Methods for Quick Consensus Estimation

By Pablo A. Goloboff, J. Farris. 2001

333 citations recorded by the source corpus.

A method that allows estimating consensus trees without exhaustive searches is described. The method consists of comparing the results of different independent superficial searches. The results of the searches are then summarized through a majority rule, consensed with the strict consensus tree of the best trees found overall. This assumes that to the extent that a group is recovered by most searches, it is more likely to be actually supported by the data. The effect of different parameters on the accuracy and reliability of the results is discussed. Increasing the cutoff frequency decreases the number of spurious groups, although it also decreases the number of correct nodes recovered. Collapsing trees during swapping reduces the number of spurious groups without significantly decreasing the number of correct nodes recovered. A way to collapse branches considering suboptimal trees is described, which can be extended as a measure of relative support for groups; the relative support is based on the Bremer support, but takes into account relative amounts of favorable and contradictory evidence. More exhaustive searches increase the number of correct nodes recovered, but leave unaffected (or increase) the number of spurious groups. Within some limits, the number of replications does not strongly affect the accuracy of the results, so that using relatively small numbers of replications normally suffices to produce a reliable estimation.

Subfields: Ecology, Ecology, Evolution, Behavior and Systematics, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/1f9f56fdb1444ce78b38f372754eb025ce1b0dfe

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Citations in the corpus

Weighting against homoplasy improves phylogenetic analysis of morphological data sets (2008, methodology): “To avoid bias due to unequal frequency of groups in optimal and quasi-optimal trees (see discussion in Goloboff and Farris, 2001, and examples in Goloboff and Pol, 2005), the best trees for each addition sequence were retained even if worse than the trees for other addition sequences.”
Casting the Percomorph Net Widely: The Importance of Broad Taxonomic Sampling in the Search for the Placement of Serranid and Percid Fishes (2007, methodology): “This 85% majority-rule tree was used to quickly estimate the groups present in the consensus of large data sets (Goloboff and Farris, 2001).”
A phylogeny of extant penguins (Aves: Sphenisciformes) combining morphology and mitochondrial sequences (2005, methodology): “Finally, as recommended by Goloboff and Farris (2001), relative support values were calculated considering only those trees within the absolute Bremer support for each group.”
THE AMPHIBIAN TREE OF LIFE (2006, methodology): “Ideally, indicators of search adequacy (e.g., multiple independent minimumlength hits, stable consensus; see Goloboff, 1999; Goloboff and Farris, 2001; Goloboff et al., 2003) should be employed to judge the adequacy of analysis, as is now reasonable in parsimony analysis of large prealigned…”
TNT, a free program for phylogenetic analysis (2008, background): “In the case of impossibly large data sets (or easier data sets but very impatient users), a conservative estimate of the actual consensus of most parsimonious trees that does not require actually finding them (i.e. a quick consensus estimation; Goloboff and Farris, 2001) can be produced by selecting”
Phylogeny of Asilidae Inferred from Morphological Characters of Imagines (Insecta: Diptera: Brachycera: Asiloidea) (2009, methodology): “Griffiths (1994), therefore, concluded that surstyli in Leptogastrinae (sensu Martin) are not appendages (5 styli) musculated from the epandrium itself and therefore should not be called surstyli. For lack of a better term, I use surstyli in the following sense: secondary, movable lobate differentia”
TNT version 1.5, including a full implementation of phylogenetic morphometrics (2016, methodology): “TNT also implements the option of collapsing trees based on branch-swapping (as in Goloboff and Farris, 2002), and this is implemented for landmark data in the same way as for standard characters: for any rear-rangement that produces a tree of the same score (or within the score difference speciﬁed…”
Improvements to resampling measures of group support (2003, background): “The absolute (Bremer, 1988, 1994) and relative (Goloboff and Farris, 2001) Bremer supports measure two different aspects of group support.”
A Phylogeny of the Tropical Genus Piper Using Its and the Chloroplast Intron psbJ–petA (2008, background): “TNT produces trees until the consensus tree reaches stability (Goloboff and Farris 2001).”
Phylogeny and classification of tribe Aedini (Diptera: Culicidae) (2009, methodology): “In our previous studies, we assessed clade support using Bremer support (Bremer, 1994) and relative Bremer support (Goloboff & Farris, 2001), which © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2009, 157, 700–794 measure the amount of evidence in favour of a group…”
The Morphology And Phylogeny Of Dionychan Spiders (Araneae: Araneomorphae) (2014, background): “The proportion of opposing and supporting characters is then calculated as C/F, where F is the sum of fit of all characters favoring a group, and C of those opposing it (Goloboff and Farris, 2001).”