License: Creative Commons Attribution 3.0 Unported license (CC BY 3.0)
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DOI: 10.4230/LIPIcs.WABI.2018.5
URN: urn:nbn:de:0030-drops-93079
URL: http://dagstuhl.sunsite.rwth-aachen.de/volltexte/2018/9307/
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Dondi, Riccardo ; Lafond, Manuel ; Scornavacca, Celine

Reconciling Multiple Genes Trees via Segmental Duplications and Losses

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Abstract

Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families is interconnected. In this paper, we extend a previous approach to reconcile a set of gene trees with a species tree based on segmental macro-evolutionary events, where segmental duplication events and losses are associated with cost delta and lambda, respectively. We show that the problem is polynomial-time solvable when delta <= lambda (via LCA-mapping), while if delta > lambda the problem is NP-hard, even when lambda = 0 and a single gene tree is given, solving a long standing open problem on the complexity of the reconciliation problem. On the positive side, we give a fixed-parameter algorithm for the problem, where the parameters are delta/lambda and the number d of segmental duplications, of time complexity O(ceil[delta/lambda]^d * n * delta/lambda). Finally, we demonstrate the usefulness of this algorithm on two previously studied real datasets: we first show that our method can be used to confirm or refute hypothetical segmental duplications on a set of 16 eukaryotes, then show how we can detect whole genome duplications in yeast genomes.

BibTeX - Entry

@InProceedings{dondi_et_al:LIPIcs:2018:9307,
  author =	{Riccardo Dondi and Manuel Lafond and Celine Scornavacca},
  title =	{{Reconciling Multiple Genes Trees via Segmental Duplications and Losses}},
  booktitle =	{18th International Workshop on Algorithms in  Bioinformatics (WABI 2018)},
  pages =	{5:1--5:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-082-8},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{113},
  editor =	{Laxmi Parida and Esko Ukkonen},
  publisher =	{Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{http://drops.dagstuhl.de/opus/volltexte/2018/9307},
  URN =		{urn:nbn:de:0030-drops-93079},
  doi =		{10.4230/LIPIcs.WABI.2018.5},
  annote =	{Keywords: Gene trees/species tree reconciliation, phylogenetics, computational complexity, fixed-parameter algorithms}
}

Keywords: Gene trees/species tree reconciliation, phylogenetics, computational complexity, fixed-parameter algorithms
Collection: 18th International Workshop on Algorithms in Bioinformatics (WABI 2018)
Issue Date: 2018
Date of publication: 02.08.2018

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