Environmental DNA in Biodiversity Studies

Getting to the core of the matter: Assessing the role of replication in sedimentary DNA metabarcoding

This study evaluates the impact of replication on sedimentary DNA metabarcoding by analyzing variation in community composition across biological, technical, and stratigraphic replicates.

City life: airborne DNA metagenomic biodiversity monitoring reveals dynamic changes across time and space

This study uses airborne DNA metagenomics to monitor biodiversity across time and space, revealing seasonal and spatial shifts in species composition.

Optimizing DNA extraction from environmentally degraded bone samples for molecular identification of cetacean species

This paper presents an optimized DNA extraction protocol for degraded cetacean bone samples, successfully amplifying mitochondrial DNA from 55.6% of samples for species identification.

Temporal persistence of airborne environmental DNA in a natural open-air setting

This study investigates the temporal persistence of airborne eDNA from a wallaby carcass, finding that DNA remains detectable up to 100 meters for three days, with active sampling improving detection rates.

The Metabarcoding Analysis Pipeline (MAP): Simple, accurate, and flexible metabarcoding

The paper introduces MAP, a metabarcoding pipeline that handles long-read data and provides accurate biodiversity estimates, outperforming existing platforms for COI metabarcoding.

Patterns and Drivers of Diatom Diversity and Biogeography in the North Pacific

The paper assesses North Pacific diatom communities using rbcL metabarcoding, identifying environmental drivers and a previously overlooked species.

Assessment of Leaf-Litter Invertebrate Biodiversity Using High Throughput Sequencing

The paper assesses leaf-litter invertebrate biodiversity using high-throughput sequencing, finding that the Qiagen Blood and Tissue Kit is most effective and that temperature influences community composition.

Optimising passive eDNA sampling: A theoretical framework for time-dependent eDNA accumulation

This paper develops a theoretical model to understand how deployment duration affects eDNA accumulation in passive samplers, showing that recovery dynamics depend on DNA input, degradation, and substrate capacity.

Targeted hybridization capture enables comprehensive detection of freshwater bioassessment invertebrates from environmental DNA

This study uses targeted hybridization capture to detect freshwater macroinvertebrates from eDNA, recovering 450 genera across 8 phyla with high taxonomic resolution.

Characterizing mitochondrial copy number variation and PCR amplification bias as sources of quantitative constraints in DNA metabarcoding

COI metabarcoding of 81 arthropod mock communities shows PCR amplification bias is taxon-specific but non-exponential, so cycle calibration fails while a constant-bias model recovers mtDNA copies.

eDNA metabarcoding provides scalable and continuous biodiversity monitoring across the tree of life

This study uses eDNA metabarcoding to monitor biodiversity across aquatic habitats, finding it provides more species data at lower cost than traditional methods.

Assessing fish diversity in the Amazon: The impact of primers and reference libraries in eDNA surveys

This study evaluates the impact of primers and reference databases on fish species detection in eDNA surveys of the Teles Pires River basin, finding that modified primers and local databases improve detection.

Mechanistic assessment of eDNA passive samplers: a case study with invasive freshwater bivalves

This study assesses the mechanisms of eDNA capture by passive samplers using invasive bivalves, showing dynamic equilibrium rather than cumulative accumulation.

Improving metazoan biodiversity inventories associated with rocky subtidal habitats of the North Colombian Pacific through eDNA metabarcoding and DNA barcodes

The paper uses eDNA metabarcoding and DNA barcoding to document marine biodiversity in Colombian Pacific rocky shores, identifying over 1,400 taxa and highlighting site-specific diversity differences.

Beyond DNA barcodes: an open-source workflow for recovering and organizing barcoded vouchers for ecological and evolutionary research

The paper presents an open-source workflow to recover and organize barcoded vouchers for ecological and evolutionary research, enabling efficient linking of specimens to molecular data and metadata.

Jelly belly: Recovery of fish eDNA from Cassiopea medusae gastrovascular cavities across the Florida Keys

The paper explores fish eDNA recovery from Cassiopea medusae gastrovascular cavities in the Florida Keys, identifying species not found in water or sediment samples.

Assessing RNA as a tool to detect scavenging in a riparian invertebrate predator

This study tests if carabid beetles consume carrion by analyzing RNA and DNA in their gut after feeding on fresh or dead Drosophila.

Metabarcoding replicate detection frequency tracks ddPCR copy number for cod and herring eDNA in ancient marine sediments

The paper quantifies eDNA abundance using ddPCR and compares it with metabarcoding detection frequency in ancient marine sediments, finding a positive correlation and ecological relevance.

A depositional taphonomy model for sedimentary ancient DNA based on biotic profiles of contrasting sedimentation regimes

This study develops a depositional taphonomy model for sedimentary ancient DNA (sedaDNA) to determine its origins from local or distant sources across different sedimentation regimes.

The Barcode Inference Pipeline (BIP): From Sequencer Output to DNA Barcodes

The paper introduces BIP, a pipeline for DNA barcode inference from sequencing data, which outperforms existing tools by accurately distinguishing target and non-target sequences.

Estimating absolute microbial abundances from metabarcoding anchored to cytometry data

This paper calibrates metabarcoding data using flow cytometry to estimate absolute microbial abundances and gene concentrations in oceanic samples.

Improving sensitivity in environmental DNA measurement by reconcentrating DNA extracts

This study improves eDNA measurement sensitivity by reconcentrating DNA extracts without additional equipment or reagents, increasing DNA concentration by sevenfold when pooling ten samples.

Tracing the 'Panda of the Sea': Species-Specific qPCR Assays for eDNA Monitoring of Critically Endangered Bahaba taipingensis in the Pearl River Estuary

The paper develops and validates species-specific qPCR assays for detecting Bahaba taipingensis eDNA in the Pearl River Estuary, finding detectable eDNA in September samples.

Extracellular vesicle associated nucleic acids and proteins as a complementary fraction for fish biodiversity monitoring and physiological signal recovery

The paper evaluates EV-associated nucleic acids and proteins as a complementary method to eDNA/eRNA for biodiversity monitoring and physiological signal recovery in aquatic environments.

Efficacy of natural marine sponges as a passive environmental DNA sampler for freshwater fish diversity monitoring

This study evaluates the effectiveness of sponge skeletons as passive eDNA samplers for freshwater fish diversity, finding comparable species richness and community structure to water filtration.

Evaluating DNA metabarcoding to characterise diet diversity and foraging strategies in a generalist mesopredator, the lesser black-backed gull (Larus fuscus)

This study evaluates DNA metabarcoding for diet analysis in lesser black-backed gulls, revealing diverse diets and foraging strategies across different age and colony groups.

Discovering the unseen: a performance comparison of taxonomic classification methods under unknown DNA barcodes

This study compares taxonomic classification methods for DNA barcoding, finding that phylogenetic placement methods excel for arthropod COI barcodes while composition-based classifiers perform better for fungal ITS.

CurateMake: an auditable workflow for multi-source ITS reference database harmonisation and phylogenetic validation

CurateMake is a workflow for harmonizing and validating ITS reference databases, improving taxonomic coherence and error correction through nomenclatural standardization and phylogenetic validation.

Extraction workflow determines marker-specific recovery andreproducibility in leaf-litter eDNA metabarcoding

The paper compares DNA extraction workflows for leaf-litter eDNA metabarcoding, finding that recovery and reproducibility depend on workflow and marker, with site-level ecological signals retained across methods.

SSUplex: fast, both-strand extraction and origin-sorting of small-subunit rRNA for environmental DNA metabarcoding

SSUplex is a tool for extracting and sorting small-subunit rRNA reads by origin, improving accuracy in environmental DNA metabarcoding.