Robinson-Foulds Supertrees

Abstract

BackgroundSupertree methods synthesize collections of small phylogenetic trees with incomplete taxon overlap into comprehensive trees, or supertrees, that include all taxa found in the input trees. Supertree methods based on the well established Robinson-Foulds (RF) distance have the potential to build supertrees that retain much information from the input trees. Specifically, the RF supertree problem seeks a binary supertree that minimizes the sum of the RF distances from the supertree to the input trees. Thus, an RF supertree is a supertree that is consistent with the largest number of clusters (or clades) from the input trees.ResultsWe introduce efficient, local search based, hill-climbing heuristics for the intrinsically hard RF supertree problem on rooted trees. These heuristics use novel non-trivial algorithms for the SPR and TBR local search problems which improve on the time complexity of the best known (naïve) solutions by a factor of Θ(n) and Θ(n2) respectively (where n is the number of taxa, or leaves, in the supertree). We use an implementation of our new algorithms to examine the performance of the RF supertree method and compare it to matrix representation with parsimony (MRP) and the triplet supertree method using four supertree data sets. Not only did our RF heuristic provide fast estimates of RF supertrees in all data sets, but the RF supertrees also retained more of the information from the input trees (based on the RF distance) than the other supertree methods.ConclusionsOur heuristics for the RF supertree problem, based on our new local search algorithms, make it possible for the first time to estimate large supertrees by directly optimizing the RF distance from rooted input trees to the supertrees. This provides a new and fast method to build accurate supertrees. RF supertrees may also be useful for estimating majority-rule(-) supertrees, which are a generalization of majority-rule consensus trees.

An Experimental Study of Quartets MaxCut and Other Supertree Methods

“…In this paper, we report results from a study in which we explored several encodings of the source trees by quartet trees and applied QMC to the resultant sets of quartet trees. We compared these different QMC-based supertree methods to MRP and five other supertree methods: Robinson-Foulds Supertrees (RFS) [15], Q-imputation (Q-Imp) [16], MinFlip [17][18][19], SFIT [20], and PhySIC [21]. We find:…”

Cause of gene tree discord? Distinguishing incomplete lineage sorting and lateral gene transfer in phylogenetics

“…Just as ILS, multiple methods have been developed to tree reconstruction Lhen genes have conflicting evolutionary history due to LGT events (Bansal et al, 2013;Sjostrand et al, 2014). Studies have proposed various optimizing criteria, from minimizing the total Robinson-Foulds distance of the supertree (Bansal et al, 2010) to the Subtree Prune-and-Regraft distance (Whidden et al, 2014), and robustness to LGT Las compared betLeen tree-building approaches (e.g., supertrees versus supermatrix; Lapierre et al, 2014). HoLever, most of the methods dealing Lith LGT do not model coalescent process, except that a revieL paper by Szollosi et al (2015) discussed a potential model by extending and combining current methods (Szollosi et al, 2015).…”

1001 - A tool for binary representations of unordered multistate characters (with examples from genomic data)

“…The 1001 binary representations of molecular data (not necessary polarized) may also be Robinson-Foulds consensus (reviewed in Kitching et al 1998 andBansal et al 2010) calculated using program RFS v. 2.0 (Bansal et al 2010). Majority-Rule consensus calculated in PAUP* (Swofford 2002).…”