RECOMB-CG 2007: Comparative Genomics pp 177-191 | Cite as

A Rigorous Analysis of the Pattern of Intron Conservation Supports the Coelomata Clade of Animals

  • Jie Zheng
  • Igor B. Rogozin
  • Eugene V. Koonin
  • Teresa M. Przytycka
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4751)

Abstract

Many intron positions are conserved in varying subsets of eukaryotic genomes and, consequently, comprise a potentially informative class of phylogenetic characters. Roy and Gilbert developed a method of phylogenetic reconstruction using the patterns of intron presence-absence in eukaryotic genes and, applying this method to the analysis of animal phylogeny, obtained support for an Ecdysozoa clade ([1]). The critical assumption in the method was the independence of the rates of intron loss in different branches of the phylogenetic. Here, this assumption is refuted by showing that the branch-specific intron loss rates are strongly correlated. We show that different tree topologies are obtained, in each case with a significant statistical support, when different subsets of intron positions are analyzed. The analysis of the conserved intron positions supports the Coelomata topology, i.e., a clade comprised of arthropods and chordates, whereas the analysis of more variable intron positions favors the Ecdysozoa topology, i.e., a clade of arthropods and nematodes. We show, however, that the support for Ecdysozoa is fully explained by parallel loss of introns in nematodes and arthropods, a factor that does not contribute to the analysis of the conserved introns. The developed procedure for the identification and analysis of conserved introns and other characters with minimal or no homoplasy is expected to be useful for resolving many hard phylogenetic problems.

Keywords

Retention Rate Tree Topology Intron Position Variable Intron Intron Loss 
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 2007

Authors and Affiliations

  • Jie Zheng
    • 1
  • Igor B. Rogozin
    • 1
  • Eugene V. Koonin
    • 1
  • Teresa M. Przytycka
    • 1
  1. 1.National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894USA

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