Environmental DNA in Biodiversity Studies

Towards population genetic assessments and species abundance from environmental DNA: A case study with zebrafish in controlled aquaria

This study demonstrates the use of microhaplotypes from environmental DNA to estimate population genetic diversity and species abundance in zebrafish aquaria.

The long and the short of it: Nanopore based eDNA metabarcoding of marine vertebrates works; sensitivity and specificity depend on amplicon lengths

This paper compares nanopore-based eDNA metabarcoding using 2kb and 170bp amplicons for marine fish species identification, finding that longer amplicons improve taxonomic resolution in controlled settings but yield fewer species in field samples.

DNA data (genome skims and metabarcodes) paired with chemical data demonstrate utility for retrospective analysis of forage linked to fatal poisoning of cattle

The paper uses DNA data and chemical analysis to identify toxic plants in contaminated forage linked to cattle poisoning.

AI-based prediction of herbarium sequencing success across the plant tree of life

The paper develops an AI model to predict successful genomic DNA sequencing from herbarium specimens using morphological, metadata, and DNA quantity features.

Metazoan diversity in Chilean hypersaline lakes unveiled by environmental DNA

This study uses environmental DNA to assess metazoan diversity in Chilean hypersaline lakes, revealing high biodiversity and validating eDNA as a tool for conservation.

A long-term ecological research data set from the marine genetic monitoring programme ARMS-MBON 2018-2020

The paper presents a marine biodiversity dataset from ARMS-MBON 2018-2020, showing its potential for ecological research and monitoring.

Lessons learned from applying eDNA surveying to diadromous fish detection across the north-east Atlantic region

This study uses eDNA sampling and qPCR/dPCR assays to monitor diadromous fish distribution in the Northeast Atlantic, finding dPCR's higher sensitivity is crucial for detecting low-abundance species like sea lamprey.

Arctic plant species display contrasting levels of chloroplast DNA copy numbers

The paper quantifies chloroplast DNA copy number variation in Arctic plants and shows significant differences between species and tissue types, highlighting its impact on DNA metabarcoding accuracy.

A short cut to sample coverage standardization in meta-barcoding data provides new insights into land use effects on insect diversity

This study standardizes sample coverage in metabarcoding data to assess land use effects on insect diversity, finding significant declines in both taxonomic and phylogenetic diversity in agricultural areas.

Insights into the representativeness of biodiversity assessment in large reservoir through eDNA metabarcoding

This study uses eDNA metabarcoding to assess biodiversity in a large reservoir, revealing previously unreported species and demonstrating that 30% sampling can effectively capture biodiversity.

Complementary assessment of fish biodiversity across the upper/lower mesophotic interface in a subtropical coral reef using eDNA metabarcoding and baited cameras

This study assesses fish biodiversity at the upper/lower mesophotic interface using eDNA metabarcoding and baited cameras, finding complementary species detections and continuity with shallow reef systems.

An accessible metagenomic strategy allows for better characterization of invertebrate bulk samples

This study presents a metagenomic strategy using low-coverage whole genome sequencing reads to construct genomic references, improving species biomass estimation in bulk samples compared to metabarcoding.

A Preliminary Application of Bird Surveys Using Environmental DNA Technology: in Futian Mangrove Nature Reserve

This study uses environmental DNA metabarcoding to survey bird diversity in Futian Mangrove Nature Reserve, finding higher bird OTU detection in air samples compared to water and soil.

Understanding detection probability in a low-density population to inform optimal eDNA sampling for freshwater mussels

This study evaluates eDNA detection probabilities for freshwater mussels in low-density populations, showing that higher replication is needed for reliable detection compared to visual sampling.

From Nets to Molecules: A Comparative Study of Stream Fish Diversity Recovery Using Different Sampling Methods in Eastern Amazonia

This study compares fish diversity recovery using netting, eDNA, and dietary metabarcoding in three Neotropical streams to improve biodiversity assessment.

What we can find in what's left behind: DNA metabarcoding of semi-aquatic insect exuviae

This study shows that DNA metabarcoding of exuviae can identify more insect orders and higher diversity than emergence traps in freshwater habitats.

eDNA sampling systems for salmon ecosystem monitoring

This study develops and tests modular eDNA sampling systems that enable high filtration volumes and rapid sample collection, demonstrating their utility for ecosystem monitoring in diverse aquatic environments.

Safeguarding Iguana diversity: Enabling rapid and low-effort tracking of non-native iguanas through terrestrial eDNA innovations

This paper develops an eDNA toolkit using KASP technology to detect native and invasive iguanas and their hybrids, enabling rapid and low-effort tracking for conservation.

A Novel Taxonomic Database for eukaryotic Mitochondrial Cytochrome Oxidase subunit I Gene (eKOI): Enhancing taxonomic resolution at community-level in metabarcoding analyses

The paper introduces eKOI, a curated mitochondrial COI gene database to improve taxonomic resolution in metabarcoding, revealing new biodiversity in protists.

Targeting terrestrial vertebrates with eDNA: Trends, perspectives, and considerations for sampling

This paper reviews eDNA sampling methods for terrestrial vertebrates, identifies challenges, and proposes best practices for detection and monitoring.

Benchmarking beta-diversity measures and transfer functions for sedimentary ancient DNA

This study benchmarks beta-diversity measures and transfer functions for sedimentary ancient DNA, showing that newer ordination methods are more robust to ancient DNA noise.

Untrimmed ITS2 metabarcode sequences cause artificially reduced abundances of specific fungal taxa

The paper identifies quality biases in ITS2 metabarcoding that reduce specific fungal taxa abundances and recommends sliding window trimming to mitigate these biases.

Unveiling the Mystery of the Petroleum Genome Archive: Paleofauna Activities, Geological History, and aDNA Identification Methods in Nanyang Oilfield

This study extracts and classifies DNA fragments from petroleum samples, revealing genetic insights into ancient environments and human history, while challenging traditional aDNA methods.

Performance of eDNA capture methods for monitoring fish biodiversity in a hyper-tidal estuary

This study compares eDNA filtering methods for fish biodiversity monitoring in estuaries, finding that 0.45 µm filters yield the highest species richness and consistency.

The use of iconPCR for 16S library preparation improves data quality and workflow

The paper introduces iconPCR, a novel PCR technology that improves data quality and workflow by ensuring uniform amplification across reactions, leading to more accurate microbial community analysis.

Characterisation of coastal reef fish assemblages across an estuarine-urbanisation gradient using underwater visual survey and environmental DNA metabarcoding

The paper characterizes coastal reef fish diversity across an estuarine-urbanisation gradient using underwater visual surveys and environmental DNA metabarcoding, finding reduced richness in highly turbid areas and novel species detection.

AmpliPiper: A versatile amplicon-seq analysis tool for multilocus DNA barcoding

AmpliPiper is a software pipeline for analyzing multilocus amplicon-seq data, enabling accurate and sensitive DNA barcoding with Oxford Nanopore sequencing.

mbctools: A User-Friendly Metabarcoding and Cross-Platform Pipeline for Analyzing Multiple Amplicon Sequencing Data across a Large Diversity of Organisms

mbctools is a cross-platform pipeline for metabarcoding analysis that simplifies amplicon sequencing data processing with a menu-driven interface and integrates VSEARCH for diverse tasks.

Host-Exclusive Primer Design Enables Effective Metabarcoding via Nanopore Long-Read Sequencing

The paper develops a host-exclusive primer design workflow for long-read metabarcoding, enabling efficient amplification of fungal rDNA from mixed DNA samples.

NAMERS: a purpose-built reference DNA sequence database to support applied eDNA metabarcoding

NAMERS provides a curated DNA sequence database to improve eDNA metabarcoding workflows by offering high-quality reference sequences for freshwater fish in British Columbia.