MBE Advance Access published online on September 24, 2007
Molecular Biology and Evolution, doi:10.1093/molbev/msm207
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Research Article |
Support for the Coelomata Clade of Animals From a Rigorous Analysis of the Pattern of Intron Conservation
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
* Corresponding authors E-mail: przytyck{at}ncbi.nlm.nih.gov or koonin{at}ncbi.nlm.nih.gov
Received for publication June 22, 2007. Revision received September 4, 2007. Accepted for publication September 18, 2007.
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 (Roy and Gilbert 2005). The critical assumption in the method was the independence of intron loss in different branches of the phylogenetic tree. 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.
Key Words: Intron loss • Intron conservation • Phylogenetic analysis • coelomata • ecdysozoa
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