Improvements to resampling measures of group support

  title={Improvements to resampling measures of group support},
  author={Pablo A. Goloboff and James S Farris and Mari K{\"a}llersj{\"o} and Bengt Oxelman and Martıacute;n J Ramıacute;rez and Claudia A Szumik},
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… 

Resampling measures of group support: a reply to Grant and Kluge

Grant and Kluge (2003) associated resampling measures of group support with the aim of evaluating statistical stability, confidence, or the probability of recovering a true phylogenetic group. This

Behaviour of resampling methods under different weighting schemes, measures and variable resampling strengths

We compared general behaviour trends of resampling methods (bootstrap, bootstrap with Poisson distribution, jackknife, and jackknife with symmetric resampling) and different ways to summarize the

Ratio of explanatory power (REP): a new measure of group support.

Branch support via resampling: an empirical study

Two datasets were explored for a range of search parameters using jackknifing, and strict consensus summary of resampling replicates is preferable to frequency‐within‐replicates summary because it is a more conservative approach to the reporting of replicate results.

Evaluating the clade size effect in alternative measures of branch support

The role of homoplasy is corroborated as a possible cause of the clade size effect, increasing the number of random trees during the resampling, which together with the higher chances that medium-sized clades have of being contradicted generates the bias during the perturbation of the original matrix, making it stronger in resamplings measures of support.

Bias in tree searches and its consequences for measuring group supports.

Two methods commonly used for finding phylogenetic trees consist of randomizing the input order of species in multiple addition sequences followed by branch swapping, or using random trees as the starting point for branch swapping.

Problems with supertrees based on the subtree prune‐and‐regraft distance, with comments on majority rule supertrees

  • P. GoloboffC. Szumik
  • Computer Science
    Cladistics : the international journal of the Willi Hennig Society
  • 2016
This paper examines a recent proposal to calculate supertrees by minimizing the sum of subtree prune‐and‐regraft distances to the input trees, and it is dubious that so‐called majority rulesupertrees can always be interpreted as displaying those clades present (or compatible with) with a majority of the trees.

An empirical test of the relationship between the bootstrap and likelihood ratio support in maximum likelihood phylogenetic analysis

It is shown decisively that BS is not an efficient indirect method of measuring support and it is suggested that even quite superficial searches to calculate S provide better estimates of support.

Support and stability

  • P. Hovenkamp
  • Computer Science
    Cladistics : the international journal of the Willi Hennig Society
  • 2009
The purpose of this note is to help the reader to form an opinion on both types of justification of jackknifing, mainly by reiterating a few points made by Hovenkamp (2004) in some greater detail.

Weighting against homoplasy improves phylogenetic analysis of morphological data sets

The problem of character weighting in cladistic analysis is revisited. The finding that, in large molecular data sets, removal of third positions (with more homoplasy) decreases the number of well




  • J. Felsenstein
  • Economics
    Evolution; international journal of organic evolution
  • 1985
The recently‐developed statistical method known as the “bootstrap” can be used to place confidence intervals on phylogenies and shows significant evidence for a group if it is defined by three or more characters.

RASA Attributes Highly Significant Structure to Randomized Data

  • J. Farris
  • Computer Science
    Cladistics : the international journal of the Willi Hennig Society
  • 2002
The claim that RASA is a deductive procedure is unfounded and seems to have been used as part of a strategy for avoiding tests of the method.

On the Interpretation of Bootstrap Trees: Appropriate Threshold of Clade Selection and Induced Gain

This study proposes two analytical approximations of the optimum threshold of clade selection to interpret (i.e., reduce) the bootstrap tree and investigates error measures that stem from a generalization of Robinson and Foulds’ (1981) distance, used to quantify the divergence between the true phylogeny and the estimated trees.


  • P. Goloboff
  • Computer Science
    Cladistics : the international journal of the Willi Hennig Society
  • 1993
Abstract— A new method for weighting characters according to their homoplasy is proposed; the method is non‐iterative and does not require independent estimations of weights. It is based on searching


Abstract— Branch support is quantified as the extra length needed to lose a branch in the consensus of near‐most‐parsimonious trees. This approach is based solely on the original data, as opposed to

The effect of irrelevant characters on bootstrap values

1 E-mail: conveniently its inverse, relevance?can be defined recursively, at least for binary characters. A binary character is relevant to a node if any of these conditions


  • J. Farris
  • Biology
    Cladistics : the international journal of the Willi Hennig Society
  • 1995
Faith (1992) feels that those trees are leastcorroborated instead, and in arriving at his view of most-parsimonious trees he repeats most of the same mistakes, as will be seen here.

A Successive Approximations Approach to Character Weighting

Results indicate that the successive weighting procedure can be highly successful, even when cladistically reliable characters are heavily outnumbered by unreliable ones, and computer simulation tests of the technique are described.

A Report on “One Day Symposium on Numerical Cladistics”

  • I. Horovitz
  • Computer Science
    Cladistics : the international journal of the Willi Hennig Society
  • 1999
A recent symposium on numerical cladistics addressed novel methods for searching tree space, applications of randomizations in cladistic analysis, and data management, and modifications to parsimony jackknifing that improved its accuracy when compared to normal heuristic searches.


For analysis of large matrices, parsimony jackknifing is hundreds of thousands of times faster than extensive branch‐swapping, yet is better able to screen out poorly‐supported groups.