DNA Barcodes pp 127-152 | Cite as

DNA Barcoding Birds: From Field Collection to Data Analysis

  • Darío A. LijtmaerEmail author
  • Kevin C. R. Kerr
  • Mark Y. Stoeckle
  • Pablo L. Tubaro
Part of the Methods in Molecular Biology book series (MIMB, volume 858)


As of February 2011, COI DNA barcode sequences (a 648-bp segment of the 5′ end of the mitochondrial gene cytochrome c oxidase I, the standard DNA barcode for animals) have been collected from over 23,000 avian specimens representing 3,800 species, more than one-third of the world’s avifauna. Here, we detail the methodology for obtaining DNA barcodes from birds, covering the entire process from field collection to data analysis. We emphasize key aspects of the process and describe in more detail those that are particularly relevant in the case of birds. We provide elemental information about collection of specimens, detailed protocols for DNA extraction and PCR, and basic aspects of sequencing methodology. In particular, we highlight the primer pairs and thermal cycling profiles associated with successful amplification and sequencing from a broad range of avian species. Finally, we succinctly review the methodology for data analysis, including the detection of errors (such as contamination, misidentifications, or amplification of pseudogenes), assessment of species resolution, detection of divergent intraspecific lineages, and identification of unknown specimens.

Key words

Birds Cytochrome c oxidase I DNA barcodes Collection DNA extraction Neighbor joining Polymerase chain reaction Pectoral muscle Sequencing Toe pad 



Our work related to barcoding has been possible thanks to the financial support provided by the National Research Council of Argentina (CONICET), the Agencia Nacional de Promoción Científica y Tecnológica (ANPCyT), Lounsbery Foundation, Fundación Williams, the Consortium for the Barcode of Life (CBOL), the iBOL, the International Development Research Centre of Canada (IDRC), and the Biodiversity Institute of Ontario—Canadian Centre for DNA Barcoding (BIO-CCDB). We also thank the authorities of National Fauna and the provincial offices of fauna of Argentina, the National Parks Administration of Argentina, and Fundación Pearson. Finally, we thank N. Ivanova and A. Borisenko for their invaluable help in diverse aspects of the barcoding process.


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Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  • Darío A. Lijtmaer
    • 1
    Email author
  • Kevin C. R. Kerr
    • 2
  • Mark Y. Stoeckle
    • 3
  • Pablo L. Tubaro
    • 1
  1. 1.Ornithology“Bernardino Rivadavia”Buenos AiresArgentina
  2. 2.Department of Natural HistoryRoyal Ontario MuseumTorontoCanada
  3. 3.The Rockefeller UniversityNew YorkUSA

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