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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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What this work says

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

inferredcites →https://doi.org/10.1002/ece3.1272openalex-snapshot

The application of eDNA for monitoring of the Great Crested Newt in the UK

inferredcites →https://doi.org/10.1002/ece3.3346openalex-snapshot

Distinct seasonal migration patterns of Japanese native and non‐native genotypes of common carp estimated by environmental DNA

inferredcites →https://doi.org/10.1007/s10201-016-0508-5openalex-snapshot

A simple method for preserving environmental DNA in water samples at ambient temperature by addition of cationic surfactant

inferredcites →https://doi.org/10.1007/s13280-016-0776-7openalex-snapshot

Lack of recognition of genetic biodiversity: International policy and its implementation in Baltic Sea marine protected areas

inferredcites →https://doi.org/10.1016/j.biocon.2014.11.019openalex-snapshot

Environmental DNA – An emerging tool in conservation for monitoring past and present biodiversity

inferredcites →https://doi.org/10.1016/j.biocon.2017.04.023openalex-snapshot

Tropical-forest mammals as detected by environmental DNA at natural saltlicks in Borneo

inferredcites →https://doi.org/10.1038/ismej.2014.195openalex-snapshot

Minimum entropy decomposition: Unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences

inferredcites →https://doi.org/10.1038/ismej.2017.119openalex-snapshot

Exact sequence variants should replace operational taxonomic units in marker-gene data analysis

inferredcites →https://doi.org/10.1038/ismej.2017.29openalex-snapshot

Ecological dynamics and co-occurrence among marine phytoplankton, bacteria and myoviruses shows microdiversity matters

inferredcites →https://doi.org/10.1038/nmeth.3869openalex-snapshot

DADA2: High-resolution sample inference from Illumina amplicon data

inferredcites →https://doi.org/10.1038/s41559-016-0004openalex-snapshot

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

inferredcites →https://doi.org/10.1038/srep16963openalex-snapshot

MIG-seq: an effective PCR-based method for genome-wide single-nucleotide polymorphism genotyping using the next-generation sequencing platform

inferredcites →https://doi.org/10.1038/srep40368openalex-snapshot

Environmental DNA metabarcoding reveals local fish communities in a species-rich coastal sea

inferredcites →https://doi.org/10.1046/j.1444-2906.2002.00399.xopenalex-snapshot

Genetic structure of land-locked ayu within the Biwa Lake system

inferredcites →https://doi.org/10.1093/bioinformatics/btg412openalex-snapshot

APE: Analyses of Phylogenetics and Evolution in R language

inferredcites →https://doi.org/10.1093/bioinformatics/btv401openalex-snapshot

Error filtering, pair assembly and error correction for next-generation sequencing reads

inferredcites →https://doi.org/10.1093/molbev/mst141openalex-snapshot

MitoFish and MitoAnnotator: A Mitochondrial Genome Database of Fish with an Accurate and Automatic Annotation Pipeline

inferredcites →https://doi.org/10.1093/molbev/mst197openalex-snapshot

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

inferredcites →https://doi.org/10.1093/molbev/msy074openalex-snapshot

MitoFish and MiFish Pipeline: A Mitochondrial Genome Database of Fish with an Analysis Pipeline for Environmental DNA Metabarcoding

inferredcites →https://doi.org/10.1093/nar/gkr344openalex-snapshot

Sequence-specific error profile of Illumina sequencers

inferredcites →https://doi.org/10.1098/rsbl.2008.0118openalex-snapshot

Species detection using environmental DNA from water samples

inferredcites →https://doi.org/10.1098/rsos.150088openalex-snapshot

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

inferredcites →https://doi.org/10.1098/rsos.180537openalex-snapshot

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

inferredcites →https://doi.org/10.1101/074252openalex-snapshot

UCHIME2: improved chimera prediction for amplicon sequencing

inferredcites →https://doi.org/10.1101/081257openalex-snapshot

UNOISE2: improved error-correction for Illumina 16S and ITS amplicon sequencing

inferredcites →https://doi.org/10.1101/212134openalex-snapshot

Impact of sequence variant detection and bacterial DNA extraction methods on the measurement of microbial community composition in human stool

inferredcites →https://doi.org/10.1111/1365-2664.12392openalex-snapshot

A basin‐scale application of environmental DNA assessment for rare endemic species and closely related exotic species in rivers: a case study of giant salamanders in Japan

inferredcites →https://doi.org/10.1111/1365-2664.12467openalex-snapshot

Applications and limitations of measuring environmental DNA as indicators of the presence of aquatic animals

inferredcites →https://doi.org/10.1111/1755-0998.12460openalex-snapshot

A novel environmental DNA approach to quantify the cryptic invasion of non‐native genotypes

inferredcites →https://doi.org/10.1111/2041-210x.12114openalex-snapshot

Oligotyping: differentiating between closely related microbial taxa using 16S rRNA gene data

inferredcites →https://doi.org/10.1111/fwb.12846openalex-snapshot

Environmental DNA analysis for estimating the abundance and biomass of stream fish

inferredcites →https://doi.org/10.1111/j.1365-2664.2012.02171.xopenalex-snapshot

Improved detection of an alien invasive species through environmental DNA barcoding: the example of the American bullfrog Lithobates catesbeianus

inferredcites →https://doi.org/10.1111/j.1365-294x.2011.05418.xopenalex-snapshot

Monitoring endangered freshwater biodiversity using environmental DNA

inferredcites →https://doi.org/10.1111/j.1365-294x.2012.05550.xopenalex-snapshot

Bioinformatic challenges for DNA metabarcoding of plants and animals

inferredcites →https://doi.org/10.1111/j.1365-294x.2012.05600.xopenalex-snapshot

Conservation in a cup of water: estimating biodiversity and population abundance from environmental DNA

inferredcites →https://doi.org/10.1111/j.1755-263x.2010.00158.xopenalex-snapshot

“Sight‐unseen” detection of rare aquatic species using environmental DNA

inferredcites →https://doi.org/10.1111/mec.13650openalex-snapshot

Using dense locality sampling resolves the subtle genetic population structure of the dispersive fish species Plecoglossus altivelis

inferredcites →https://doi.org/10.1128/msystems.00003-15openalex-snapshot

Open-Source Sequence Clustering Methods Improve the State Of the Art

inferredcites →https://doi.org/10.1139/cjfas-2013-0047openalex-snapshot

Estimating occupancy and abundance of stream amphibians using environmental DNA from filtered water samples

inferredcites →https://doi.org/10.1146/annurev.es.18.110187.001413openalex-snapshot

EVOLUTION OF ANIMAL MITOCHONDRIAL DNA: RELEVANCE FOR POPULATION BIOLOGY AND SYSTEMATICS

inferredcites →https://doi.org/10.1186/1471-2105-13-283openalex-snapshot

Denoising PCR-amplified metagenome data

inferredcites →https://doi.org/10.1371/journal.pone.0003376openalex-snapshot

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

inferredcites →https://doi.org/10.1371/journal.pone.0025232openalex-snapshot

Evaluation of Intra-Host Variants of the Entire Hepatitis B Virus Genome

inferredcites →https://doi.org/10.1371/journal.pone.0027310openalex-snapshot

Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies

inferredcites →https://doi.org/10.1371/journal.pone.0035868openalex-snapshot

Estimation of Fish Biomass Using Environmental DNA

inferredcites →https://doi.org/10.1371/journal.pone.0058807openalex-snapshot

Genetic Diversity and Evolution of Chinese Traditional Medicinal Fungus Polyporus umbellatus (Polyporales, Basidiomycota)

inferredcites →https://doi.org/10.1371/journal.pone.0086175openalex-snapshot

Using Environmental DNA to Census Marine Fishes in a Large Mesocosm

inferredcites →https://doi.org/10.1371/journal.pone.0149786openalex-snapshot

Environmental DNA as a ‘Snapshot’ of Fish Distribution: A Case Study of Japanese Jack Mackerel in Maizuru Bay, Sea of Japan

inferredcites →https://doi.org/10.1371/journal.pone.0153291openalex-snapshot

Correction: Environmental DNA as a 'Snapshot' of Fish Distribution: A Case Study of Japanese Jack Mackerel in Maizuru Bay, Sea of Japan

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.0173073openalex-snapshot

Environmental DNA reflects spatial and temporal jellyfish distribution

inferredcites →https://doi.org/10.1371/journal.pone.0176541openalex-snapshot

Environmental DNA method for estimating salamander distribution in headwater streams, and a comparison of water sampling methods

inferredcites →https://doi.org/10.3390/ijms14036436openalex-snapshot

Thermostable Mismatch-Recognizing Protein MutS Suppresses Nonspecific Amplification during Polymerase Chain Reaction (PCR)

inferredcites →https://doi.org/10.7717/peerj.4644openalex-snapshot

Estimating intraspecific genetic diversity from community DNA metabarcoding data

What points at this work

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

inferred← citeshttps://doi.org/10.1002/edn3.143openalex-snapshot

Population differentiation from environmental DNA: Investigating the potential of haplotype presence/absence‐based analysis of molecular variance

inferred← citeshttps://doi.org/10.1002/edn3.70029openalex-snapshot

Estimating Rapid Diversity Changes During Acute Herbicide Contamination Using Environmental DNA

inferred← citeshttps://doi.org/10.1007/978-981-19-8218-7_1openalex-snapshot

Revisiting the Genomic Approaches in the Cereals and the Path Forward

inferred← citeshttps://doi.org/10.1016/bs.amb.2020.01.001openalex-snapshot

Marine environmental DNA: Approaches, applications, and opportunities

inferred← citeshttps://doi.org/10.1016/j.scitotenv.2020.142622openalex-snapshot

Methodology of fish eDNA and its applications in ecology and environment

inferred← citeshttps://doi.org/10.1101/2021.08.04.455111openalex-snapshot

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

inferred← citeshttps://doi.org/10.22541/au.166756789.99942137/v1openalex-snapshot

Experimental evaluation of species and genetic variability based on DNA metabarcoding from the aquatic environment: extra OTUs formed by NUMTS may reduce the diversity of ASVs

inferred← citeshttps://doi.org/10.3897/mbmg.4.53455openalex-snapshot

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

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