Environmental DNA in Biodiversity Studies

Development of environmental DNA surveillance for the threatened crucian carp (Carassius carassius)

This study develops an eDNA qPCR assay for detecting crucian carp in UK ponds and evaluates its effectiveness compared to traditional methods.

New mitochondrial primers for metabarcoding of insects, designed and evaluated using in silico methods

The paper designs and evaluates new mitochondrial primers for insect metabarcoding using in silico methods, showing improved taxonomic resolution compared to existing primers.

A novel environmental DNA (eDNA) sampling method for aye-ayes from their feeding traces

This paper tests a target capture method to retrieve mitochondrial DNA from aye-aye feeding traces, successfully obtaining near-complete genomes for population genetic monitoring.

A quantitative PCR based environmental DNA assay for detecting Atlantic salmon (Salmo salar L.)

This study develops a quantitative PCR assay to detect Atlantic salmon in water samples using species-specific primers and a MGB probe targeting the COI gene, showing its sensitivity for in situ detection.

Taxonomic identification from metagenomic and metabarcoding data using any genetic marker

The paper updates Metaxa2 to support taxonomic classification using any genetic marker for metagenomic and metabarcoding data.

Needle in a haystack? A comparison of eDNA metabarcoding and targeted qPCR for detection of the great crested newt (Triturus cristatus)

This study compares eDNA metabarcoding and targeted qPCR for detecting the great crested newt, finding qPCR more sensitive but metabarcoding with no threshold comparable at a stringent qPCR threshold.

A MinION-based pipeline for fast and cost-effective DNA barcoding

The paper develops a MinION-based pipeline for DNA barcoding that generates accurate barcodes for up to 1000 specimens per flowcell at a low cost.

Automated high throughput animal DNA metabarcode classification

The paper develops a method to classify animal DNA metabarcodes more efficiently and accurately using a large reference database and the RDP naive Bayesian classifier.

Holmes-ITS2: Consolidated ITS2 resources and search engines for plant DNA-based marker analyses

The paper develops a comprehensive ITS2 sequence database and search tools for plant species identification, providing a web service for accurate and efficient marker analysis.

A simple centrifugation protocol increases mitochondrial DNA yield 140-fold and facilitates mitogenomic studies

The paper introduces a centrifugation protocol that increases mitochondrial DNA yield 140-fold, enabling efficient sequencing of whole mitochondrial genomes for biodiversity studies.

DNA Metabarcoding For High-Throughput Monitoring Of Estuarine Macrobenthic Communities

This study demonstrates that COI metabarcoding can provide robust species-level identifications for estuarine macrobenthic communities, outperforming morphology-based methods in species richness detection.

New barcoded primers for efficient retrieval of cercozoan sequences in high-throughput environmental diversity surveys, with emphasis on worldwide biological soil crusts

The paper introduces new barcoded primers for efficient metabarcoding of Cercozoa in environmental surveys, showing high specificity and detection of diverse cercozoan sequences.

Environmental DNA metabarcoding of rivers: Not all eDNA is everywhere, and not all the time

This study shows that eDNA metabarcoding results vary with sampling time and location in rivers, highlighting the need for careful sampling design.

Metacoder: An R Package for Visualization and Manipulation of Community Taxonomic Diversity Data

Metacoder is an R package that enables parsing, manipulation, and visualization of hierarchical community taxonomic data through flexible plotting and analysis functions.

Environmental DNA Barcode Sequence Capture: Targeted, PCR-free Sequence Capture for Biodiversity Analysis from Bulk Environmental Samples

Hybridization baits pull COI barcodes straight out of bulk terrestrial and benthic samples without PCR, recovering several more arthropod orders per sample than amplicon sequencing.