Journal of Mathematical Biology

, Volume 72, Issue 7, pp 1811–1844 | Cite as

Inferring gene duplications, transfers and losses can be done in a discrete framework

  • Vincent Ranwez
  • Celine Scornavacca
  • Jean-Philippe Doyon
  • Vincent Berry
Article
First Online:
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Abstract

In the field of phylogenetics, the evolutionary history of a set of organisms is commonly depicted by a species tree—whose internal nodes represent speciation events—while the evolutionary history of a gene family is depicted by a gene tree—whose internal nodes can also represent macro-evolutionary events such as gene duplications and transfers. As speciation events are only part of the events shaping a gene history, the topology of a gene tree can show incongruences with that of the corresponding species tree. These incongruences can be used to infer the macro-evolutionary events undergone by the gene family. This is done by embedding the gene tree inside the species tree and hence providing a reconciliation of those trees. In the past decade, several parsimony-based methods have been developed to infer such reconciliations, accounting for gene duplications (\(\mathbb {D}\)), transfers (\(\mathbb {T}\)) and losses (\(\mathbb {L}\)). The main contribution of this paper is to formally prove an important assumption implicitly made by previous works on these reconciliations, namely that solving the (maximum) parsimony \(\mathbb {DTL}\) reconciliation problem in the discrete framework is equivalent to finding a most parsimonious \(\mathbb {DTL}\) scenario in the continuous framework. In the process, we also prove several intermediate results that are useful on their own and constitute a theoretical toolbox that will likely facilitate future theoretical contributions in the field.

Keywords

Tree reconciliation Tree embedding Gene evolution Phylogenetics Parsimony Equivalence 

Mathematics Subject Classification

68R05 68R10 92-08 05C30 
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Notes

Acknowledgments

This work was funded by the French Agence Nationale de la Recherche (ANR) through Grants ANR-09-PEXT-000 “Phylospace” and ANR-10-BINF-01-01 “Ancestrome”, and by the Institut de Biologie Computationnelle. This publication is Contribution No. 2015-098 of the Institut des Sciences de l’Evolution de Montpellier (ISEM, UMR 5554).

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Copyright information

© Springer-Verlag Berlin Heidelberg 2015

Authors and Affiliations

  • Vincent Ranwez
    • 1
    • 4
  • Celine Scornavacca
    • 2
    • 4
  • Jean-Philippe Doyon
    • 2
    • 3
  • Vincent Berry
    • 3
    • 4
  1. 1.SupAgro, UMR-AGAPMontpellierFrance
  2. 2.ISEM, UMR 5554 (Univ. Montpellier, CNRS, IRD, EPHE)MontpellierFrance
  3. 3.LIRMM, CNRS, Univ. MontpellierMontpellierFrance
  4. 4.Institut de Biologie ComputationnelleMontpellierFrance

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