Environmental DNA in Biodiversity Studies

Forensics and DNA Barcodes - Do Identification Errors Arise in the Lab or in the Sequence Libraries?

This study investigates whether misidentifications in DNA barcoding of insect species stem from reference libraries or query sequences, finding that errors originated from the latter and proposing a workflow to reduce them.

Environmental DNA analysis shows high potential as a tool for estimating intraspecific genetic diversity in a wild fish population

This study demonstrates that eDNA analysis can accurately detect haplotypes in wild fish populations, comparable to traditional capture-based methods.

PriSeT: Efficient De Novo Primer Discovery

PriSeT is a tool for discovering optimal primer sets for DNA metabarcoding, balancing taxonomic coverage and resolution by analyzing reference sequences.

PEMA: from the raw .fastq files of 16S rRNA and COI marker genes to the (M)OTU-table, a thorough metabarcoding analysis

PEMA streamlines metabarcoding analysis by containerizing tools for 16S rRNA and COI data, enabling efficient and customizable processing pipelines.

Identifying spawning activity in aquatic species based on environmental DNA spikes

The paper demonstrates that spikes in environmental DNA (eDNA) concentration can indicate spawning activity in aquatic species, specifically showing that eDNA spikes are caused by sperm release during spawning.

On the impact of contaminants on the accuracy of genome skimming and the effectiveness of exclusion read filters

The paper evaluates how contaminant DNA affects genome skimming accuracy and proposes a filtering method using Kraken-II to improve sample identification.

Combining metabarcoding and morphological approaches to identify phytoplankton taxa associated with harmful algal blooms

The paper evaluates the effectiveness of combining morphological and molecular methods for identifying harmful algal bloom taxa, finding that multiple-marker metabarcoding outperforms morphology.

Rapid assessment of phytoplankton assemblages using Next Generation Sequencing - Barcode of Life database: a widely applicable toolkit to monitor biodiversity and harmful algal blooms (HABs)

The paper develops a molecular toolset using DNA barcoding and NGS to rapidly assess phytoplankton communities, focusing on harmful algal blooms and toxin-producing cyanobacteria.

Optimizing an environmental DNA protocol for monitoring threatened Chinook Salmon in the San Francisco Estuary: balancing sensitivity, cost and time.

The paper evaluates eDNA protocols for Chinook Salmon monitoring, finding a method that balances time, cost, and DNA yield in the San Francisco Estuary.

Beyond traditional biodiversity fish monitoring: environmental DNA metabarcoding and simultaneous underwater visual census detect different sets of a complex fish community at a marine biodiversity hotspot

The paper compares eDNA metabarcoding and underwater visual census for fish community detection in marine environments, finding they identify different taxa due to differences in detection capabilities and reference database limitations.

MetaCurator: A hidden Markov model-based toolkit for extracting and curating sequences from taxonomically-informative genetic markers

MetaCurator curates reference sequences for genetic markers by trimming and dereplicating sequences, improving taxonomic characterization in metagenomic studies.

COI metabarcoding primer choice affects richness and recovery of indicator taxa in freshwater systems

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.

Enhancing DNA metabarcoding performance and applicability with bait capture enrichment and DNA from conservative ethanol

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.

Environmental DNA (eDNA) metabarcoding of pond water as a tool to survey conservation and management priority mammals

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.

Understanding PCR Processes to Draw Meaningful Conclusions from Environmental DNA Studies

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.

Detection of introduced and resident marine species using environmental DNA metabarcoding of sediment and water

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

A validated workflow for rapid taxonomic assignment and monitoring of a national fauna of bees (Apiformes) using high throughput barcoding

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

Limited dispersion and quick degradation of environmental DNA in fish ponds inferred by metabarcoding

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.

A rapid and accurate MinION-based workflow for tracking species biodiversity in the field

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.

Field application of an eDNA assay for the endangered white-clawed crayfish Austropotamobius pallipes

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.

Evaluating intraspecific genetic diversity of a fish population using environmental DNA: An approach to distinguish true haplotypes from erroneous sequences

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

Environmental (e)DNA detection of the invasive pink salmon Oncorhynchus gorbuscha during the 2017 Norwegian invasion

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.

Influence of Preservation Methods, Sample Medium and Sampling Time on eDNA Recovery in a Neotropical River

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.

Anacapa Toolkit: an environmental DNA toolkit for processing multilocus metabarcode datasets

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

Using eDNA to biomonitor the fish community in a tropical oligotrophic lake

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.

Comprehensive biodiversity analysis via ultra-deep patterned flow cell technology: a case study of eDNA metabarcoding seawater

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

An efficient and robust laboratory workflow and tetrapod database for larger scale eDNA studies

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

Environmental DNA: a new low-cost monitoring tool for pathogens in salmonid aquaculture.

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.

DNA metabarcoding from sample fixative as a quick and voucher preserving biodiversity assessment method

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.

Evaluating metabarcoding to analyse diet composition of species foraging in anthropogenic landscapes using Ion Torrent and Illumina sequencing

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.