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Discovering Local Patterns of Co-evolution

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Comparative Genomics (RECOMB-CG 2008)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 5267))

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Abstract

Co-evolution is the process in which a set of orthologs exhibits a similar or correlative pattern of evolution. Co-evolution is a powerful way to learn about the functional interdependencies between sets of genes and cellular functions, about their complementary and backup relations, and more generally, for answering fundamental questions about the evolution of biological systems.

Orthologs that exhibit strong signal of co-evolution in part of the evolutionary tree may show mild signal of co-evolution in other parts of the tree. The major reasons for this phenomenon are noise in the biological input, genes that gain or lose functions, and the fact that some measures of co-evolution relate to rare events such as positive evolution. Previous works in the field dealt with the problem of finding sets of genes that co-evolved along an entire underlying phylogenetic tree, without considering the fact that often co-evolution is local.

In this work, we describe a new set of biological problems that are related to finding patterns of local co-evolution. We discuss their computational complexity and design algorithms for solving them. These algorithms outperform other bi-clustering methods as they are designed specifically for solving the set of problems mentioned above. We use our approach to trace the co-evolution of fungal and Eukaryotic genes at a high resolution across the different parts of the corresponding phylogenetic trees. Our analysis shows that local co-evolution is a wide-scale phenomenon.

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Author information

Authors and Affiliations

  1. School of Computer Science, Tel Aviv University,  

    Yifat Felder

  2. Department of Molecular Microbiology and Biotechnology, Tel Aviv University,  

    Tamir Tuller

Authors
  1. Yifat Felder
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  2. Tamir Tuller
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Editor information

Editors and Affiliations

  1. Molecular and Cell Biology, University of Connecticut, Division of Genetics and Genomics, Beach Hall, 354 Mansfiled Rd, CT 06269, Storrs, USA

    Craig E. Nelson

  2. Université Paris-Est, IGM-LabInfo, 5 Bd Descartes, Champs sur Marne, 77454, Marne la Vallée, France

    Stéphane Vialette

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© 2008 Springer-Verlag Berlin Heidelberg

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Felder, Y., Tuller, T. (2008). Discovering Local Patterns of Co-evolution. In: Nelson, C.E., Vialette, S. (eds) Comparative Genomics. RECOMB-CG 2008. Lecture Notes in Computer Science(), vol 5267. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-87989-3_5

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  • DOI: https://doi.org/10.1007/978-3-540-87989-3_5

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-87988-6

  • Online ISBN: 978-3-540-87989-3

  • eBook Packages: Computer ScienceComputer Science (R0)

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