Journal of Molecular Evolution

, Volume 64, Issue 1, pp 50–60 | Cite as

Evaluating Neanderthal Genetics and Phylogeny

  • Martin B. Hebsgaard
  • Carsten Wiuf
  • M. Thomas P. Gilbert
  • Henrik Glenner
  • Eske WillerslevEmail author


The retrieval of Neanderthal (Homo neanderthalsensis) mitochondrial DNA is thought to be among the most significant ancient DNA contributions to date, allowing conflicting hypotheses on modern human (Homo sapiens) evolution to be tested directly. Recently, however, both the authenticity of the Neanderthal sequences and their phylogenetic position outside contemporary human diversity have been questioned. Using Bayesian inference and the largest dataset to date, we find strong support for a monophyletic Neanderthal clade outside the diversity of contemporary humans, in agreement with the expectations of the Out-of-Africa replacement model of modern human origin. From average pairwise sequence differences, we obtain support for claims that the first published Neanderthal sequence may include errors due to postmortem damage in the template molecules for PCR. In contrast, we find that recent results implying that the Neanderthal sequences are products of PCR artifacts are not well supported, suffering from inadequate experimental design and a presumably high percentage (>68%) of chimeric sequences due to “jumping PCR” events.


Ancient DNA Human evolution Neanderthal DNA Bayesian inference PCR artifacts DNA damage 



We thank A. Krogh, L. G. T. Jørgensen, and W. Hughes for valuable help and J. P. Huelsenbeck, S. Y. W. Ho, M. Phillips, and J. Haile for helpful discussion. G. Gutierrez was very helpful in providing an electronic version of their data. M.B.H. was supported by the Danish Research Council. C.W. was supported by The Danish Cancer Society. M.T.P.G. was supported by the Marie Curie FP6 Action. H.G. was supported by the Danish National Science Research Council. E.W. was supported by Wellcome Trust, the Carlsberg Foundation, and the Danish Research Council.

Supplementary material

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Supplementary material


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Copyright information

© Springer Science+Business Media, Inc. 2006

Authors and Affiliations

  • Martin B. Hebsgaard
    • 1
  • Carsten Wiuf
    • 2
    • 3
  • M. Thomas P. Gilbert
    • 1
  • Henrik Glenner
    • 1
  • Eske Willerslev
    • 1
    Email author
  1. 1.Centré for Ancient GeneticsNiels Bohr Institute and Biological Institute, University of CopenhagenCopenhagenDenmark
  2. 2.Bioinformatics Research CenterUniversity of AarhusAarhusDenmark
  3. 3.Molecular Diagnostic LaboratoryAarhus University HospitalAarhusDenmark

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