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Use of DNA barcode in the identification of fish species from Ribeira de Iguape Basin and coastal rivers from São Paulo State (Brazil)

Jefferson Monteiro Henriques
  • Corresponding author
  • Departamento de Morfologia - Instituto de Biocięncias Universidade Estadual Paulista - UNESP Botucatu 18618-970 Săo Paulo Brazil
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Guilherme José Costa Silva
  • Departamento de Morfologia - Instituto de Biociências Universidade Estadual Paulista - UNESP Botucatu 18618-970 São Paulo Brazil
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Fernando Yuldi Ashikaga
  • Departamento de Morfologia - Instituto de Biociências Universidade Estadual Paulista - UNESP Botucatu 18618- 970 São Paulo Brazil
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Robert Hanner
  • Biodiversity Institute of Ontario and Department of Integrative Biology University of Guelph Guelph N1G 2W1 Ontario Canada
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Fausto Foresti
  • Departamento de Morfologia - Instituto de Biociências Universidade Estadual Paulista - UNESP Botucatu 18618-970 São Paulo Brazil
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Claudio Oliveira
  • Departamento de Morfologia - Instituto de Biociências Universidade Estadual Paulista - UNESP Botucatu 18618-970 São Paulo Brazil
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  • De Gruyter OnlineGoogle Scholar
Published Online: 2015-11-26 | DOI: https://doi.org/10.1515/dna-2015-0015


Species identification is a difficult task, ranging from the definition of the species concept itself to the definition of the threshold for speciation. DNA Barcode technology uses a fragment of the Cytochrome Oxidase I (COI) gene as a molecular tool that many studies have already validated as a tool for species identification. DNA barcode sequences for COI were generated and analyzed from 805 specimens. The General Mixed Yule Coalescent (GMYC) analysis recognized 99 independent evolution units, and the Barcode Index Numbers (BIN) approach pointed to the existence of 104 BINs (interpreted as distinct species). By cross-tabulating the results of all approaches, we identified 109 Molecular Operational Taxonomic Units (MOTU) by at least one methodology. In most cases (89 MOTUs), the genetic approaches are in agreement with morphological identification, and the discrepant results of MOTUs are in the complex groups, which have many morphological similarities but may represent species complexes.

This article offers supplementary material which is provided at the end of the article.

Keywords: Single locus analysis; species identification and delimitation; COI gene


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About the article

Received: 2015-02-25

Accepted: 2015-07-20

Published Online: 2015-11-26

Published in Print: 2015-01-01

Citation Information: DNA Barcodes, Volume 3, Issue 1, Pages 118–128, ISSN (Online) 2299-1077, DOI: https://doi.org/10.1515/dna-2015-0015.

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© 2015. This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License. BY-NC-ND 3.0

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