Minimum Leaf Removal for Reconciliation: Complexity and Algorithms

Dondi, Riccardo; El-Mabrouk, Nadia

doi:10.1007/978-3-642-31265-6_32

Cited by 3 publications

(3 citation statements)

References 32 publications

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“…Evolutionary scenarios under this model can be computed efficiently by algorithms that are implemented in various software packages (Górecki and Tiuryn, 2007;Chaudhary et al, 2010), and despite its simplicity appear to have produced some credible evolutionary studies for small rates of gene duplication and loss events (e.g., Page, 2000;Page and Cotton, 2002;Martin and Burg, 2002;Sanderson and McMahon, 2007). Subsequent programs based on variations of the parsimony model have attempted to improve biological realism (e.g., error correction of the given trees and unrooted gene trees) (Chaudhary et al, 2012;Dondi and El-Mabrouk, 2012;Górecki and Eulenstein, 2012). Moreover, many higher level approaches in evolutionary biology are based on this model, which includes the estimation of gene duplication episodes (e.g., Bansal and Eulenstein, 2008;Burleigh et al, 2009) and supertree inference (e.g., Wehe et al, 2008).…”

Section: Related Workmentioning

confidence: 99%

DrML: Probabilistic Modeling of Gene Duplications

Górecki

Eulenstein

2014

Journal of Computational Biology

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DrML is a software program for inferring evolutionary scenarios from a gene tree and a species tree with speciation time estimates that is based on a general maximum likelihood model. The program implements novel algorithms that efficiently infer most likely scenarios of gene duplication and loss events. Our comparative studies suggest that the general maximum likelihood model provides more credible estimates than standard parsimony reconciliation, especially when speciation times differ significantly. DrML is an open source project written in Python, and along with an on-line manual and sample data sets publicly available.

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Section: Related Workmentioning

confidence: 99%

DrML: Probabilistic Modeling of Gene Duplications

Górecki

Eulenstein

2014

Journal of Computational Biology

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“…We presented algorithmic results for removing, from a given gene tree, the minimum number of leaves or leaf-labels (species) leading to a tree without a NAD vertex, under conditions of a known or an unknown species tree [16,53]. All known formulations of this version of the problem are NP-hard [14,15].…”

Section: Introductionmentioning

confidence: 99%

Error Detection and Correction of Gene Trees

Lafond

Swenson

El-Mabrouk

2013

Models and Algorithms for Genome Evolution

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Reconstructing the phylogeny of a gene family and reconciling the obtained gene tree with the species tree reveals the history of duplications, losses and other events that have shaped the gene family, with important implications towards the functional specificity of genes. However, evolutionary histories inferred by reconciliation are strongly dependent upon the accuracy of the trees, and few misplaced leaves will lead to a completely different history. Furthermore, sequence data alone often lack the information to confidently support a gene tree topology. We outline a number of criteria that can be used to detect erroneous gene trees. Analysing Ensembl gene trees of the fish genomes Stickleback, Medaka, Tetraodon, and Zebrafish reveals a significant number of erroneous gene trees. Finally, some potential directions for error correction of gene trees are explored.

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“…Here, we present algorithmic results for removing, for a given gene tree (or a forest of gene trees), the minimum number of leaves or leaf-labels (species) leading to a tree without any NAD vertex, in both cases of a known or an unknown species tree. The minimum leaf removal problem in case of a known species tree has been recently proved to be APX-hard [21]. …”

Section: Introductionmentioning

confidence: 99%

Gene tree correction for reconciliation and species tree inference

Swenson

Doroftei

El-Mabrouk

2012

Algorithms Mol Biol

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Background: Reconciliation is the commonly used method for inferring the evolutionary scenario for a gene family. It consists in "embedding" inferred gene trees into a known species tree, revealing the evolution of the gene family by duplications and losses. When a species tree is not known, a natural algorithmic problem is to infer a species tree from a set of gene trees, such that the corresponding reconciliation minimizes the number of duplications and/or losses. The main drawback of reconciliation is that the inferred evolutionary scenario is strongly dependent on the considered gene trees, as few misplaced leaves may lead to a completely different history, with significantly more duplications and losses. Results: In this paper, we take advantage of certain gene trees' properties in order to preprocess them for reconciliation or species tree inference. We flag certain duplication vertices of a gene tree, the "non-apparent duplication" (NAD) vertices, as resulting from the misplacement of leaves. In the case of species tree inference, we develop a polynomial-time heuristic for removing the minimum number of species leading to a set of gene trees that exhibit no NAD vertices with respect to at least one species tree. In the case of reconciliation, we consider the optimization problem of removing the minimum number of leaves or species leading to a tree without any NAD vertex. We develop a polynomial-time algorithm that is exact for two special classes of gene trees, and show a good performance on simulated data sets in the general case.

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Minimum Leaf Removal for Reconciliation: Complexity and Algorithms

Cited by 3 publications

References 32 publications

DrML: Probabilistic Modeling of Gene Duplications

DrML: Probabilistic Modeling of Gene Duplications

Error Detection and Correction of Gene Trees

Gene tree correction for reconciliation and species tree inference

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