Comparing species detection success between molecular markers in DNA metabarcoding of coastal macroinvertebrates

Barbara R. Leite; Pedro E. Vieira; Jesús S. Troncoso; Filipe O. Costa

doi:10.3897/mbmg.5.70063

Michelle Scriver, Ulla von Ammon, Xavier Pochon, Martin Zirngibl, Francois Audrezet, Kaeden Leonard, Kylie Pedersen, Nick Bamford, Ngairo Tahere, Jo‐Ann L. Stanton, Neil J. Gemmell, Anastasija Zaiko (2024)
Ebbs and Flows of Marine Biodiversity: Navigating Spatiotemporal Patterns of Environmental DNA in a Coastal Tidal Ecosystem. Environmental DNA 6: .

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Pedro E. Vieira, Andrea Desiderato, Sofia L. Azevedo, Patricia Esquete, Filipe O. Costa, Henrique Queiroga (2022)
Molecular evidence for extensive discontinuity between peracarid (Crustacea) fauna of Macaronesian islands and nearby continental coasts: over fifty candidate endemic species. Marine Biology 169: .

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Nauras Daraghmeh, Katrina Exter, Justine Pagnier, Piotr Balazy, Ibon Cancio, Giorgos Chatzigeorgiou, Eva Chatzinikolaou, Maciej Chelchowski, Nathan Alexis Mitchell Chrismas, Thierry Comtet, Thanos Dailianis, Klaas Deneudt, Oihane Diaz de Cerio, Markos Digenis, Vasilis Gerovasileiou, José González, Laura Kauppi, Jon Bent Kristoffersen, Piotr Kukliński, Rafał Lasota, Liraz Levy, Magdalena Małachowicz, Borut Mavrič, Jonas Mortelmans, Estefania Paredes, Anita Poćwierz‐Kotus, Henning Reiss, Ioulia Santi, Georgia Sarafidou, Grigorios Skouradakis, Jostein Solbakken, Peter A. U. Staehr, Javier Tajadura, Jakob Thyrring, Jesus S. Troncoso, Emmanouela Vernadou, Frederique Viard, Haris Zafeiropoulos, Małgorzata Zbawicka, Christina Pavloudi, Matthias Obst (2025)
A Long‐Term Ecological Research Data Set From the Marine Genetic Monitoring Program ARMS‐MBON 2018–2020. Molecular Ecology Resources 25: .

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Audrey Bourret, Claude Nozères, Eric Parent, Geneviève J. Parent (2023)
Maximizing the reliability and the number of species assignments in metabarcoding studies using a curated regional library and a public repository. Metabarcoding and Metagenomics 7: .

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Barbara R. Leite, Sofia Duarte, Jesús S. Troncoso, Filipe O. Costa (2023)
Artificial Seaweed Substrates Complement ARMS in DNA Metabarcoding-Based Monitoring of Temperate Coastal Macrozoobenthos. Diversity 15: 657.

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Yuri S. Bukin, Ivan S. Mikhailov, Darya P. Petrova, Yuri P. Galachyants, Yulia R. Zakharova, Yelena V. Likhoshway (2023)
The effect of metabarcoding 18S rRNA region choice on diversity of microeukaryotes including phytoplankton. World Journal of Microbiology and Biotechnology 39: .

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Ana Ramón‐Laca, Ramón Gallego, Krista M. Nichols (2023)
Affordable de novo generation of fish mitogenomes using amplification‐free enrichment of mitochondrial DNA and deep sequencing of long fragments. Molecular Ecology Resources 23: 818.

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Joana Marujo Neves, Marta Martins, Helena Adão, Mário Mil-Homens, Maria Helena Costa, Jorge Lobo-Arteaga (2025)
Ecological quality assessment of estuarine macrobenthic communities using an integrative approach. Marine Pollution Bulletin 210: 117316.

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André O. Ferreira, Olga M. Azevedo, Cristina Barroso, Sofia Duarte, Conceição Egas, João T. Fontes, Pedro Ré, A. Miguel P. Santos, Filipe O. Costa (2024)
Multi-marker DNA metabarcoding for precise species identification in ichthyoplankton samples. Scientific Reports 14: .

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Katrin Kiemel, Guntram Weithoff, Ralph Tiedemann (2023)
DNA metabarcoding reveals impact of local recruitment, dispersal, and hydroperiod on assembly of a zooplankton metacommunity. Molecular Ecology 32: 6190.

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Marion Chevrinais, Audrey Bourret, Geneviève Côté, Geneviève Faille, Nellie Gagné, Geneviève J. Parent (2025)
Improving an endangered marine species distribution using reliable and localized environmental DNA detections combined with trawl captures. Scientific Reports 15: .

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Jorge Moutinho, Diego Carreira-Flores, Pedro T. Gomes, Filipe O. Costa, Sofia Duarte (2023)
Assessing the Seasonal and Spatial Dynamics of Zooplankton through DNA Metabarcoding in a Temperate Estuary. Animals 13: 3876.

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Ana S. Lavrador, Fábio G. Amaral, Jorge Moutinho, Pedro E. Vieira, Filipe O. Costa, Sofia Duarte (2024)
Comprehensive DNA metabarcoding-based detection of non-indigenous invertebrates in recreational marinas through a multi-substrate approach. Marine Environmental Research 200: 106660.

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Alica Ohnesorge, Uwe John, Lucie Kuczynski, Stefan Neuhaus, Kingsly Chuo Beng, Bernd Krock, Silke Laakmann (2024)
Roaming the Seas—Assessing Marine Invertebrate Biodiversity Along Salinity Gradients With Zooplankton and eDNA Metabarcoding. Environmental DNA 6: .

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Sofia Duarte, Pedro E. Vieira, Barbara R. Leite, Marcos A.L. Teixeira, João M. Neto, Filipe O. Costa (2023)
Macrozoobenthos monitoring in Portuguese transitional waters in the scope of the water framework directive using morphology and DNA metabarcoding. Estuarine, Coastal and Shelf Science 281: 108207.

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Jia Jin Marc Chang, Yin Cheong Aden Ip, Wan Lin Neo, Maxine A. D. Mowe, Zeehan Jaafar, Danwei Huang (2024)
Primed and ready: nanopore metabarcoding can now recover highly accurate consensus barcodes that are generally indel-free. BMC Genomics 25: .

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