Environmental DNA in Biodiversity Studies

PIMENTO: A PrIMEr infereNce TOolkit to facilitate large-scale calling of amplicon sequence variants

PIMENTO identifies and removes primer sequences from amplicon sequencing data to enable large-scale variant calling.

A ground surface rolling method for detecting environmental DNA of terrestrial animals

The paper introduces a ground surface rolling method for collecting environmental DNA from terrestrial habitats, detecting 53 bird and mammal species with 92% accuracy compared to camera surveys.

Unraveling long-term trends and drivers of fish biodiversity change using environmental DNA metabarcoding of archived samples

The paper uses environmental DNA metabarcoding of archived samples to track long-term fish biodiversity trends and identify drivers of change across six European river systems over 17 years.

Detecting the Indo-Pacific finless porpoises (Neophocaena phocaenoides) in Hong Kong waters using environmental DNA

This study detects Indo-Pacific finless porpoise eDNA in Hong Kong waters using qPCR and metabarcoding, showing comparable detection rates and potential for cetacean monitoring.

Sorting States of Environmental DNA Reveals State-Specific Biodiversity Signals and Transport Patterns in Eight Alpine Watersheds

This study sorts eDNA into three states to analyze biodiversity and transport patterns in alpine watersheds, finding membrane-bound eDNA dominates diversity and transport.

Towards a global barcode reference library for subterranean fauna

The paper presents a barcode reference library (BRL) for subterranean fauna, demonstrating its effectiveness in eDNA metabarcoding by identifying species not found in GenBank.

The future is faeces: Using faecal genomic sequencing to understand dietary choices of an endangered arboreal marsupial

This study uses faecal genomic sequencing to identify dietary components of greater gliders, revealing new plant species in their diet and highlighting conservation implications.

DNA metabarcoding and environmental DNA across Brazilian biomes: trends, challenges, and conservation applications

This paper reviews DNA metabarcoding and eDNA applications in Brazilian biomes, highlighting trends, challenges, and the need for investment in infrastructure and collaboration.

Unlocking karst biodiversity with eDNA: a validated qPCR toolkit for discovery and monitoring the worlds largest cavefish radiation (Cyprinidae: Sinocyclocheilus)

The paper develops and validates a qPCR toolkit for detecting and identifying Sinocyclocheilus cavefish using eDNA, showing high specificity and detection limits in both lab and field settings.

Metabarcoding of sedimentary ancient DNA reveals centuries of species turnover and introductions of non-indigenous species in a highly urbanised estuary

This study uses sedimentary ancient DNA metabarcoding to track species turnover and non-indigenous species introductions in an urban estuary over centuries.

Noninvasive reconstruction of complete mitochondrial genomes from aquatic environmental DNA using PCR-free long-read sequencing

This paper develops a long-read sequencing workflow to reconstruct complete mitochondrial genomes from environmental DNA, demonstrating effectiveness through both PCR-free and PCR-based approaches.

A case for multi-gear assessments: Detection probabilities of nearshore fish with eDNA and seine nets vary by functional traits

The paper compares detection probabilities of nearshore fish using eDNA and seine nets, finding trait-specific selectivity differences.

Environmental DNA reveals temporal and spatial variability of invertebrate communities in arid-lands ephemeral water bodies

The paper uses environmental DNA to study invertebrate communities in arid-land rock-holes, finding seasonal and spatial variability in species richness and composition.

Tiger diet in Ranthambore Tiger Reserve: how do metabarcoding and mechanical sorting compare?

This study compares DNA metabarcoding and mechanical sorting for analyzing tiger diets in Ranthambore Tiger Reserve, finding metabarcoding more effective at detecting prey diversity and biomass.

Advancing ecological assessment: The integration of eDNA metabarcoding into an estuarine fish index

This study integrates eDNA metabarcoding into an estuarine fish index to assess ecological status, finding that eDNA detects higher species richness but differs in species assemblages compared to bottom trawling.

Modeling cetacean eDNA distribution along the Washington coast using metabarcoding from opportunistic samples and generalized additive models

The paper uses eDNA metabarcoding and generalized additive models to model cetacean distribution along the Washington coast, finding spatial patterns consistent with historical records.

Linking sediment porosity to taxon-specific patterns of eDNA preservation in a temperate, semi-enclosed bay

The paper examines how sediment porosity affects taxon-specific eDNA preservation in a temperate bay, finding contrasting preservation patterns across different phyla.

Sensitive environmental DNA methods for low-risk surveillance of at-risk bumble bees

The paper demonstrates that environmental DNA (eDNA) methods can sensitively detect bumble bee species, including rare ones, comparable to traditional netting surveys.

Phylo-MIP: Phylogeny-based Molecular Identification Pipeline for DNA metabarcoding, and assessment of insect communities in subalpine river ecosystems

Phylo-MIP improves species identification in eDNA metabarcoding by integrating phylogenetic analysis, increasing detected species by 28% over BLAST-based methods.

HAPP: High-Accuracy Pipeline for Processing deep metabarcoding data

HAPP improves deep metabarcoding data processing by enhancing signal-to-noise ratio through four steps, showing significant performance improvements over existing methods.

Detection of environmental DNA of the Indo-Pacific humpback dolphins in Hong Kong waters using quantitative PCR

This study develops a qPCR assay to detect Indo-Pacific humpback dolphin eDNA in Hong Kong waters, revealing their presence in specific coastal regions.

Quantitative, Multispecies Monitoring at a Continental Scale

The paper combines qPCR and metabarcoding to estimate eDNA quantities for multiple fish species, creating spatial maps that align with known ecological niches and identify biodiversity hotspots.

Benchmarking fungal species classification using Oxford Nanopore Technologies long-read ITS metabarcodes

This study benchmarks species classification of fungal ITS metabarcodes using ONT long-read sequencing, showing that threshold-based and machine learning classifiers outperform others in accuracy and consistency.

Surveying Tropical Faunal Diversity via Airborne DNA Analyses

This study evaluates airborne eDNA metabarcoding for assessing tropical arthropod and vertebrate diversity, finding it comparable to traditional methods and highlighting the importance of standardized sampling effort.

Evaluation of nanopore sequencing for increasing accessibility of eDNA studies in biodiverse countries

The paper evaluates nanopore sequencing for eDNA metabarcoding in Zambia, showing it can match or exceed Illumina sequencing for biodiversity assessments in remote areas.

From short to long reads: enhanced protist diversity profiling via Nanopore metabarcoding

This paper introduces BaNaNA, a pipeline for generating high-quality OTUs from Nanopore long-read sequencing data, showing its effectiveness for protist biodiversity studies and its advantages over short-read methods.

Extending sampling approaches for great crested newt (Triturus cristatus) eDNA monitoring

This study investigates extending the eDNA survey season for great crested newts and compares ethanol precipitation and filtration methods for eDNA capture.

Advancing eDNA methods for monitoring the reproduction of quagga and zebra mussels in lakes

This study evaluates eDNA methods for monitoring quagga and zebra mussel reproduction, finding that integrated water and bulk sampling are more effective than sub-surface sampling for quantifying larvae and estimating reproductive periods.

Globally unified analysis of riverine eDNA reveals common associations of fish biodiversity with drainage characteristics

This study uses global eDNA data to show how riverine fish biodiversity relates to drainage characteristics, revealing climate and human activity effects vary by biodiversity facet and catchment size.

Maximizing vegetation representation of the catchment in sedimentary DNA with targeted cores in small lakes

This study shows that central-core samples in small lakes capture more taxonomic richness than marginal samples, improving sedimentary DNA-based vegetation representation.