title: DNA Metabarcoding of Amazonian Ichthyoplankton Swarms.
abstract: Tropical rainforests harbor extraordinary biodiversity. The Amazon basin is thought to hold 30% of all river fish species in the world. Information about the ecology, reproduction, and recruitment of most species is still lacking, thus hampering fisheries management and successful conservation strategies. One of the key understudied issues in the study of population dynamics is recruitment. Fish larval ecology in tropical biomes is still in its infancy owing to identification difficulties. Molecular techniques are very promising tools for the identification of larvae at the species level. However, one of their limits is obtaining individual sequences with large samples of larvae. To facilitate this task, we developed a new method based on the massive parallel sequencing capability of next generation sequencing (NGS) coupled with hybridization capture. We focused on the mitochondrial marker cytochrome oxidase I (COI). The results obtained using the new method were compared with individual larval sequencing. We validated the ability of the method to identify Amazonian catfish larvae at the species level and to estimate the relative abundance of species in batches of larvae. Finally, we applied the method and provided evidence for strong temporal variation in reproductive activity of catfish species in the Ucayalí River in the Peruvian Amazon. This new time and cost effective method enables the acquisition of large datasets, paving the way for a finer understanding of reproductive dynamics and recruitment patterns of tropical fish species, with major implications for fisheries management and conservation.
authors.affiliation: Institut de Recherche pour le Développement, Université de Montpellier, Unité Mixte de Recherche Diversité Adaptation et Développement des Plantes (UMR DIADE), Montpellier, France.
authors.forename: M E
authors.initials: ME
authors.lastname: Maggia
authors.affiliation: Institut de Recherche pour le Développement, Université de Montpellier, Unité Mixte de Recherche Diversité Adaptation et Développement des Plantes (UMR DIADE), Montpellier, France.
authors.forename: Y
authors.initials: Y
authors.lastname: Vigouroux
authors.affiliation: Institut de Recherche pour le Développement, Unité Mixte de Recherche Biologie des Organismes et Ecosystèmes Aquatiques (UMR BOREA), MNHN-CNRS-7208-UPMC-UCBN-IRD-207, Montpellier, France.|Laboratoire Mixte International-Evolution et Domestication de l'Ichtyofaune Amazonienne (LMI-EDIA), IIAP-UAGRM-IRD, UMR BOREA, 7 rue Cuvier, CP 32, Paris, France.
authors.forename: J F
authors.initials: JF
authors.lastname: Renno
authors.affiliation: Institut de Recherche pour le Développement, Unité Mixte de Recherche Biologie des Organismes et Ecosystèmes Aquatiques (UMR BOREA), MNHN-CNRS-7208-UPMC-UCBN-IRD-207, Montpellier, France.|Laboratoire Mixte International-Evolution et Domestication de l'Ichtyofaune Amazonienne (LMI-EDIA), IIAP-UAGRM-IRD, UMR BOREA, 7 rue Cuvier, CP 32, Paris, France.
authors.forename: F
authors.initials: F
authors.lastname: Duponchelle
authors.affiliation: Institut des Sciences de l'Évolution (UMR ISEM), Université Montpellier-CNRS-IRD-EPHE, Place Eugène Bataillon-CC 065, Montpellier, France.
authors.forename: E
authors.initials: E
authors.lastname: Desmarais
authors.affiliation: Institut de Recherche pour le Développement, Unité Mixte de Recherche Biologie des Organismes et Ecosystèmes Aquatiques (UMR BOREA), MNHN-CNRS-7208-UPMC-UCBN-IRD-207, Montpellier, France.|Laboratoire Mixte International-Evolution et Domestication de l'Ichtyofaune Amazonienne (LMI-EDIA), IIAP-UAGRM-IRD, UMR BOREA, 7 rue Cuvier, CP 32, Paris, France.
authors.forename: J
authors.initials: J
authors.lastname: Nunez
authors.affiliation: Laboratoire Mixte International-Evolution et Domestication de l'Ichtyofaune Amazonienne (LMI-EDIA), IIAP-UAGRM-IRD, UMR BOREA, 7 rue Cuvier, CP 32, Paris, France.|Instituto de Investigaciones de la Amazonía Peruana (IIAP), Laboratorio de Biología y Genética Molecular (LBGM), Iquitos, Perú.
authors.forename: C
authors.initials: C
authors.lastname: García-Dávila
authors.affiliation: FAUNAGUA, ULRA-UMSS, ECOSINTEGRALES SRL, Cochabamba, Plurinational State of Bolivia.
authors.forename: F M
authors.initials: FM
authors.lastname: Carvajal-Vallejos
authors.affiliation: Institut des Sciences de l'Évolution (UMR ISEM), Université Montpellier-CNRS-IRD-EPHE, Place Eugène Bataillon-CC 065, Montpellier, France.
authors.forename: E
authors.initials: E
authors.lastname: Paradis
authors.affiliation: Montpellier-SupAgro, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Montferrier-sur-Lez, France.
authors.forename: J F
authors.initials: JF
authors.lastname: Martin
authors.affiliation: Institut de Recherche pour le Développement, Université de Montpellier, Unité Mixte de Recherche Diversité Adaptation et Développement des Plantes (UMR DIADE), Montpellier, France.
authors.forename: C
authors.initials: C
authors.lastname: Mariac
mesh_terms: D000818:Animals; D058893:DNA Barcoding, Taxonomic / Q000379:methods*; D005399:Fishes / Q000145:classification / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D007814:Larva / Q000235:genetics*