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Increasing confidence for discerning species and population compositions from metabarcoding assays of environmental samples: case studies of fishes in the Laurentian Great Lakes and Wabash River

https://doi.org/10.3897/mbmg.4.53455

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Organic matter reduces the amount of detectable environmental DNA in freshwater

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Temporal and spatial variation in distribution of fish environmental DNA in England’s largest lake

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Analysis of a coastal North Sea fish community: Comparison of aquatic environmental DNA concentrations to fish catches

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Maximizing fish detection with eDNA metabarcoding

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Mitochondrial DNA molecules and virtual number of mitochondria per cell in mammalian cells

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Representing biodiversity: Data and procedures for identifying priority areas for conservation

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Early detection of invasive species in marine ecosystems using high-throughput sequencing: technical challenges and possible solutions

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The ecology of environmental DNA and implications for conservation genetics

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Diagnostics based on nucleic acid sequence variant profiling: PCR, hybridization, and NGS approaches

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Comparison of environmental DNA metabarcoding and conventional fish survey methods in a river system

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Detecting aquatic invasive species in bait and pond stores with targeted environmental (e)DNA high-throughput sequencing metabarcode assays: Angler, retailer, and manager implications

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From molecules to management: Adopting DNA-based methods for monitoring biological invasions in aquatic environments

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Community and population indicators of ecosystem health: targeting links between levels of biological organisation

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Stream Transport and Retention of Environmental DNA Pulse Releases in Relation to Hydrogeomorphic Scaling Factors

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Environmental Conditions Influence eDNA Persistence in Aquatic Systems

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Why biodiversity surveys are good value

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Biodiversity hotspots for conservation priorities

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DADA2: High-resolution sample inference from Illumina amplicon data

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Population characteristics of a large whale shark aggregation inferred from seawater environmental DNA

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Environmental DNA reveals quantitative patterns of fish biodiversity in large rivers despite its downstream transportation

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Optimizing environmental DNA sampling effort for fish inventories in tropical streams and rivers

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Introduction: Population Biology, Evolution, and Control of Invasive Species

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Sequence-specific error profile of Illumina sequencers

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MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species

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Water, water everywhere: environmental DNA can unlock population structure in elusive marine species

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Evaluating intraspecific genetic diversity of a fish population using environmental DNA: An approach to distinguish true haplotypes from erroneous sequences

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Unlocking biodiversity and conservation studies in high‐diversity environments using environmental DNA (eDNA): A test with Guianese freshwater fishes

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Particle size distribution and optimal capture of aqueous macrobial eDNA

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Assessing the cost‐efficiency of environmental DNA sampling

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Scrutinizing key steps for reliable metabarcoding of environmental samples

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ANALYZING TABLES OF STATISTICAL TESTS

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Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows

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Next‐generation monitoring of aquatic biodiversity using environmental DNA metabarcoding

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Assessing vertebrate biodiversity in a kelp forest ecosystem using environmental DNA

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Environmental DNA metabarcoding of lake fish communities reflects long‐term data from established survey methods

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Genetic patterns across an invasion's history: a test of change versus stasis for the Eurasian round goby in North America

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Environmental DNA metabarcoding: Transforming how we survey animal and plant communities

inferredcites →https://doi.org/10.1111/mec.15060openalex-snapshot

DNA metabarcoding—Need for robust experimental designs to draw sound ecological conclusions

inferredcites →https://doi.org/10.1111/mec.15382openalex-snapshot

eDNA metabarcoding survey reveals fine‐scale coral reef community variation across a remote, tropical island ecosystem

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Geographic Distribution of Endangered Species in the United States

inferredcites →https://doi.org/10.1139/cjfas-2016-0306openalex-snapshot

Fish community assessment with eDNA metabarcoding: effects of sampling design and bioinformatic filtering

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An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform

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Illumina error profiles: resolving fine-scale variation in metagenomic sequencing data

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Unique, dual-indexed sequencing adapters with UMIs effectively eliminate index cross-talk and significantly improve sensitivity of massively parallel sequencing

inferredcites →https://doi.org/10.1186/s12866-015-0450-4openalex-snapshot

Phasing amplicon sequencing on Illumina Miseq for robust environmental microbial community analysis

inferredcites →https://doi.org/10.1371/journal.pone.0088786openalex-snapshot

Transport Distance of Invertebrate Environmental DNA in a Natural River

inferredcites →https://doi.org/10.1371/journal.pone.0157366openalex-snapshot

Spatial Representativeness of Environmental DNA Metabarcoding Signal for Fish Biodiversity Assessment in a Natural Freshwater System

inferredcites →https://doi.org/10.1371/journal.pone.0165252openalex-snapshot

Environmental DNA from Seawater Samples Correlate with Trawl Catches of Subarctic, Deepwater Fishes

inferredcites →https://doi.org/10.1371/journal.pone.0175186openalex-snapshot

Aquatic environmental DNA detects seasonal fish abundance and habitat preference in an urban estuary

inferredcites →https://doi.org/10.1371/journal.pone.0177643openalex-snapshot

Environmental DNA (eDNA) metabarcoding assays to detect invasive invertebrate species in the Great Lakes

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Clearing muddied waters: Capture of environmental DNA from turbid waters

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Invasion genetics of the silver carp Hypophthalmichthys molitrix across North America: Differentiation of fronts, introgression, and eDNA metabarcode detection

inferredcites →https://doi.org/10.1371/journal.pone.0208592openalex-snapshot

Direct fishing and eDNA metabarcoding for biomonitoring during a 3-year survey significantly improves number of fish detected around a South East Asian reservoir

inferredcites →https://doi.org/10.1371/journal.pone.0210357openalex-snapshot

Environmental DNA metabarcoding for fish community analysis in backwater lakes: A comparison of capture methods

inferredcites →https://doi.org/10.18637/jss.v053.i09openalex-snapshot

fastcluster : Fast Hierarchical, Agglomerative Clustering Routines for R and Python

inferredcites →https://doi.org/10.3389/fmars.2016.00283openalex-snapshot

Genetic and Manual Survey Methods Yield Different and Complementary Views of an Ecosystem

inferredcites →https://doi.org/10.3389/fmars.2018.00322openalex-snapshot

Advantages and Limitations of Environmental DNA/RNA Tools for Marine Biosecurity: Management and Surveillance of Non-indigenous Species

inferredcites →https://doi.org/10.3897/mbmg.2.30457openalex-snapshot

Monitoring riverine fish communities through eDNA metabarcoding: determining optimal sampling strategies along an altitudinal and biodiversity gradient

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← backgroundhttps://doi.org/10.3897/mbmg.4.53455.suppl1zenodo-depositor-declared

Supplementary material 1 from: Snyder MR, Stepien CA (2020) Increasing confidence for discerning species and population compositions from metabarcoding assays of environmental samples: case studies of fishes in the Laurentian Great Lakes and Wabash River. Metabarcoding and Metagenomics 4: e53455.…

inferred← citeshttps://doi.org/10.1002/edn3.337openalex-snapshot

An efficient early‐pooling protocol for environmental DNA metabarcoding

inferred← citeshttps://doi.org/10.1038/s41467-024-48640-3openalex-snapshot

An integrated spatio-temporal view of riverine biodiversity using environmental DNA metabarcoding

inferred← citeshttps://doi.org/10.1111/1755-0998.13990openalex-snapshot

Testing the applicability of environmental DNA metabarcoding to landscape genetics

inferred← citeshttps://doi.org/10.1111/mec.16364openalex-snapshot

Meta‐analysis shows both congruence and complementarity of DNA and eDNA metabarcoding to traditional methods for biological community assessment

inferred← citeshttps://doi.org/10.1139/cjfas-2023-0061openalex-snapshot

Identifying early life stages of Great Lakes fishes using a metabarcoding approach

inferred← citeshttps://doi.org/10.3390/dna4010001openalex-snapshot

Evaluating Metabarcoding Markers for Identifying Zooplankton and Ichthyoplankton Communities to Species in the Salish Sea: Morphological Comparisons and Rare, Threatened or Invasive Species

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