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Article Dans Une Revue Algorithms for Molecular Biology Année : 2019

Reconciling multiple genes trees via segmental duplications and losses

Résumé

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 δ and , respectively. We show that the problem is polynomial-time solvable when δ ≤ (via LCA-mapping), while if δ > the problem is NP-hard, even when = 0 and a single gene tree is given, solving a long standing open problem on the complexity of multi-gene reconciliation. On the positive side, we give a fixed-parameter algorithm for the problem, where the parameters are δ/ and the number d of segmental duplications, of time complexity O ⌈ δ ⌉ d · n · δ. 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 raise doubt on 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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Dates et versions

hal-02154306 , version 1 (18-12-2019)

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Riccardo Dondi, Manuel Lafond, Celine Scornavacca. Reconciling multiple genes trees via segmental duplications and losses. Algorithms for Molecular Biology, 2019, 14 (1), ⟨10.1186/s13015-019-0139-6⟩. ⟨hal-02154306⟩
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