Phylogenomics pp 171-184 | Cite as

Computational Reconstruction of Ancestral DNA Sequences

  • Mathauieu Blanchette
  • Abdoulaye Baniré Diallo
  • Eric D. Green
  • Webb Miller
  • David Haussler
Part of the Methods in Molecular Biology™ book series (MIMB, volume 422)


This chapter introduces the problem of ancestral sequence reconstruction: given a set of extant orthologous DNA genomic sequences (or even whole-genomes), together with a phylogenetic tree relating these sequences, predict the DNA sequence of all ancestral species in the tree. Blanchette et al. (1) have shown that for certain sets of species (in particular, for eutherian mammals), very accurate reconstruction can be obtained. We explain the main steps involved in this process, including multiple sequence alignment, insertion and deletion inference, substitution inference, and gene arrangement inference. We also describe a simulation-based procedure to assess the accuracy of the reconstructed sequences. The whole reconstruction process is illustrated using a set of mammalian sequences from the CFTR region.

Key Words

Ancestral DNA sequence reconstruction multiple sequences alignment mammalian phylogeny; mammalian evolution substitutions and indels reconstruction ancestral sequence reconstruction accuracy 


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Copyright information

© Humana Press Inc., Totowa, NJ 2008

Authors and Affiliations

  • Mathauieu Blanchette
    • 1
  • Abdoulaye Baniré Diallo
    • 1
  • Eric D. Green
    • 2
  • Webb Miller
    • 3
  • David Haussler
    • 4
  1. 1.McGill Centre for BioinformaticsMcGill UniversityMontrealCanada
  2. 2.National Human Genome Research Institute, National Institutes of HealthBethesda
  3. 3.Center for Comparative Genomics and BioinformaticsPenn StateUniversity Park
  4. 4.Howard Hughes Medical InstituteUniversity of CaliforniaSanta Cruz

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