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Identifying North American freshwater invertebrates using DNA barcodes: are existing COI sequence libraries fit for purpose?

https://doi.org/10.1086/696613
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What this work says

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

inferredcites →https://doi.org/10.1002/(sici)1099-0755(199807/08)8:4<617::aid-aqc255>3.0.co;2-#openalex-snapshot
River classification using invertebrates: RIVPACS applications
inferredcites →https://doi.org/10.1007/s10452-013-9460-1openalex-snapshot
The tiny mayfly in the room: implications of size-dependent invertebrate taxonomic identification for biomonitoring data properties
inferredcites →https://doi.org/10.1007/s10661-007-9749-4openalex-snapshot
Which group is best? Attributes of different biological assemblages used in freshwater biomonitoring programs
inferredcites →https://doi.org/10.1007/s10750-007-9003-7openalex-snapshot
Global diversity of rotifers (Rotifera) in freshwater
inferredcites →https://doi.org/10.1007/s10750-007-9235-6openalex-snapshot
An introduction to the Freshwater Animal Diversity Assessment (FADA) project
inferredcites →https://doi.org/10.1016/j.pt.2010.11.002openalex-snapshot
Combined effects of parasites and contaminants on animal health: parasites do matter
inferredcites →https://doi.org/10.1016/j.ympev.2006.11.021openalex-snapshot
A comprehensive DNA sequence library is essential for identification with DNA barcodes
inferredcites →https://doi.org/10.1016/j.ympev.2012.07.033openalex-snapshot
The effect of sampling from subdivided populations on species identification with DNA barcodes using a Bayesian statistical approach
inferredcites →https://doi.org/10.1016/j.ympev.2013.05.012openalex-snapshot
Barcoding in the dark?: A critical view of the sufficiency of zoological DNA barcoding databases and a plea for broader integration of taxonomic knowledge
inferredcites →https://doi.org/10.1016/s0169-5347(98)01583-3openalex-snapshot
Nematode community structure as a bioindicator in environmental monitoring
inferredcites →https://doi.org/10.1016/s1470-160x(03)00016-5openalex-snapshot
Sensitivity of aquatic insect species richness to disturbance in the Adour–Garonne stream system (France)
inferredcites →https://doi.org/10.1038/srep09687openalex-snapshot
Massively parallel multiplex DNA sequencing for specimen identification using an Illumina MiSeq platform
inferredcites →https://doi.org/10.1038/srep12162openalex-snapshot
Potential for DNA-based identification of Great Lakes fauna: match and mismatch between taxa inventories and DNA barcode libraries
inferredcites →https://doi.org/10.1046/j.1365-2427.1999.00430.xopenalex-snapshot
AusRivAS: using macroinvertebrates to assess ecological condition of rivers in Western Australia
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The biology and ecology of lotic nematodes
inferredcites →https://doi.org/10.1071/mf14173openalex-snapshot
How much wetland has the world lost? Long-term and recent trends in global wetland area
inferredcites →https://doi.org/10.1071/mf15190openalex-snapshot
Emergent technologies and analytical approaches for understanding the effects of multiple stressors in aquatic environments
inferredcites →https://doi.org/10.1071/mf16304openalex-snapshot
A DNA barcode database of Australia’s freshwater macroinvertebrate fauna
inferredcites →https://doi.org/10.1071/mf96096openalex-snapshot
A multivariate method for determining optimal subsample size in the analysis of macroinvertebrate samples
inferredcites →https://doi.org/10.1073/pnas.1406468111openalex-snapshot
Simultaneous assessment of the macrobiome and microbiome in a bulk sample of tropical arthropods through DNA metasystematics
inferredcites →https://doi.org/10.1080/03014223.2015.1011592openalex-snapshot
Assessing the diversity of New Zealand freshwater harpacticoid copepods (Crustacea: Copepoda) using mitochondrial DNA (COI) barcodes
inferredcites →https://doi.org/10.1086/674782openalex-snapshot
Does DNA barcoding improve performance of traditional stream bioassessment metrics?
inferredcites →https://doi.org/10.1086/674982openalex-snapshot
Comparison of four species-delimitation methods applied to a DNA barcode data set of insect larvae for use in routine bioassessment
inferredcites →https://doi.org/10.1086/675225openalex-snapshot
Cryptic biodiversity in streams: a comparison of macroinvertebrate communities based on morphological and DNA barcode identifications
inferredcites →https://doi.org/10.1093/molbev/msr121openalex-snapshot
MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods
inferredcites →https://doi.org/10.1093/nar/gku1216openalex-snapshot
GenBank
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Species detection using environmental DNA from water samples
inferredcites →https://doi.org/10.1098/rstb.2005.1725openalex-snapshot
Defining operational taxonomic units using DNA barcode data
inferredcites →https://doi.org/10.1098/rstb.2015.0330openalex-snapshot
A new way to contemplate Darwin's tangled bank: how DNA barcodes are reconnecting biodiversity science and biomonitoring
inferredcites →https://doi.org/10.1111/1365-2664.12300openalex-snapshot
FORUM: Ecological networks: the missing links in biomonitoring science
inferredcites →https://doi.org/10.1111/1755-0998.12236openalex-snapshot
Next‐generation DNA barcoding: using next‐generation sequencing to enhance and accelerate DNA barcode capture from single specimens
inferredcites →https://doi.org/10.1111/1755-0998.12240openalex-snapshot
Rapid and accurate taxonomic classification of insect (class Insecta) cytochrome c oxidase subunit 1 ( COI ) DNA barcode sequences using a naïve Bayesian classifier
inferredcites →https://doi.org/10.1111/icad.12123openalex-snapshot
Chironomids as indicators in freshwater ecosystems: an assessment of the literature
inferredcites →https://doi.org/10.1111/j.1096-0031.2012.00408.xopenalex-snapshot
An update on DNA barcoding: low species coverage and numerous unidentified sequences
inferredcites →https://doi.org/10.1111/j.1365-2427.2011.02724.xopenalex-snapshot
Congruence of biodiversity measures among larval dragonflies and caddisflies from three Canadian rivers
inferredcites →https://doi.org/10.1111/j.1365-294x.2012.05519.xopenalex-snapshot
Biomonitoring 2.0: a new paradigm in ecosystem assessment made possible by next‐generation DNA sequencing
inferredcites →https://doi.org/10.1111/j.1365-294x.2012.05537.xopenalex-snapshot
New environmental metabarcodes for analysing soil DNA: potential for studying past and present ecosystems
inferredcites →https://doi.org/10.1111/j.1365-294x.2012.05538.xopenalex-snapshot
Next‐generation sequencing technologies for environmental DNA research
inferredcites →https://doi.org/10.1111/j.1442-9993.1995.tb00532.xopenalex-snapshot
Biological guidelines for freshwater sediment based on BEnthic Assessment of SedimenT (the BEAST) using a multivariate approach for predicting biological state
inferredcites →https://doi.org/10.1111/j.1471-8286.2007.01678.xopenalex-snapshot
bold : The Barcode of Life Data System (http://www.barcodinglife.org)
inferredcites →https://doi.org/10.1139/cjfas-58-7-1395openalex-snapshot
Comparison of models predicting invertebrate assemblages for biomonitoring in the Fraser River catchment, British Columbia
inferredcites →https://doi.org/10.1186/1471-2164-9-214openalex-snapshot
A universal DNA mini-barcode for biodiversity analysis
inferredcites →https://doi.org/10.1186/1472-6785-11-18openalex-snapshot
When species matches are unavailable are DNA barcodes correctly assigned to higher taxa? An assessment using sphingid moths
inferredcites →https://doi.org/10.1186/1742-9994-6-30openalex-snapshot
Towards a comprehensive barcode library for arctic life - Ephemeroptera, Plecoptera, and Trichoptera of Churchill, Manitoba, Canada
inferredcites →https://doi.org/10.1371/journal.pone.0017497openalex-snapshot
Environmental Barcoding: A Next-Generation Sequencing Approach for Biomonitoring Applications Using River Benthos
inferredcites →https://doi.org/10.1371/journal.pone.0038063openalex-snapshot
A DNA Barcode Library for North American Ephemeroptera: Progress and Prospects
inferredcites →https://doi.org/10.1371/journal.pone.0125485openalex-snapshot
Molecular Barcoding of Aquatic Oligochaetes: Implications for Biomonitoring
inferredcites →https://doi.org/10.1371/journal.pone.0138432openalex-snapshot
Large-Scale Biomonitoring of Remote and Threatened Ecosystems via High-Throughput Sequencing
inferredcites →https://doi.org/10.1371/journal.pone.0157505openalex-snapshot
Large-Scale Monitoring of Plants through Environmental DNA Metabarcoding of Soil: Recovery, Resolution, and Annotation of Four DNA Markers
inferredcites →https://doi.org/10.1899/07-175.1openalex-snapshot
Data quality, performance, and uncertainty in taxonomic identification for biological assessments
inferredcites →https://doi.org/10.1899/0887-3593(2006)025[0730:ftnona]2.0.co;2openalex-snapshot
Functional trait niches of North American lotic insects: traits-based ecological applications in light of phylogenetic relationships
inferredcites →https://doi.org/10.1899/10-012.1openalex-snapshot
Incorporation of DNA barcoding into a large-scale biomonitoring program: opportunities and pitfalls
inferredcites →https://doi.org/10.1899/10-016.1openalex-snapshot
Can DNA barcodes of stream macroinvertebrates improve descriptions of community structure and water quality?
inferredcites →https://doi.org/10.2307/1467284openalex-snapshot
Commentary on the Subsampling Procedures Used for Rapid Bioassessments
inferredcites →https://doi.org/10.2307/1467286openalex-snapshot
Effects of Sampling Area and Subsampling Procedure on Comparisons of Taxa Richness among Streams
inferredcites →https://doi.org/10.2307/1468195openalex-snapshot
Rare species in multivariate analysis for bioassessment: some considerations

What points at this work

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

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Comparing morphological and DNA-based bioassessment methodologies for macroinvertebrates in Neotropical streams: a case study from Ecuador
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The first DNA barcode library of Chironomidae from the Tibetan Plateau with an evaluation of the status of the public databases
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DNA Metabarcoding as a Complementary Approach to Traditional Surveys for Monitoring the Plant Diversity in the Amazon canga
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Diversity and Potential Endemism of New Zealand Freshwater Rotifers Revealed Using Mitochondrial DNA Barcodes
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If You Build It, Will They Come? An Environmental DNA Assessment of Fish Assemblages on Artificial Reefs in the Northern Gulf of Mexico
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High diversity of freshwater invertebrates on inuinnait nuna, the canadian arctic, revealed using mitochondrial DNA barcodes
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Molecular characterization and phylogenetics of Indian polychaete fauna: scope for implementation in ecological monitoring
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Capacity of United States federal government and its partners to rapidly and accurately report the identity (taxonomy) of non-native organisms intercepted in early detection programs
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Biodiversity analyses in freshwater meiofauna through DNA sequence data
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Metabarcoding meiofauna biodiversity assessment in four beaches of Northern Colombia: effects of sampling protocols and primer choice
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Fresh insights into Mediterranean biodiversity: environmental DNA reveals spatio-temporal patterns of stream invertebrate communities on Sicily
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eDNA and Bioassessment of Rivers
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Arthropoda
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Environmental DNA and toxicogenomics in ecological health risk assessment
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Linking DNA Metabarcoding and Text Mining to Create Network-Based Biomonitoring Tools: A Case Study on Boreal Wetland Macroinvertebrate Communities
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Prioritizing taxa for genetic reference database development to advance inland water conservation
inferred← citeshttps://doi.org/10.1016/j.ecolind.2019.01.014openalex-snapshot
Metabarcoding of storage ethanol vs. conventional morphometric identification in relation to the use of stream macroinvertebrates as ecological indicators in forest management
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Implications of taxonomic and numerical resolution on DNA metabarcoding-based inference of benthic macroinvertebrate responses to river restoration
inferred← citeshttps://doi.org/10.1016/j.jglr.2019.10.004openalex-snapshot
A reference inventory for aquatic fauna of the Laurentian Great Lakes
inferred← citeshttps://doi.org/10.1016/j.rsma.2023.103069openalex-snapshot
DNA barcoding reveals cryptic diversity of fish eggs in Equatorial Southwestern Atlantic
inferred← citeshttps://doi.org/10.1016/j.scitotenv.2019.04.247openalex-snapshot
DNA barcode reference libraries for the monitoring of aquatic biota in Europe: Gap-analysis and recommendations for future work
inferred← citeshttps://doi.org/10.1016/j.scitotenv.2024.173621openalex-snapshot
Effectiveness of eDNA for monitoring riverine macroinvertebrates
inferred← citeshttps://doi.org/10.1016/j.scitotenv.2024.177308openalex-snapshot
Environmental DNA barcoding reveals general biodiversity patterns in the large tropical rift Lake Albert
inferred← citeshttps://doi.org/10.1021/acs.est.7b06494openalex-snapshot
Omics Advances in Ecotoxicology
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A reference library for Canadian invertebrates with 1.5 million barcodes, voucher specimens, and DNA samples
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Evaluation of genetic markers for the metabarcoding of Australian marsupials from predator scats
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DNA metabarcoding reveals metacommunity dynamics in a threatened boreal wetland wilderness
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Strengthening marine amphipod DNA barcode libraries for environmental monitoring
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Implications of taxonomic and numerical resolution on DNA metabarcoding-based inference of benthic macroinvertebrate responses to river restoration
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Dealing with the promise of metabarcoding in mega-event biomonitoring: EXPO2015 unedited data
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A reference library for the identification of Canadian invertebrates: 1.5 million DNA barcodes, voucher specimens, and genomic samples
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Metabarcoding a Metacommunity: detecting change in a wetland wilderness
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Identifying error and accurately interpreting environmental DNA metabarcoding results: A case study to detect vertebrates at arid zone waterholes
inferred← citeshttps://doi.org/10.1111/1755-0998.13262openalex-snapshot
BAGS: An automated Barcode, Audit & Grade System for DNA barcode reference libraries
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Advancing aquatic biodiversity assessments of invertebrates using eDNA metabarcoding: A systematic evaluation of primers for marine and freshwater communities
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Environmental DNA of preservative ethanol performed better than water samples in detecting macroinvertebrate diversity using metabarcoding
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Environmental DNA metabarcoding for insect biodiversity surveys: Current status and future prospects for potential applications in highly diverse insect taxa
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Scaling up DNA metabarcoding for freshwater macrozoobenthos monitoring
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Towards routine DNA metabarcoding of macroinvertebrates using bulk samples for freshwater bioassessment: Effects of debris and storage conditions on the recovery of target taxa
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Two hundred and five newly assembled mitogenomes provide mixed evidence for rivers as drivers of speciation for Amazonian primates
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Nematode biodiversity assessments need vouchered databases: A BOLD reference library for plant-parasitic nematodes in the superfamily Criconematoidea
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Efficient COI barcoding using high throughput single-end 400 bp sequencing
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Over 2.5 million COI sequences in GenBank and growing
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Assessment of BOLD and GenBank – Their accuracy and reliability for the identification of biological materials
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COI metabarcoding primer choice affects richness and recovery of indicator taxa in freshwater systems
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Using DNA barcoding to improve invasive pest identification at U.S. ports-of-entry
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Increased performance of DNA metabarcoding of macroinvertebrates by taxonomic sorting
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Haplotype-level metabarcoding of freshwater macroinvertebrate species: A prospective tool for population genetic analysis
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Efficiency of the cytochrome c oxidase subunit II gene for the delimitation of termite species (Blattodea: Isoptera) in the state of Paraíba, northeastern Brazil
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Documenting Emerging Insects, Environmental DNA, and Metal Concentrations in a Small Appalachian Stream
inferred← citeshttps://doi.org/10.21203/rs.3.rs-8253547/v1openalex-snapshot
DNA barcoding vs morphology: Assessing different methods for invertebrate identification and determination of industrial effluent impacts
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Molecular techniques to assess fish diet and describe prey availability
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Ecological and morphological differentiation among COI haplotype groups in the plant parasitic nematode species Mesocriconema xenoplax
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Bioinformatics is a BLAST: Engaging First-Year Biology Students on Campus Biodiversity Using DNA Barcoding
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Assessing the DNA barcoding readiness of Spanish Lake macrophytes for aquatic bioassessment under European water and nature directives (WFD/HD)
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Studying Ecosystems With DNA Metabarcoding: Lessons From Biomonitoring of Aquatic Macroinvertebrates
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Putting COI Metabarcoding in Context: The Utility of Exact Sequence Variants (ESVs) in Biodiversity Analysis
inferred← citeshttps://doi.org/10.3389/fevo.2020.581835openalex-snapshot
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Biodiversity between sand grains: Meiofauna composition across southern and western Sweden assessed by metabarcoding
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A DNA barcode library for ground beetles of Germany: the genus Agonum Bonelli, 1810 (Insecta, Coleoptera, Carabidae)
inferred← citeshttps://doi.org/10.3897/mbmg.4.51433openalex-snapshot
Exploring the potential of metabarcoding to disentangle macroinvertebrate community dynamics in intermittent streams
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Surprisingly high genetic divergence of the mitochondrial DNA barcode fragment (COI) within Central European woodlice species (Crustacea, Isopoda, Oniscidea)
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Diptera of Canada
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A DNA barcode library for ground beetles of Germany: the genus Pterostichus Bonelli, 1810 and allied taxa (Insecta, Coleoptera, Carabidae)
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Confirmation and Description of the Larva of the Aquatic Dance Fly, Proclinopyga Melander (Diptera: Empididae: Clinocerinae)
inferred← citeshttps://doi.org/10.4289/0013-8797.124.1.131openalex-snapshot
DNA Barcoding Takes Bioassessment Further: New Distribution Records for Aquatic Macroinvertebrates from Alaskan National Parks
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Molecular insights into the diversity of odonates in the Andaman and Nicobar Islands using 16S rRNA gene
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Additional file 1 of Efficient COI barcoding using high throughput single-end 400 bp sequencing
inferred← citeshttps://doi.org/10.6084/m9.figshare.13336519openalex-snapshot
Additional file 3 of Efficient COI barcoding using high throughput single-end 400 bp sequencing
inferred← citeshttps://doi.org/10.6084/m9.figshare.13336525openalex-snapshot
Additional file 4 of Efficient COI barcoding using high throughput single-end 400 bp sequencing
inferred← citeshttps://doi.org/10.6084/m9.figshare.13336531openalex-snapshot
Additional file 5 of Efficient COI barcoding using high throughput single-end 400 bp sequencing
inferred← citeshttps://doi.org/10.7287/peerj.4644v0.1/reviews/1openalex-snapshot
Peer Review #1 of "Estimating intraspecific genetic diversity from community DNA metabarcoding data (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.4644v0.1/reviews/2openalex-snapshot
Peer Review #2 of "Estimating intraspecific genetic diversity from community DNA metabarcoding data (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.4644v0.1/reviews/3openalex-snapshot
Peer Review #3 of "Estimating intraspecific genetic diversity from community DNA metabarcoding data (v0.1)"
inferred← citeshttps://doi.org/10.7717/peerj.14071openalex-snapshot
A manager’s guide to using eDNA metabarcoding in marine ecosystems
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taxalogue: a toolkit to create comprehensive CO1 reference databases
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Estimating intraspecific genetic diversity from community DNA metabarcoding data
Editorial review for independent work. ICSAC — the Institute for Complexity Science and Advanced Computing — runs a structured editorial panel for researchers publishing outside journals, and publishes on CiteStamp rails. Submission is free and goes through ORCID: icsacinstitute.org/submit.