RANDOM DATA, HOMOPLASY AND INFORMATION

@article{Goloboff1991RANDOMDH,
  title={RANDOM DATA, HOMOPLASY AND INFORMATION},
  author={Pablo A. Goloboff},
  journal={Cladistics},
  year={1991},
  volume={7}
}
  • P. Goloboff
  • Published 1 December 1991
  • Computer Science
  • Cladistics
It is often assumed that homoplasy makes cladistic results uncertain. The minimum values that the consistency index C (Kluge and Fart-is, 1969) can achieve on most parsimonious trees decrease with number of taxa and have a more complex dependence with number of characters. Those minimum values have never been calculated, and therefore it is not known which values of C would indicate that there is as much homoplasy as is possible in a data set of a given size. Several authors have examined this… 
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).
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The paper by Faith and Cranston (1991) is but the latest manifestation ofa disturbing phenomenon in cladistics. In their paper, as well as in Archie ( 1989) and Faith ( I99 1) ~ randomizations of
THE RELATIONSHIP BETWEEN HOMOPLASY AND CONFIDENCE IN A PHYLOGENETIC TREE
This chapter provides a statistical assessment of confidence in a phylogenetic tree. The analysis is done with the help of bootstrap procedure. A set of 101 phylogenetic studies was extracted from
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TLDR
This study shows that the removal of even a single taxon in an analysis can cause a solution of relatively few multiple equally parsimonious trees in an inclusive matrix to result in hundreds of equally parsimony trees with the single removal of a taxon.
MEASURES OF HOMOPLASY
This chapter discusses the measures of character homoplasy followed by measures of homoplasy for entire data sets or ensembles of characters. It attempts to compare both the standard measures of
Assessing progress in systematics with continuous jackknife function analysis.
TLDR
Convergence of data on a reference tree does not guarantee historical accuracy, but it does predict that the accumulation of further data under the sampling model will not lead to rapid changes in the hypothesis.
STOR Cladistic Characters and Cladogram Stability
Phylogenetic stability is the tendency for monophyletic groups that are resolved by an analysis to continue to be resolved when either the data or the analytical method is altered. Bootstrapping and
Maximum Parsimony and the Skewness Test: A Simulation Study of the Limits of Applicability
TLDR
Large-scale computations with simulated phylogenetic data are employed to estimate the probability that MP succeeds in finding the true phylogeny for up to twelve taxa and 256 characters, and the skewness test of Hillis is found to perform well on simulated data.
The Role of Permutation Tail Probability Tests in Phylogenetic Systematics
TLDR
Investigation of cladistic structure (Faith and Cranston, 1991) and Karl Popper's (1959) concept of corroboration demonstrated that PTP testing is hypothetico-deductive and consistent with Popperian corroboration and suggested that P TP-style testing provides a Popperians justification for cladistic parsimony.
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References

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  • 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).
Homoplasy Excess Ratios: New Indices for Measuring Levels of Homoplasy in Phylogenetic Systematics and a Critique of the Consistency Index
TLDR
Hers is shown to be more appropriate than CI in comparative taxonomic studies that wish to measure the average level of homoplasy in data sets involving different groups of taxa or different characters, and a new index, the Homoplasy excess ratio (HER), is introduced that takes into account the expected increase in overall homoplASY levels with increasing numbers ofTaxa in systematic studies.
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TLDR
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Abstract Archie (1990) prefers his “homoplasy excess ratio” HER to Farris' (1989) 1 ensemble retention index R. HER, he writes, lacks R's defects: R's minimum is not zero, and varies with number of
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TLDR
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