ArticleBMC evolutionary biology2014
EM for phylogenetic topology reconstruction on nonhomogeneous data.
Article in BMC evolutionary biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
backgroundThe 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.
methodsWe 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.
resultsIn 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.
conclusionsThe 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.
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