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Common Intervals and Symmetric Difference in a Model-Free Phylogenomics, with an Application to Streptophyte Evolution

  • Zaky Adam
  • Monique Turmel
  • Claude Lemieux
  • David Sankoff
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4205)

Abstract

The common intervals of two permutations on n elements are the subsets of terms contiguous in both permutations. They constitute the most basic representation of conserved local order. We use d, the size of the symmetric difference (the complement of the common intervals) of the two subsets of 2{ 1, ⋯ ,n} thus determined by two permutations, as an evolutionary distance between the gene orders represented by the permutations. We consider the Steiner Tree problem in the space (2{ 1, ⋯ ,n},d) as the basis for constructing phylogenetic trees, including ancestral gene orders. We extend this to genomes with unequal gene content and to genomes containing gene families. Applied to streptophyte phylogeny, our method does not support the positioning of the complex algae Charales as a sister group to the land plants.

Keywords

Gene Order Binary Tree Land Plant Chloroplast Genome Steiner Tree 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Zaky Adam
    • 1
  • Monique Turmel
    • 2
  • Claude Lemieux
    • 2
  • David Sankoff
    • 1
  1. 1.School of Information Technology and Engineering, and Department of Mathematics and StatisticsUniversity of OttawaOttawaCanada
  2. 2.Département de biochimie et de microbiologieUniversité LavalQuébecCanada

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