Character Stability in 39 Data Sets

Sokal, Robert R.; Shao, Kwang‐Tsao

doi:10.1093/sysbio/34.1.83

Cited by 10 publications

(3 citation statements)

References 51 publications

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“…changes appear along the internode immediately below that group (Felsenstein, 1985b; see also Sokal and Shao, 1985, for a discussion of the influence ofcharacter/taxon ratios on taxonomic congruence). High character/taxon ratios tend to be found in molecular studies using nucleotide sequence data or restriction fragment data, since such studies typically generate many more characters than do most morphological studies.…”

Section: Simple Hypotheses About Group Membershipmentioning

confidence: 99%

Confidence Limits on Phylogenies: The Bootstrap Revisited

1989

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Abstract— The bootstrap, a non‐parametric statistical analysis, can be used to assess confidence limits on phylogcnics. The method most widely used tests the monophyly of individual clades. This paper proposes additional applications of the bootstrap which provide useful information about phylogeny even when many clades are found not to be supported with confidence (as often occurs in practice). In such cases it is still possible to place a constraint on the phylogenetic position of taxa by examining the relative size of the smallest monophyletic groups that contain them. In addition, the taxonomic composition of these larger clades can be determined, as well as the relative likelihood of their occurrence. The distinction between hypotheses about membership in particular clades and hypotheses about entire topologies is also discussed. To investigate the latter, the bootstrap is used to estimate the sampling distribution of tree similarity indices. All methods are illustrated by reference to a large data set on the angiosperm family Asteraccae, selected from the literature.

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Section: Simple Hypotheses About Group Membershipmentioning

confidence: 99%

Confidence Limits on Phylogenies: The Bootstrap Revisited

1989

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“…See text and the Appendix for details. The numbers of characters were standardized to the numbers of binary-character equivalents (Sokal and Shao, 1985). Wighton and Wilson, 1987 40 animal morph genus 17 18 5 0.54 Cutler and Gibbs, 1985 41 animal morph genus 27 323 78 0.49 Fink, 1985 42 animal morph genus 57 307 24 0.45 Kitching, 1987 43 animal morph family 13 59 0 0.66 Cracraft, 1985 44 animal morph family 22 113 43 0.63 Nelson, 1984 45 animal morph class 8 84 0 0.89 Gauthier, 1986 46 animal morph class 9 39 II 0.93 Brooks et al, 1985 47 animal molec" species 6 118 87 0.56 George and Ryder, 1986 48 animal molec" species 32 76 55 0.66 Hillis and Davis, 1986 49 animal melee" order 13 19 0 0.59 Wyss et al, 1987 50 Vilgalys, 1986Baum and Saville, 1985Churchill et al, 1984Lipscomb, 1985 nation for their recurrence may differ from an explanation that is adequate to account for broad convergences that are not positionally or developmentally similar (Rensch, 1959 p. 191).…”

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confidence: 99%

Patterns of Variation in Levels of Homoplasy

1989

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Patterns of variation in levels of homoplasy were explored through statistical analyses of standardized consistency indexes. Data were obtained from 60 recent cladistic analyses of a wide variety of organisms based on several different kinds of characters. Consistency index is highly correlated with the number of taxa included in an analysis, with homoplasy increasing as the number of taxa increases. This observation is compatible with a simple model of character evolution in which 1) the probability of character-state change increases with the total number of branches in a tree and 2) the number of possible states of a character is limited. Consistency index does not show a significant relationship to the number of characters utilized in an analysis or to the taxonomic rank of the terminal taxa. When the relationship between consistency index and number of taxa is taken into account, there is no significant difference between plant and animal data sets in the amount of homoplasy. Likewise, the level of homoplasy in morphological and molecular data sets does not appear to differ significantly, although there are still too few molecular studies to be confident of this result. Future comparisons of consistency indexes, including studies along the lines established here, must take into account the influence of the number of taxa on homoplasy.

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“…lade is defined as the ratio Np,,,,/(2';.S-3), where Npreu stands for the number of binary codelcharacters and S denotes the number of species (cf. SOKAL 1983 andSOKAL andSHAO 1985). As a measure of the symmetry of the tree, an index, Ice/, proposed by COLLESS (1982: 103) was used.…”

Section: Tree Statisticsmentioning

confidence: 99%

Adequacy of numerical taxonomic methods: Further experiments using simulated data

Heijerman¹

2009

Journal of Zoological Systematics and Evolutionary Research

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The adequacy of various phenetic and phylogenetic estimation methods was evaluated using simulated data sets. Two parsimony programs were used to construct maximum parsimony trees (WAGNER 78 and HENNIG 86). The CAFCA program was used to perform group‐compatibility analysis. Four UPGMA clustering strategies were employed. The simulation model GENESIS was used to generate data sets under different evolutionary conditions. The effects of input parameters and tree properties on the accuracy of the estimated trees were evaluated. UPGMA based on product moment correlations of unstandardized characters appeared to perform best, under all evolutionary conditions tested. The effect of input parameters on the accuracy was not very significant. Among the tree statistics the stemminess of the true tree appeared to be the most important estimator of accuracy.

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Character Stability in 39 Data Sets

Cited by 10 publications

References 51 publications

Confidence Limits on Phylogenies: The Bootstrap Revisited

Confidence Limits on Phylogenies: The Bootstrap Revisited

Patterns of Variation in Levels of Homoplasy

Adequacy of numerical taxonomic methods: Further experiments using simulated data

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