+- Mapping individual gene data on an evolutionary tree

Mapping individual gene data on an evolutionary tree
 

B. Mirkin, T.I. Fenner, G. Loizou

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Project outline and aims
 

Evolutionary trees are an important instrument in inter-genome analysis. Traditionally, computational biology focuses on the problem of tree building. This problem can be formulated as follows: given a set of extant species and data on similarities between them, build a (rooted) tree whose leaves correspond to the extant species and interior nodes to their ancestors. This project is devoted to a related problem - developing methods of interpretation of various types of data on the extant species by mapping them in a biologically meaningful way onto an evolutionary tree and annotating the tree nodes with relevant evolutionary events.

In particular, we are concerned with two types of mapping:

  • given an evolutionary species tree and a set of trees built on the same extant species according to similarity between individual gene families, find a mapping of the individual gene trees onto the species tree exhibiting gene duplications and losses to account for the differences;
  • given an evolutionary species tree and a pattern of presence/absence of a specific gene in the extant species, find a parsimonious evolutionary scenario explaining the pattern by phenomena of gene emergence, horizontal transfer, and gene loss.

    Solving problems of this type will help in reconstructing the genome contents of ancestor species.
     

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    Publications:

    O. Eulenstein, B. Mirkin, and M. Vingron (1997) Comparison of annotating duplication, tree mapping, and copying as methods to compare gene trees with species trees, in B. Mirkin, F. McMorris, F. Roberts, and A. Rzhetsky (Eds.) Mathematical Hierarchies and Biology, DIMACS Series, V. 37, Providence: AMS, 71-94.

    O. Eulenstein, B. Mirkin, and M. Vingron (1998) Duplication-Based Measures of Difference Between Gene and Species Trees, Journal of Computational Biology, 5, 135-148.

    B. Mirkin, T. Fenner, M. Galperin and E. Koonin (2003) Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes, BMC Evolutionary Biology 2003, 3:2.

    B. Mirkin and E. Koonin (2003) A top-down method for building genome classification trees with linear binary hierarchies, in M. Janowitz, J.-F. Lapointe, F. McMorris, B. Mirkin, and F. Roberts (Eds.) Bioconsensus, DIMACS Series, V. 61, Providence: AMS, 97-112.