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DNA Barcoding Birds: From Field Collection to Data Analysis

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Book cover DNA Barcodes

Part of the book series: Methods in Molecular Biology ((MIMB,volume 858))

Abstract

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.

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Acknowledgments

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.

Author information

Authors and Affiliations

  1. Ornithology, “Bernardino Rivadavia”, Buenos Aires, Argentina

    Darío A. Lijtmaer & Pablo L. Tubaro

  2. Department of Natural History, Royal Ontario Museum, Toronto, ON, Canada

    Kevin C. R. Kerr

  3. The Rockefeller University, New York, NY, USA

    Mark Y. Stoeckle

Authors
  1. Darío A. Lijtmaer
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  2. Kevin C. R. Kerr
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  3. Mark Y. Stoeckle
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  4. Pablo L. Tubaro
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Corresponding author

Correspondence to Darío A. Lijtmaer .

Editor information

Editors and Affiliations

  1. National Museum of Natural History, Dept. Botany, Smithsonian Institution, 10th St. & Constitution Ave. NW.,, Washington, 20560-0166, District of Columbia, USA

    W. John Kress

  2. National Museum of Natural History, Dept. Botany, Smithsonian Institution, 10th St. & Constitution Ave. NW.,, Washington, 20560-0166, District of Columbia, USA

    David L. Erickson

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© 2012 Springer Science+Business Media, LLC

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Lijtmaer, D.A., Kerr, K.C.R., Stoeckle, M.Y., Tubaro, P.L. (2012). DNA Barcoding Birds: From Field Collection to Data Analysis. In: Kress, W., Erickson, D. (eds) DNA Barcodes. Methods in Molecular Biology, vol 858. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-61779-591-6_7

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  • DOI: https://doi.org/10.1007/978-1-61779-591-6_7

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-61779-590-9

  • Online ISBN: 978-1-61779-591-6

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