DNA Barcodes pp 79-107 | Cite as

DNA Barcoding Amphibians and Reptiles

  • Miguel VencesEmail author
  • Zoltán T. Nagy
  • Gontran Sonet
  • Erik Verheyen
Part of the Methods in Molecular Biology book series (MIMB, volume 858)


Only a few major research programs are currently targeting COI barcoding of amphibians and reptiles (including chelonians and crocodiles), two major groups of tetrapods. Amphibian and reptile species are typically old, strongly divergent, and contain deep conspecific lineages which might lead to problems in species assignment with incomplete reference databases. As far as known, there is no single pair of COI primers that will guarantee a sufficient rate of success across all amphibian and reptile taxa, or within major subclades of amphibians and reptiles, which means that the PCR amplification strategy needs to be adjusted depending on the specific research question. In general, many more amphibian and reptile taxa have been sequenced for 16S rDNA, which for some purposes may be a suitable complementary marker, at least until a more comprehensive COI reference database becomes available. DNA barcoding has successfully been used to identify amphibian larval stages (tadpoles) in species-rich tropical assemblages. Tissue sampling, DNA extraction, and amplification of COI is straightforward in amphibians and reptiles. Single primer pairs are likely to have a failure rate between 5 and 50% if taxa of a wide taxonomic range are targeted; in such cases the use of primer cocktails or subsequent hierarchical usage of different primer pairs is necessary. If the target group is taxonomically limited, many studies have followed a strategy of designing specific primers which then allow an easy and reliable amplification of all samples.

Key words

Amphibia Testudines Crocodylia Sphenodontia Squamata COI primers 



We thank the Belgian Science Policy Office for supporting the Joint Experimental Molecular Unit.


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Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  • Miguel Vences
    • 1
    Email author
  • Zoltán T. Nagy
    • 2
  • Gontran Sonet
    • 2
  • Erik Verheyen
    • 3
  1. 1.Division of Evolutionary Biology Zoological InstituteTechnical University of BraunschweigBraunschweigGermany
  2. 2.Joint Experimental Molecular UnitRoyal Belgian Institute of Natural SciencesBrusselsBelgium
  3. 3.Vertebrate departmentRoyal Belgian Institute of Natural SciencesBrusselsBelgium

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