2026-07-26T04:14:54Z https://drops.dagstuhl.de/oai

oai:drops-oai.dagstuhl.de:9307 2024-03-06T10:44:00Z ddc:004 open_access

Reconciling Multiple Genes Trees via Segmental Duplications and Losses Dondi, Riccardo Lafond, Manuel Scornavacca, Celine Gene trees/species tree reconciliation phylogenetics computational complexity fixed-parameter algorithms 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. Schloss Dagstuhl – Leibniz-Zentrum für Informatik Riccardo Dondi and Manuel Lafond and Celine Scornavacca 2018 Is Part Of LIPIcs, Volume 113, 18th International Workshop on Algorithms in Bioinformatics (WABI 2018) InProceedings Text doc-type:ResearchArticle publishedVersion application/pdf doi:10.4230/LIPIcs.WABI.2018.5 urn:nbn:de:0030-drops-93079 https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018.5 eng https://creativecommons.org/licenses/by/3.0/legalcode