ArticleMolecular ecology2021
Nuclear eDNA estimates population allele frequencies and abundance in experimental mesocosms and field samples.
Article in Molecular ecology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 84 citations in OpenAlex.
- Article
- Enhancing Intra-Specific Population Genetic Studies of Bottlenose Dolphins (Ecology and evolution · 2026Article
- Prospects of multipurpose biomonitoring for fisheries assessment based on environmental nucleic acids.Journal of fish biology · 2026Review
- Individual Identification of Prey in Carnivore Scats.Molecular ecology resources · 2026Article
- Hybrid Horizons: Screening Hybridisation Through Nuclear Environmental DNA.Molecular ecology resources · 2026Article
- Estimating Organism Abundance Using Within-Sample Haplotype Frequencies of eDNA Data.Molecular ecology resources · 2026Article
- Unlocking Demography: Developing an eDNA-Based Toolkit to Measure Sex Ratios From Populations.Molecular ecology resources · 2026Article
- Unlocking natural history collections to improve eDNA reference databases and biodiversity monitoring.Bioscience · 2025Article
- Environmental DNA as a tool for hydropower impact assessments: current status, special considerations, and future integration.Biological reviews of the Cambridge Philosophical Society · 2025Review
- Counting the Invisible: New Tools to Estimate the Number of Contributors From Sequence-Based Microsatellite Genotyping of Environmental DNA Samples.Molecular ecology resources · 2025Article
- gmmDenoise: A New Method and R Package for High-Confidence Sequence Variant Filtering in Environmental DNA Amplicon Analysis.Molecular ecology resources · 2025Article
- Biomonitoring 2.0 Refined: observing local change through metaphylogeography using a community-based eDNA metabarcoding monitoring network.BMC biology · 2025Article
- Experimental evaluation of genetic variability based on DNA metabarcoding from the aquatic environment: Insights from the LerayEcology and evolution · 2024Article
- Nuclear environmental DNA resolves fine-scale population genetic structure in an aquatic habitat.iScience · 2024Article
- Article
- Plants, pollinators and their interactions under global ecological change: The role of pollen DNA metabarcoding.Molecular ecology · 2023Article
- Environmental DNA reveals the genetic diversity and population structure of an invasive species in the Laurentian Great Lakes.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Inadvertent human genomic bycatch and intentional capture raise beneficial applications and ethical concerns with environmental DNA.Nature ecology & evolution · 2023Article
- Managing human-mediated range shifts: understanding spatial, temporal and genetic variation in marine non-native species.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2022Article
- Reinforcement of Environmental DNA Based Methods (Biology · 2021Review
Corrections and comments
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Authors and funding
4 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Advances in environmental DNA (eDNA) methodologies have led to improvements in the ability to detect species and communities in aquatic environments, yet the majority of studies emphasize biological diversity at the species level by targeting variable sites within the mitochondrial genome. Here, we demonstrate that eDNA approaches also have the capacity to detect intraspecific diversity in the nuclear genome, allowing for assessments of population-level allele frequencies and estimates of the number of genetic contributors in an eDNA sample. Using a panel of microsatellite loci developed for the round goby (Neogobius melanostomus), we tested the similarity between eDNA-based and individual tissue-based estimates of allele frequencies from experimental mesocosms and in a field-based trial. Subsequently, we used a likelihood-based DNA mixture framework to estimate the number of unique genetic contributors in eDNA samples and in simulated mixtures of alleles. In both mesocosm and field samples, allele frequencies from eDNA were highly correlated with allele frequencies from genotyped round goby tissue samples, indicating nuclear markers can be reliably amplified from water samples. DNA mixture analyses were able to estimate the number of genetic contributors from mesocosm eDNA samples and simulated mixtures of DNA from up to 58 individuals, with the degree of positive or negative bias dependent on the filtering scheme of low-frequency alleles. With this study we document the application of eDNA and multiple amplicon-based methods to obtain intraspecific nuclear genetic information and estimate the absolute abundance of a species in eDNA samples. With proper validation, this approach has the potential to advance noninvasive survey methods to characterize populations and detect population-level genetic diversity.
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