Are the Duplication Cost and Robinson-Foulds Distance Equivalent?

Zheng, Yu; Zhang, Louxin

doi:10.1089/cmb.2014.0021

Cited by 5 publications

(2 citation statements)

References 34 publications

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“…Furthermore, these distances are not equivalent as shown by distinct results using the DL or the ILS costs under iGTP . Indeed, the distances used are not redundant ( Zheng and Zhang 2014 ), but even the inclusion of a distance partially correlated with an existing one should not be alarming, as long as there are cases where it can add new information. Actually, even a distance that is completely equivalent to another metric should not bias the performance, with the only drawbacks of wasting computing time and increasing the variance over their penalty parameters (since the model can not distinguish between them).…”

Section: Discussionmentioning

confidence: 99%

A Bayesian Supertree Model for Genome-Wide Species Tree Reconstruction

2014

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Current phylogenomic data sets highlight the need for species tree methods able to deal with several sources of gene tree/species tree incongruence. At the same time, we need to make most use of all available data. Most species tree methods deal with single processes of phylogenetic discordance, namely, gene duplication and loss, incomplete lineage sorting (ILS) or horizontal gene transfer. In this manuscript, we address the problem of species tree inference from multilocus, genome-wide data sets regardless of the presence of gene duplication and loss and ILS therefore without the need to identify orthologs or to use a single individual per species. We do this by extending the idea of Maximum Likelihood (ML) supertrees to a hierarchical Bayesian model where several sources of gene tree/species tree disagreement can be accounted for in a modular manner. We implemented this model in a computer program called guenomu whose inputs are posterior distributions of unrooted gene tree topologies for multiple gene families, and whose output is the posterior distribution of rooted species tree topologies. We conducted extensive simulations to evaluate the performance of our approach in comparison with other species tree approaches able to deal with more than one leaf from the same species. Our method ranked best under simulated data sets, in spite of ignoring branch lengths, and performed well on empirical data, as well as being fast enough to analyze relatively large data sets. Our Bayesian supertree method was also very successful in obtaining better estimates of gene trees, by reducing the uncertainty in their distributions. In addition, our results show that under complex simulation scenarios, gene tree parsimony is also a competitive approach once we consider its speed, in contrast to more sophisticated models.

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Section: Discussionmentioning

confidence: 99%

A Bayesian Supertree Model for Genome-Wide Species Tree Reconstruction

2014

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“…While varies costs have been proposed [ 23 - 26 ], here we are concerned with the well-researched Robinson-Foulds, duplication, and deep coalescence costs. The Robinson-Foulds cost is measuring quantitative dissimilarities between two trees without relying on an evolutionary model, and is therefore well suited to address discordance caused by error [ 27 , 28 ]. In difference, the costs for the evolutionary events gene duplication and deep coalescence are both based on an evolutionary parsimony model allowing to resolve discord based on such events [ 29 , 30 ].…”

Section: Introductionmentioning

confidence: 99%

Refining discordant gene trees

Górecki

Eulenstein

2014

BMC Bioinformatics

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BackgroundEvolutionary studies are complicated by discordance between gene trees and the species tree in which they evolved. Dealing with discordant trees often relies on comparison costs between gene and species trees, including the well-established Robinson-Foulds, gene duplication, and deep coalescence costs. While these costs have provided credible results for binary rooted gene trees, corresponding cost definitions for non-binary unrooted gene trees, which are frequently occurring in practice, are challenged by biological realism.ResultWe propose a natural extension of the well-established costs for comparing unrooted and non-binary gene trees with rooted binary species trees using a binary refinement model. For the duplication cost we describe an efficient algorithm that is based on a linear time reduction and also computes an optimal rooted binary refinement of the given gene tree. Finally, we show that similar reductions lead to solutions for computing the deep coalescence and the Robinson-Foulds costs.ConclusionOur binary refinement of Robinson-Foulds, gene duplication, and deep coalescence costs for unrooted and non-binary gene trees together with the linear time reductions provided here for computing these costs significantly extends the range of trees that can be incorporated into approaches dealing with discordance.

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