Environmental DNA in Biodiversity Studies

From fluke to fragment: a multifaceted method for molecular sex identification and mitochondrial haplotyping from environmental DNA samples

This paper develops a method to identify molecular sex and mitochondrial haplotypes from environmental DNA samples, achieving high concordance with tissue samples and resolving lineage-level genetic diversity.

The Leray-XT COI primer pair is not suitable for observing ciliates and radiolarians

The paper assesses the suitability of the Leray-XT COI primer pair for amplifying ciliates and radiolarians, finding that the forward primer cannot bind to either taxon.

NeMO: a flexible R package for nested multi-species occupancy modelling and eDNA study optimization

NeMO is an R package that models multi-species occupancy from eDNA data, estimates detectability, and optimizes survey design by calculating minimal sampling effort.

Large river eDNA sampling designs with remote-sensing-based clustering stratification

This paper proposes a remote-sensing-based stratification method for eDNA sampling in rivers, showing improved detection efficiency compared to random sampling and highlighting the need for hydrological integration.

Eukaryotic biodiversity and ecological networks from the surface to the mesopelagic in the Northwest Atlantic Slope Water

The paper uses eDNA metabarcoding to study eukaryotic biodiversity and ecological networks in the Northwest Atlantic Slope Water, revealing depth-specific communities and the role of protists in network stability.

Fine-scale ecological biomonitoring in a large, complex agriculturally impacted watershed via eDNA metabarcoding

This study uses eDNA metabarcoding to assess biodiversity in an agriculturally impacted watershed, finding greater taxonomic richness and clearer land-use patterns compared to traditional morphology-based methods.

Comparing freshwater eDNA with conventional survey methods to detect vertebrate biodiversity in a Malagasy tropical rainforest

This study compares eDNA metabarcoding with conventional surveys in a Malagasy rainforest, finding eDNA outperforms in detecting vertebrates but has limitations due to primer bias and taxonomic gaps.

Sampling intensity and temporal persistence of airborne eDNA in partially enclosed spaces

This study estimates the sampling intensity and signal persistence of airborne eDNA in an enclosed space to inform effective biomonitoring strategies.

Evaluating eDNA Detection from Live and Dead Control Sources

This study compares eDNA release from live and dead fish, finding dead fish emit significantly higher concentrations, with no significant effect of temperature or velocity on detection.

Biomonitoring in the Anthropocene: Urban estuary environmental DNA tracks marine fish, terrestrial wildlife, and human diet

The paper uses eDNA metabarcoding to monitor marine fish, terrestrial wildlife, and human diet in an urban estuary, finding seasonal patterns and dietary insights through wastewater analysis.

Environmental DNA monitoring of waterfowl reveals community changes during migration

This study evaluates environmental DNA (eDNA) as a tool for monitoring waterfowl communities during migration, showing it can detect species composition and relative abundance but not absolute numbers.

Environmental DNA reveals hidden eukaryotic diversity and fine-scale community patterns across seascape areas in the Northern Red Sea

The paper uses environmental DNA to assess eukaryotic diversity and community patterns in the Northern Red Sea, finding that eDNA captures broader diversity and fine-scale spatial structuring not fully explained by benthic composition.

Generating, curating, and evaluating trnL reference sequence databases: Benchmarking OBITools3/ecoPCR, RESCRIPt, and MetaCurator

The paper evaluates three trnL reference sequence databases generated using different curation tools and assesses their classification performance across trnL regions.

Topography structures of arthropod communities revealed by leaf-derived environmental DNA on Oahu, Hawaii

The paper uses leaf-derived eDNA to study arthropod community structure and invasion dynamics on Oahu, Hawaii, revealing elevation-based transitions and plant species effects.

Vertebrate Biodiversity via eDNA at the air-water interface

This paper uses eDNA sequencing to show that genetic material moves between water and air, revealing a continuous ecological interface and offering new monitoring approaches for vertebrates.

Integrated reanalysis of global riverine fish eDNA datasets shows robustness and congruence of biodiversity conclusions

This study reanalyzes global riverine fish eDNA datasets to show that biodiversity conclusions are robust despite varying bioinformatic workflows and reference databases.

OligoN-design: A simple and versatile tool to design specific probes and primers from large heterogeneous datasets

OligoN-design designs taxon-specific oligonucleotides from target and non-target sequences, outperforming existing tools by handling large datasets efficiently.

Environmental DNA Metabarcoding Effectively Detects Invasive Species, Pests, and Community Changes in Taiwan Rice Fields

The paper demonstrates that eDNA metabarcoding effectively detects invasive species, pests, and community changes in Taiwan rice fields using limited sampling.

Assessing the potential of bee-collected pollen sequence data to train machine learning models for geolocation of sample origin

This study uses bee-collected pollen sequence data to train machine learning models for predicting sample origin, finding that Random Forest and k-Nearest Neighbors models achieve high accuracy.

A breath of fresh air: comparative evaluation of passive versus active airborne eDNA sampling strategies

Passive 3D-printed Nutshell air eDNA samplers hung up to 96 hours at Rotterdam Zoo detected 76 vertebrate species, versus 50 and 25 for two active samplers.

eDNA provides accurate population abundance estimates with bioenergetics and particle mass-balance modelling

This study develops a model integrating bioenergetics and mass-balance to estimate freshwater fish abundance from eDNA, improving accuracy and detecting population changes.

On-site metabarcoding analysis of environmental DNA samples

This paper presents a portable eDNA metabarcoding pipeline for rapid ecological assessment, demonstrating its feasibility in remote settings with on-site analysis.

A Novel eDNA-Based Approach for Hybrid Detection: Implications for Conservation Management

This paper introduces an eDNA-based method to detect hybrid individuals, validated through controlled experiments, offering a scalable tool for conservation management.

Long-read nanopore shotgun eDNA sequencing for river biodiversity, pollution and environmental health monitoring

Species-specific versus community-wide assays in eDNA monitoring of European eel Anguilla anguilla: Trade-offs between detection sensitivity and the value of additional community data

This study compares eDNA metabarcoding and qPCR for detecting European eel in river catchments, finding metabarcoding more effective for broader ecological insights despite slightly lower sensitivity.

Developing terrestrial environmental DNA sampling methods for detecting arboreal invasive reptiles: a case study of the green anole in the Ogasawara Island, Japan

This paper develops terrestrial eDNA sampling methods to detect arboreal invasive green anoles in Ogasawara Islands, finding that eDNA concentrations reflect population density and enable early detection.

State of mangrove biodiversity assessment in Kenya and the prospect of environmental DNA in strengthening surveys

This study evaluates the current state of mangrove biodiversity assessments in Kenya and assesses the feasibility of environmental DNA (eDNA) as a complementary tool for biodiversity monitoring.

Monitoring terrestrial vertebrates with airborne DNA in the Luangwa Valley, Zambia

This study uses airborne eDNA to monitor terrestrial vertebrates in the Luangwa Valley, detecting 120 taxa with high sensitivity and showing that extended sampling improves detection of less common species.

Enhanced reconstruction of Holocene bryophytes from sedimentary ancient DNA using bryophyte-specific primers

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

Applying environmental DNA metabarcoding to calculate an index of biotic integrity for freshwater fish

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.