Improvements to resampling measures of group support

Abstract

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).

Coalescence vs. concatenation: Sophisticated analyses vs. first principles applied to rooting the angiosperms

“…Bootstrap values were mapped onto the strict consensus (Schuh and Polhemus, 1980) of the most likely trees by using TreeGraph2 ver. 2.1 (Stöver and Müller, 2010) to ensure that only supported clades are presented (Goloboff et al, 2003;Simmons and Freudenstein, 2011).…”

“…Xi et al (2014) reported that the clade of (Amborella, Nuphar) was highly supported (99% partitioned bootstrap support) by MP-EST, but even 99% resampling support does not guarantee that a clade is actually supported by the complete, original data set (Goloboff and Farris, 2001;Sharkey and Leathers, 2001;Goloboff and Pol, 2005;Simmons and Freudenstein, 2011). Only those clades present in the strict consensus of all equally optimal trees are unambiguously supported by the data (Nixon and Carpenter, 1996b;Goloboff et al, 2003). Xi et al (2014) tested the sensitivity of their inference that the clade of (Amborella, Nuphar) is sister to the remaining angiosperms to the number of genes sampled.…”

A preliminary phylogenetic study of late Palaeozoic spiriferoid brachiopods using cladistic and Bayesian approaches

“…However, Goloboff et al (2003) pointed out that results from these traditional approaches could be distorted by differences in character weightings and/or transformation costs, developing symmetric resampling as an alternative method unbiased from the heterogeneity of characters.…”

Tacuarembemys kusterae, gen. et sp. nov., a new Late Jurassic–?earliest Cretaceous continental turtle from western Gondwana

“…Branch support is measured using Bremer support, jackknife, and bootstrap resamplings. Jackknife and bootstrap resamplings were obtained after 1000 replicates, and the values are shown as the difference in the frequency of a clade and the frequency when it is contradicted (GC values of Goloboff et al, 2003). If more than one MPT was found, a strict consensus was calculated.…”