Abstract
A variety of DNA extraction methods have been employed successfully to extract DNA from museum specimens. Toe pads are a common source of ancient DNA in birds, as they are generally not an informative character and can be removed without significant destruction of precious specimens. However, the DNA in these tissues is often highly degraded, both by natural postmortem decay and due to treatment by preservatives. In this case study chapter, we describe the use of both a commercial DNA extraction method and a silica-based method to extract ancient DNA from desiccated toe pads from the extinct passenger pigeon, Ectopistes migratorius. Successful amplification of nuclear DNA was achieved from both methods, representing the first nuclear DNA sequence recovered from this extinct species. We describe simple modifications to both protocols that we employed during the DNA extraction process.
*Note: In the case study presented in this chapter, we describe the extraction of DNA from toe pads of museum-preserved specimens of the passenger pigeon, Ectopistes migratorius, using a method similar to that presented in Chap. 3. Other methods, such as those described in Chap. 2, may also be appropriate to extract DNA from this type of sample. We discuss specific challenges associated with applying this extraction method to ancient toe pad samples, including the use of dithiothreitol (DTT) for tissue dissolution. For more information, see the original publication of the scientific results in (1).
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References
Fulton TL, Wagner SW, Fisher C, Shapiro B (in press) Nuclear DNA from the extinct Passenger Pigeon (Ectopistes migratorius) confirms its phylogenetic placement within Columbinae. Ann Anat
Wandeler P, Hoeck PEA, Keller LF (2007) Back to the future: museum specimens in population genetics. Trends Ecol Evol 22:634–642
Mundy NI, Unitt P, Woodruff DS (1997) Skin from feet of museum specimens as a non-destructive source of DNA for avian genotyping. Auk 114:126–129
Schorger AW (1973) The passenger pigeon; its natural history and extinction. University of Oklahoma Press, Norman
Goodwin D (1967) Pigeons and doves of the world. British Museum (Natural History), London
Shapiro B, Sibthorpe D, Rambaut A, Austin J, Wragg GM, Bininda-Emonds ORP, Lee PLM, Cooper A (2002) Flight of the dodo. Science 295:1683
Johnson KP, Clayton DH, Dumbacher JP, Fleischer RC (2010) The flight of the passenger pigeon: phylogenetics and biogeographic history of an extinct species. Mol Phylogenet Evol 57:455–458
Stamatakis A (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688–2690
Huelsenbeck JP, Ronquist F (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17:754–755
Ronquist F, Huelsenbeck JP (2003) MrBayes3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572–1574
Posada D (2008) jModelTest: Phylogenetic model averaging. Mol Biol Evol 25:1253–1256
Acknowledgments
We thank Clemency Fisher and the National Museums Liverpool for providing Ectopistes material for analysis. Funding for this research was provided by the Pennsylvania State University to BS and an Undergraduate Discovery Grant to SMW.
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© 2012 Springer Science+Business Media, LLC
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Fulton, T.L., Wagner, S.M., Shapiro, B. (2012). Case Study: Recovery of Ancient Nuclear DNA from Toe Pads of the Extinct Passenger Pigeon. In: Shapiro, B., Hofreiter, M. (eds) Ancient DNA. Methods in Molecular Biology, vol 840. Humana Press. https://doi.org/10.1007/978-1-61779-516-9_4
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DOI: https://doi.org/10.1007/978-1-61779-516-9_4
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