Environmental DNA in Biodiversity Studies

The paper develops a quantitative insect metabarcoding method using COI and multilocus markers to accurately identify and quantify mosquito species in pooled samples.

This study tests if benthic kick-net sampling can be used for diatom metabarcoding, finding it comparable to traditional scraping methods and suitable for ecological monitoring.

The paper compares traditional and eDNA methods for detecting quagga mussels, finding that targeted PCR and metabarcoding outperform kick-net sampling, with qPCR being most sensitive at low densities.

This study shows that eDNA metabarcoding read counts correlate with fish biomass and abundance in ponds, and results are consistent across different DNA capture methods.

This study compares propylene glycol-based antifreeze and ethanol as preservatives for DNA metabarcoding of benthic arthropods, finding antifreeze provides similar taxonomic coverage with simpler processing.

The paper develops a metabarcoding workflow to identify vulture species, sex, and diet from fecal samples, finding domestic livestock dominate the diet.

The paper reports mitochondrial genomes of 11 aquatic macroinvertebrate species from Cyprus, highlighting gaps in reference databases for species identification.

Alfie is a Python package that classifies COI DNA barcode sequences into taxonomic kingdoms using k-mer frequencies and a neural network classifier with over 99% accuracy.

This paper describes a method combining automatic light traps and DNA metabarcoding to assess nocturnal flying insect communities, showing higher efficiency and taxonomic coverage compared to traditional methods.

The paper demonstrates the use of a mobile genetics lab in Madagascar to conduct in situ DNA sequencing and provide training for local scientists.

This study evaluates if DNA metabarcoding can assess mitochondrial genetic diversity changes in response to environmental stressors in river macrozoobenthic communities.

The paper uses metabarcoding to show distinct zooplankton communities in northern and southern North Sea regions, consistent with known species distributions and abundance patterns.

The paper introduces Tagsteady, a metabarcoding library preparation protocol that minimizes tag-jumps by avoiding steps that cause them, resulting in accurate sequence assignment.

The paper investigates optimal size sorting and pooling strategies for malaise trap samples to maximize taxon recovery using metabarcoding.

This study evaluates twelve COI and 16S metabarcoding primer sets for insectivorous diet analysis using in silico and empirical methods, finding primer degeneracy and amplicon length are key factors affecting detection and reliability.

The paper introduces the coil R package for cleaning, translating, and evaluating errors in COI-5P DNA barcode data, showing high accuracy in identifying technical errors but limitations in detecting biological contaminants.

CommDivMap transforms metabarcoding OTU tables into species richness maps, tested on arthropod samples from agricultural plots.

This study evaluates eDNA metabarcoding protocols for deep-sea biodiversity, finding that DNA is more reliable than RNA and larger sediment samples improve accuracy.

The paper evaluates MinION sequencing for generating accurate DNA barcode sequences from preserved and non-invasively collected wildlife samples using a clustering-based pipeline.

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.

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

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

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

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.

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

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

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.

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

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