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Inferring Evolutionary Scenarios in the Duplication, Loss and Horizontal Gene Transfer Model

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Book cover Logic and Program Semantics

Part of the book series: Lecture Notes in Computer Science ((LNPSE,volume 7230))

Abstract

An H-tree is a formal model of evolutionary scenario. It can be used to represent any processes with gene duplication and loss, horizontal gene transfer (HGT) and speciation events. The model of H-trees, introduced in [26], is an extension of the duplication-loss model (DL-model). Similarly to its ancestor, it has a number of interesting mathematical and biological properties. It is, however, more computationally complex than the DL-model. In this paper, we primarily address the problem of inferring H-trees that are compatible with a given gene tree and a given phylogeny of species with HGTs. These results create a mathematical and computational foundation for a more general and practical problem of inferring HGTs from given gene and species trees with HGTs. We also demonstrate how our model can be used to support HGT hypotheses based on empirical data sets.

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Author information

Authors and Affiliations

  1. Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Banacha 2, 02-097, Warszawa, Poland

    Paweł Górecki & Jerzy Tiuryn

Authors
  1. Paweł Górecki
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  2. Jerzy Tiuryn
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Editors and Affiliations

  1. Computer Science Department, Cornell University, 4149 Upson Hall, 14853, Ithaca, NY, USA

    Robert L. Constable

  2. Intelligent Systems Faculty of Science, Institute for Computing and Information Sciences, Radboud University Nijmegen, Postbus 9010, 6500 GL, Nijmegen, The Netherlands

    Alexandra Silva

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Górecki, P., Tiuryn, J. (2012). Inferring Evolutionary Scenarios in the Duplication, Loss and Horizontal Gene Transfer Model. In: Constable, R.L., Silva, A. (eds) Logic and Program Semantics. Lecture Notes in Computer Science, vol 7230. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-29485-3_7

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  • DOI: https://doi.org/10.1007/978-3-642-29485-3_7

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-29484-6

  • Online ISBN: 978-3-642-29485-3

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