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eDNA metabarcoding: a non-invasive method to track temporal community dynamics in temporary rivers. Limnetica 45: 1.
DOI: 10.23818/limn.45.02
Beyond borders: The role of protected areas in promoting bat-mediated pest suppression in rural areas of Madagascar. Agriculture, Ecosystems & Environment 387: 109590.
DOI: 10.1016/j.agee.2025.109590
Bone appétit: DNA metabarcoding as a non-lethal alternative to morphological dietary assessment in Atlantic bonefish (Albula vulpes). Environmental Biology of Fishes 106: 337.
DOI: 10.1007/s10641-022-01328-3
DNA Metabarcoding Reveals Insights into Diet Partitioning and Pest Suppression by Open Space Bats in Agricultural Landscapes. Acta Chiropterologica 26: .
DOI: 10.3161/15081109ACC2024.26.2.003
Anthropogenic activities altering the ecosystem in Lake Yamzhog Yumco, southern Qinghai-Tibetan Plateau. Science of The Total Environment 904: 166715.
DOI: 10.1016/j.scitotenv.2023.166715
How non-target chironomid communities respond to mosquito control: Integrating DNA metabarcoding and joint species distribution modelling. Science of The Total Environment 913: 169735.
DOI: 10.1016/j.scitotenv.2023.169735
Persisting roadblocks in arthropod monitoring using non-destructive metabarcoding from collection media of passive traps. PeerJ 11: e16022.
DOI: 10.7717/peerj.16022
Feeding ecology of a highly aerial bird during its long breeding season. Avian Research 14: 100073.
DOI: 10.1016/j.avrs.2022.100073
Hidden diversity: DNA metabarcoding reveals hyper-diverse benthic invertebrate communities. BMC Ecology and Evolution 23: .
DOI: 10.1186/s12862-023-02118-w
DNA metabarcoding and morphological identification reveal similar richness, taxonomic composition and body size patterns among flying insect communities. Insect Conservation and Diversity 17: 449.
DOI: 10.1111/icad.12710
Mitochondrial cytochrome c oxidase subunit I (COI) metabarcoding of Foraminifera communities using taxon-specific primers. PeerJ 10: e13952.
DOI: 10.7717/peerj.13952
Maximizing Identification Precision of Hymenoptera and Brachycera (Diptera) With a Non‐Destructive DNA Metabarcoding Approach. Ecology and Evolution 15: .
DOI: 10.1002/ece3.70770
Synchronised monitoring of plant and insect diversity: a case study using automated Malaise traps and DNA-based methods. Biodiversity Data Journal 12: .
DOI: 10.3897/BDJ.12.e127669
Ecological networks reveal strong pest suppression complementarity between birds and bats within rice-dominated agroecosystems in West Africa. Agriculture, Ecosystems & Environment 396: 110020.
DOI: 10.1016/j.agee.2025.110020
Repeated subsamples during DNA extraction reveal increased diversity estimates in DNA metabarcoding of Malaise traps. Ecology and Evolution 12: .
DOI: 10.1002/ece3.9502
TaxonTableTools: A comprehensive, platform‐independent graphical user interface software to explore and visualise DNA metabarcoding data. Molecular Ecology Resources 21: 1705.
DOI: 10.1111/1755-0998.13358
Successive accumulation of biotic assemblages at a fine spatial scale along glacier-fed waters. iScience 27: 109476.
DOI: 10.1016/j.isci.2024.109476
How dispersal rates depend on the prey capture strategy: A case study of Georgia's spiders. Ecology and Evolution 14: .
DOI: 10.1002/ece3.11372
Is it worth the extra mile? Comparing environmental DNA and RNA metabarcoding for vertebrate and invertebrate biodiversity surveys in a lowland stream. PeerJ 12: e18016.
DOI: 10.7717/peerj.18016
Can metabarcoding resolve intraspecific genetic diversity changes to environmental stressors? A test case using river macrozoobenthos. Metabarcoding and Metagenomics 4: .
DOI: 10.3897/mbmg.4.51925
Seasonal shift in the diet of the notched-eared bat (Myotis emarginatus) in the Basque Country: from flies to spiders. Mammalian Biology 103: 419.
DOI: 10.1007/s42991-023-00353-8
Upscaling biodiversity monitoring: Metabarcoding estimates 31,846 insect species from Malaise traps across Germany. Molecular Ecology Resources 25: .
DOI: 10.1111/1755-0998.14023
Birds as potential suppressing agents of eucalypt plantations’ insect pests. BioControl 67: 571.
DOI: 10.1007/s10526-022-10164-4
Using eDNA metabarcoding to capture a snapshot of plankton community composition in the western Marmara Sea and northeastern Aegean Sea. Marine Biodiversity 55: .
DOI: 10.1007/s12526-025-01544-x
Assessing flower‐visiting arthropod diversity in apple orchards through metabarcoding of environmental DNA from flowers and visual census. Environmental DNA 5: 117.
DOI: 10.1002/edn3.362
Reference Sequence Browser: An R application with a user-friendly GUI to rapidly query sequence databases. PLOS ONE 19: e0309707.
DOI: 10.1371/journal.pone.0309707
A metabarcoding framework for wild bee assessment in Luxembourg. Journal of Hymenoptera Research 94: 215.
DOI: 10.3897/jhr.94.84617
Investigating pelagic biodiversity and gelatinous zooplankton communities in the rapidly changing European Arctic: An eDNA metabarcoding survey. Environmental DNA 6: .
DOI: 10.1002/edn3.569
Improved freshwater macroinvertebrate detection from environmental DNA through minimized nontarget amplification. Environmental DNA 3: 261.
DOI: 10.1002/edn3.177
To share or not to share: DNA metabarcoding reveals trophic niche overlap between sympatric trawling bats. European Journal of Wildlife Research 69: .
DOI: 10.1007/s10344-023-01712-z
Prokaryotic communities as proxies for eukaryotic soil beta diversity in forest ecosystems. Ecological Indicators 178: 113930.
DOI: 10.1016/j.ecolind.2025.113930
Eukaryotic biodiversity of sub-ice water in the marginal ice zone of the European Arctic: A multi-marker eDNA metabarcoding survey. Science of The Total Environment 968: 178840.
DOI: 10.1016/j.scitotenv.2025.178840
Opportunistic feeding habits of two African freshwater clupeid fishes: DNA metabarcoding unravels spatial differences in diet and microbiome, and identifies new prey taxa. Hydrobiologia 850: 3777.
DOI: 10.1007/s10750-023-05267-7
DNA metabarcoding improves the detection of multiple stressor responses of stream invertebrates to increased salinity, fine sediment deposition and reduced flow velocity. Science of The Total Environment 750: 141969.
DOI: 10.1016/j.scitotenv.2020.141969
Cooking small and large portions of “biodiversity‐soup”: Miniaturized DNA metabarcoding PCRs perform as good as large‐volume PCRs. Ecology and Evolution 11: 9092.
DOI: 10.1002/ece3.7753
Use of massive DNA barcoding to monitor biodiversity: A test on forest soil macrofauna. Forest Ecology and Management 595: 123004.
DOI: 10.1016/j.foreco.2025.123004
Profile hidden Markov model sequence analysis can help remove putative pseudogenes from DNA barcoding and metabarcoding datasets. BMC Bioinformatics 22: .
DOI: 10.1186/s12859-021-04180-x
Specific gut bacterial responses to natural diets of tropical birds. Scientific Reports 12: .
DOI: 10.1038/s41598-022-04808-9
‘Vampire birds’: diet metabarcoding reveals that migrating Woodchat Shrikes Lanius senator consume engorged camel ticks in a desert stopover site . Ostrich 95: 296.
DOI: 10.2989/00306525.2024.2386454
Evaluating the potential of DNA metabarcoding for ecological status assessment under the Water Framework Directive: A case study on benthic invertebrates from Western Carpathian streams. Metabarcoding and Metagenomics 9: .
DOI: 10.3897/mbmg.9.163640
Streamlining large-scale oceanic biomonitoring using passive eDNA samplers integrated into vessel's continuous pump underway seawater systems. Science of The Total Environment 946: 174354.
DOI: 10.1016/j.scitotenv.2024.174354
The secret meal of Antarctic mesopelagic fish (Myctophidae: Electrona) revealed by multi-marker metabarcoding. Frontiers in Marine Science 11: .
DOI: 10.3389/fmars.2024.1474424
DNA metabarcoding reveals the influence of land cover and farming on the dietary composition of a spider-specialist bat. Metabarcoding and Metagenomics 9: .
DOI: 10.3897/mbmg.9.144371
Implications of taxonomic and numerical resolution on DNA metabarcoding-based inference of benthic macroinvertebrate responses to river restoration. Ecological Indicators 135: 108508.
DOI: 10.1016/j.ecolind.2021.108508
Sources of uncertainty in DNA metabarcoding of whole communities: Implications for its use in biomonitoring. Methods in Ecology and Evolution 16: 1658.
DOI: 10.1111/2041-210X.70093
MetaWorks: A flexible, scalable bioinformatic pipeline for high-throughput multi-marker biodiversity assessments. PLOS ONE 17: e0274260.
DOI: 10.1371/journal.pone.0274260
APSCALE: advanced pipeline for simple yet comprehensive analyses of DNA metabarcoding data. Bioinformatics 38: 4817.
DOI: 10.1093/bioinformatics/btac588
Catch effectiveness, complementarity and costs of five sampling techniques for flying insects across different land use types. Insect Conservation and Diversity 18: 970.
DOI: 10.1111/icad.12839
taxalogue: a toolkit to create comprehensive CO1 reference databases. PeerJ 11: e16253.
DOI: 10.7717/peerj.16253
Eyeing DNA barcoding for species identification of fish larvae. Journal of Fish Biology 105: 1784.
DOI: 10.1111/jfb.15920
Integrating eDNA and community science to monitor urban Odonata diversity. Insect Conservation and Diversity : .
DOI: 10.1111/icad.70006
Soft-sediment surrogacy: acoustic remote sensing relates more strongly to marine sediment eDNA than to infauna. Estuarine, Coastal and Shelf Science : 109592.
DOI: 10.1016/j.ecss.2025.109592
Comparison of destructive and nondestructiveDNAextraction methods for the metabarcoding of arthropod bulk samples. Molecular Ecology Resources 23: 92.
DOI: 10.1111/1755-0998.13694
DNA metabarcoding reveals a diverse, omnivorous diet of Arctic amphipods during the polar night, with jellyfish and fish as major prey. Frontiers in Marine Science 11: .
DOI: 10.3389/fmars.2024.1327650
Insight into Invertebrate Community in Solonchak Soil Type Using EDNA Metabarcoding – A Pilot Study. Contemporary Agriculture 73: 200.
DOI: 10.2478/contagri-2024-0024
Spineless and overlooked: DNA metabarcoding of autonomous reef monitoring structures reveals intra‐ and interspecific genetic diversity in Mediterranean invertebrates. Molecular Ecology Resources 23: 1689.
DOI: 10.1111/1755-0998.13836
MitoGeneExtractor: Efficient extraction of mitochondrial genes from next‐generation sequencing libraries. Methods in Ecology and Evolution 14: 1017.
DOI: 10.1111/2041-210X.14075
A belly full of jelly? DNA metabarcoding shows evidence for gelatinous zooplankton predation by several fish species in Greenland waters. Royal Society Open Science 11: .
DOI: 10.1098/rsos.240797
Putting COI Metabarcoding in Context: The Utility of Exact Sequence Variants (ESVs) in Biodiversity Analysis. Frontiers in Ecology and Evolution 8: .
DOI: 10.3389/fevo.2020.00248
Identifying conservation hotspots and assessing species commonness and rarity: Baseline arthropod diversity in German nature reserves via national Malaise trap monitoring. Insect Conservation and Diversity 18: 510.
DOI: 10.1111/icad.12818
Technical challenges in the implementation of macroinvertebrate DNA metabarcoding in river biomonitoring: A case study from peninsular Spain—Advantages, limitations and roadmap. Ecological Solutions and Evidence 6: .
DOI: 10.1002/2688-8319.70125
Pelvic spine reduction affects diet but not gill raker morphology in two polymorphic brook stickleback (Culaea inconstans) populations. Ecology and Evolution 13: .
DOI: 10.1002/ece3.10526
Unlocking rivers' hidden diversity and ecological status using DNA metabarcoding in Northwest Spain. Ecology and Evolution 14: .
DOI: 10.1002/ece3.70110
The impact of wildfires on the diet of Podarcis lusitanicus revealed by DNA metabarcoding. PLOS One 20: e0319238.
DOI: 10.1371/journal.pone.0319238
Unearthing soil arthropod diversity through DNA metabarcoding. PeerJ 10: e12845.
DOI: 10.7717/peerj.12845
Establishing DNA‐Based Strategies for Soil Biodiversity Assessment: Insights From Carabid Beetles. Ecology and Evolution 15: .
DOI: 10.1002/ece3.72461
Double-blind validation of alternative wild bee identification techniques: DNA metabarcoding and in vivo determination in the field. Journal of Hymenoptera Research 93: 189.
DOI: 10.3897/jhr.93.86723
Assessing the response of an urban stream ecosystem to salinization under different flow regimes. Science of The Total Environment 926: 171849.
DOI: 10.1016/j.scitotenv.2024.171849
Curation of a reference database of COI sequences for insect identification through DNA metabarcoding: COins. Database 2022: .
DOI: 10.1093/database/baac055
Capture—Incubate—Release: An Animal‐Friendly Approach to Assess Local Aquatic Macroinvertebrate Species Diversity Through Environmental DNA Metabarcoding. Environmental DNA 7: .
DOI: 10.1002/edn3.70112
Ground-lying deadwood volume promotes soil beta diversity but not alpha diversity in European temperate forests. Plant and Soil : .
DOI: 10.1007/s11104-025-07600-6
Homogenization of insect bulk samples yields more comprehensive yet comparable biodiversity data than non-destructive lysis. Metabarcoding and Metagenomics 8: .
DOI: 10.3897/mbmg.8.129814
Illuminating Entomological Dark Matter with DNA Barcodes in an Era of Insect Decline, Deep Learning, and Genomics. Annual Review of Entomology 70: 185.
DOI: 10.1146/annurev-ento-040124-014001
Bat diversity boosts ecosystem services: Evidence from pine processionary moth predation. Science of The Total Environment 912: 169387.
DOI: 10.1016/j.scitotenv.2023.169387
Cross-comparing different protocols for DNA metabarcoding of freshwater macroinvertebrates. Hydrobiologia : .
DOI: 10.1007/s10750-025-05993-0
Learning to Hunt on the Go: Dietary Changes During Development of Rhinolophid Bats. Animals 14: 3303.
DOI: 10.3390/ani14223303
Exploring the influence of natural features on soil mesofaunal communities in agricultural landscapes through DNA metabarcoding. Frontiers in Sustainable Food Systems 9: .
DOI: 10.3389/fsufs.2025.1443215
Gradient patterns in the Tatra Mountain lakes revisited with invertebrate DNA metabarcoding. Metabarcoding and Metagenomics 9: .
DOI: 10.3897/mbmg.9.150825
Environmental DNA for assessing impact and recovery of aquatic communities in an invaded mountain lake. Lake and Reservoir Management 40: 111.
DOI: 10.1080/10402381.2024.2309632
Effects of Bti on the diversity and community composition of three Chironomidae subfamilies across different micro-habitats. Environmental Pollution 366: 125490.
DOI: 10.1016/j.envpol.2024.125490
Using the long-term genetic monitoring network ARMS-MBON to detect marine non-indigenous species along the European coasts. Biological Invasions 27: .
DOI: 10.1007/s10530-024-03503-2
Fresh insights into Mediterranean biodiversity: environmental DNA reveals spatio-temporal patterns of stream invertebrate communities on Sicily. Hydrobiologia 849: 155.
DOI: 10.1007/s10750-021-04718-3
Introduced fish reduce the occurrence of shrews in alpine lakes. Biological Conservation 299: 110830.
DOI: 10.1016/j.biocon.2024.110830
Phylogeographic study using autonomous reef monitoring structures indicates fast range expansion of the invasive bryozoan Juxtacribrilina mutabilis. Hydrobiologia 850: 4115.
DOI: 10.1007/s10750-023-05184-9
Rapid spread of a new alien and potentially invasive species, Clathrocaspia knipowitschii (Makarov, 1938) (Gastropoda: Hydrobiidae), in the Danube River. Archives of Biological Sciences 74: 81.
DOI: 10.2298/ABS220211006S
Multi-group biodiversity distributions and drivers of metacommunity organization along a glacial–fluvial–limnic pathway on the Tibetan plateau. Environmental Research 220: 115236.
DOI: 10.1016/j.envres.2023.115236
COI Metabarcoding Provides Insights into the Highly Diverse Diet of a Generalist Salamander, Salamandra salamandra (Caudata: Salamandridae). Diversity 14: 89.
DOI: 10.3390/d14020089
Benthic invertebrates in Svalbard fjords—when metabarcoding does not outperform traditional biodiversity assessment. PeerJ 10: e14321.
DOI: 10.7717/peerj.14321
Trophic interactions of an invasive gecko in an endemic-rich oceanic island: Insights using DNA metabarcoding. Frontiers in Ecology and Evolution 10: .
DOI: 10.3389/fevo.2022.1044230
Do fish gut microbiotas vary across spatial scales? A case study of Diplodus vulgaris in the Mediterranean Sea. Animal Microbiome 6: .
DOI: 10.1186/s42523-024-00319-2
Metazoan Diversity and Its Drivers: An eDNA Survey in the Pacific Gateway of a Changing Arctic Ocean. Environmental DNA 7: .
DOI: 10.1002/edn3.70082
Comparison of three strategies for local bioassessments in streams using environmental DNA and RNA metabarcoding of macroinvertebrates. Metabarcoding and Metagenomics 9: .
DOI: 10.3897/mbmg.9.148923
Exploring macroinvertebrate biodiversity in the dynamic southern Balkan stream network of the Vjosa using preservative-based DNA metabarcoding. Aquatic Sciences 85: .
DOI: 10.1007/s00027-023-00948-w
Latitudinal gradients in zooplankton communities in Norwegian fjords resolved by an integrated morphological and molecular approach. ICES Journal of Marine Science 82: .
DOI: 10.1093/icesjms/fsae147
Distinct multitrophic biodiversity composition and community organization in a freshwater lake and a hypersaline lake on the Tibetan Plateau. iScience 27: 110124.
DOI: 10.1016/j.isci.2024.110124
The Advantages of Combining Morphological and Molecular Methods to Characterise Zooplankton Communities: A Case Study of the UNESCO Biosphere Reserve of the Berlengas Archipelago, Portugal. Oceans 5: 805.
DOI: 10.3390/oceans5040046
Insights into the habitat associations, phylogeny, and diet of Pipistrellus maderensis in Porto Santo, northeastern Macaronesia. Web Ecology 23: 87.
DOI: 10.5194/we-23-87-2023
Dietary Variation Is Driven by Landscape Heterogeneity in an Insular Omnivorous Endemic Lizard, Revealed by DNA Metabarcoding. Diversity 14: 1078.
DOI: 10.3390/d14121078
It's raining species: Rainwash eDNA metabarcoding as a minimally invasive method to assess tree canopy invertebrate diversity. Environmental DNA 5: 3.
DOI: 10.1002/edn3.372
Detecting the invisible through DNA metabarcoding: The role of gelatinous taxa in the diet of two demersal Antarctic key stone fish species (Notothenioidei). Environmental DNA 6: .
DOI: 10.1002/edn3.561
Landscape influences bat suppression of pine processionary moth: Implications for pest management. Journal of Environmental Management 373: 123803.
DOI: 10.1016/j.jenvman.2024.123803
Environmental DNA Monitoring of Biodiversity Hotspots in Danish Marine Waters. Frontiers in Marine Science 8: .
DOI: 10.3389/fmars.2021.800474
The clockwork of insect activity: Advancing ecological understanding through automation. Journal of Animal Ecology 94: 597.
DOI: 10.1111/1365-2656.14246
Using Flower eDNA Metabarcoding to Identify the Effects of Forest Structure and Microclimate on Flower‐Visiting Arthropods. Environmental DNA 7: .
DOI: 10.1002/edn3.70185
Shift in diet composition of a riparian predator along a stream pollution gradient. Proceedings of the Royal Society B: Biological Sciences 291: .
DOI: 10.1098/rspb.2024.2104
Environmental DNA time series analysis of a temperate stream reveals distinct seasonal community and functional shifts. River Research and Applications 40: 850.
DOI: 10.1002/rra.4265
Wet grinding of invertebrate bulk samples – a scalable and cost-efficient protocol for metabarcoding and metagenomics. Metabarcoding and Metagenomics 5: .
DOI: 10.3897/mbmg.5.67533
Environmental gradients and optimal fixation time revealed with DNA metabarcoding of benthic sample fixative. Scientific Reports 14: .
DOI: 10.1038/s41598-024-68939-x
Fit for purpose? Evaluating benthic invertebrate DNA metabarcoding for ecological status class assessment in streams under the Water Framework Directive. Water Research 272: 122987.
DOI: 10.1016/j.watres.2024.122987
Optimizing Environmental DNA Metabarcoding of Archived Suspended Particulate Matter for River Biodiversity Monitoring. Environmental DNA 7: .
DOI: 10.1002/edn3.70130
Surveying marine biodiversity using eDNA metabarcoding of seawater and sediment in a high Arctic fjord during the polar night (Kongsfjorden, Svalbard). Marine Environmental Research 211: 107443.
DOI: 10.1016/j.marenvres.2025.107443
From DNA to diagnostics: A case study using macroinvertebrate metabarcoding to assess the effectiveness of restoration measures in a Dutch stream. Science of The Total Environment 923: 171413.
DOI: 10.1016/j.scitotenv.2024.171413
Performance of DNA Metabarcoding vs. Morphological Methods for Assessing Intertidal Turf and Foliose Algae Diversity. Molecular Ecology Resources 25: .
DOI: 10.1111/1755-0998.14115
Beware of Plant DNA in Animal Dietary Metabarcoding: Lessons From a Strictly Insectivorous Bat. Molecular Ecology Resources 25: .
DOI: 10.1111/1755-0998.14100
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