Environmental DNA in Biodiversity Studies

EukRibo provides a curated 18S rDNA database for accurate taxonomic annotation of environmental metabarcoding data, focusing on eukaryotic diversity.

This paper creates rbcL and trnL DNA barcode reference datasets for plants in semi-arid eastern South African savannas to improve metabarcoding accuracy.

MetaWorks provides a bioinformatic pipeline for processing multi-marker metabarcoding data across different domains of life, supporting various markers and taxonomic assignments.

This study shows that environmental DNA can effectively detect common haplotypes in blackfoot pua but rarely captures rare ones, supporting its use for non-invasive population genetic monitoring.

The paper tests metabarcoding for elasmobranch monitoring using published primers and identifies practical constraints and adjustments needed for effective application.

This paper presents a non-invasive molecular pipeline using fecal DNA to generate whole genome and metagenomic data for African savanna elephants, demonstrating its utility for conservation.

This study uses environmental DNA metabarcoding to track the spatial and temporal patterns of Arctic charr spawning in a lake, confirming its effectiveness compared to traditional methods.

This study compares the accuracy and efficiency of DNA barcode sequencing using Oxford Nanopore Technologies and Pacific Biosciences, finding ONT's R10 & Q20+ chemistry combination provides the highest success rate.

This study optimises DNA isolation from marine sponges for metabarcoding, finding that blotting tissue dry and using a non-commercial protocol improves taxon recovery and sequence reads.

The paper uses DNA metabarcoding to detect environmental gradients in an urban harbour, showing greater variation in species rank assessments compared to morphological methods.

This paper uses convolutional neural networks to process eDNA metabarcoding data, achieving faster speeds than OBITools while maintaining comparable accuracy.

This study evaluates how shotgun metagenomics captures composition and biomass in artificial soil invertebrate communities, showing taxon-specific biases and the influence of reference genome properties.

This study evaluates the use of universal primers as capture probes to isolate or remove DNA from eDNA samples, finding that COI capture probes fail to exclude bacterial DNA while 16S capture misses metazoans.

This study compares three preservation protocols for diatom samples over different storage durations, finding that DNA quality and diversity are largely unaffected, but rare taxa vary, highlighting the importance of method choice for detecting low-density species.

This paper develops and validates an eDNA assay to detect sea lamprey larvae in river sediments, showing it can effectively detect low-abundance larvae.

This study uses eDNA metabarcoding to assess nearshore fish communities in Southeast Alaska, finding that habitat type significantly influences species richness and composition, while tide effects are more subtle and habitat-dependent.

The paper describes a portable sequencing pipeline for detecting harmful algal blooms using environmental DNA from Lake Erie, showing significant differences in HAB-associated taxa abundance before and after a bloom.

This paper introduces 3D-printed hydroxyapatite samplers for passive environmental DNA collection, showing they efficiently recover DNA but with variable results.

This paper compares two DNA extraction methods for metabarcoding Malaise trap samples, finding that wet material processing is more efficient and less prone to contamination.

DnoisE is a denoising tool for sequence datasets that uses codon entropy to merge erroneous reads with correct ones, improving accuracy for coding markers.

This study demonstrates that airborne environmental DNA can detect terrestrial vertebrate taxa, offering a new method for biodiversity monitoring.

The paper evaluates DNA metabarcoding's effectiveness in monitoring biodiversity changes during the EXPO2015 mega-event using air and water samples.

This study uses DNA metabarcoding to analyze plant traces in Malaise trap samples, revealing insect-plant interactions and detecting rare and neophyte species.

The paper curates DNA barcode records for marine invertebrates, identifying and tagging problematic records in BOLD with specific annotations.

This study uses a two-step metagenomic approach to accurately identify prey from common vampire bat blood meals using shotgun sequencing and validates results with metabarcoding.

This study introduces and validates a targeted next generation sequencing (tNGS) method for eDNA analysis, showing improved detection and quantification of invasive European green crab compared to qPCR.

The paper develops a DNA barcode database for Japanese woody plants, covering 834 species and showing high identification rates using chloroplast DNA regions.

The paper examines how eDNA signatures vary across depth and space in a kelp forest, showing microhabitat partitioning and temporal changes in marine vertebrate communities.

The paper introduces DARN, a tool to analyze COI amplicon data, revealing that bacterial and archaeal sequences are often present in eDNA samples and should be included in reference databases.

The paper develops a multi-gene targeted capture method to improve species-level identification of flowering plants in environmental DNA samples.