DNA metabarcoding of Neotropical ichthyoplankton: Enabling high accuracy with lower cost

André B. Nobile; Diogo Freitas-Souza; Francisco J. Ruiz-Ruano; Maria Lígia M. O. Nobile; Gabriela O. Costa; Felipe P. de Lima; Juan Pedro M. Camacho; Fausto Foresti; Claudio Oliveira

doi:10.3897/mbmg.3.35060

Ashrenee Govender, Sean T. Fennessy, Sean N. Porter, Johan C. Groeneveld, Vitor Hugo Rodrigues Paiva (2023)
Metabarcoding of ichthyoplankton communities associated with a highly dynamic shelf region of the southwest Indian Ocean. PLOS ONE 18: e0284961.

DOI: 10.1371/journal.pone.0284961

Kavishka S. Gallage, Alexander Van Nynatten, Nathan K. Lujan, Nathan R. Lovejoy, Nicholas E. Mandrak (2023)
Identifying early life stages of Great Lakes fishes using a metabarcoding approach. Canadian Journal of Fisheries and Aquatic Sciences 80: 1813.

DOI: 10.1139/cjfas-2023-0061

Paulo Santos Pompeu, Lídia Wouters, Heron Oliveira Hilário, Raquel Coelho Loures, Alexandre Peressin, Ivo Gavião Prado, Fábio Mineo Suzuki, Daniel Cardoso Carvalho (2023)
Inadequate Sampling Frequency and Imprecise Taxonomic Identification Mask Results in Studies of Migratory Freshwater Fish Ichthyoplankton. Fishes 8: 518.

DOI: 10.3390/fishes8100518

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: .

DOI: 10.1038/s41598-024-69963-7

Joeselle M. Serrana, Kozo Watanabe, Claudia Isabella Pogoreutz (2023)
Haplotype-level metabarcoding of freshwater macroinvertebrate species: A prospective tool for population genetic analysis. PLOS ONE 18: e0289056.

DOI: 10.1371/journal.pone.0289056

C. David de Santana, Lynne R. Parenti, Casey B. Dillman, Jonathan A. Coddington, Douglas A. Bastos, Carole C. Baldwin, Jansen Zuanon, Gislene Torrente-Vilara, Raphaël Covain, Naércio A. Menezes, Aléssio Datovo, T. Sado, M. Miya (2021)
The critical role of natural history museums in advancing eDNA for biodiversity studies: a case study with Amazonian fishes. Scientific Reports 11: .

DOI: 10.1038/s41598-021-97128-3

Jessica Guerchon, Arseniy R. Morov, Aviyam Tagar, Maxim Rubin-Blum, Yaron Tikochinski, Igal Berenshtein, Gil Rilov, Nir Stern (2023)
Marine top secrets: Ichthyoplankton in surface water uncover hidden knowledge on fish diversity and distribution. Estuarine, Coastal and Shelf Science 282: 108226.

DOI: 10.1016/j.ecss.2023.108226

A Veríssimo, P Fonseca, S Garrido (2024)
Molecular barcoding reveals patterns of egg predation in small pelagic fish. Marine Ecology Progress Series 741: 113.

DOI: 10.3354/meps14498

Frances C. Ratcliffe, Tamsyn M. Uren Webster, Deiene Rodriguez‐Barreto, Richard O'Rorke, Carlos Garcia de Leaniz, Sofia Consuegra (2021)
Quantitative assessment of fish larvae community composition in spawning areas using metabarcoding of bulk samples. Ecological Applications 31: .

DOI: 10.1002/eap.2284

Lara E. Silva, Rodrigo R. Domingues, Naiara G. Sales, Priscila M.S. Villela, Camila Barbosa Silva, Alexandre W.S. Hilsdorf (2023)
Amazonian ichthyoplankton assessment via DNA metabarcoding: A baseline for detecting spawning sites of migratory fishes. Biological Conservation 284: 110180.

DOI: 10.1016/j.biocon.2023.110180

Eric Toro-Delgado, Juan Hernández-Roldán, Vlad Dincă, Juan Carlos Vicente, Mark R Shaw, Donald Lj Quicke, Raluca Vodă, Martin Albrecht, José Fernández-Triana, Blai Vidiella, Sergi Valverde, Leonardo Dapporto, Paul D N Hebert, Gerard Talavera, Roger Vila (2022)
Butterfly–parasitoid–hostplant interactions in Western Palaearctic Hesperiidae: a DNA barcoding reference library. Zoological Journal of the Linnean Society 196: 757.

DOI: 10.1093/zoolinnean/zlac052

Natália Lima Lira, Sandro Tonello, Roberto Laridondo Lui, Josiane Baccarin Traldi, Heleno Brandão, Claudio Oliveira, Daniel Rodrigues Blanco (2023)
Identifying fish eggs and larvae: from classic methodologies to DNA metabarcoding. Molecular Biology Reports 50: 1713.

DOI: 10.1007/s11033-022-08091-9

Carol A. Stepien, Haila K. Schultz, Sean M. McAllister, Emily L. Norton, Julie E. Keister (2023)
Evaluating Metabarcoding Markers for Identifying Zooplankton and Ichthyoplankton Communities to Species in the Salish Sea: Morphological Comparisons and Rare, Threatened or Invasive Species. DNA 4: 1.

DOI: 10.3390/dna4010001

Paulo Eduardo Aguiar Saraiva Câmara, Natana Rabelo, Fabyano Alvares Cardoso Lopes, Micheline Carvalho-Silva, Peter Convey, Marcelo Carvalho, Sandro Scheffler, Gustavo Santiago, Paula Sucerquia, Vivian Gonçalves, Luiz Rosa (2025)
Assessing cryptic non-fungal eukaryotic diversity associated with rocks at Lions Rump, South Shetland Islands, Maritime Antarctica. Antarctic Science : 1.

DOI: 10.1017/S0954102025100333

Cédric Mariac, Jean‐François Renno, Carmen Garcia‐Davila Carmen Garcia‐Davila, Yves Vigouroux, Eduardo Mejia, Carlos Angulo, Diana Castro Ruiz, Guillain Estivals, Christian Nolorbe, Aurea García Vasquez, Jesus Nuñez, Gérard Cochonneau, Mayra Flores, Jhon Alvarado, José Vertiz, Werner Chota‐Macuyama, Homero Sánchez, Guido Miranda, Fabrice Duponchelle (2022)
Species‐level ichthyoplankton dynamics for 97 fishes in two major river basins of the Amazon using quantitative metabarcoding. Molecular Ecology 31: 1627.

DOI: 10.1111/mec.15944

Alexander Van Nynatten, Kavishka S. Gallage, Nathan K. Lujan, Nicholas E. Mandrak, Nathan R. Lovejoy (2023)
Ichthyoplankton metabarcoding: An efficient tool for early detection of invasive species establishment. Molecular Ecology Resources 23: 1319.

DOI: 10.1111/1755-0998.13803

Daniel Fonseca Teixeira, Heron Oliveira Hilário, Gilmar Bastos Santos, Daniel Cardoso Carvalho (2023)
DNA metabarcoding assessment of Neotropical ichthyoplankton communities is marker‐dependent. Ecology and Evolution 13: .

DOI: 10.1002/ece3.10649

Alejandro Mateos‐Rivera, Rasmus Skern‐Mauritzen, Geir Dahle, Svein Sundby, Bahar Mozfar, Anders Thorsen, Henning Wehde, Bjørn A. Krafft (2020)
Comparison of visual and molecular taxonomic methods to identify ichthyoplankton in the North Sea. Limnology and Oceanography: Methods 18: 599.

DOI: 10.1002/lom3.10387

Joel Christopher Hoffman, Christy Meredith, Erik Pilgrim, Anett Trebitz, Chelsea Hatzenbuhler, John Russell Kelly, Gregory Peterson, Julie Lietz, Sara Okum, John Martinson (2021)
Comparison of larval fish detections using morphology-based taxonomy versus high-throughput sequencing for invasive species early detection. Canadian Journal of Fisheries and Aquatic Sciences 78: 752.

DOI: 10.1139/cjfas-2020-0224

David T. Milan, Izabela S. Mendes, Júnio S. Damasceno, Daniel F. Teixeira, Naiara G. Sales, Daniel C. Carvalho (2020)
New 12S metabarcoding primers for enhanced Neotropical freshwater fish biodiversity assessment. Scientific Reports 10: .

DOI: 10.1038/s41598-020-74902-3

(2020)
Tropical Ecosystems in the 21st Century. : 331.

DOI: 10.1016/bs.aecr.2020.01.001