Improvements to resampling measures of group support

By Pablo A. Goloboff, J. Farris, M. Källersjö, Bengt Oxelman, Martıacute;n J Ramıacute;rez, C. Szumik. 2003

814 citations recorded by the source corpus.

Several aspects of current resampling methods to assess group support are reviewed. When the characters have different prior weights or some state transformation costs are different, the frequencies under either bootstrapping or jackknifing can be distorted, producing either under‐ or overestimations of the actual group support. This is avoided by symmetric resampling, where the probability p of increasing the weight of a character equals the probability of decreasing it. Problems with interpreting absolute group frequencies as a measure of the support are discussed; group support does not necessarily vary with the frequency itself, since in some cases groups with positive support may have much lower frequencies than groups with no support at all. Three possible solutions for this problem are suggested. The first is measuring the support as the difference in frequency between the group and its most frequent contradictory group. The second is calculating frequencies for values of p below the threshold under which the frequency ranks the groups in the right order of support (this threshold may vary from data set to data set). The third is estimating the support by using the slope of the frequency as a function of different (low) values of p; when p is low, groups with actual support have negative slopes (closer to 0 when the support is higher), and groups with no support have positive slopes (larger when evidence for and against the group is more abundant).

Subfields: Ecology, Evolution, Behavior and Systematics, Insect Science, Plant Science

View Paper: https://www.semanticscholar.org/paper/83cf63df840f3c233e74a025063ead6544116277

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Citations in the corpus

Phylogeny and classification of tribe Aedini (Diptera: Culicidae) (2009, methodology): “We applied symmetric resampling, as implemented in TNT, to our data and recorded both the absolute frequencies of group occurrence and the frequency differences (‘Groups present/ Contradicted’ or GC values; Goloboff et al., 2003a).”
Phylogenetic Analysis of Araucariaceae: Integrating Molecules, Morphology, and Fossils (2013, methodology): “Group support was assessed and also by absolute jackknifing frequencies with the following settings: five RAS per replicate followed by Tree Drifting and Sectorial Searches and an independent probability of character removal of 0.36 (Goloboff et al. 2003).”
The More the Merrier? A Large Cladistic Analysis of Mysticetes, and Comments on the Transition from Teeth to Baleen (2011, methodology): “…were summarized using strict consensus trees with zero-length branches collapsed, and Bremer support values (Bremer 1994) and symmetric resampling (Goloboff et al. 2003a) based on 2000 replicates and reported as GC frequency differences (Goloboff et al. 2003a) were used to estimate branch support…”
Varying rates of diversification in the genus Melitaea (Lepidoptera: Nymphalidae) during the past 20 million years (2009, methodology): “favourable and contradictory evidences in the data with the given assumptions used to interpret those (Goloboff et al., 2003).”
TNT version 1.5, including a full implementation of phylogenetic morphometrics (2016, background): “…of resampling, either the entire conﬁguration or the individual landmarks can be resam-pled — whether the resampling is done with standard bootstrapping (Felsenstein, 1985), independent-removal jackniﬁng (Farris et al., 1996), Poisson bootstrapping or symmetric resampling (Goloboff et al., 2003).”
A taxonomic and phylogenetic re-evaluation of Therizinosauria (Dinosauria: Maniraptora) (2010, methodology): “Resampling methods were also conducted in TNT and included standard bootstrapping (1000 replicates; Felsenstein 1985) and symmetrical resampling (1000 replicates; Goloboff et al. 2003).”
Cryptic genetic diversity in "widespread" Southeast Asian bird species suggests that Philippine avian endemism is gravely underestimated. (2010, methodology): “After increasing the maximum number of saved trees to 5000, we performed a bootstrap analysis using symmetric resampling (Goloboff et al., 2003) implementing a traditional search with 33% change probability (5000 replicates).”
Systematics of Fraxinus (Oleaceae) and evolution of dioecy (2008, background): “An additional output with GC values (Goloboff et al. 2003) provided a measure of group frequency minus greatest frequency of a conflicting group.”
Weighting against homoplasy improves phylogenetic analysis of morphological data sets (2008, methodology): “…justified by reference to ‘‘stability’’ (e.g., Siddall, 2002, p. 85; Hovenkamp, 2004), other authors (e.g., Farris et al., 1996; Farris, 2002, p. 352; Goloboff et al., 2003a, p. 326) have justified jackknifing as intended primarily as a measure of degree of support; that is, a measure of whether…”
Phylogenetic History of Simosuchus clarki (Crocodyliformes: Notosuchia) from the Late Cretaceous of Madagascar (2010, methodology): “This phylogenetic data set was analyzed with equally weighted parsimony using TNT v. 1.0 (Goloboff et al., 2003).”
Revision and Cladistic Analysis of the Nocturnal Social Wasp Genus, Apoica Lepeletier (Hymenoptera: Vespidae; Polistinae, Epiponini) (2007, neutral): “Because all characters are equally weighted and are nonadditive, the bias in typical resampling support that is corrected by symmetric resampling is not present (Goloboff et al., 2003).”
Osteology of the Late Jurassic Portuguese sauropod dinosaur Lusotitan atalaiensis (Macronaria) and the evolutionary history of basal titanosauriforms (2013, methodology): “Symmetric resampling is similar to bootstrapping and jack-knifing, but the probability of downweighting a given character is equal to the probability of up-weighting it (Goloboff et al., 2003).”
A phylogeny of extant penguins (Aves: Sphenisciformes) combining morphology and mitochondrial sequences (2005, background): “0 (Goloboff et al., 2003) to search for optimal trees under equal weights.”