Reconciling multiple genes trees via segmental duplications and losses View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2019-12

AUTHORS

Riccardo Dondi, Manuel Lafond, Celine Scornavacca

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 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. More... »

PAGES

7

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/s13015-019-0139-6

DOI

http://dx.doi.org/10.1186/s13015-019-0139-6

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1112898345

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/30930955


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