Environmental DNA in Biodiversity Studies

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

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.

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.

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

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.

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