Environmental DNA in Biodiversity Studies

First national survey of terrestrial biodiversity using airborne eDNA

This study conducts the first national terrestrial biodiversity survey using airborne eDNA, identifying over 1,100 taxa and showing its potential to complement citizen science for conservation.

Environmental RNA/DNA Metabarcoding for Ecological Risk Assessment of Chemicals Based on Response of Benthic Communities in Natural Environments

The paper estimates a safe concentration of LAS using eRNA metabarcoding to assess ecological risk, finding eRNA more sensitive than eDNA for detecting community changes.

DNA Divers: volunteer-based eDNA capture for local and global marine biodiversity monitoring

This paper evaluates a volunteer-based eDNA capture method using swimming motion to collect marine biodiversity data, finding it effective for detecting diverse species across wide latitudinal ranges.

Fish from the sky: Airborne eDNA tracks aquatic life

The paper demonstrates that airborne eDNA can reliably detect aquatic life, showing that passive air samplers capture eDNA signals comparable to water samples.

Data of the Insect Biome Atlas: a metabarcoding survey of the terrestrial arthropods of Sweden and Madagascar

The paper presents comprehensive DNA metabarcoding data from Sweden and Madagascar, characterizing terrestrial arthropod faunas and providing insights into community composition and dynamics.

The profiles of mammals, birds and fish in twelve water bodies on the Island of Montreal by mitochondrial DNA: detection of invasive animals and meat and fish waste

The paper uses mitochondrial DNA analysis of water samples to detect invasive and unexpected animal species in Montreal's water bodies, finding invasive fish and potential meat/fish waste contamination.

A rapid and inexpensive universal PCR protocol for DNA (meta)barcoding using a one-tube, 2-step PCR

The paper introduces a rapid, inexpensive, single-tube two-step PCR protocol for DNA barcoding and metabarcoding that improves PCR product yield compared to a one-step protocol.

eDNA enables proof-of-origin of samples from reservoirs with rich and abundant biodiversity

The paper shows that eDNA profiles from water samples can indicate sample provenance across reservoirs using multi-marker metabarcoding and blockchain traceability.

Towards large-scale museomics projects: a cost-effective and high-throughput extraction method for obtaining historical DNA from museum insect specimens

This paper introduces a cost-effective DNA extraction method for museum insect specimens, validated against existing protocols and applied to a large sample set.

Seasonal changes in fish eDNA signal vary between contrasting river types

This study examines seasonal changes in fish eDNA signals across different river types, finding inconsistent patterns and highlighting the importance of considering priority species in survey design.

High-throughput biodiversity surveying sheds new light on the brightest of insect taxa

One year of COI metabarcoding of 197 Malaise traps across Sweden detected 1,535 of 2,990 known Lepidoptera species, plus specimen-validated new country records, range extensions and putative undescribed species.

Spatial and seasonal biodiversity variation in a large Mediterranean lagoon using environmental DNA metabarcoding through sponge tissue collection

The paper assesses faunal composition and its spatial and temporal variation in a Mediterranean lagoon using eDNA metabarcoding from sponge tissues collected in different seasons and areas.

eDNA replicates, polymerase and amplicon size impact inference of richness across habitats

This study investigates how replicates, PCR polymerases, and amplicon size affect species richness estimates in eDNA metabarcoding across different habitats.

Automating the Curation of DNA Barcode Databases for Vascular Plants

This paper introduces a new workflow to improve the reliability and accuracy of plant DNA barcode databases by addressing post-analytical validation shortcomings and demonstrating the impact of clustering and threshold-based identification.

eDNA metabarcoding shows highly diverse but distinct shallow, mid-water, and deep-water eukaryotic communities within a marine biodiversity hotspot

The paper uses eDNA metabarcoding to show that deep-water eukaryotic communities in the Gulf of California are as diverse as shallow ones but distinct, supporting the need for deeper habitat conservation.

A Method for Preparing Morphologically Preserved Wildlife Fecal Specimens for Long-Term Ecological Studies

This paper introduces a method to preserve wildlife fecal specimens for long-term ecological studies, maintaining morphology, DNA integrity, and chemical composition.

Data Fusion for Integrative Species Identification Using Deep Learning

This paper develops a deep learning framework that integrates molecular and image data to improve species identification, showing significant accuracy gains for genetically similar and morphologically indistinguishable species.

Development of a Comprehensive Analytical Workflow for eDNA Analysis of Vertebrates, Arthropods, and Mollusks

This paper develops an eDNA analysis workflow using long-read sequencing and expanded databases to improve detection of vertebrates, arthropods, and mollusks.

An annotated reference library for supporting DNA metabarcoding analysis of aquatic macroinvertebrates in French freshwater environments

This paper constructs a COI-based DNA barcode library for French freshwater macroinvertebrates to improve DNA metabarcoding accuracy and highlights challenges with primer specificity and genetic diversity.

Improving whole biodiversity monitoring and discovery with environmental DNA metagenomics

The paper introduces SEQIDIST, a framework to improve eDNA metagenomics accuracy by reducing false positives and discovering new biodiversity, tested on riverine eDNA data.

Scalable environmental DNA methods reveal associations between landscape-scale forest habitat and insect richness

The paper develops scalable terrestrial eDNA methods to link landscape-scale forest habitat with insect richness using flower and leaf surface samples.

Cas9-based enrichment for targeted long-read metabarcoding

This paper introduces a Cas9-based method for targeted long-read metabarcoding, enabling multiplexed enrichment of marker genes without PCR, and demonstrates its effectiveness in characterizing complex microbial and nematode communities.

Assessing the combined performance of supervised learning and spike-in constructs for bias correction in eDNA metabarcoding

This study evaluates supervised learning models for bias correction in eDNA metabarcoding, showing significant performance improvements with experiment-specific data.

Development and validation of five native Aotearoa New Zealand genera-specific large brown macroalgal eDNA ddPCR assays

The paper develops and validates five ddPCR assays for detecting eDNA of specific large brown macroalgal genera in Aotearoa New Zealand.

μCeta: a set of cetacean-specific primers for environmental DNA metabarcoding with minimal amplification of non-target vertebrates

The paper develops and validates μCeta, a cetacean-specific primer set for eDNA metabarcoding that minimizes non-target vertebrate amplification, successfully detecting Indo-Pacific humpback dolphin eDNA in Hong Kong waters.

Inferring species interactions from co-occurrence networks with environmental DNA metabarcoding data in a coastal marine food-web

The paper evaluates co-occurrence networks from eDNA metabarcoding data to infer species interactions in a coastal marine ecosystem, finding limited trophic interactions and methodological challenges.

Monitoring of the invasive round goby in an estuarine seascape based on eDNA

The paper develops and evaluates an eDNA monitoring method using qPCR to detect the invasive round goby in a marine environment, showing high sensitivity and correlation with field sampling.

Challenges in detecting ecological interactions using sedimentary ancient DNA data

The paper evaluates five methods for detecting ecological interactions from sedimentary ancient DNA data and finds high false discovery rates and poor detection performance under realistic conditions.

Water volume, biological and PCR replicates influence the characterization of deep-sea pelagic fish communities.

This study evaluates how water volume and replicates affect eDNA-based characterization of deep-sea pelagic fish communities, finding that 5L water volume and 5-10 PCR replicates are sufficient for reliable results.

Freshwater fish community assessment using eDNA metabarcoding vs. capture-based methods: differences in efficiency and resolution coupled to habitat and ecology

This study compares eDNA metabarcoding and electrofishing for assessing freshwater fish communities, finding similar species richness but differing compositions influenced by habitat and ecology.