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Reconciling Multiple Genes Trees via Segmental Duplications and Losses

Authors Riccardo Dondi, Manuel Lafond, Celine Scornavacca

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ACM Subject Classification
  • Applied computing → Computational biology
  • Theory of computation → Fixed parameter tractability
  • Theory of computation → Problems, reductions and completeness
Keywords
  • Gene trees/species tree reconciliation
  • phylogenetics
  • computational complexity
  • fixed-parameter algorithms

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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.

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Riccardo Dondi, Manuel Lafond, and Celine Scornavacca. Reconciling Multiple Genes Trees via Segmental Duplications and Losses. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 5:1-5:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018) https://doi.org/10.4230/LIPIcs.WABI.2018.5

Author Details

Riccardo Dondi
  • Dipartimento di Filosofia, Lettere, Comunicazione, Università degli Studi di Bergamo, Bergamo, Italy,
Manuel Lafond
  • Department of Computer Science, Université de Sherbrooke, Québec, Canada,
Celine Scornavacca
  • ISEM, CNRS, Université de Montpellier, IRD, EPHE, Montpellier, France,

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