Environmental DNA in Biodiversity Studies

Particle size distribution shift and diurnal concentration changes of environmental DNA caused by fish spawning behaviour

This study examines changes in eDNA particle size distribution and concentrations during Ayu fish spawning, showing increased sperm-derived eDNA and diurnal concentration peaks, which can enhance eDNA-based spawning detection.

Diet of Andean leaf-eared mice (Phyllotis) living at extreme elevations on Atacama volcanoes: insights from metagenomics, DNA metabarcoding, and stable isotopes

The paper investigates the diet of Andean leaf-eared mice at extreme elevations using metagenomics, DNA metabarcoding, and stable isotopes, finding evidence of herbivory and potential cryptic vegetation.

Environmental DNA and wildlife camera traps uncover complimentary vertebrate visitation patterns at freshwater granite rock-holes

The paper compares eDNA metabarcoding and camera trapping to monitor vertebrate visitation in arid-lands freshwater ecosystems, finding complementary results between the methods.

Reference Sequence Browser: An R application with a User-Friendly GUI to rapidly query sequence databases

The paper introduces an R-based GUI tool called Reference Sequence Browser to efficiently query multiple genetic databases for reference sequences in eDNA studies.

Barcode 100K Specimens: In a Single Nanopore Run

This study demonstrates a cost-effective method for DNA barcoding using Oxford Nanopore Technologies, enabling the processing of 100,000 specimens per flow cell at $0.01 per specimen.

soibean: High-resolution Taxonomic Identification of Ancient Environmental DNA Using Mitochondrial Pangenome Graphs

soibean improves species-level classification of ancient environmental DNA using mitochondrial pangenome graphs, revealing new insights from archaeological datasets.

Comprehensive Sequencing of Environmental RNA from Japanese Medaka at Various Size Fractions and Comparison with Skin RNA

The paper analyzes environmental RNA from Japanese medaka at different size fractions and compares it with skin RNA to determine optimal filtration methods and sources of eRNA.

CV.eDNA: A hybrid approach to invertebrate biomonitoring using computer vision and DNA metabarcoding

The paper combines computer vision and DNA metabarcoding to improve invertebrate classification accuracy and taxonomic granularity using a hybrid approach.

tombRaider - improved species and haplotype recovery from metabarcoding data through artefact and pseudogene exclusion.

tombRaider improves species and haplotype identification in metabarcoding by removing artefacts and pseudogenes, enhancing data accuracy and reliability.

A rapid phylogeny-based method for accurate community profiling of large-scale metabarcoding datasets

The paper introduces a fast approximate likelihood method for phylogenetic assignment of DNA sequences, showing improved accuracy in taxonomic classification compared to existing methods.

Environmental DNA Surveys of Invertebrate Community on Forest Canopies Using Rainwater Analysis

This study evaluates using rainwater eDNA analysis for canopy invertebrate surveys, finding it potentially efficient but needing further validation.

Enhancing metabarcoding efficiency and ecological insights through integrated taxonomy and DNA reference barcoding: a case study on beach meiofauna

The paper improves metabarcoding efficiency for beach meiofauna by integrating DNA barcoding with morphological taxonomy, increasing sequence annotation and species-level OTU identification.

Unlocking Antarctic molecular time-capsules - recovering historical environmental DNA from museum-preserved sponges

The paper recovers historical environmental DNA (heDNA) from Antarctic sponge specimens to reconstruct past fish biodiversity and community composition.

DNA barcode developement based on chloroplast and ITS genes for species identification of endangered and threated species of Western Ghats, India

This study develops a DNA barcoding system using chloroplast and ITS genes to identify endangered species in the Western Ghats, finding high amplification rates for specific markers.

Tigers in North Dakota; Tiger Salamander (Ambystoma tigrinum) eDNA Surveying for Presence in Cattle Ponds

The paper uses eDNA sampling to detect tiger salamanders in North Dakota cattle ponds, finding presence at 5 out of 8 sites with moderate occupancy and detection probabilities.

Megabarcoding reveals a tale of two very different dark taxa along the same elevational gradient

The paper uses megabarcoding to show that two Diptera taxa have distinct spatio-temporal distributions along an elevational gradient in a temperate forest.

Rapid molecular species identification of mammalian scat samples using nanopore adaptive sampling

This paper develops a method using nanopore adaptive sampling to rapidly identify mammalian species from scat samples, achieving accurate identifications for most samples and detecting a misidentification in one case.

Identification of Large Japanese field mouse Apodemus speciosus food plant resources in an industrial green space using DNA metabarcoding

The paper uses DNA metabarcoding to identify food plant resources of Apodemus speciosus in an industrial green space, finding 72 plant taxa with comprehensive coverage.

Recovering short DNA fragments from minerals and marine sediments: a comparative study evaluating lysis and isolation approaches

This study evaluates DNA extraction methods from marine sediments, finding that lysis buffer choice significantly affects DNA recovery and fragment length, with EDTA and phosphate buffers performing best.

PIMENTA: PIpeline for MEtabarcoding through Nanopore Technology used for Authentication

PIMENTA is a Nanopore DNA metabarcoding pipeline that improves taxonomic identification accuracy and efficiency through optimized processing and parallelization.

Picturing plant biodiversity from airborne environmental DNA.

This study demonstrates that airborne environmental DNA sampling can detect plant biodiversity in a botanical garden, with flowering plants and trees being more detectable than non-flowering herbs.

Experimental evaluation of environmental DNA methods for detection of a rare fish in turbid water

This study evaluates eDNA detection methods in turbid water, finding that filter type and prefiltration impact detection success for a rare fish species.

A CRISPR-based strategy for targeted sequencing in biodiversity science

The paper develops a CRISPR-based method for targeted sequencing of plant DNA, showing improved sequence length and abundance estimates compared to traditional metabarcoding.

rCRUX: A Rapid and Versatile Tool for Generating Metabarcoding Reference libraries in R

rCRUX generates comprehensive metabarcoding reference libraries for user-defined loci, outperforming existing tools in creating diverse and accurate databases.

Mitochondrial genomes of Pleistocene megafauna retrieved from recent sediment layers of two Siberian lakes

The paper retrieves mitochondrial genomes of extinct Pleistocene megafauna from recent sediment layers in Siberian lakes, showing that permafrost thawing affects aeDNA preservation and stratigraphic signal.

THAPBI PICT - a fast, cautious, and accurate metabarcoding analysis pipeline

THAPBI PICT is a metabarcoding pipeline that processes Illumina paired-end reads, reduces noise, and classifies sequences using a curated database, providing interpretable outputs for non-specialists.

Semi-automated curation and manual addition of sequences to build reliable and extensive reference databases for ITS2 vascular plant DNA (meta-)barcoding

The paper curates and expands reference databases for ITS2 DNA barcoding in vascular plants by automating curation and manually adding new sequences.

Distinguishing Signal from Noise: Understanding Patterns of Non-Detections to Inform Accurate Quantitative Metabarcoding

This study investigates non-detections in metabarcoding data to improve quantitative accuracy by modeling amplification biases and stochastic sampling effects.

Taxonomic identification accuracy from BOLD and GenBank databases using over a thousand insect barcodes from Colombia

The paper evaluates the accuracy of insect taxonomic identification using BOLD and GenBank databases with 1160 Colombian insect sequences, finding BOLD more accurate overall.

euka: Robust detection of eukaryotic taxa from modern and ancient environmental DNA using pangenomic reference graphs.

euka improves taxonomic identification and abundance estimation in ancient eDNA by using pangenomic graphs and maximum-likelihood methods, outperforming existing tools.