Stratigraphic Indices and Tree Balance

Hitchin, Rebecca; Benton, Michael J.

doi:10.1093/sysbio/46.3.563

Cited by 28 publications

(30 citation statements)

References 40 publications

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“…A more detailed comparison yielded mixed results, with b Siddall (1996) has suggested, on the basis of simulations, that the SCI metric may be affected by tree balance. Empirical studies, however (Hitchin and Benton, 1997b), show that neither the RCI nor the SCI depends on tree balance. In addition, there is no evidence for a strong association of values for these metrics and tree size.…”

Section: Results Of Congruence Testingmentioning

confidence: 96%

Molecular and Morphological Phylogenies of Mammals: Congruence with Stratigraphic Data

Benton

1998

Molecular Phylogenetics and Evolution

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Section: Results Of Congruence Testingmentioning

confidence: 96%

Molecular and Morphological Phylogenies of Mammals: Congruence with Stratigraphic Data

Benton

1998

Molecular Phylogenetics and Evolution

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“…Using a sample of 376 cladograms, Hitchin and Benton (1997) demonstrated that balanced trees yielded SCI and RCI values as high (on average) as unbalanced trees, despite the theoretical expectation of an inverse relationship between balance and stratigraphic consistency (Siddall, 1996(Siddall, , 1997. Theoretical expectation and observation should not be confused.…”

Section: Observations From Real Data Setsmentioning

confidence: 87%

“…Siddall (1996Siddall ( , 1997 also argued from simulations and empirical observations that SCI tends to decrease as the number of taxa in a cladogram increases. However, this trend was not observed by Hitchin and Benton (1997) in a sample of 376 cladograms (see also Benton and Hitchin, 1997b).…”

Section: Constraints On the Scimentioning

confidence: 95%

Congruence Between Phylogeny and Stratigraphy: Randomization Tests and the Gap Excess Ratio

1999

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Stratigraphic congruence indices (e.g., stratigraphic consistency index [SCI] of Huelsenbeck, 1994, Paleobiology 40:563-569; relative completeness index [RCI] of Benton, 1994, Trends Ecol. Evol. 9:181-185 [not to be confused with the rescaled consistency index of Farris, 1989, Cladistics 5:417-419]) are increasingly being quoted for cladograms containing fossil taxa. However, like the character consistency index (CI, summed over all characters), these values cannot be compared for trees derived from different data sets. Just as the number of characters and taxa in data matrices affects typical CI values, so tree balance and the distribution of stratigraphic ranges (and indirectly tree size) delimit the range of congruence indices that can be obtained. Because investigators often seek to compare the performance of cladograms from different sources (e.g., different taxa, habitats, periods in history), indices of t insensitive to these factors are desirable. Two approaches are proposed here: (1) The gap excess ratio (GER) is a new metric that controls for the distribution of range data but is sensitive to differences in tree balance. The GER expresses the difference between the minimum implied gap (MIG; the total ghost range implied by a given set of stratigraphic ranges on a given tree) and G min (the minimum possible ghost range for those data on any tree) as a fraction of the range of values possible for those stratigraphic data on any tree. Rather than re ecting inferred completeness of the fossil record (as does the RCI, which is only partially determined by cladistic constraints), the GER indicates congruence alone. (2) Randomization tests hold most potentially con ated parameters constant and compare the observed RCI or GER index with the distribution of indices obtained by randomly reassigning range data over the tree. This enables us to deduce whether the MIG is signi cantly less (i.e., shows greater congruence) than for random permutations of the same range data. Stratigraphic congruence indices have been invoked as an ancillary criterion for assessing competing hypotheses of relationships derived from different sources or for choosing between equally parsimonous trees derived from the same character matrix. The rst application is illustrated with comparisons of actinopterygian and eutherian phylogenies, and the second is illustrated with a study of trees for fossil and Recent arthropods. [Ghost ranges; homoplasy excess ratios; permutation tail probability; relative completeness index; retention index; stratigraphic consistency index.] 1 Present address: Oxford University Museum of Natural History, Parks Road, Oxford OX1 3PW,

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“…In order to evaluate how to measure the fit of stratigraphy to a phylogenetic tree we must first determine what is being measured and what are the properties of different measures. We will only briefly consider the first of these, because it has been the main focus of prior work (Hitchin and Benton, 1997a,b; Siddall, 1998; Wagner and Sidor, 2000; Pol and Norell, 2001). The second aspect, concerning the properties and biases of measures, is particularly relevant for inferring the suitability of these measures for different purposes.…”

Section: Introductionmentioning

confidence: 99%

Measures of stratigraphic fit to phylogeny and their sensitivity to tree size, tree shape, and scale

2004

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Measures of stratigraphic fit to phylogeny are analyzed to test how they are affected by the shape and size of the phylogenetic trees and by the number of stratigraphic intervals encompassed. Monte Carlo randomizations are used to investigate the sensitivity of three commonly used measures (SCI, GER and MSM*) approximating their distribution of possible values under certain conditions. All are shown to vary in different ways as parameters are varied, although MSM* seems to be the most invariant in the analyzed parameter space. These results suggest that the raw metrics should not be used for comparing the fit of different taxonomic groups or competing phylogenetic trees of the same group that differ in tree size or balance. Tree balance also affects the distributions used in significance tests based on randomization and therefore their results should not be interpreted in terms of the amount of conflict implied by a phylogenetic tree.

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Stratigraphic Indices and Tree Balance

Cited by 28 publications

References 40 publications

Molecular and Morphological Phylogenies of Mammals: Congruence with Stratigraphic Data

Molecular and Morphological Phylogenies of Mammals: Congruence with Stratigraphic Data

Congruence Between Phylogeny and Stratigraphy: Randomization Tests and the Gap Excess Ratio

Measures of stratigraphic fit to phylogeny and their sensitivity to tree size, tree shape, and scale

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