Environmental DNA in Biodiversity Studies

This study shows that COI primer choice affects arthropod richness and indicator taxa recovery in freshwater samples, suggesting multiple primer sets should be used for maximum diversity detection.

This study improves DNA metabarcoding by using bait capture enrichment and ethanol-extracted DNA, showing better accuracy and efficiency compared to traditional PCR and bulk DNA methods.

This study evaluates eDNA metabarcoding for detecting terrestrial mammals in pond water, finding uneven distribution in natural ponds and detection of species missed by other methods.

This study uses simulations to understand how PCR processes affect species detection in eDNA studies and finds that proportional read indices accurately reflect taxon biomass when amplification efficiency is high.

This study compares eDNA metabarcoding of sediment and water samples to detect marine species, finding greater diversity in sediment and detecting non-indigenous species.

The paper develops a high-throughput DNA barcoding workflow for bee species identification, revealing molecular entities and potential contaminants in a UK bee fauna.

This study uses eDNA metabarcoding to show that eDNA from introduced fish species peaks within days and degrades quickly, indicating localized and transient eDNA signals in ponds.

This paper introduces a portable workflow for on-site DNA barcoding using MinION sequencing and ONTrack pipeline, achieving high accuracy and low computational demand for field biodiversity tracking.

This paper develops an eDNA assay using COI gene primers and MGB probe for detecting the endangered white-clawed crayfish in water samples, showing its effectiveness in lotic systems.

This study evaluates methods to reduce false positive haplotypes in eDNA sequencing data by combining denoising and low detection rate filtering.

The paper develops eDNA detection methods for pink salmon in Norway and finds they can detect the species during spawning, suggesting potential establishment of odd-year populations.

This study evaluates how preservation methods, sample medium, and sampling time affect eDNA recovery for fish detection in a Neotropical river, finding that cooling water samples outperforms surfactant preservation.

The paper introduces Anacapa, a toolkit for processing multilocus eDNA metabarcoding data, enabling comprehensive reference database creation and accurate taxonomic assignment.

This study uses eDNA to survey fish and vertebrate communities in a tropical lake, finding new species records and confirming methods for detecting invasive species.

This study compares sequencing depth and platform performance in eDNA metabarcoding, finding that NovaSeq detects more biodiversity than MiSeq even at equivalent sequencing depths.

The paper presents a lab workflow and bioinformatic pipeline to improve eDNA metabarcoding accuracy by reducing contamination and taxonomic mis-assignment risks.

This study evaluates the accuracy and cost-effectiveness of Ion Torrent sequencing for eDNA monitoring in aquaculture, finding it comparable to Illumina for detecting pathogens and microalgae.

This paper tests a non-destructive DNA metabarcoding method using ethanol fixative to assess biodiversity, finding it effective for some taxa but lacking for others.

The paper evaluates DNA metabarcoding using Ion Torrent and Illumina sequencing to identify diet composition in domestic cats, finding MiSeq more sensitive and reproducible for detecting food items.

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

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

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.

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.

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

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.

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.

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.

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.

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

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