Environmental DNA in Biodiversity Studies

This study compares eDNA filtering methods for fish biodiversity monitoring in estuaries, finding that 0.45 µm filters yield the highest species richness and consistency.

The paper introduces iconPCR, a novel PCR technology that improves data quality and workflow by ensuring uniform amplification across reactions, leading to more accurate microbial community analysis.

The paper characterizes coastal reef fish diversity across an estuarine-urbanisation gradient using underwater visual surveys and environmental DNA metabarcoding, finding reduced richness in highly turbid areas and novel species detection.

AmpliPiper is a software pipeline for analyzing multilocus amplicon-seq data, enabling accurate and sensitive DNA barcoding with Oxford Nanopore sequencing.

mbctools is a cross-platform pipeline for metabarcoding analysis that simplifies amplicon sequencing data processing with a menu-driven interface and integrates VSEARCH for diverse tasks.

The paper develops a host-exclusive primer design workflow for long-read metabarcoding, enabling efficient amplification of fungal rDNA from mixed DNA samples.

The paper develops a hierarchical model to better understand eDNA fate and transport dynamics, particularly in low concentration samples, and provides evidence of eDNA removal rates and inhibitor effects.

NAMERS provides a curated DNA sequence database to improve eDNA metabarcoding workflows by offering high-quality reference sequences for freshwater fish in British Columbia.

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.

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.

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

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

This study uses environmental DNA to characterize cetacean communities and their prey in coastal waters, finding similar results to visual surveys and identifying year-round presence.

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

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.

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

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

This paper develops a DNA-based index using ancient sediment DNA to assess past and present phytoplankton dominance in the Baltic Sea, revealing historical shifts in species composition.

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

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

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

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

This study identifies cost-effective primer pairs and develops a tool to enhance eDNA-based monitoring of freshwater biodiversity.

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.

The paper assesses freshwater biodiversity in the Lower Rhine using morphological and molecular methods, finding discrepancies between sequencing and morphotype richness, and highlighting limitations in reference databases.

This paper develops a DNA metabarcoding method to analyze fish stomach contents, improving trophic interaction data collection for ecosystem-based fisheries management.

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.

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

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.