ArticlePloS one2018
Metabarcoding by capture using a single COI probe (MCSP) to identify and quantify fish species in ichthyoplankton swarms.
Article in PloS one, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- A Roadmap for Using Hybridisation Capture-Based Target Enrichment of Ancient Environmental DNA in Palaeoecology.Molecular ecology resources · 2026Review
- Unlocking natural history collections to improve eDNA reference databases and biodiversity monitoring.Bioscience · 2025Article
- DNA metabarcoding assessment of Neotropical ichthyoplankton communities is marker-dependent.Ecology and evolution · 2023Article
- Evaluation of DNA metabarcoding for identifying fish eggs: a case study on the West Florida Shelf.PeerJ · 2023Review
- Genome-scale target capture of mitochondrial and nuclear environmental DNA from water samples.Molecular ecology resources · 2021Article
- Metabarcoding of Fish Larvae in the Merbok River Reveals Species Diversity and Distribution Along its Mangrove Environment.Zoological studies · 2021Article
- New 12S metabarcoding primers for enhanced Neotropical freshwater fish biodiversity assessment.Scientific reports · 2020Article
- Assessing species diversity of Coral Triangle artisanal fisheries: A DNA barcode reference library for the shore fishes retailed at Ambon harbor (Indonesia).Ecology and evolution · 2020Article
- Population-level inferences from environmental DNA-Current status and future perspectives.Evolutionary applications · 2020Review
- Reappraising plastid markers of the red algae for phylogenetic community ecology in the genomic era.Ecology and evolution · 2020Article
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Authors and funding
7 authors.
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Abstract
The ability to determine the composition and relative frequencies of fish species in large ichthyoplankton swarms could have extremely important ecological applications However, this task is currently hampered by methodological limitations. We proposed a new method for Amazonian species based on hybridization capture of the COI gene DNA from a distant species (Danio rerio), absent from our study area (the Amazon basin). The COI sequence of this species is approximately equidistant from all COI of Amazonian species available. By using this sequence as probe we successfully facilitated the simultaneous identification of fish larvae belonging to the order Siluriformes and to the Characiformes represented in our ichthyoplankton samples. Species relative frequencies, estimated by the number of reads, showed almost perfect correlations with true frequencies estimated by a Sanger approach, allowing the development of a quantitative approach. We also proposed a further improvement to a previous protocol, which enables lowering the sequencing effort by 40 times. This new Metabarcoding by Capture using a Single Probe (MCSP) methodology could have important implications for ecology, fisheries management and conservation in fish biodiversity hotspots worldwide. Our approach could easily be extended to other plant and animal taxa.
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