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Miguel Vences, Zoltán T. Nagy, Gontran Sonet and Erik Verheyen (2012)

DNA Barcoding Amphibians and Reptiles

In: DNA Barcodes: Methods and Protocols, ed. by Kress, W. John and Erickson, David L., vol. 858(February 2008), pp. 79–107, Humana Press, Totowa, NJ. Methods in Molecular Biology™. (ISBN: 978-1-61779-590-9).

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 conspecifi c 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 suffi cient rate of success across all amphibian and reptile taxa, or within major subclades of amphibians and reptiles, which means that the PCR amplifi cation strategy needs to be adjusted depending on the specifi c 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 amplifi cation 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 specifi c primers which then allow an easy and reliable amplifi cation of all samples.

Peer Review, International Redaction Board, Impact Factor
Crocodylia, Squamata, Sphenodontia, Testudines, Amphibia, COI primers
Related content
Taxonomy and Phylogeny

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