Ancient DNA pp 29-35 | Cite as

Case Study: Recovery of Ancient Nuclear DNA from Toe Pads of the Extinct Passenger Pigeon

  • Tara L. Fulton
  • Stephen M. Wagner
  • Beth Shapiro
Part of the Methods in Molecular Biology book series (MIMB, volume 840)


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.

Key words

Columbidae pigeons toe pads DTT dithiothreitol ancient DNA silica extraction 


  1. 1.
    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 AnatGoogle Scholar
  2. 2.
    Wandeler P, Hoeck PEA, Keller LF (2007) Back to the future: museum specimens in population genetics. Trends Ecol Evol 22:634–642PubMedCrossRefGoogle Scholar
  3. 3.
    Mundy NI, Unitt P, Woodruff DS (1997) Skin from feet of museum specimens as a non-destructive source of DNA for avian genotyping. Auk 114:126–129Google Scholar
  4. 4.
    Schorger AW (1973) The passenger pigeon; its natural history and extinction. University of Oklahoma Press, NormanGoogle Scholar
  5. 5.
    Goodwin D (1967) Pigeons and doves of the world. British Museum (Natural History), LondonGoogle Scholar
  6. 6.
    Shapiro B, Sibthorpe D, Rambaut A, Austin J, Wragg GM, Bininda-Emonds ORP, Lee PLM, Cooper A (2002) Flight of the dodo. Science 295:1683PubMedCrossRefGoogle Scholar
  7. 7.
    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 57:455–458PubMedCrossRefGoogle Scholar
  8. 8.
    Stamatakis A (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688–2690PubMedCrossRefGoogle Scholar
  9. 9.
    Huelsenbeck JP, Ronquist F (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17:754–755PubMedCrossRefGoogle Scholar
  10. 10.
    Ronquist F, Huelsenbeck JP (2003) MrBayes3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572–1574PubMedCrossRefGoogle Scholar
  11. 11.
    Posada D (2008) jModelTest: Phylogenetic model averaging. Mol Biol Evol 25:1253–1256PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  • Tara L. Fulton
    • 1
  • Stephen M. Wagner
    • 1
  • Beth Shapiro
    • 2
  1. 1.Department of BiologyThe Pennsylvania State UniversityUniversity ParkUSA
  2. 2.Department of Ecology and Evolutionary BiologyUniversity of California Santa CruzSanta CruzUSA

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