EM for phylogenetic topology reconstruction on nonhomogeneous data
Ibáñez-Marcelo, Esther (Centre de Recerca Matemàtica)
Casanellas i Rius, Marta (Universitat Politècnica de Catalunya. Departament de Matemàtica Aplicada I)

Fecha:	2014
Resumen:	The reconstruction of the phylogenetic tree topology of four taxa is, still nowadays, one of the main challenges in phylogenetics. Its difficulties lie in considering not too restrictive evolutionary models, and correctly dealing with the long-branch attraction problem. The correct reconstruction of 4-taxon trees is crucial for making quartet-based methods work and being able to recover large phylogenies. We adapt the well known expectation-maximization algorithm to evolutionary Markov models on phylogenetic 4-taxon trees. We then use this algorithm to estimate the substitution parameters, compute the corresponding likelihood, and to infer the most likely quartet. In this paper we consider an expectation-maximization method for maximizing the likelihood of (time nonhomogeneous) evolutionary Markov models on trees. We study its success on reconstructing 4-taxon topologies and its performance as input method in quartet-based phylogenetic reconstruction methods such as QFIT and QuartetSuite. Our results show that the method proposed here outperforms neighbor-joining and the usual (time-homogeneous continuous-time) maximum likelihood methods on 4-leaved trees with among-lineage instantaneous rate heterogeneity, and perform similarly to usual continuous-time maximum-likelihood when data satisfies the assumptions of both methods. The method presented in this paper is well suited for reconstructing the topology of any number of taxa via quartet-based methods and is highly accurate, specially regarding largely divergent trees and time nonhomogeneous data.
Ayudas:	Ministerio de Economía y Competitividad MTM2012-38122-C03-01 Agència de Gestió d'Ajuts Universitaris i de Recerca 2009/SGR-1284
Derechos:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.
Lengua:	Anglès
Documento:	Article ; recerca ; Versió publicada
Materia:	Tree topology reconstruction ; Expectation-maximization ; Quartet-based method ; Evolutionary Markov model
Publicado en:	BMC evolutionary biology, Vol. 14 (June 2014) , p. 132, ISSN 1471-2148

DOI: 10.1186/1471-2148-14-132
PMID: 24938507

12 p, 1.5 MB

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