ReviewMolecular ecology resources2023
Extracting abundance information from DNA-based data.
Review in Molecular ecology resources, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
17 citing papers in PubMed.
- Conservation Planning and Reporting Implications of qPCR-based Multi-species eDNA Detection Under EU Environmental Regulations.Environmental management · 2026Article
- A multi-modal dataset for insect biodiversity with imagery and DNA at the trap and individual level.Scientific data · 2026Article
- Limitations of Common Molecular Markers in Fungal Biodiversity Analysis and the Benefits of Their Synergistic Use.Molecular ecology resources · 2026Article
- Accuracy of occurrence and abundance estimates from insect metabarcoding.bioRxiv : the preprint server for biology · 2026Article
- Compact bacterial recombination complexes drive efficient kilobase-scale knock-in in mammalian cells.Nucleic acids research · 2026Article
- Comparison of Morphological and DNA-Based Identification Methods to Assess Earthworm (Clitellata: Lumbricidae) Diversity at 25 Permanent Soil Monitoring Sites in Germany.Ecology and evolution · 2025Article
- Comparative Analysis of Pasture Composition: DNA Metabarcoding Versus Quadrat-Based Botanical Surveys in Experimental Grassland Plots.Ecology and evolution · 2025Article
- Combining environmental DNA and remote sensing for efficient, fine-scale mapping of arthropod biodiversity.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2024Article
- Three steps towards comparability and standardization among molecular methods for characterizing insect communities.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2024Article
- Towards holistic insect monitoring: species discovery, description, identification and traits for all insects.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2024Review
- Capacity and establishment rules govern the number of nonnative species in communities of ground-dwelling invertebrates.Ecology and evolution · 2024Article
- Consistent effects of independent domestication events on the plant microbiota.Current biology : CB · 2024Article
- Conceptual and empirical bridges between micro- and macroevolution.Nature ecology & evolution · 2023Review
- Optimizing insect metabarcoding using replicated mock communities.Methods in ecology and evolution · 2023Article
- Extracting abundance information from DNA-based data.Molecular ecology resources · 2023Review
- Article
- FAVIS: Fast and versatile protocol for non-destructive metabarcoding of bulk insect samples.PloS one · 2023Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
The accurate extraction of species-abundance information from DNA-based data (metabarcoding, metagenomics) could contribute usefully to diet analysis and food-web reconstruction, the inference of species interactions, the modelling of population dynamics and species distributions, the biomonitoring of environmental state and change, and the inference of false positives and negatives. However, multiple sources of bias and noise in sampling and processing combine to inject error into DNA-based data sets. To understand how to extract abundance information, it is useful to distinguish two concepts. (i) Within-sample across-species quantification describes relative species abundances in one sample. (ii) Across-sample within-species quantification describes how the abundance of each individual species varies from sample to sample, such as over a time series, an environmental gradient or different experimental treatments. First, we review the literature on methods to recover across-species abundance information (by removing what we call "species pipeline biases") and within-species abundance information (by removing what we call "pipeline noise"). We argue that many ecological questions can be answered with just within-species quantification, and we therefore demonstrate how to use a "DNA spike-in" to correct for pipeline noise and recover within-species abundance information. We also introduce a model-based estimator that can be used on data sets without a physical spike-in to approximate and correct for pipeline noise.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.