Environmental DNA in Biodiversity Studies

This study improves bryophyte recovery from sedimentary ancient DNA using species-specific primers, revealing taxonomic and functional patterns in Arctic ecosystems over time.

This study uses eDNA metabarcoding to calculate a fish-based Index of Biotic Integrity (IBI) in the Tennessee River Basin and compares it to conventional and macroinvertebrate-based indices.

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.

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.

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.

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.

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.

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.

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.

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.

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

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.

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

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

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

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.

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.

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.

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.

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.

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.

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.

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.

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

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.

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.

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.

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

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