Environmental DNA in Biodiversity Studies

DnoisE: Distance denoising by Entropy. An open-source parallelizable alternative for denoising sequence datasets

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

Airborne environmental DNA for terrestrial vertebrate community monitoring

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

Dealing with the promise of metabarcoding in mega-event biomonitoring: EXPO2015 unedited data

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

Metabarcoding malaise trap plant components enables monitoring the diversity of plant-insect interactions

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

Revision and annotation of DNA barcode records for marine invertebrates: report of the 8th iBOL conference hackathon

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

A two-step metagenomics approach for prey identification from the blood meals of common vampire bats (Desmodus rotundus)

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.

Targeted Next Generation Sequencing of environmental DNA improves detection and quantification of invasive European green crab (Carcinus maenas)

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.

A DNA barcode database for the woody plants of Japan

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

eDNA Captures Microhabitat Partitioning in a Kelp Forest Ecosystem

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.

Bacteria are everywhere, even in your COI marker gene data!

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.

A multi-gene region targeted capture approach to detect plant DNA in environmental samples: A case study from coastal environments

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

Efficacy and accuracy responses of DNA mini-barcodes in species identification under a supervised machine learning approach

This study evaluates the effectiveness of DNA mini-barcodes for species identification using supervised machine learning and determines the optimal length for accuracy.

Ferries and environmental DNA: underway sampling from commercial vessels provides new opportunities for systematic genetic surveys of marine biodiversity

This study demonstrates the feasibility of using commercial ferries to collect marine eDNA samples, enabling systematic biodiversity surveys in hard-to-reach areas.

The potential of aquatic haematophagous, liquidosomatophagous and macrophagous leeches as a tool for iDNA characterisation

This study uses DNA metabarcoding to analyze the diet of non-haemadipsid leeches and assess their potential for vertebrate and invertebrate monitoring through iDNA.

Towards the extended barcode concept: Generating DNA reference data through genome skimming of danish plants

The paper generates DNA reference data for 184 Danish plant species using genome skimming, enhancing molecular identification capabilities and improving species resolution in metagenomic studies.

Environmental DNA from a small sample of reservoir water can tell volumes about its biodiversity.

The paper evaluates eDNA metabarcoding in a reservoir to assess biodiversity, finding it detects many taxa including previously unreported species and provides insights into fish population genetics.

Utility of Occupancy Models with Environmental DNA (eDNA) fromOlympic Coast National Marine Sanctuary

The paper evaluates occupancy models with eDNA to estimate species presence and optimal sampling design in Olympic Coast National Marine Sanctuary.

Endpoint PCR coupled with capillary electrophoresis (celPCR) provides sensitive and quantitative measures of environmental DNA in singleplex and multiplex reactions

This study compares the sensitivity of endpoint PCR with capillary electrophoresis (celPCR) to digital PCR (dPCR) for quantifying environmental DNA in singleplex and multiplex reactions.

Beyond fish eDNA metabarcoding: Field replicates disproportionately improve the detection of stream associated vertebrate species

This paper shows that increasing field replicates improves detection of non-fish vertebrates in stream eDNA metabarcoding, while fish detection increases less.

Non-invasive surveys of mammalian viruses using environmental DNA

The paper detects and identifies known and novel mammalian viruses from environmental DNA and invertebrate-derived DNA using hybridization capture and sequencing.

Profile hidden Markov model sequence analysis can help remove putative pseudogenes from DNA barcoding and metabarcoding datasets

The paper develops a method using HMM profile analysis to identify and remove pseudogenes from COI metabarcode datasets, improving accuracy in DNA barcoding.

eDNA metabarcoding outperforms traditional fisheries sampling and reveals fine-scale heterogeneity in a temperate freshwater lake

The paper compares eDNA metabarcoding with traditional fishing methods in a freshwater lake, finding eDNA more efficient at detecting species diversity and revealing spatial patterns.

CONSTAX2: Improved taxonomic classification of environmental DNA markers

CONSTAX2 improves taxonomic classification of environmental DNA markers by integrating BLAST-based classifiers and enhancing performance metrics and usability.

Linked machine learning classifiers improve species classification of fungi when using error-prone long-reads on extended metabarcodes

This paper demonstrates that linked machine learning classifiers improve species classification of fungi using error-prone long-reads on extended metabarcodes, achieving high recall and low false positives.

Assessment of current taxonomic assignment strategies for metabarcoding eukaryotes

This study evaluates seven taxonomic assignment methods for metabarcoding eukaryotes using mock communities, finding that BLAST top hit performs competitively when optimized and that reference database quality impacts accuracy.

A flexible pipeline combining clustering and correction tools for prokaryotic and eukaryotic metabarcoding

The paper develops a flexible metabarcoding pipeline for prokaryotic and eukaryotic data, showing clustering and LULU-curation improve biodiversity inventory reliability.

Environmental DNA sampling provides new management strategies for vernal pool branchiopods in California

The paper develops qPCR-based eDNA assays to monitor vernal pool branchiopods, achieving high detection rates compared to traditional methods.

To denoise or to cluster? That is not the question. Optimizing pipelines for COI metabarcoding and metaphylogeography

The paper compares denoising and clustering methods for COI metabarcoding, arguing they are complementary and should be used together to better capture biodiversity information.

debar, a sequence-by-sequence denoiser for COI-5P DNA barcode data

debar is an R package that denoises COI-5P DNA barcode data using a profile hidden Markov model, reducing indel errors by 75-94% with a low false correction rate.

A validation scale to determine the readiness of environmental DNA assays for routine species monitoring

The paper introduces a 5-level validation scale to assess the readiness of eDNA assays for species monitoring, showing most assays are inadequately validated.