ESTIMATING CHARACTER WEIGHTS DURING TREE SEARCH

@article{Goloboff1993ESTIMATINGCW,
  title={ESTIMATING CHARACTER WEIGHTS DURING TREE SEARCH},
  author={Pablo A. Goloboff},
  journal={Cladistics},
  year={1993},
  volume={9}
}
  • P. Goloboff
  • Published 1 March 1993
  • Medicine, Mathematics
  • Cladistics
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 trees with maximum total fit, with character fits defined as a concave function of homoplasy. Then, when comparing trees, differences in steps occurring in characters which show more homoplasy on the trees are less influential. The reliability of the characters is estimated, during the analysis, as… 
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TLDR
A corrected parsimony criterion for reconstructing phylogenies is presented, which states that character rather than step is the most fundamental unit and the most parsimonious tree should maximize the sum or average of the phylogenetic signals, quantified by retention index, contributed by each character.
BRANCH SUPPORT AND TREE STABILITY
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
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References

SHOWING 1-10 OF 18 REFERENCES
TESTING METHODS OF EVOLUTIONARY TREE CONSTRUCTION
  • D. Penny, M. Hendy
  • Medicine, Mathematics
    Cladistics : the international journal of the Willi Hennig Society
  • 1985
Abstract— Evaluating the reliability of methods for reconstructing evolutionary trees is discussed under the four headings of: evaluating criteria for an optimal tree, finding the optimal tree for
A likelihood approach to character weighting and what it tells us about parsimony and compatibility
TLDR
The statistical framework of maximum likelihood estimation is used to examine character weighting in inferring phylogenies and provides a spectrum of intermediates between these methods that may be of use in analysing real data.
HOMOPLASY AND THE CHOICE AMONG CLADOGRAMS
  • P. Goloboff
  • Medicine, Mathematics
    Cladistics : the international journal of the Willi Hennig Society
  • 1991
TLDR
Despite some recent assertions to the contrary, the consistency index is an appropriate measure of homoplasy (= deviation from hierarchy).
A Successive Approximations Approach to Character Weighting
TLDR
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.
Two Optimality Criteria for Selecting Subsets of most Parsimonious Trees
TLDR
Two new optimality indices are developed for selecting subsets of trees from a set of most parsimonious trees, one of which quantifies the proportion of characters that are postulated to have changed only once, and the other selects the tree that is most likely to give the observed data under certain assumptions.
Outgroup Analysis and Parsimony
TLDR
Methods that use outgroups in the reconstruction of phylogeny are described and evaluated by the criterion of parsimony, and algorithms and rules are presented that find the most parsimonious estimates of ancestral states for binary and multistate characters when outgroup relationships are well resolved.
The Out-Group Comparison Method of Character Analysis
TLDR
The goals here are to discuss some problems with one criterion in particular, the so-called "commonality principle" (Eldredge, 1979), and to develop a general method of character analysis based on out-group comparison, which receives wide support in both botanical and zoological circles.
A Hypothesis‐Independent Method of Character Weighting for Cladistic Analysis
TLDR
The proposed hypothesis‐independent method of weighting cladistir characters, based on character compatibility, is used in two fashions, to generate cladograms, and to select from multiple minimum length cladograms.
Choosing Among Multiple Equally Parsimonious Cladograms
TLDR
The issue of choice among multiple equally parsimonious cladograms, and three statistics considered, are addressed: the consistency index, F-ratio, D and the D measure, an application of the Shannon entropy statistic from Gatlin (1972).
PARSIMONY AND CHARACTER WEIGHTING
Abstract— The likelihood justification of parsimony proposed in Sober (1983, 1984a) is applied to some problems posed by character weighting. An argument is provided for thinking that the point
...
1
2
...