Reconciling multiple genes trees via segmental duplications and losses

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 appr...

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Bibliographic Details
Published in:Algorithms for molecular biology Vol. 14; no. 1; pp. 7 - 19
Main Authors: Dondi, Riccardo, Lafond, Manuel, Scornavacca, Celine
Format: Journal Article
Language:English
Published: London BioMed Central 20.03.2019
Springer Nature B.V
BMC
Subjects:
Algorithms
Bioinformatics
Biological evolution
Biomedical and Life Sciences
Cellular and Medical Topics
Complexity
Computational Biology/Bioinformatics
Computer Science
Eukaryotes
Evolution
Fixed-parameter tractability
Gene families
Gene mapping
Gene trees
Genes
Genomes
Genomics
Life Sciences
Mapping
Parameters
Phylogenetics
Physiological
Polynomials
Reconciliation
Reproduction (copying)
Segmental duplications
Selected papers from WABI 2018
Species trees
Trees
Yeast
NP-hardness
Reconciliation
Phylogenetics
Segmental duplications
Gene trees
Species trees
Fixed-parameter tractability
Whole genome duplications
ISSN:1748-7188, 1748-7188
Online Access:Get full text
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Summary: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 λ , respectively. We show that the problem is polynomial-time solvable when δ ≤ λ (via LCA-mapping), while if δ > λ the problem is NP-hard, even when λ = 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 / λ and the number d of segmental duplications, of time complexity O ⌈ δ λ ⌉ d · n · δ λ . 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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ISSN:1748-7188
1748-7188
DOI:10.1186/s13015-019-0139-6