Divergence thresholds and divergent biodiversity estimates: can metabarcoding reliably describe zooplankton communities? (Q35664770)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26078859%20AND%20SRC:MED&resulttype=core&format=json

17 February 2020

title

Divergence thresholds and divergent biodiversity estimates: can metabarcoding reliably describe zooplankton communities? (English)

1 reference

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17 February 2020

0 references

0 references

1 reference

3

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17 February 2020

4

Hugh J MacIsaac

1 reference

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17 February 2020

5

Melania E Cristescu

1 reference

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17 February 2020

author name string

Emily A Brown

series ordinal

1

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17 February 2020

Frédéric J J Chain

series ordinal

2

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17 February 2020

publication date

13 May 2015

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17 February 2020

number of pages

18

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based on heuristic

inferred from page(s)

published in

Ecology and Evolution

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17 February 2020

volume

5

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17 February 2020

issue

11

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17 February 2020

page(s)

2234-2251

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Toward accurate molecular identification of species in complex environmental samples: testing the performance of sequence filtering and clustering methods

17 February 2020

cites work

1 reference

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12 July 2018

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12 July 2018

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Intracellular diversity of the V4 and V9 regions of the 18S rRNA in marine protists (radiolarians) assessed by high-throughput sequencing

12 July 2018

1 reference

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Characterization of the 18S rRNA gene for designing universal eukaryote specific primers.

12 July 2018

1 reference

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Next generation sequencing reveals the hidden diversity of zooplankton assemblages

12 July 2018

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454 pyrosequencing to describe microbial eukaryotic community composition, diversity and relative abundance: a test for marine haptophytes

12 July 2018

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UPARSE: highly accurate OTU sequences from microbial amplicon reads

12 July 2018

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Employing 454 amplicon pyrosequencing to reveal intragenomic divergence in the internal transcribed spacer rDNA region in fungi

12 July 2018

1 reference

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Characterization of the two intra-individual sequence variants in the 18S rRNA gene in the plant parasitic nematode, Rotylenchulus reniformis

12 July 2018

1 reference

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Assessing the consequences of denoising marker-based metagenomic data

12 July 2018

1 reference

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MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

12 July 2018

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The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

12 July 2018

1 reference

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Accuracy of protist diversity assessments: morphology compared with cloning and direct pyrosequencing of 18S rRNA genes and ITS regions using the conspicuous tintinnid ciliates as a case study

12 July 2018

1 reference

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Culturing captures members of the soil rare biosphere

12 July 2018

1 reference

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Using high throughput sequencing to explore the biodiversity in oral bacterial communities

12 July 2018

1 reference

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Copy number variation of ribosomal DNA and Pokey transposons in natural populations of Daphnia.

12 July 2018

1 reference

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Sequencing our way towards understanding global eukaryotic biodiversity

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4461424

Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4461424

UCHIME improves sensitivity and speed of chimera detection

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4461424

A large-scale benchmark study of existing algorithms for taxonomy-independent microbial community analysis

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4461424

Depicting more accurate pictures of protistan community complexity using pyrosequencing of hypervariable SSU rRNA gene regions.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4461424

Removing noise from pyrosequenced amplicons

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4461424

Evolution of the nuclear ribosomal DNA intergenic spacer in four species of the Daphnia pulex complex.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4461424

Clustering 16S rRNA for OTU prediction: a method of unsupervised Bayesian clustering

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4461424

Second-generation environmental sequencing unmasks marine metazoan biodiversity

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4461424

454 Pyrosequencing and Sanger sequencing of tropical mycorrhizal fungi provide similar results but reveal substantial methodological biases

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4461424

Freshwater Perkinsea and marine-freshwater colonizations revealed by pyrosequencing and phylogeny of environmental rDNA.

12 July 2018

1 reference

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Ironing out the wrinkles in the rare biosphere through improved OTU clustering

12 July 2018

1 reference

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FastTree 2--approximately maximum-likelihood trees for large alignments

12 July 2018

1 reference

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Massively parallel tag sequencing reveals the complexity of anaerobic marine protistan communities

12 July 2018

1 reference

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Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates

12 July 2018

1 reference

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454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity

12 July 2018

1 reference

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Accurate determination of microbial diversity from 454 pyrosequencing data

12 July 2018

1 reference

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Length variation in 18S rRNA expansion segment 43/e4 of Daphnia obtusa: ancient or recurring polymorphism?

12 July 2018

1 reference

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Repetitive sequence variation and dynamics in the ribosomal DNA array of Saccharomyces cerevisiae as revealed by whole-genome resequencing

12 July 2018

1 reference

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Microbial population structures in the deep marine biosphere

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4461424

Accuracy and quality of massively parallel DNA pyrosequencing

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4461424

Microbial diversity in the deep sea and the underexplored "rare biosphere"

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4461424

Mapping of picoeucaryotes in marine ecosystems with quantitative PCR of the 18S rRNA gene

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4461424

Monitoring the mode and tempo of concerted evolution in the Drosophila melanogaster rDNA locus

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4461424

Genome sequencing in microfabricated high-density picolitre reactors

12 July 2018

1 reference

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Biological identifications through DNA barcodes

12 July 2018

1 reference

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Distribution of substitution rates and location of insertion sites in the tertiary structure of ribosomal RNA.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4461424

Comparative analysis of more than 3000 sequences reveals the existence of two pseudoknots in area V4 of eukaryotic small subunit ribosomal RNA.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4461424

Basic local alignment search tool

12 July 2018

1 reference

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DNA recombination during PCR.

12 July 2018

1 reference

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Comparisons of the fungal and protistan communities among different marine sponge holobionts by pyrosequencing

12 July 2018

1 reference

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Comparing clustering and pre-processing in taxonomy analysis

25 September 2018

1 reference

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Seasonal trends in the biomass and structure of bryophyte-associated fungal communities explored by 454 pyrosequencing.

25 September 2018

1 reference

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New primers to amplify the fungal ITS2 region--evaluation by 454-sequencing of artificial and natural communities.

25 September 2018

1 reference

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Selection on the structural stability of a ribosomal RNA expansion segment in Daphnia obtusa

25 September 2018

1 reference

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The correlation between rDNA copy number and genome size in eukaryotes

25 September 2018

1 reference

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The origin and evolution of variable-region helices in V4 and V7 of the small-subunit ribosomal RNA of branchiopod crustaceans

25 September 2018

1 reference

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The unusually long small subunit ribosomal RNA gene found in amitochondriate amoeboflagellate Pelomyxa palustris: its rRNA predicted secondary structure and phylogenetic implication

25 September 2018

1 reference

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Analysis of the primary sequence and secondary structure of the unusually long SSU rRNA of the soil bug, Armadillidium vulgare

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4461424

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

25 September 2018

1 reference

Ecology. Dipping into the rare biosphere.

21 January 2018

1 reference

High sensitivity of 454 pyrosequencing for detection of rare species in aquatic communities

21 January 2018

1 reference

The 'rare biosphere': a reality check

21 January 2018

1 reference

Changes in the root-associated fungal communities along a primary succession gradient analysed by 454 pyrosequencing

21 January 2018

1 reference

Picobiliphytes: a marine picoplanktonic algal group with unknown affinities to other eukaryotes

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26078859

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Some Unusual Small-Subunit Ribosomal RNA Sequences of Metazoans

1 reference

inferred from DOI database lookup

7 January 2021

based on heuristic

Identifiers

DOI

10.1002/ECE3.1485

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26078859%20AND%20SRC:MED&resulttype=core&format=json

17 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26078859%20AND%20SRC:MED&resulttype=core&format=json

17 February 2020

PubMed publication ID

26078859

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26078859%20AND%20SRC:MED&resulttype=core&format=json