A formula for maximum possible steps in multistate characters: isolating matrix parameter effects on measures of evolutionary convergence

@article{Cuthill2010AFF,
  title={A formula for maximum possible steps in multistate characters: isolating matrix parameter effects on measures of evolutionary convergence},
  author={Jennifer F Hoyal Cuthill and Simon J. Braddy and Philip C. J. Donoghue},
  journal={Cladistics},
  year={2010},
  volume={26}
}
To identify a biological signal in the distribution of homoplasy, it is first necessary to isolate non‐biological factors affecting its measurement. The number of states per character in a phylogenetic data matrix may indicate evolutionary flexibility and, consequently, the likelihood of recurrent evolution. However, we show here that the number of states per character limits the maximum number of steps that may be inferred using parsimony. A formula is provided for the maximum number of steps… 
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13 Citations
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13 Citations

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The size of the character state space affects the occurrence and detection of homoplasy: modelling the probability of incompatibility for unordered phylogenetic characters.
The size of the character state space affects the occurrence and detection of homoplasy: modelling the probability of incompatibility for unordered phylogenetic characters.
Exploring the effects of character construction and choice, outgroups and analytical method on phylogenetic inference from discrete characters in extant crocodilians
Phylogenies for fossil taxa must be inferred from morphology, but accuracy of inference is questionable. Here, morphological characters for extant crocodilians are investigated to assess how to…
The morphological state space revisited: what do phylogenetic patterns in homoplasy tell us about the number of possible character states?
TLDR
This work explores what the morphological state space of phylogenetic character evolution might be like, by analysing trends in homoplasy, by comparing character matrices against computer simulations with different state space models: infinite states, finite states, ordered states and an ‘inertial' model, simulating phylogenetic constraints.
The morphological state space revisited: what do phylogenetic patterns in homoplasy tell us about the number of possible character states?
TLDR
This work explores what the morphological state space of phylogenetic character evolution might be like, by analysing trends in homoplasy, by comparing character matrices against computer simulations with different state space models: infinite states, finite states, ordered states and an 'inertial' model, simulating phylogenetic constraints.
Fossils and the Tree of Life : ghost ranges, stratigraphic congruence and data quality
TLDR
A novel script was developed to automatically carry out continuous taxon jackknifing to investigate the effect of taxon sampling on the stability of phylogenetic trees and it was found that measures of homoplasy and support could serve as partial indicators of whether a tree was likely to be sensitive toTaxon sampling.
Measuring Stratigraphic Congruence Across Trees, Higher Taxa, and Time
TLDR
The center of gravity of FO dates had not been investigated hitherto, and this was found to correlate most strongly with some measures of stratigraphic congruence in this empirical study, and the modified GER was the index least susceptible to bias.
Journeys through discrete‐character morphospace: synthesizing phylogeny, tempo, and disparity
TLDR
It is argued that there are clear advantages to considering these three lines of enquiry in a single space: the phylomorphospace, which contains fundamentally different approaches used to generate such spaces, with no direct comparison between them, despite the differing evolutionary histories they imply.
Comparative Cladistics: Fossils, Morphological Data Partitions and Lost Branches in the Fossil Tree of Life
TLDR
In this thesis, a wide range of cladistic analysis of fossil and extant taxa representing a diverse array of phylogenetic groups is gathered and a modification to a rarely used measure of homoplasy is devised that will hopefully encourage its wider usage.
Sampling diverse characters improves phylogenies: Craniodental and postcranial characters of vertebrates often imply different trees
TLDR
It is concluded that trees inferred largely from either craniodental or postcranial characters in isolation may differ significantly from those that would result from a more holistic approach.
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References

SHOWING 1-10 OF 34 REFERENCES
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.
Consistency, characters, and the likelihood of correct phylogenetic inference.
Computer simulations of character-state evolution in 8, 16, 32, and 64 ingroup taxa with a known set of relationships demonstrate that the maximum probability of correct phylogenetic inference…
Character‐state space versus rate of evolution in phylogenetic inference
TLDR
Although increased character‐state space greatly improved the accuracy of topology inference, improvements in the estimation of the correct tree length were less apparent and accuracy and inferred tree length improved most when character‐ state space increased initially; further increases provided more modest improvements.
PATTERNS OF VARIATION IN LEVELS OF HOMOPLASY
TLDR
There is no significant difference between plant and animal data sets in the amount of homoplasy when the relationship between consistency index and number of taxa is taken into account, although there are still too few molecular studies to be confident of this result.
Proportional Change and Patterns of Homoplasy: Sanderson and Donoghue Revisited
TLDR
In data sets with more than seven taxa, the APC explains more variation in homoplasy than does the number of taxa and the retention index (RI) and the consistency index (CI) are significantly correlated with the CI.
The Accuracy of the Maximum Parsimony Method for Phylogeny Reconstruction with Morphological Characters
TLDR
Caution is advised in using phylogenies reconstructed from morphological data to make inferences about biological processes or patterns that rely on knowledge of the true phylogeny, as maximum parsimony is less accurate when there are fewer characters, more character states per character, and more character state changes per speciation event.
A randomization test for phylogenetic information in systematic data
-A randomization procedure is proposed to determine if sets of data used for phylogenetic analysis contain phylogenetically nonrandom information. The method compares the observed number of steps on…
MEASURES OF HOMOPLASY
Cases in which Parsimony or Compatibility Methods will be Positively Misleading
TLDR
Parsimony or minimum evolution methods were first introduced into phylogenetic inference by Camin and Sokal (1965), and a number of other parsimony methods have since appeared in the systematic literature and found widespread use in studies of molecular evolution.
Homoplasy and Developmental Constraint: A Model and an Example from Plants1
TLDR
A simple model relating homoplasy to the rate of character change and the number of evolvable states is outlined, both of which may reflect developmental constraints.
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