferal eDNA across intertidal habitats and its implications for accurate sea-level reconstruction

This study examines how foraminiferal eDNA from different life stages affects sea-level reconstruction in mangrove and mudflat environments, finding that bulk sediment eDNA is reliable in mangroves but less so in transitional zones.

Sampling design and sample processing affect soil biodiversity assessments

This study evaluates how soil sampling design and processing affect biodiversity estimates, finding significant variation in diversity metrics based on subsample numbers and pooling strategies.

Molecular detection of a cryptic salamander: Development of an eDNA assay for the detection of the mud salamander (Pseudotriton montanus).

The paper develops a species-specific eDNA qPCR assay for detecting the cryptic mud salamander, confirming its presence in eight out of 68 sampled sites.

Resolving eukaryotic river biofilm communities using long-read sequencing for biomonitoring

This study compares short-read and long-read sequencing of 18S rRNA gene amplicons in river biofilms, showing that long-read sequencing improves taxonomic resolution while trimming can introduce mismatches.

Seasonal patterns of environmental DNA detection for freshwater unionid mussels

This study evaluates eDNA detection for freshwater mussels across seasons, finding consistent detection with visual surveys but noting seasonal factors affecting efficiency.

Environmental DNA as an Indicator of Seasonal Reproductive Phenology in Freshwater Mussels

This study uses environmental DNA to monitor freshwater mussel reproduction, finding that male mitotype signals align with spawning periods but are sporadic and may be influenced by multiple factors.

Metabarcoding and microtomography reveal new insights into the dietary niche of near-extinct amphibians

This study uses DNA metabarcoding and microtomography to analyze the diet of near-extinct harlequin toads, revealing ecological segregation and hymenopteran specialization.

MitoNGS: an online platform to analyze fish metabarcoding data in high-resolution

MitoNGS improves fish metabarcoding analysis by enhancing reference databases and introducing a species group strategy to resolve ambiguous taxa.

A conservation planning assessment of basin wide Unionid mussel assemblages using environmental DNA

This study evaluates eDNA metabarcoding for monitoring freshwater mussel assemblages, finding it detects more species than visual surveys and identifies rare species.

Environmental DNA/RNA metabarcoding in estuaries of Sao Paulo, Brazil, reveals fish diversity and the presence of invasive species

The paper uses eDNA and eRNA metabarcoding to assess fish diversity in Brazilian estuaries, finding higher diversity in less impacted areas and invasive species in urbanized systems.

Assessment of Environmental DNA Surveys for the Cryptic Salamander Mussel (Simpsonaias ambigua)

This study compares eDNA sampling with visual surveys to detect the rare Salamander Mussel, finding eDNA more efficient and sensitive for detection in difficult habitats.

Unveiling protist composition and diversity patterns with eDNA metabarcoding: comparing short- and long-read approaches

This study compares short- and long-read eDNA metabarcoding for protist diversity in coastal waters, finding that long-read sequencing provides deeper taxonomic resolution and detects ecologically relevant taxa.

Process-based model predicts seasonal variation in eDNA transport - a case study on Eurasian beavers in a small river

This study uses a process-based model to predict seasonal eDNA transport in a river, showing longer transport distances in winter and shorter in summer for Eurasian beavers.

Balancing Barcoding and Genomics: gDNA Quality in Insect Vouchers after HotSHOT DNA extraction

The paper evaluates gDNA quality after HotSHOT extraction in insect vouchers under different storage conditions and finds that HotSHOT preserves sufficient gDNA for genomic sequencing, though field storage impacts DNA integrity.

Performance and limitations of out-of-distribution detection for insect DNA (meta)barcoding

This study evaluates out-of-distribution detection in DNA barcoding using genetic distance and deep learning metrics, finding that detection is more sensitive to sequence noise and lack of diagnosable characters than identification accuracy.

Unveiling vertebrate biodiversity in arid and semi-arid terrestrial ecosystems through eDNA metabarcoding at savanna waterholes

This study evaluates eDNA metabarcoding effectiveness in detecting terrestrial vertebrates in arid ecosystems, finding that sediment samples detect abundant taxa better while water samples detect rare taxa more frequently.

Development of metagenomic methods for non-invasive health monitoring of endangered species: Unveiling hidden microbial threats in fecal samples

This paper develops a metagenomic pipeline to detect pathogenic bacteria in fecal samples of endangered species, identifying 19 potentially harmful bacterial species in Iberian desmans.

Extraction-free iDNA metabarcoding of small dung beetles is an efficient method for surveying arboreal mammals in tropical forests

This paper introduces an extraction-free iDNA metabarcoding method using small dung beetles to survey arboreal mammals in tropical forests, detecting 42 vertebrate species from 105 beetles.

Scalable isolation of soil genomic DNA from microbes to multicellular micro- and mesofauna

The paper develops a scalable DNA extraction method for soil samples, showing it improves detection of eukaryotic and metazoan diversity compared to conventional methods.

Long-range PCR amplification and nanopore sequencing of 8-10 kb mitochondrial fragments from environmental DNA

The paper demonstrates the use of long-range PCR and nanopore sequencing to obtain and analyze long mitochondrial fragments from environmental DNA samples, enabling species identification despite sequencing errors.

Dynamic sedimentary ancient DNA models of Fennoscandic Holocene plant communities reveal the role of temperature and competition

This study uses sedimentary ancient DNA data from 10 lakes in Fennoscandia to model Holocene plant community dynamics, showing that temperature and competition, especially shading, significantly influence community structure.

Targeted Airborne eDNA Detection of Pest Wallabies: Effects of Sampler Type and Distance

This study evaluates airborne eDNA detection of Bennetts wallabies using active and passive samplers, finding active samplers and coarse filters improve detection, especially at short distances.

Fast, Flexible, Feasible: A Transparent Framework for Evaluating eDNA Workflow Trade-offs in Resource-Limited Settings

The paper evaluates eDNA workflows to identify cost-effective and sensitive methods for biodiversity monitoring in resource-limited settings.

Explainable Multimodal Machine Learning Using Combined Environmental DNA and Biogeographic Features for Ecosystem Biomonitoring

The paper introduces a multimodal machine learning approach combining eDNA and biogeographic data to improve ecosystem biomonitoring accuracy.

Tracking the phenology of riverine insect communities using environmental DNA

This study shows that eDNA can capture seasonal changes in aquatic insect communities across a river catchment, revealing phenological trends and species dynamics over time.

BirT: a novel primer pair for avian environmental DNA metabarcoding

The paper introduces a new primer pair (BirT) for avian eDNA metabarcoding, demonstrating its effectiveness in detecting bird species from water samples with high specificity and taxonomic resolution.