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T. Przytycka’s Research Group

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Teresa M. Przytycka’s research group

Algorithmic and Graph Theoretical methods in

Computational and Systems Biology

 Evolutionary inference based on conserved introns

Group members:

Jie Zhang

Teresa M. Przytycka

Collaborators

Igor B. Rogozin

Eugene V. Koonin

References:

· Zheng J, Rogozin IB, Koonin EV, Przytycka TM . Support for the Coelomata clade of animals from a rigorous analysis of the pattern of intron conservation. , Mol.Bio.Evo. PubMed

· Jie Zheng, Igor Rogozin, Eugene Koonin and Teresa M. Przytycka. A rigorous analysis of the pattern of intron conservation supports the Coelomata clade of animals. RECOMB Comparative Genomics 2007. LNCS 4751 p.177-92.

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 SW, Gilbert W. 2005. Resolution of a deep animal divergence by the pattern of intron conservation. Proc Natl Acad Sci USA. 102:4403-4408). 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, that is, a clade comprised of arthropods and chordates, whereas the analysis of more variable intron positions favors the Ecdysozoa topology, that is, 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.

Supplementary materials

Data:

11 genomes used in the main experiments

13 genomes used for control experiments