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Peer-reviewedCC BY-NC-ND 4.0Molecular Ecology Resources

A Museum‐Curated, Voucher‐Backed 12S Barcode Reference Library for Fishes of the Ecuadorian Amazon

  • Evan W. Hessels1,2
  • José V. Montoya3,4
  • Corey Yuen2
  • Jonathan Valdiviezo‐Rivera5
  • Blanca Rios‐Touma3,6
  • Gabriela Echevarría3
  • Nathan K. Lujan1,2
6 affiliations
  1. 1Department of Natural History Royal Ontario Museum Toronto Ontario Canada
  2. 2Department of Ecology and Evolutionary Biology University of Toronto Toronto Ontario Canada
  3. 3Universidad de las Américas Quito Pichincha Ecuador
  4. 4Laboratorio de Ecología Acuática, Centro de Ecología Instituto Venezolano de Investigaciones Científicas (IVIC) Caracas Venezuela
  5. 5Instituto Nacional de Biodiversidad (INABIO) Quito Ecuador
  6. 6Colegio de Ciencias Biológicas y Ambientales (COCIBA) and Global Research & Solutions Center Universidad San Francisco de Quito Quito Ecuador
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Abstract

Environmental DNA (eDNA) metabarcoding is an emerging method that promises to expedite and improve biodiversity surveys by identifying species from the genetic material they shed into the environment. eDNA methods offer many advantages over conventional specimen‐based surveys, but their effectiveness hinges on reference libraries, which for highly biodiverse regions such as the Ecuadorian Amazon are too often incomplete, inconsistently curated and disconnected from morphological voucher specimens needed to reliably identify and revise taxa. To address this gap, we collected approximately 5000 fish specimens and 1500 tissues of an estimated 311 morphologically defined species from Ecuador's Aguarico, Napo and Pastaza river basins, and built a new, rigorously curated, museum voucher–backed 12S reference library spanning 748 barcodes from over 303 species across 12 orders, 46 families and 171 genera. When tested against unknown haplotypes from concurrently collected eDNA samples, the library nearly doubled the proportion identified to species (40.0%, vs. 21.3% using GenBank). It also enabled the empirical estimation of new species‐level barcode thresholds: 0.4% for the full‐length barcode, 0.9% for a general vertebrate mini‐barcode, and 0.6% for a fish‐specific mini‐barcode. By linking museum vouchers, updated taxonomy, and operational scalability, this reference library helps transform eDNA metabarcoding from an exciting possibility to a practical tool for understanding, monitoring and safeguarding Amazonian freshwater biodiversity.

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Cite

BibTeXRIS
BibTeX
@article{hessels2026museumcurated,
  title = {{A Museum‐Curated, Voucher‐Backed 12S Barcode Reference Library for Fishes of the Ecuadorian Amazon}},
  author = {Evan W. Hessels and José V. Montoya and Corey Yuen and Jonathan Valdiviezo‐Rivera and Blanca Rios‐Touma and Gabriela Echevarría and Nathan K. Lujan},
  journal = {Molecular Ecology Resources},
  year = {2026},
  month = nov,
  doi = {10.1111/1755-0998.70220},
  url = {https://doi.org/10.1111/1755-0998.70220},
  note = {CC BY-NC-ND 4.0},
}
RIS
TY  - JOUR
TI  - A Museum‐Curated, Voucher‐Backed 12S Barcode Reference Library for Fishes of the Ecuadorian Amazon
AU  - Evan W. Hessels
AU  - José V. Montoya
AU  - Corey Yuen
AU  - Jonathan Valdiviezo‐Rivera
AU  - Blanca Rios‐Touma
AU  - Gabriela Echevarría
AU  - Nathan K. Lujan
PY  - 2026
DA  - 2026/11/04
JO  - Molecular Ecology Resources
DO  - 10.1111/1755-0998.70220
UR  - https://doi.org/10.1111/1755-0998.70220
AB  - Environmental DNA (eDNA) metabarcoding is an emerging method that promises to expedite and improve biodiversity surveys by identifying species from the genetic material they shed into the environment. eDNA methods offer many advantages over conventional specimen‐based surveys, but their effectiveness hinges on reference libraries, which for highly biodiverse regions such as the Ecuadorian Amazon are too often incomplete, inconsistently curated and disconnected from morphological voucher specimens needed to reliably identify and revise taxa. To address this gap, we collected approximately 5000 fish specimens and 1500 tissues of an estimated 311 morphologically defined species from Ecuador's Aguarico, Napo and Pastaza river basins, and built a new, rigorously curated, museum voucher–backed 12S reference library spanning 748 barcodes from over 303 species across 12 orders, 46 families and 171 genera. When tested against unknown haplotypes from concurrently collected eDNA samples, the library nearly doubled the proportion identified to species (40.0%, vs. 21.3% using GenBank). It also enabled the empirical estimation of new species‐level barcode thresholds: 0.4% for the full‐length barcode, 0.9% for a general vertebrate mini‐barcode, and 0.6% for a fish‐specific mini‐barcode. By linking museum vouchers, updated taxonomy, and operational scalability, this reference library helps transform eDNA metabarcoding from an exciting possibility to a practical tool for understanding, monitoring and safeguarding Amazonian freshwater biodiversity.
SN  - 1755-098X
SN  - 1755-0998
ER  -