Environmental DNA in Biodiversity Studies

Computational Evaluation of DNA Metabarcoding for Universal Diagnostics of Invasive Insect Pests

The paper evaluates COI primers for DNA metabarcoding to detect invasive insect pests, finding that mini-barcodes can effectively distinguish pests from non-pests despite taxonomic challenges.

Single-cell metabarcoding reveals biotic interactions of the Arctic calcifier Neogloboquadrina pachyderma with the eukaryotic pelagic community

This study uses single-cell metabarcoding to analyze the eukaryotic interactome of Neogloboquadrina pachyderma in Baffin Bay, revealing dominant diatom interactions and potential parasitic Syndiniales.

eDNA metabarcoding as a biomonitoring tool for marine protected areas

eDNA metabarcoding at a California marine reserve recovered 76% of diver-recorded fish species, distinguished communities 50 m apart, yet reversed the visual inside-versus-outside richness pattern.

Environmental palaeogenomic reconstruction of an Ice Age algal population

This paper uses shotgun metagenomics to reconstruct population genomic data for the algae Nannochloropsis from lake sediment samples dated to the Last Glacial Maximum.

TaxonTableTools - A comprehensive, platform-independent graphical user interface software to explore and visualise DNA metabarcoding data

TaxonTableTools provides a GUI for analysing and visualising DNA metabarcoding data, enabling users to perform ecological analyses and generate visualisations without bioinformatic expertise.

A deep learning model for fish classification base on DNA barcode

This paper introduces ESK-model, a deep learning approach for fish classification using DNA barcode data, achieving accurate family-level classification.

Hybridisation capture allows DNA damage analysis of ancient marine eukaryotes

The paper uses hybridisation capture and a new bioinformatic tool to authenticate and analyze DNA damage in ancient marine eukaryote sedaDNA, revealing DNA damage profiles of Emiliania huxleyi.

A workflow for accurate metabarcoding using nanopore MinION sequencing

This study evaluates the use of Nanopore MinION sequencing for metabarcoding, showing high accuracy with a custom pipeline and RCA amplification.

metabaR : an R package for the evaluation and improvement of DNA metabarcoding data quality

metabaR is an R package that improves DNA metabarcoding data quality by identifying artefacts, assessing filtering thresholds, and providing visualisation tools for ecological analysis.

PIMBA: a PIpeline for MetaBarcoding Analysis

PIMBA is a pipeline for DNA metabarcoding analysis that supports custom databases and integrates multiple reference databases into a user-friendly, open-source tool.

Quantitative PCR assays to detect humpback whale (Megaptera novaeangliae), shortbelly rockfish (Sebastes jordani), and common murre (Uria aalge) in marine water samples

The paper develops qPCR assays for detecting three marine species in environmental water samples, showing high sensitivity but varying specificity.

From qualitative to quantitative insect metabarcoding: an in tandem multilocus mosquito identification methodology

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

Freshwater diatom biomonitoring through benthic kick-net metabarcoding

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.

Targeted and passive environmental DNA approaches outperform established methods for detection of quagga mussels, Dreissena rostriformis bugensis in flowing water

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.

Read counts from environmental DNA (eDNA) metabarcoding reflect fish abundance and biomass in drained ponds

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.

Propylene glycol-based antifreeze as an effective preservative for DNA metabarcoding of benthic arthropods

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.

Metabarcoding for parallel identification of species, sex and diet: an application to the conservation of globally-threatened Gyps vultures

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

The mitochondrial genomes of 11 aquatic macroinvertebrate species from Cyprus

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

Alignment-free identification of COI DNA barcode data with the Python package Alfie

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.

Efficient assessment of nocturnal flying insect communities by combining automatic light traps and DNA metabarcoding

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.

Next-generation in situ conservation and educational outreach in Madagascar using a mobile genetics lab

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

Can metabarcoding resolve intraspecific genetic diversity changes to environmental stressors? A test case using river macrozoobenthos

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

Metabarcoding reveals different zooplankton communities in northern and southern areas of the North Sea

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

Tagsteady: a metabarcoding library preparation protocol to avoid false assignment of sequences to samples

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

Pooling size sorted malaise trap fractions to maximise taxon recovery with metabarcoding

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

In silico and empirical evaluation of twelve COI & 16S metabarcoding primer sets for insectivorous diet analyses

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.

coil: an R package for cytochrome C oxidase I (COI) DNA barcode data cleaning, translation, and error evaluation.

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: Modelling and mapping species richness at different spatial scales

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

An assessment of environmental metabarcoding protocols aiming at favouring contemporary biodiversity in inventories of deep-sea communities

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

MinION-based DNA barcoding of preserved and non-invasively collected wildlife samples

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