The DOI matches its Crossref record; 59 of the 60 references it cites were found in a registry or an index; none of the 35 sources its claims cite is checked for support yet.
Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol
Open accessAbstract
Metabarcoding is an emerging genetic tool to rapidly assess biodiversity in ecosystems. It involves high-throughput sequencing of a standard gene from an environmental sample and comparison to a reference database. However, no consensus has emerged regarding laboratory pipelines to screen species diversity and infer species abundances from environmental samples. In particular, the effect of primer bias and the detection limit for specimens with a low biomass has not been systematically examined, when processing samples in bulk. We developed and tested a DNA metabarcoding protocol that utilises the standard cytochrome c oxidase subunit I (COI) barcoding fragment to detect freshwater macroinvertebrate taxa. DNA was extracted in bulk, amplified in a single PCR step, and purified, and the libraries were directly sequenced in two independent MiSeq runs (300-bp paired-end reads). Specifically, we assessed the influence of specimen biomass on sequence read abundance by sequencing 31 specimens of a stonefly species with known haplotypes spanning three orders of magnitude in biomass (experiment I). Then, we tested the recovery of 52 different freshwater invertebrate taxa of similar biomass using the same standard barcoding primers (experiment II). Each experiment was replicated ten times to maximise statistical power. The results of both experiments were consistent across replicates. We found a distinct positive correlation between species biomass and resulting numbers of MiSeq reads. Furthermore, we reliably recovered 83% of the 52 taxa used to test primer bias. However, sequence abundance varied by four orders of magnitudes between taxa despite the use of similar amounts of biomass. Our metabarcoding approach yielded reliable results for high-throughput assessments. However, the results indicated that primer efficiency is highly species-specific, which would prevent straightforward assessments of species abundance and biomass in a sample. Thus, PCR-based metabarcoding assessments of biodiversity should rely on presence-absence metrics.
Overview
AI snapshot
Written from the paper’s full text.
TL;DR
This study developed and tested a replicated COI metabarcoding protocol for freshwater macroinvertebrates, using bulk DNA extraction and Illumina MiSeq sequencing. It found a strong biomass–read relationship within a single species, but strong species-specific primer bias across taxa, concluding that PCR-based metabarcoding cannot reliably quantify species abundance or biomass and should be used for presence–absence assessments.
Key findings
- In experiment I, all 31 *Dinocras cephalotes* specimens were recovered across ten replicates, including the smallest specimen at 0.023% (0.145 mg) of total biomass; specimen biomass and sequence abundance showed a highly significant positive linear correlation in all ten replicates (p<0.001, R² = 0.65).
- In experiment II, 83% (43/52) of taxa were reliably recovered; 34 taxa were recovered in all ten replicates. Recovery by group was Ephemeroptera 7/8 (88%), Plecoptera 4/4 (100%), Trichoptera 13/15 (86%), Diptera 7/8 (88%), and Others 12/17 (71%).
- Despite similar biomass, sequence abundance varied by four orders of magnitude among taxa, and there was no correlation between taxon biomass and number of recovered sequences. Primer efficiency was highly species-specific, preventing straightforward abundance or biomass inference.
- LCO and HCO sequencing direction had small effects on final sequence abundance (2.7% and 4.4% differences in experiments I and II), though LCO was 34% more frequent in experiment I (p = 0.006) and no primer bias was detected in experiment II (p = 0.41).
Methods
- Two controlled experiments with ten replicates each were sequenced on two independent MiSeq runs using 300-bp paired-end reads; experiment I used 31 *D. cephalotes* stonefly specimens spanning three orders of magnitude in biomass, and experiment II used 52 freshwater invertebrate taxa with similar tissue biomass.
- DNA was extracted in bulk, amplified in a single PCR step with tagged fusion primers based on standard COI LCO1490/HCO2198, purified, and directly sequenced; experiment I used 1.4% and 20% tissue aliquots, while experiment II pooled roughly equal tissue amounts per taxon.
- Bioinformatic analysis used demultiplexing, cutadapt primer removal, read concatenation, blastn against reference haplotypes for experiment I, and UPARSE OTU clustering at 97% identity with BOLD identification for experiment II; sequence counts were normalised to total sequence abundance and tissue weight.
Limitations
- The paper states that PCR-based metabarcoding cannot accurately estimate species biomass or even abundance in diverse environmental samples because primer efficiency is highly species-specific; it recommends presence–absence metrics and notes that PCR-free approaches are needed for biomass estimates.
- The paper states that only 83% of taxa were recovered with one universal COI primer pair, that barcode reference databases remain incomplete, that DNA-based assessments cannot assign biological traits, and that PCR replication effects were not evaluated due to a small number of replicates.
- Evident from the text: the experiments are limited to freshwater macroinvertebrates from western Germany and a specific MiSeq/COI Folmer protocol; some morphotaxa were identified only to family or order and contained multiple MOTUs, so species-level amplification behaviour may be more variable than the morphotaxon-level summaries suggest.
Model-written summary. Check it against the paper before relying on it.
Integrity signals
Registry
Cites
Statistics
Figures
Verification
Claims the paper makes
44 Own result · 24 Own interpretation · 22 Not checked yet · 8 No basis given · 5 Own method
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“However, sequence abundance varied by four orders of magnitudes between taxa despite the use of similar amounts of biomass.”
§ Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol > Abstract
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“we found significant differences between the LCO and HCO primers with respect to the number of reads with no hits in experiment I (t-test, p = 0.01, S3A Fig) and final hits in experiment II (t-test, p = 0.01, S3B Fig).”
§ Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol > Results > Sequencing success and statistics
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“We detected few outliers and low standard deviations for the ratio of LCO- to HCO-based haplotype read abundance for each of the five DNA extractions (Fig 2B and S8 Fig).”
§ Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol > Results > Experiment I
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The sequencing results for the ten replicates were highly reproducible.”
§ Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol > Results > Experiment I
boosted- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“We did not observe significant differences in sequence abundance among the replicates using different amounts of extracted tissue as a template.”
§ Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol > Results > Experiment I
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“From the DNA extractions performed with the TissueLyser LT, six more specimens (2.31%) were recovered than when DNA was extracted with liquid nitrogen.”
§ Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol > Results > Experiment II
plaindirectn = 6- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Sequences starting with the LCO primer for the first read were significantly overrepresented in experiment I (34% more frequent than sequences beginning with the HCO primer, t-test, p = 0.006, S4A Fig).”
§ Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol > Results > Sequencing success and statistics
plaincorrelationaln = 31- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“A much higher per-site nucleotide diversity was observed using the consensus sequences of the 31 unique Dinocras cephalotes COI haplotypes (see experiment I below) (S2 Fig). Fewer peaks of low diversity (only up to 70% identical bases) were detected using both primers than using one primer at a time (100% identical bases).”
§ Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol > Materials and Methods > Primer design and sequencing strategy
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“In experiment II, we did not detect primer bias (t-test, p = 0.41, S4B Fig).”
§ Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol > Results > Sequencing success and statistics
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Specimens with a low biomass tend to show relatively high variation in sequence abundance among the ten replicates.”
§ Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol > Results > Experiment I
hedgedcorrelationaln = 31- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
- Probably not a substantial claim. 23
- It may state two separate claims as one. 23
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The two independent weight measurements differed in mean by 0.1 mg (SD = 0.03).”
§ Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol > Results > Experiment I
plainn = 31- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The MiSeq runs of experiments I and II yielded 9.63 and 14.07 Gb of read data, respectively.”
§ Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol > Results > Sequencing success and statistics
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“In all 10 replicates, we recovered all 31 D. cephalotes specimens based on their unique haplotypes, including the smallest specimens, which only made up 0.023% (0.145 mg) of the total specimen biomass (Fig 2A).”
§ Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol > Results > Experiment I
plainn = 31- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The mean normalised sequence abundances had low standard deviations and the linear model fit well (p<0.001, R 2 = 0.65, S8 Fig).”
§ Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol > Results > Experiment I
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“For two specimens, we recovered sequence artefacts (see S6 Fig); these did not affect further analyses.”
§ Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol > Results > Experiment I
plainn = 2- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Both MiSeq runs showed good read quality (sequences with Q30 ≥ 85.3% and 83.3%).”
§ Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol > Results > Sequencing success and statistics
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Sequences that did not match the target species were similar to sequences derived from a variety of benthic organisms, but also fungi and plants.”
§ Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol > Results > Experiment II
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Using our protocol, it is possible to assess community compositions within a week, from sampling to species identification.”
§ Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol > Discussion > Implications for large-scale monitoring and future challenges
hedgeddirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: fails — The paper may give no reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. The paper may give no reason why it holds.
In the paper
“Furthermore, we used a universal COI primer with a broad target range [41], and only 17% of taxa went undetected.”
§ Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol > Discussion > Implications for large-scale monitoring and future challenges
What the sources say
- Not checked yetcites [41] O Folmer, 1994, DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates, Mol Marine Biol Biotechnol
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Of all recovered 213 OTUs, 31 could not be identified using the BOLD database (S9B Fig).”
§ Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol > Results > Experiment II
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“We detected a slightly different sequencing efficiency between forward and reverse primers, but this only affected total sequence abundance and did not systematically alter the inferences from the data.”
§ Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol > Discussion > Experiment I: Relationship between specimen biomass and sequence abundance
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Our parallel sequencing strategy leads to an increase in per-site sequence diversity and read quality.”
§ Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol > Discussion > Implications for large-scale monitoring and future challenges
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: fails — The paper may give no reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. The paper may give no reason why it holds. It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“different species within a genus or subfamily can have different ecological preferences and stress tolerances and belong to different functional feeding groups [11,12] see [13] for review.”
§ Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol > Introduction
What the sources say
- Not checked yetcites [11] Merritt RW, Berg MB, Cummins KW. An Introduction to the Aquatic Insects of North America. 2009.
- Not checked yetcites [12] SU Pauls, 2008, Grazers, shredders and filtering carnivores—The evolution of feeding ecology in Drusinae (Trichoptera: Limnephilidae): Insights from a molecular phylogeny, Mol Phylogenet Evol source
- Not checked yetcites [13] FC Jones, 2008, Taxonomic sufficiency: The influence of taxonomic resolution on freshwater bioassessments using benthic macroinvertebrates, Environ Rev source
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“The same PCR master mix was used for all reactions to ensure identical PCR conditions for all replicates.”
§ Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol > Materials and Methods > Experiment I: Relationship between specimen biomass and sequence abundance
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“many benthic invertebrate larvae are difficult to identify at the species level, and thus the most practical taxonomic level for the identification of these organisms is often only the genus or family [10].”
§ Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol > Introduction
What the sources say
- Not checked yetcites [10] P Haase, 2010, First audit of macroinvertebrate samples from an EU Water Framework Directive monitoring program: human error greatly lowers precision of assessment results, J North Am Benthol Soc source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“To ensure reliable hits, only sequences that had a maximum of five mismatches and gaps were included in the analysis.”
§ Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol > Materials and Methods > Experiment I: Relationship between specimen biomass and sequence abundance
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The parallel sequencing approach thus substantially reduced regions of low per-site diversity, improving read quality.”
§ Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol > Materials and Methods > Primer design and sequencing strategy
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“DNA barcoding allows for standardized and accurate species identification [15–18].”
§ Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol > Introduction
What the sources say
- Not checked yetcites [15] PDN Hebert, 2003, Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species, Proc R Soc Lond B Biol Sci source
- Not checked yetcites [16] X Zhou, 2009, Towards a comprehensive barcode library for arctic life—Ephemeroptera, Plecoptera, and Trichoptera of Churchill, Manitoba, Canada, Front Zool source
- Not checked yetcites [17] X Zhou, 2010, Ephemeroptera, Plecoptera, and Trichoptera fauna of Churchill (Manitoba, Canada): insights into biodiversity patterns from DNA barcoding, J North Am Benthol Soc source
- Not checked yetcites [18] BW Sweeney, 2011, Can DNA barcodes of stream macroinvertebrates improve descriptions of community structure and water quality?, J North Am Benthol Soc source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
In the paper
“frequent identification errors occur and many specimens are not detected in samples [10]”
§ Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol > Introduction
What the sources say
- Not checked yetcites [10] P Haase, 2010, First audit of macroinvertebrate samples from an EU Water Framework Directive monitoring program: human error greatly lowers precision of assessment results, J North Am Benthol Soc source
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“All analyses were performed with ten replicates to improve statistical robustness.”
- Also stated in: § Abstract · plain
“Each experiment was replicated ten times to maximise statistical power.”
§ Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol > Introduction
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
- Also stated in: § Abstract · plain
In the paper
“Stein and co-authors showed that ten of 16 assessment metrics had higher statistical power using DNA barcoding than morphological assessment [14].”
§ Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol > Introduction
What the sources say
- Not checked yetcites [14] ED Stein, 2014, Is DNA Barcoding Actually Cheaper and Faster than Traditional Morphological Methods: Results from a Survey of Freshwater Bioassessment Efforts in the United States?, PLoS ONE source
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“For animals, a 658-bp standardized fragment of the mitochondrial gene COI (cytochrome c oxidase subunit 1) is typically used [19].”
§ Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol > Introduction
What the sources say
- Not checked yetcites [19] PDN Hebert, 2003, Biological identifications through DNA barcodes, Proc R Soc Lond B Biol Sci source
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Presumably, these morphotaxa contained several taxonomically distant species, which are unequally well amplified with the Folmer primers.”
§ Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol > Discussion > Experiment II: Primer amplification bias between species
hedgedcorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“We used a highly replicated and standardised approach for species detection using DNA metabarcoding”
§ Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol > Discussion > Implications for large-scale monitoring and future challenges
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“show that several technical and logistic problems have to be overcome before this protocol can be used for large-scale monitoring.”
§ Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol > Discussion > Implications for large-scale monitoring and future challenges
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“However, our results indicate that the amount of tissue used in the DNA extraction was sufficient and did not lead to the systematic exclusion of small specimens as long as tissues are well ground and specimens have similar amplification efficiencies.”
§ Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol > Discussion > Experiment I: Relationship between specimen biomass and sequence abundance
hedgedn = 31- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“However degraded DNA and contamination as in eDNA studies with amplicons is not a concern for organisms collected directly from streams.”
§ Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol > Discussion > Implications for large-scale monitoring and future challenges
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: fails — The paper may give no reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. The paper may give no reason why it holds.
None of the sources cited for this claim have been checked yet.
In the paper
“Several studies show that DNA-based assessments are superior to morphological assessments in freshwater ecosystems (e.g., [14,25,33])”
§ Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol > Discussion
What the sources say
- Not checked yetcites [14] ED Stein, 2014, Is DNA Barcoding Actually Cheaper and Faster than Traditional Morphological Methods: Results from a Survey of Freshwater Bioassessment Efforts in the United States?, PLoS ONE source
- Not checked yetcites [25] JK Jackson, 2014, Cryptic biodiversity in streams: a comparison of macroinvertebrate communities based on morphological and DNA barcode identifications, Freshw Sci source
- Not checked yetcites [33] Zimmermann J, Glöckner G, Jahn R, Enke N, Gemeinholzer B. Metabarcoding vs. morphological identification to assess diatom diversity in environmental studies. Mol Ecol Resour. 2014; 1–17. <comment>doi: 10.1111/1755-0998.12336</comment> source
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“but not its abundance because many small organisms generate the same number of sequence reads as a few large organisms.”
§ Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol > Discussion > Implications for large-scale monitoring and future challenges
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Thus, it is not possible to accurately estimate species biomass or even abundance in diverse environmental samples using amplification-based sequencing protocols.”
§ Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol > Discussion > Implications for large-scale monitoring and future challenges
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“The efforts of large national and international barcoding consortia (BOLD, iBOL, and GBOL) have contributed to a substantial increase in both the size and quality of reference databases [56]”
§ Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol > Discussion > Implications for large-scale monitoring and future challenges
What the sources say
- Not checked yetcites [56] P Taberlet, 2012, Towards next-generation biodiversity assessment using DNA metabarcoding, Mol Ecol source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
None of the sources cited for this claim have been checked yet.
In the paper
“we are confident that metabarcoding will widely replace present biomonitoring methods over time because 1) it has a higher taxonomic resolution [14], 2) it is cost efficient and fast and, most importantly, 3) it reduces human bias enabling comparisons among studies [57].”
§ Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol > Discussion > Implications for large-scale monitoring and future challenges
What the sources say
- Not checked yetcites [14] ED Stein, 2014, Is DNA Barcoding Actually Cheaper and Faster than Traditional Morphological Methods: Results from a Survey of Freshwater Bioassessment Efforts in the United States?, PLoS ONE source
- Not checked yetcites [57] Y Ji, 2013, Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding, Ecol Lett source
boosteddirect- Asserted: passes — The authors put it forward as true.
- Checkable: fails — It may be too vague to check against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. It may be too vague to check against evidence. The paper’s conclusions may not depend on it. It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“We provide a highly reproducible laboratory protocol for processing macroinvertebrate samples in bulk and identified species using metabarcoding with the standard COI region.”
§ Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol > Conclusions
boosted- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“Piñol et al. [39] proposed a relationship between biomass and sequence reads, but did not systematically examine this hypothesis.”
§ Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol > Discussion > Experiment I: Relationship between specimen biomass and sequence abundance
What the sources say
- Not checked yetcites [39] Piñol J, Mir G, Gomez-Polo P, Agustí N. Universal and blocking primer mismatches limit the use of high-throughput DNA sequencing for the quantitative metabarcoding of arthropods. Mol Ecol Resour. 2014; 1–12. <comment>doi: 10.1111/1755-0998.12355</comment> source
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“This is consistent with the primer bias which we already observed between morphotaxa and support the overall findings of strong taxon-specific amplification bias.”
§ Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol > Discussion > Experiment II: Primer amplification bias between species
boostedcorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The methods developed in this study can easily be adapted to assess the communities of other ecosystems.”
§ Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol > Discussion > Implications for large-scale monitoring and future challenges
plain- Asserted: passes — The authors put it forward as true.
- Checkable: fails — It may be too vague to check against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: fails — The paper may give no reason why it holds.
Probably not a substantial claim. It may be too vague to check against evidence. The paper’s conclusions may not depend on it. The paper may give no reason why it holds.
In the paper
“However, while this approach could have comparable taxonomic resolution as the COI barcode, it is currently limited by the lack of reference databases [55].”
§ Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol > Discussion > Implications for large-scale monitoring and future challenges
What the sources say
- Not checked yetcites [55] LJ Clarke, 2014, Environmental metabarcodes for insects: in silicoPCR reveals potential for taxonomic bias, Mol Ecol Resour source
hedgeddirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“A combination of both data types, i.e., DNA species barcodes and ecological traits, will maximise the power of metabarcoding for the reliable assessment of ecosystem responses under stress and for biomonitoring.”
§ Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol > Discussion > Implications for large-scale monitoring and future challenges
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: fails — It may be too vague to check against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. It may be too vague to check against evidence.
- Rests on an assumption: DNA-based assessments cannot assign biological traits to species.
The paper relies on this without support.
Precise estimates of biomass with respect to specimen recovery and primer bias have not been performed.
“Precise estimates of biomass with respect to specimen recovery and primer bias have not been performed.”
The paper relies on this without support.
COI amplicons are typically similar in base composition.
“COI amplicons are typically similar in base composition; therefore, three strategies were used to increase sequence diversity.”
The paper relies on this without support.
Sanger sequencing requires that each specimen is processed individually in the laboratory, which is costly and extremely time-consuming for routine community assessments involving hundreds or thousands of specimens per sample.
“However, Sanger sequencing requires that each specimen is processed individually in the laboratory, which is costly and extremely time-consuming for routine community assessments involving hundreds or thousands of specimens per sample.”
The paper relies on this without support.
Benthic indicator organisms vary in biomass, and this variation depends on taxonomic group and life stage.
“Benthic indicator organisms vary in biomass, and this variation depends on taxonomic group and life stage.”
The paper relies on this without support.
Morphotaxa could often only be identified at family or order level, and several species per morphotaxon may occur in the sampled aquatic habitats even at the same habitat patch.
“This was expected, as morphotaxa could often only be identified at family or order level, and several species per morphotaxon may occur in the sampled aquatic habitats even at the same habitat patch.”
The paper relies on this without support.
Stochastic effects increase with reduced specimen biomass.
“This result is expected because stochastic effects increase with reduced specimen biomass.”
The paper relies on this without support.
Currently, the monitoring of freshwater ecosystems is based on abundance metrics, which cannot be generated using the metabarcoding solutions currently available.
“Currently, the monitoring of freshwater ecosystems is based on abundance metrics, which cannot be generated using the metabarcoding solutions currently available.”
The paper relies on this without support.
All assessment protocols rely on reference catalogues against which inventory data of a species from an ecosystem are compared.
“All assessment protocols rely on reference catalogues against which inventory data of a species from an ecosystem are compared.”
The paper relies on this without support.
Changes in species traits in a community (e.g. functional feeding groups, tolerance against pollution) are used as indicator values to evaluate the biological significance of inferred community changes.
“In particular, changes in species traits in a community (e.g. functional feeding groups, tolerance against pollution) are used as indicator values to evaluate the biological significance of inferred community changes.”
The paper relies on this without support.
DNA-based assessments cannot assign biological traits to species.
“However, DNA-based assessments cannot assign biological traits to species.”
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“This was done to increase the likelihood of detecting small-bodied and rare species in samples, as individuals with a larger biomass provide disproportionate amounts of DNA and can therefore be over-represented when metabarcoding bulk samples65.”
From Soundscapes and deep learning enable tracking biodiversity recovery in tropical forests (2023) · cites this paper as [65]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
Each contradiction between two passages listed here was confirmed by an independent check.
Rated minor: it would not touch a result — a value no result rests on, a p-value that stays on the same side of the significance level, or a conflict that is clerical, resolved elsewhere in the paper, or outside its own findings.
In the paper
§ Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol > Results > Experiment II
“We were able to reliably assign OTUs to all 52 taxa included in the extraction.”
§ Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol > Discussion > Implications for large-scale monitoring and future challenges
“Furthermore, we used a universal COI primer with a broad target range [41], and only 17% of taxa went undetected.”
Citations
Cites
R: A Language and Environment for Statistical Computing
R Core Team (2000) · doi:10.32614/r.manuals · Cited by 355,893
QIIME allows analysis of high-throughput community sequencing data
Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D., Costello, E. K., Fierer, N., Peña, A. G., Goodrich, J. K., Gordon, J. I., et al. (2010) · Nature Methods · doi:10.1038/nmeth.f.303 · Cited by 34,887
Cutadapt removes adapter sequences from high-throughput sequencing reads
Martin, M. (2011) · EMBnet.journal · doi:10.14806/ej.17.1.200 · Cited by 33,889
BLAST+: architecture and applications
Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., & Madden, T. L. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-421 · Cited by 22,074
Schloss, P. D., Westcott, S. L., Ryabin, T., Hall, J. R., Hartmann, M., Hollister, E. B., Lesniewski, R. A., Oakley, B. B., Parks, D. H., Robinson, C. J., et al. (2009) · Applied and Environmental Microbiology · doi:10.1128/aem.01541-09 · Cited by 19,549
UPARSE: highly accurate OTU sequences from microbial amplicon reads
Edgar, R. C. (2013) · Nature Methods · doi:10.1038/nmeth.2604 · Cited by 16,770
Folmer, O., Black, M., Hoeh, W., Lutz, R., & Vrijenhoek, R. (1994) · PubMed · doi:10.5281/zenodo.15145663 · Cited by 15,546
Biological identifications through DNA barcodes
Hebert, P. D. N., Cywinska, A., Ball, S. L., & deWaard, J. R. (2003) · Proceedings of the Royal Society of London. Series B: Biological Sciences · doi:10.1098/rspb.2002.2218 · Cited by 13,376
A safe operating space for humanity
Rockström, J., Steffen, W., Noone, K., Persson, Å., Chapin, F. S., Lambin, E. F., Lenton, T. M., Scheffer, M., Folke, C., Schellnhuber, H. J., et al. (2009) · Nature · doi:10.1038/461472a · Cited by 13,333
Ecosystems and Human Well-being: Synthesis
Assessment, M. E. (2005) · Island Press · doi:10.5281/zenodo.18167309 · Cited by 10,665
Cited by
Sorted by citations
Items 301–400 of 765
Guri, G., Westgaard, J., Yoccoz, N. G., Wangensteen, O. S., Præbel, K., Ray, J. L., Kelly, R. P., Shelton, A. O., Hanebrekke, T., & Johansen, T. (2023) · Environmental DNA · doi:10.1002/edn3.409 · Cited by 25
Using surface environmental DNA to assess arthropod biodiversity within a forested ecosystem
Allen, M. C., Lockwood, J. L., Kwait, R., Vastano, A. R., Peterson, D. L., Tkacenko, L. A., Kisurin, A., Stringham, O., Angle, J. C., & Jaffe, B. D. (2023) · Environmental DNA · doi:10.1002/edn3.487 · Cited by 25
Macher, J.-N., Macher, T., & Leese, F. (2017) · Metabarcoding and Metagenomics · doi:10.3897/mbmg.1.22262 · Cited by 25
“These techniques are becoming standard in many fields of research (Deiner et al. 2015, Choo et al. 2017, Macher et al. 2017), as well as application (Elbrecht et al. 2017).”
MethodSelf-citationBeentjes, K. K., Speksnijder, A. G. C. L., Schilthuizen, M., Schaub, B. E. M., & van der Hoorn, B. (2018) · Metabarcoding and Metagenomics · doi:10.3897/mbmg.2.26744 · Cited by 24
“…these novel strategies, especially the relationship between input biomass or specimen counts and output HTS sequence abundances (Amend et al. 2010, Aylagas et al. 2018, Deagle et al. 2013, Kelly et al. 2014, Elbrecht and Leese 2015, Piñol et al. 2015, Gibson et al. 2015, Hering et al. 2018).”
BackgroundBiases in the metabarcoding of plant pathogens using rust fungi as a model system
Makiola, A., Dickie, I. A., Holdaway, R. J., Wood, J. R., Orwin, K. H., Lee, C. K., & Glare, T. R. (2018) · MicrobiologyOpen · doi:10.1002/mbo3.780 · Cited by 25
“This suggests that previous problems when using quantitative next-generation sequencing data (Elbrecht & Leese, 2015; Piñol, Mir, Gomez‐Polo, & Agustí, 2015) were probably induced by PCR, and not by the method or sequencing platform per se.”
InfluentialGarcía‐Machado, E., Normandeau, É., Côté, G., & Bernatchez, L. (2023) · Environmental DNA · doi:10.1002/edn3.444 · Cited by 24
“We then trimmed the sequences outside the 5 ′ and 3 ′ primer regions and used PrimerMiner (Elbrecht & Leese, 2015) for in silico evaluation and optimization of the amplification primers for 16S and cytb (Appendix S2).”
MethodFAVIS: Fast and versatile protocol for non-destructive metabarcoding of bulk insect samples
Iwaszkiewicz-Eggebrecht, E., Łukasik, P., Buczek, M., Deng, J., Hartop, E., Havnås, H., Prus-Frankowska, M., Ugarph, C., Viteri, P., Andersson, A. F., et al. (2023) · PLoS ONE · doi:10.1371/journal.pone.0286272 · Cited by 24
Cram, J. A., Hollins, A., McCarty, A. J., Martinez, G., Cui, M., Gomes, M. L., & Fuchsman, C. A. (2024) · Environmental Microbiology · doi:10.1111/1462-2920.16557 · Cited by 24
Gösser, F., Schweinsberg, M., Mittelbach, P., Schoenig, E., & Tollrian, R. (2022) · Environmental DNA · doi:10.1002/edn3.378 · Cited by 25
Chapuis, S., Malewski, T., Suchecka, E., Geiger, M. F., Herder, F., & Bogdanowicz, W. (2018) · Fisheries Research · doi:10.1016/j.fishres.2018.02.007 · Cited by 23
Ritter, C. D., Zizka, A., Roger, F., Tuomisto, H., Barnes, C. J., Nilsson, R. H., & Antonelli, A. (2018) · PeerJ · doi:10.7717/peerj.5661 · Cited by 22
Sire, L., Gey, D., Debruyne, R., Noblecourt, T., Soldati, F., Barnouin, T., Parmain, G., Bouget, C., López‐Vaamonde, C., & Rougerie, R. (2019) · Frontiers in Ecology and Evolution · doi:10.3389/fevo.2019.00495 · Cited by 26
Atherton, S., & Jondelius, U. (2020) · Biodiversity Data Journal · doi:10.3897/bdj.8.e51813 · Cited by 22
Quantification of marine benthic communities with metabarcoding
Klunder, L., van Bleijswijk, J. D. L., Schaars, L. K., van der Veer, H. W., Luttikhuizen, P. C., & Bijleveld, A. I. (2021) · Molecular Ecology Resources · doi:10.1111/1755-0998.13536 · Cited by 24
“Methodological issues within the molecular method, which can hamper the assessment of a community, have been described extensively (e.g., Alberdi et al., 2018; Elbrecht & Leese, 2015; Kelly et al., 2019; Lanzén et al., 2017 and Piñol et al., 2019).”
MethodYates, M. C., Wilcox, T. M., Stoeckle, M. Y., & Heath, D. D. (2022) · Environmental DNA · doi:10.1002/edn3.381 · Cited by 24
“A number of factors (e.g., differences in PCR efficiency among species [Elbrecht & Leese, 2015; Leese et al., 2021], community composition [Piñol et al., 2019]) can potentially introduce substantial “noise” into the relationship between quantitative eDNA read data and organism abundance (Kelly et…”
BackgroundInfluentialTaking e DNA underground: Factors affecting e DNA detection of subterranean fauna in groundwater
van der Heyde, M., White, N. E., Nevill, P., Austin, A. D., Stevens, N., Jones, M., & Guzik, M. T. (2023) · Molecular Ecology Resources · doi:10.1111/1755-0998.13792 · Cited by 23
“Additionally, eDNAbased methods are notoriously unreliable for abundance estimates (Elbrecht & Leese, 2015), while morphological identification provides some population data on relative abundances of taxa from the specimens collected (Eberhard et al., 2009; Halse et al., 2014; Humphreys et al.,…”
MethodDrake, L. E., Cuff, J. P., Bedmar, S., McDonald, R. A., Symondson, W. O. C., & Chadwick, E. A. (2023) · Ecology and Evolution · doi:10.1002/ece3.10038 · Cited by 22
“…provides a greater insight into the species consumed by a predator, it cannot reveal the size or number of prey consumed (Deagle et al., 2013; Elbrecht & Leese, 2015; Hawlitschek et al., 2018; Mata et al., 2019; Pawluczyk et al., 2015; Piñol et al., 2015), potentially overlooking an…”
BackgroundWilson, J., Brandon-Mong, G.-J., Gan, H. M., & Sing, K. (2018) · Mitochondrial DNA Part A · doi:10.1080/24701394.2018.1455189 · Cited by 23
“While the high detection rates at shallow sequencing depths is the major advantage of metabarcoding, the major drawback (besides primer biases; Elbrecht and Leese 2015; Lee et al. 2015; Pi~ nol et al. 2015) appears to be errors introduced during PCR, which are then sequenced, and produce ‘spurious’ OTU (Flynn et al.”
BackgroundCoghlan, S. A., Currier, C. A., Freeland, J. R., Morris, T. J., & Wilson, C. C. (2021) · Environmental DNA · doi:10.1002/edn3.239 · Cited by 22
Using metatranscriptomics to estimate the diversity and composition of zooplankton communities
Lopez, M. L. D., Lin, Y., Sato, M., Hsieh, C., Shiah, F., & Machida, R. J. (2021) · Molecular Ecology Resources · doi:10.1111/1755-0998.13506 · Cited by 19
“…template mismatches across species may lead to inaccurate community analysis, with some species better amplified than others, such that the proportions in the final mixture do not reflect the original proportion of each species (Bista et al., 2018; Elbrecht & Leese, 2015; Leray et al., 2013).”
BackgroundMethodBucklin, A., Batta‐Lona, P. G., Questel, J. M., Wiebe, P. H., Richardson, D. E., Copley, N. J., & O’Brien, T. (2022) · Frontiers in Marine Science · doi:10.3389/fmars.2022.867893 · Cited by 22
Klunder, L., Lavaleye, M., Filippidi, A., van Bleijswijk, J. D. L., Reichart, G., van der Veer, H. W., Duineveld, G., & Mienis, F. (2018) · ICES Journal of Marine Science · doi:10.1093/icesjms/fsy114 · Cited by 22
Sander, M., Beermann, A. J., Buchner, D., Pimentel, I. M., Sinclair, J. S., Weiss, M., Haase, P., & Leese, F. (2024) · River Research and Applications · doi:10.1002/rra.4265 · Cited by 21
“Length variation was due to inline shifts (0 – 3 Ns) between the universal tail and the primer sequence to maximize diversity between sequences (Elbrecht & Leese, 2015).”
BackgroundSelf-citationUseros, F., García‐Cunchillos, I., Henry, N., Berney, C., & Lara, E. (2024) · Environmental Microbiology · doi:10.1111/1462-2920.16606 · Cited by 21
Macé, B., Mouillot, D., Dalongeville, A., Bruno, M., Déter, J., Varenne, A., Gudefin, A., Boissery, P., & Manel, S. (2024) · Molecular Ecology · doi:10.1111/mec.17373 · Cited by 21
“False-negative ones are more difficult to avoid, as it can be highly dependent of abiotic factors and primer bias (Burian et al., 2021; Elbrecht & Leese, 2015 ).”
BackgroundKnow your limits; miniCOI metabarcoding fails with key marine zooplankton taxa
Albaina, A., Garić, R., & Yebra, L. (2024) · Journal of Plankton Research · doi:10.1093/plankt/fbae057 · Cited by 23
Choo, L. Q., Crampton‐Platt, A., & Vogler, A. P. (2017) · Molecular Ecology · doi:10.1111/mec.14258 · Cited by 21
“…and addressed problems specifically related to the study of species abundance patterns by metabarcoding and potential artefacts from PCR biases (see Elbrecht & Leese, 2015), which in the simulations was shown to have a strong confounding effect on the community composition (Sommeria-Klein et al.,…”
BackgroundAzarian, C., Foster, S. D., Devloo‐Delva, F., & Feutry, P. (2020) · Environmental DNA · doi:10.1002/edn3.143 · Cited by 22
Fuchsman, C. A., Cherubini, L., & Hays, M. D. (2022) · Environmental Microbiology · doi:10.1111/1462-2920.15893 · Cited by 21
Chimeno, C., Hübner, J., Seifert, L., Morinière, J., Bozicevic, V., Hausmann, A., Schmidt, S., & Müller, J. C. (2022) · Insect Conservation and Diversity · doi:10.1111/icad.12609 · Cited by 20
“Although DNA metabarcoding has become a well-established method (Shum & Palumbi, 2021), a consensus workflow is still lacking in some fields of research (e.g. studies on terrestrial arthropods; see Elbrecht & Leese, 2015).”
MethodRobinson, C. V., Porter, T. M., Maitland, V. C., Wright, M., & Hajibabaei, M. (2022) · Ecological Indicators · doi:10.1016/j.ecolind.2022.109603 · Cited by 23
Baetscher, D. S., Locatelli, N. S., Won, E., Fitzgerald, T. P., McIntyre, P. B., & Therkildsen, N. O. (2023) · Environmental DNA · doi:10.1002/edn3.479 · Cited by 25
The Chironomidae (Diptera) of Svalbard and Jan Mayen
Stur, E., & Ekrem, T. (2020) · Insects · doi:10.3390/insects11030183 · Cited by 21
Towards quantitative DNA Metabarcoding: A method to overcome PCR amplification biasPreprint
Moinard, S., Piau, D., Laporte, F., Rioux, D., Taberlet, P., Melodelima, C., & Coissac, É. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.10.03.560640 · Cited by 21
“First, if the amount of DNA shed into the environment depends on the biomass of individuals (Elbrecht & Leese, 2015; Elbrecht, Peinert, & Leese, 2017; Lamb et al., 2019), it is also a function of shedding rates specific to each DNA source (Wilder, Farrell, & Green, 2023).”
BackgroundWolf, D. I., & Vis, M. L. (2019) · Journal of Phycology · doi:10.1111/jpy.12935 · Cited by 20
Eukaryotic diversity of marine biofouling from coastal to offshore areas
Portas, A., Quillien, N., Culioli, G., & Briand, J. (2022) · Frontiers in Marine Science · doi:10.3389/fmars.2022.971939 · Cited by 20
“These differences can be influenced by both PCR- bias and gene copy number that varies considerably across taxa and sometimes within taxa (Elbrecht and Leese, 2015; Jeunen et al., 2019; Lamb et al., 2019).”
BackgroundEcological network structure in response to community assembly processes over evolutionary time
Graham, N. R., Krehenwinkel, H., Lim, J. Y., Staniczenko, P. P. A., Callaghan, J., Andersen, J. C., Gruner, D. S., & Gillespie, R. G. (2023) · Molecular Ecology · doi:10.1111/mec.16873 · Cited by 20
“To reduce bias due to differently sized individuals contributing disproportionate amounts of DNA (Elbrecht & Leese, 2015) specimens were sorted following procedures described in Lim et al. (2021).”
MethodAssessing the response of an urban stream ecosystem to salinization under different flow regimes
Pimentel, I. M., Baikova, D., Buchner, D., Burfeid-Castellanos, A. M., David, G. M., Deep, A., Doliwa, A., Hadžiomerović, U., Mayombo, N. A. S., Prati, S., et al. (2024) · The Science of The Total Environment · doi:10.1016/j.scitotenv.2024.171849 · Cited by 20
Self-citationGarrido‐Sanz, L., Senar, M. À., & Piñol, J. (2020) · Metabarcoding and Metagenomics · doi:10.3897/mbmg.4.48281 · Cited by 18
“One PCR-free approach is shotgun metagenomics, where the extracted DNA is sequenced directly, so all PCR-generated biases are avoided (Taberlet et al. 2012; Yu et al. 2012; Zhou et al. 2013; Elbrecht and Leese 2015).”
MethodPan, Y., Qiu, D., Chen, J., & Yue, Q. (2020) · Journal of Food Quality · doi:10.1155/2020/2907670 · Cited by 22
Using patterns in prey DNA digestion rates to quantify predator diets
Uiterwaal, S. F., & DeLong, J. P. (2020) · Molecular Ecology Resources · doi:10.1111/1755-0998.13231 · Cited by 20
“While some studies suggest that metabarcoding data cannot be used quantitatively (Elbrecht & Leese, 2015), more recent work suggests that varying levels of quantification may be possible using relative read abundances as a proxy for biomass (Deagle et al., 2019;Edgar, 2017) or with certain primers…”
BackgroundLangat, S. K., Eyase, F. L., Bulimo, W., Lutomiah, J., Oyola, S. O., Imbuga, M., & Sang, R. C. (2021) · mSphere · doi:10.1128/msphere.00551-21 · Cited by 20
Yang, X., Yu, X., Zhang, X., Guo, H., Xing, Z., Xu, L., Wang, J., Shen, Y., Yu, J., Lv, P., et al. (2022) · Frontiers in Plant Science · doi:10.3389/fpls.2022.819822 · Cited by 18
Macher, J.-N., Bloska, D. M., Holzmann, M., Girard, E., Pawłowski, J., & Renema, W. (2022) · PeerJ · doi:10.7717/peerj.13952 · Cited by 18
Willassen, E., Westgaard, J., Kongsrud, J. A., Hanebrekke, T., Buhl‐Mortensen, P., & Holte, B. (2022) · PeerJ · doi:10.7717/peerj.14321 · Cited by 22
“However, competing non-target DNA may prevent detection of targeted species so that high proportions of the fauna fail detection with metabarcoding ( Alberdi et al., 2018 ; Collins et al., 2019 ; Cowart et al., 2015 ; Elbrecht & Leese, 2015 ).”
Macher, J., Zizka, V. M. A., Weigand, A. M., & Leese, F. (2017) · Methods in Ecology and Evolution · doi:10.1111/2041-210x.12937 · Cited by 18
“…the potential for future biodiversity assessments (Coissac, Hollingsworth, Lavergne, & Taberlet, 2016; Crampton- Platt, Yu, Zhou, & Vogler, 2016; Elbrecht & Leese, 2015; Tang et al., 2014; Zhou et al., 2013) by circumventing taxon- dependent PCR amplification biases and offering the possibility…”
BackgroundSelf-citationCobble community DNA as a tool to monitor patterns of biodiversity within kelp forest ecosystems
Shum, P., Barney, B. T., O’Leary, J. K., & Palumbi, S. R. (2019) · Molecular Ecology Resources · doi:10.1111/1755-0998.13067 · Cited by 19
“…of sample types (sediment: Guardiola et al., 2011, sub‐ strate: Wangensteen et al., 2018, seawater: Bakker et al., 2017, bulk invertebrate samples: Elbrecht & Leese, 2015, stomach con‐ tents: Siegenthaler, Wangensteen, Benvenuto, Campos, & Mariani, 2019a and scat: Berry et al., 2017), to more…”
BackgroundTzafesta, E., Zangaro, F., Specchia, V., & Pinna, M. (2021) · Diversity · doi:10.3390/d13030112 · Cited by 20
Machida, R. J., Kurihara, H., Nakajima, R., Sakamaki, T., Lin, Y., & Furusawa, K. (2021) · ICES Journal of Marine Science · doi:10.1093/icesjms/fsab084 · Cited by 20
Garrido‐Sanz, L., Senar, M. À., & Piñol, J. (2021) · Molecular Ecology Resources · doi:10.1111/1755-0998.13464 · Cited by 18
Alignment-free classification of COI DNA barcode data with the Python package Alfie
Nugent, C. M., & Adamowicz, S. J. (2020) · Metabarcoding and Metagenomics · doi:10.3897/mbmg.4.55815 · Cited by 21
“The characterization of biodiversity can be further confounded by intra-group PCR bias, where the over representation of certain taxa within the target group can result in other taxa being overlooked due to poorer amplification and sequencing coverage (Elbrecht and Leese 2015).”
BackgroundKaczmarek, M., Entling, M. H., & Hoffmann, C. (2022) · Insects · doi:10.3390/insects13060507 · Cited by 20
“Thus, no accurate conclusion can be made about the abundance of individual species in single samples [29].”
BackgroundHoenig, B. D., Trevelline, B. K., Kautz, A. R., Latta, S. C., & Porter, B. A. (2022) · Molecular Ecology · doi:10.1111/mec.16688 · Cited by 18
Emmons, S. C., Compson, Z. G., Malish, M. C., Busch, M. H., Saenz, V., Higgins, K. T., & Allen, D. C. (2023) · Environmental DNA · doi:10.1002/edn3.453 · Cited by 19
Raime, K., & Remm, M. (2018) · Frontiers in Plant Science · doi:10.3389/fpls.2018.00006 · Cited by 21
“Varied polymerase chain reaction (PCR) success for selected genes, gene copy numbers and PCR bias caused by primertemplate mismatches across species may cause species to be missed and reduce the quantitative potential of the method (Elbrecht and Leese, 2015; Piñol et al., 2015).”
MethodSelenium oxyanion bioconcentration in natural freshwater periphyton
Markwart, B. E., Liber, K., Xie, Y., Raes, K., Hecker, M., Janz, D. M., & Doig, L. E. (2019) · Ecotoxicology and Environmental Safety · doi:10.1016/j.ecoenv.2019.05.004 · Cited by 18
Matsuoka, S., Sugiyama, Y., Tateno, R., Imamura, S., Kawaguchi, E., & Osono, T. (2020) · Royal Society Open Science · doi:10.1098/rsos.191952 · Cited by 18
Reckem, E. N. V., Charmpi, C., der Veken, D. V., Borremans, W., Vuyst, L. D., Weckx, S., & Leroy, F. (2020) · Foods · doi:10.3390/foods9091247 · Cited by 18
“The fact that the genus Staphylococcus was not encountered across all Belgian and German fermented meat product samples when targeting the V4 region, did not necessarily infer its absence, as differences in biomass and 16S rRNA copy numbers may cause less abundant genera to be under the detection limit [56,57].”
BackgroundPaula, D. P., Barros, S. K. A., Pitta, R. M., Barreto, M. R., Togawa, R. C., & Andow, D. A. (2022) · GigaScience · doi:10.1093/gigascience/giac020 · Cited by 15
Correia, E., Granadeiro, J. P., Santos, B., Regalla, A., Mata, V. A., & Catry, T. (2023) · Marine Ecology Progress Series · doi:10.3354/meps14241 · Cited by 17
“However, since the number of reads may be mostly influenced by unpredictable PCR and sequencing bias (Deagle et al. 2019, Jusino et al. 2019), presence− absence results may still be considered more reliable in most case studies (Elbrecht & Leese 2015).”
BackgroundStainton, K., McGreig, S., Conyers, C. M., Ponting, S., Butler, L., Brown, P., & Jones, E. P. (2023) · Animals · doi:10.3390/ani13030511 · Cited by 17
“extracted from each organism, how quickly different species and life stages are digested in the gut, and primer biases in which species amplify better in the PCR stage [30].”
BackgroundKestel, J. H., Bateman, P. W., Field, D. L., White, N. E., Lines, R., & Nevill, P. (2023) · Molecular Ecology Resources · doi:10.1111/1755-0998.13814 · Cited by 17
Aerospace-foraging bats eat seasonably across varying habitats
Aihartza, J., Vallejo, N., Aldasoro, M., Mudarra, J. L. G., Goiti, U., Nogueras, J., & Ibáñez, C. (2023) · Scientific Reports · doi:10.1038/s41598-023-46939-7 · Cited by 21
Overlooked Role of Fungi in Drinking Water Taste and Odor Issues
Zhao, H.-X., He, H., Zeng, C., Zhang, T., Hu, C., Pan, R., Xu, M., Tang, Y., & Xu, B. (2024) · Environmental Science & Technology · doi:10.1021/acs.est.4c02575 · Cited by 17
Aylagas, E., & Rodríguez‐Ezpeleta, N. (2016) · Methods in molecular biology · doi:10.1007/978-1-4939-3774-5_16 · Cited by 17
Schmertmann, L. J., Irinyi, L., Malík, R., Powell, J. R., Meyer, W., & Krockenberger, M. B. (2019) · Ecology and Evolution · doi:10.1002/ece3.5498 · Cited by 16
“…with care, as a number of technical issues and biases inherent in amplicon‐based metabarcoding have been reported, including: PCR primer selection (Elbrecht & Leese, 2015; Pinto & Raskin, 2012), tag switching (Esling, Lejzerowicz, & Pawlowski, 2015; Schnell, Bohmann, & Gilbert, 2015), template…”
BackgroundFais, M., Bellisario, B., Duarte, S., Vieira, P. E., Sousa, R., Canchaya, C. A., & Costa, F. O. (2020) · Regional Studies in Marine Science · doi:10.1016/j.rsma.2020.101341 · Cited by 17
DNA metabarcoding reveals a broad dietary range for Tasmanian devils introduced to a naive ecosystem
McLennan, E. A., Wise, P., Lee, A. V., Grueber, C. E., Belov, K., & Hogg, C. J. (2022) · Ecology and Evolution · doi:10.1002/ece3.8936 · Cited by 16
“Attempts to correlate the number of sequence reads with the biomass of a specimen have had variable results, given the risks of amplification bias with unequal primer binding efficiency across species (Alberdi et al., 2017; Elbrecht & Leese, 2015).”
BackgroundHerrera‐Mesías, F., Bause, C., Ogan, S., Burger, H., Ayasse, M., Weigand, A. M., & Eltz, T. (2022) · Journal of Hymenoptera Research · doi:10.3897/jhr.93.86723 · Cited by 16
Broad ecological threats of an invasive hornet revealed through a deep sequencing approach
Pedersen, S., Kennedy, P. J., O’Shea-Wheller, T. A., Poidatz, J., Christie, A., Osborne, J. L., & Tyler, C. R. (2025) · The Science of The Total Environment · doi:10.1016/j.scitotenv.2025.178978 · Cited by 19
Jo, J., Lee, H.-G., Kim, K. Y., & Park, C. (2019) · ALGAE · doi:10.4490/algae.2019.34.2.26 · Cited by 17
“…the Qiagen DNeasy Blood/Tissue Kit (Qiagen, Hilden, Germany) following the manufacturer’s protocol, and the purified DNA was stored at -80°C until needed. genetic markers (e.g., mitochondrial DNA, chloroplast DNA, and rRNA genes) (Andújar et al. 2015, Greshake et al. 2016, Hillmann et al. 2018).”
MethodKlunder, L., Duineveld, G., Lavaleye, M., van der Veer, H. W., Palsbøll, P. J., & van Bleijswijk, J. D. L. (2019) · Journal of Sea Research · doi:10.1016/j.seares.2019.101764 · Cited by 15
“However, taxonomic resolution will decrease inherently (Elbrecht and Leese, 2015).”
Ustinova, E. N., Schepetov, D. М., Lysenkov, S. N., & Tiunov, A. V. (2021) · Soil Biology and Biochemistry · doi:10.1016/j.soilbio.2021.108288 · Cited by 16
Pinna, M., Saccomanno, B., Marini, G., Zangaro, F., Kabayeva, A., Khalaj, M., Shaimardan, L., D’Attis, S., Tzafesta, E., & Specchia, V. (2021) · Biology · doi:10.3390/biology10111092 · Cited by 16
Expanding network ecology in freshwater ecosystems
Windsor, F. M. (2023) · Journal of Animal Ecology · doi:10.1111/1365-2656.13947 · Cited by 15
“A limitation of molecular techniques is that generating quantitative data, although technically possible (Thomas et al., 2016), is fraught with biases and caveats (Elbrecht et al., 2017; Elbrecht & Leese, 2015).”
BackgroundPedro, P. M., Piper, R., Neto, P. B., Cullen, L., Dropa, M., Lorencao, R., Matté, M. H., Rech, T. C., Rufato, M. O., Silva, M., et al. (2017) · Environmental Entomology · doi:10.1093/ee/nvx166 · Cited by 15
Turunen, J., Mykrä, H., Elbrecht, V., Steinke, D., Braukmann, T., & Aroviita, J. (2021) · Metabarcoding and Metagenomics · doi:10.3897/mbmg.5.68938 · Cited by 13
“The poor correlation of DNA sequence abundance with species´ abundance is one of the key limitations for metabarcoding in biomonitoring applications for which abundance information is needed (Elbrecht and Leese 2015).”
BackgroundSelf-citationThe application of multi-locus DNA metabarcoding in traditional medicines
Arulandhu, A. J., Staats, M., Hagelaar, R., Peelen, T., & Kok, E. J. (2019) · Journal of Food Composition and Analysis · doi:10.1016/j.jfca.2019.03.007 · Cited by 15
Wells, C. D., Paulay, G., Nguyen, B., & Leray, M. (2021) · Environmental DNA · doi:10.1002/edn3.225 · Cited by 15
Elbrecht, V., & Leese, F. (2017) · Frontiers in Environmental Science · doi:10.3389/fenvs.2017.00038 · Cited by 15
Self-citationvan der Heyde, M., Bunce, M., Dixon, K. W., Fernandes, K., Majer, J. D., Wardell‐Johnson, G., White, N. E., & Nevill, P. (2022) · Molecular Ecology · doi:10.1111/mec.16375 · Cited by 14
“Although abundance estimates using DNA metabarcoding are often skewed by primer bias (Elbrecht & Leese, 2015), and/or DNA extraction method (Majaneva et al., 2018), presence/absence data has been used to demonstrate arthropod responses to restoration post mining (Fernandes et al., 2019) and to…”
Hintikka, S., Carlsson, J. E. L., & Carlsson, J. (2022) · Metabarcoding and Metagenomics · doi:10.3897/mbmg.6.80416 · Cited by 14
Dopheide, A., Davis, C., Wakelin, S. A., Whitehead, D. C., & Grelet, G. (2023) · Biology and Fertility of Soils · doi:10.1007/s00374-023-01710-y · Cited by 15
“In addition, inferences of organism abundances based on metabarcoding data are confounded by PCR biases (Pinto and Raskin 2012; Elbrecht and Leese 2015), and further qPCR measurements would be needed to confirm abundance changes among different taxa.”
BackgroundFueyo, Á., Sánchez, O., Coya, R., Carleos, C. E., Escudero, A., Cordón, J., Fernández, S., Granero‐Castro, J., & Borrell, Y. J. (2023) · Ecological Indicators · doi:10.1016/j.ecolind.2023.111454 · Cited by 14
Detection, movement and persistence of invertebrate eDNA in groundwater
Korbel, K. L., Hose, G. C., Karwautz, C., Greenfield, P. A., Wang, H., Chariton, A. A., & Griebler, C. (2024) · Scientific Reports · doi:10.1038/s41598-024-67349-3 · Cited by 14
BirT : A Novel Primer Pair for Avian Environmental DNA Metabarcoding
Thalinger, B., Empey, R., Cowperthwaite, M., Coveny, K., & Steinke, D. (2026) · Environmental DNA · doi:10.1002/edn3.70255 · Cited by 16
BBI: an R package for the computation of Benthic Biotic Indices from composition data
Cordier, T., & Pawlowski, J. W. (2018) · Metabarcoding and Metagenomics · doi:10.3897/mbmg.2.25649 · Cited by 14
“…as a proxy for species abundance (sensu gAMBI, see Aylagas et al. 2014), although the direct comparison is not straightforward, because the abundance of reads is not necessarily reflecting accurately the abundance of the species (Elbrecht and Leese 2015, Vivien et al. 2015, Dowle et al. 2016).”
BackgroundSilva, A. J., Kawalek, M. D., Williams-Hill, D. M., & Hellberg, R. S. R. (2020) · Frontiers in Ecology and Evolution · doi:10.3389/fevo.2020.00028 · Cited by 14
RNA metabarcoding helps reveal zooplankton community response to environmental stressors
Ankley, P. J., Xie, Y., Havens, S. M., Peters, L., Timlick, L., Rodríguez‐Gil, J. L., Giesy, J. P., & Palace, V. P. (2021) · Environmental Pollution · doi:10.1016/j.envpol.2021.118446 · Cited by 14
“For zooplankton meta-barcoding, mitochondrial COI is a protein-coding gene, with the abundance of DNA relative sequence counts being comparatively reflective of the biomass of target organisms (Ankley et al., 2021; Elbrecht and Leese, 2015; Yang et al., 2017b).”
Govender, A., Singh, S. P., Groeneveld, J. C., Pillay, S., & Willows‐Munro, S. (2022) · Molecular Ecology · doi:10.1111/mec.16567 · Cited by 13
“Lower confidence in relative abundance estimates (measured as read counts in metabarcoding) has been expressed by Elbrecht and Leese (2015), Piñol et al. (2015) and Jusino et al. (2019), although these estimates have been successfully used for nematode communities (Schenk et al., 2019), arthropod…”
MethodLaini, A., Beermann, A. J., Bolpagni, R., Burgazzi, G., Elbrecht, V., Zizka, V. M. A., Leese, F., & Viaroli, P. (2020) · Metabarcoding and Metagenomics · doi:10.3897/mbmg.4.51433 · Cited by 14
“This is especially true when considering that metabarcoding does not provide abundance estimates (Elbrecht and Leese 2015) and may fail to recover small or rare taxa (Hajibabaei et al. 2011, Leray and Knowlton 2017).”
BackgroundMethodSelf-citationPark, E., & Poulin, R. (2020) · Scientific Reports · doi:10.1038/s41598-020-73986-1 · Cited by 14
Krey, K. L., Cooper, W. R., & Renkema, J. M. (2020) · Environmental Entomology · doi:10.1093/ee/nvaa125 · Cited by 14
Taberlet, P., Bonin, A., Zinger, L., & Coissac, É. (2018) · Oxford University Press eBooks · doi:10.1093/oso/9780198767220.003.0014 · Cited by 15
Pest control services on farms vary among bird species on diversified, low-intensity farms
Mayne, S. J., King, D. I., Andersen, J. C., & Elkinton, J. S. (2023) · Global Ecology and Conservation · doi:10.1016/j.gecco.2023.e02447 · Cited by 12
“This means that 1) at present, we cannot accurately determine relative abundance of species in a sample, limiting us to presence-absence data (Elbrecht and Leese, 2015; Jusino et al., 2019), and 2) the presence or absence of species may depend on the primer pairs used (Jusino et al., 2019).”
BackgroundHawthorne, B. S. J., Cuff, J. P., Collins, L., & Evans, D. M. (2024) · Agricultural and Forest Entomology · doi:10.1111/afe.12628 · Cited by 14
“A study by Butterwort et al. (2022) tested this, however, and found non-significant inhibition of PCR with different concentrations of this solvent.”
InfluentialIntroduction to environmental DNA (eDNA)
Taberlet, P., Bonin, A., Zinger, L., & Coissac, É. (2018) · Oxford University Press eBooks · doi:10.1093/oso/9780198767220.003.0001 · Cited by 17
Mechai, S., Bilodeau, G. J., Lung, O., Roy, M., Steeves, R., Gagné, N., Baird, D. J., Lapen, D. R., Ludwig, A., & Ogden, N. H. (2021) · Journal of Medical Entomology · doi:10.1093/jme/tjab046 · Cited by 14
Domènech, M., Wangensteen, O. S., Enguídanos, A., Malumbres‐Olarte, J., & Arnedo, M. A. (2022) · Molecular Ecology Resources · doi:10.1111/1755-0998.13625 · Cited by 15
“Several studies have specifically addressed this issue (Deagle et al., 2019 ; Elbrecht & Leese, 2015 ; Lamb et al., 2019 ; Piñol et al., 2015 ), but the answer remains inconclusive.”
BackgroundTHAPBI PICT—a fast, cautious, and accurate metabarcoding analysis pipeline
Cock, P., Cooke, D. E. L., Thorpe, P., & Pritchard, L. (2023) · PeerJ · doi:10.7717/peerj.15648 · Cited by 13
Metadata
- Authors
- Elbrecht, V., & Leese, F.
- Affiliations
- Ruhr University Bochum (DE)
- Corresponding author
- Leese, Florian
- Venue
- PLOS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2015-07-08
- Volume
- 10
- Issue
- 7
- Pages
- e0130324
- ISSN
- 1932-6203 (ISSN-L)
- PMC
- PMC4496048
- OpenAlex
- W1551951435
- Semantic Scholar
- 5b5925709b20821df1f956c4c737e5fadb1e8b43
- Cited by
- 765
- References
- 60
- Citations by year
- 2026: 75 · 2025: 73 · 2024: 49 · 2023: 69 · 2022: 71 · 2021: 91 · 2020: 75 · 2019: 73 · 2018: 108 · 2017: 51 · 2016: 26 · 2015: 3
- FWCI
- 56.82
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- PLoS ONE (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Figshare (submittedVersion, cc-by)
- Topics
- Physical Sciences › Environmental Science › Ecology › Environmental DNA in Biodiversity Studies
- Life Sciences › Agricultural and Biological Sciences › Ecology, Evolution, Behavior and Systematics › Invertebrate Taxonomy and Ecology
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Keywords
- DNA metabarcoding, primer bias, species abundance estimation, COI barcoding, freshwater macroinvertebrates, Plecoptera, MiSeq sequencing, biodiversity assessment
- MeSH terms
- Animals, Electron Transport Complex IV, Diptera, DNA, Fresh Water, Haplotypes, Species Specificity, Reproducibility of Results, Polymerase Chain Reaction, Ecosystem, DNA Primers, Biomass, Biodiversity, DNA Barcoding, Taxonomic, High-Throughput Nucleotide Sequencing, Odonata
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
A language model drew the claims from the paper on 2026-10-06, under version 3 of the claim definition (model deepseek-v4.1-flash, prompt extract-v3).
A second model labelled each claim on 2026-10-06 (model jev-1.13-20260917, definition revision gold-guideline-v0.2).
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
