Some Desiderata for Liberal Supertrees

Wilkinson, Mark; Thorley, Joe; Pisani, David E.; Lapointe, François‐Joseph; McInerney, James O.

doi:10.1007/978-1-4020-2330-9_11

Cited by 37 publications

(16 citation statements)

References 70 publications

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“…The performance of supertree building methods should meet a series of properties proposed by Steel et al () and Wilkinson et al (, ) in a mathematical and practical context, respectively. Overall, these properties specify that: (i) the taxa in the output supertree should be equal to those found in all source trees; (ii) that there should be a phylogenetic agreement between the relationships featured in the output supertree and the original source trees; and furthermore (iii) whenever there are scaffold source trees, the resulting supertree should display their structure; and (iv) the supertree method should be applicable to any set of source trees, regardless of the order they are fed into the algorithm.…”

Section: Discussionmentioning

confidence: 99%

“…The design of algorithms for supertree construction is a very active field of research to the point where currently there are at least 20 supertree construction methods (Bininda‐Emonds, ; Bordewich et al, ; Ranwez et al, ; Bansal et al, ; Swenson et al, ). Since these methods perform differently (because of their inherent algorithmic diversity), Steel et al () and Wilkinson et al () suggested several properties that are desirable in supertree methods that can be summarized in three main points. First, there should be a close phylogenetic correspondence between the primary source trees and the resulting supertree.…”

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confidence: 99%

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A phylogeny of Bromeliaceae (Poales, Monocotyledoneae) derived from an evaluation of nine supertree methods

Escobedo-Sarti

Ramirez

Leopardi

et al. 2013

J of Sytematics Evolution

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There are 26 phylogenetic studies for Bromeliaceae based on different sources of evidence. Despite this broad phylogenetic coverage of Bromeliaceae, however, the available phylogenetic data display a scattered sampling, with little overlap among different types of evidence. The aim of this study is to integrate the available phylogenetic information of the Bromeliaceae in one hypothesis using a supertree. To test which of them integrates best the information for Bromeliaceae, nine supertree methods were employed: Avcon, MSS, MinFlip, MMC, MRP, PhySIC_IST, Robinson-Foulds Supertree, Sfit, and SuperFine. Supertrees were compared with a reference tree, generated from the maximum likelihood (ML) analysis of a supermatrix integrated by 120 taxa of Bromeliaceae and seven cpDNA regions. In order to select which method best reconstructs the most robust phylogeny, two different sets of source trees were used: (i) those generated from the analysis of each individual DNA regions; and (ii) four selected phylogenies (from the 26 published works). We used the consensus fork index, normalized partition metric, patristic distance coefficient, and the Shimodaira-Hasegawa test to compare supertrees with the reference tree. The best performing methods were used to construct a supertree using all phylogenies of Bromeliaceae. The SuperFine method generated the best supertree. The lack of overlapping among phylogenies was the major limiting factor for the integration of the phylogenetic information of Bromeliaceae. Nonetheless, supertree methods helped in the identification of poorly sampled groups, as well as to explore levels of agreement among published phylogenetic studies for Bromeliaceae.

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Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

A phylogeny of Bromeliaceae (Poales, Monocotyledoneae) derived from an evaluation of nine supertree methods

Escobedo-Sarti

Ramirez

Leopardi

et al. 2013

J of Sytematics Evolution

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“…With this novel approach rogue taxa exist only when there is some 'reduced' consensus, i.e. a consensus of pruned trees, that, according to the RNR optimality criterion, is better than the corresponding plenary consensus, i.e., a consensus including all the leaves (Wilkinson, Thorley, Pisani, Lapointe, & McInerney, 2004 RNR has two alternative optimality criteria. The relative information content (Pattengale, Aberer, Swenson, Stamatakis, & Moret, 2011) is simply the degree of resolution of the consensus (i.e., the number of internal branches), maximization of which is also what Wilkinson (1995b) used to distinguish primary from other reduced consensus trees.…”

Section: Roguenarok (Rnr)mentioning

confidence: 99%

Comments on detecting rogue taxa using RogueNaRok

Wilkinson

Crotti

2016

Systematics and Biodiversity

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Rogues are relatively unstable taxa in phylogenetic analyses that are of concern if they obfuscate relationships, or support for relationships, of interest among more stable taxa. RogueNaRok is a recently developed heuristic solution to the problem of identifying rogue taxa. We illustrate the performance of RogueNaRok with simple examples designed to clarify its behaviour. We argue that the optimality criterion currently used by RogueNaRok may sometimes be poorly suited to the task of detecting rogues and that the scores reported by RogueNaRok should not be interpreted as measures of taxon instability. We suggest how RogueNaRok might be enhanced and recommend that it not be relied upon exclusively for detecting rogues.

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“…In recent contributions, Wilkinson et al. (2004, in press) have discussed the bias that asymmetric measures of fit introduce in supertree analysis.…”

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Minority rule supertrees? MRP, Compatibility, and Minimum Flip may display the least frequent groups

Goloboff¹

2005

Cladistics

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New examples are presented, showing that supertree methods such as matrix representation with parsimony, minimum flip trees, and compatibility analysis of the matrix representing the input trees, produce supertrees that cannot be interpreted as displaying the groups present in the majority of the input trees. These methods may produce a supertree displaying some groups present in the minority of the trees, and contradicted by the majority. Of the three methods, compatibility analysis is the least used, but it seems to be the one that differs the least from majority rule consensus. The three methods are similar in that they choose the supertree(s) that best fit the set of input trees (quantified as some measure of the fit to the matrix representation of the input trees); in the case of complete trees, it is argued that, for a supertree method to be equivalent to majority rule or frequency difference consensus, two necessary (but not sufficient) conditions must be met. First, the measure of fit between a supertree and an input tree must be symmetrical. Second, the fit for a character representing a group must be measured as absolute: either it fits or it does not fit. In the restricted case of complete and equally resolved input trees, compatibility analysis (unlike MRP and minimum flipping) fulfils these two conditions: it is symmetrical (i.e., as long as the trees have the same taxon sets and are equally resolved, the number of characters in the matrix representation of tree A that require homoplasy in tree B is always the same as the number of characters in the matrix representation of tree B that require homoplasy in tree A) and it measures fit as all-or-none. In the case of just two complete and equally resolved input trees, the two conditions (symmetry and absolute fit) are necessary and sufficient, which explains why the compatibility analysis of such trees behaves as majority consensus. With more than two such trees, these conditions are still necessary but no longer sufficient for the equivalence; in such cases, the compatibility supertree may differ significantly from the majority rule consensus, even when these conditions apply (as shown by example). MRP and minimum flipping are asymmetric and measure various degrees of fit for each character, which explains why they often behave very differently from majority rule procedures, and why they are very likely to have groups contradicted by each of the input trees, or groups supported by a minority of the input trees.

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Some Desiderata for Liberal Supertrees

Cited by 37 publications

References 70 publications

A phylogeny of Bromeliaceae (Poales, Monocotyledoneae) derived from an evaluation of nine supertree methods

A phylogeny of Bromeliaceae (Poales, Monocotyledoneae) derived from an evaluation of nine supertree methods

Comments on detecting rogue taxa using RogueNaRok

Minority rule supertrees? MRP, Compatibility, and Minimum Flip may display the least frequent groups

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