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Communication Dans Un Congrès Année : 2018

On the Weighted Quartet Consensus problem

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 $\delta$ and $\lambda$, respectively. We show that the problem is polynomial-time solvable when $\delta \leq \lambda$ (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 $O(\lceil \frac{\delta}{\lambda} \rceil^{d} \cdot n \cdot \frac{\delta}{\lambda})$. 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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Dates et versions

hal-02155127 , version 1 (13-06-2019)

Identifiants

Citer

Manuel Lafond, Celine Scornavacca. On the Weighted Quartet Consensus problem. CPM, 2018, Warsaw, Poland. pp.28:1-28:18, ⟨10.4230/LIPIcs.CPM.2017.28⟩. ⟨hal-02155127⟩
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