An idealized concept of the true cladistic character

Abstract

Estimating evolutionary relationships is basic to the objectives of systematics. Comparative data, structured as taxonomic characters, are usually the esssential considerations on which such estimates are founded. Some taxonomic characters are more useful than others for structuring plausible estimates of evolutionary relationship. Thus, one of the primary challenges to the systematist is the construction of taxonomic characters most useful for this purpose. Since taxonomic characters are the result of action on the part of the systematist, they must be defined operationally. It is our hope, however, that these operationally defined characters will conform to an ideal that, itself, cannot be operationally defined insofar as the concept depends on history that is, usually, inherently unknowable. It is, nonetheless, essential to our conceptual methods that this ideal concept be well defined. Here we present a series of definitions leading to a clear ideal concept of irue cladistic character. This series includes definitions of the concepts: evolutionary unit, qualitative taxonomic character, monophyletic group, divergent character, true cladistic character, operational cladistic character, and the post-factum ideal relation between an operational cladistic character and an estimate of cladistic history. A concise characterization of true cladistic character is presented and proved.

Trait-based diversification shifts reflect differential extinction among fossil taxa

“…Compatible characters should represent slowly evolving characters (26,27). Simulations confirm this expectation (29) (SI Appendix, Fig.…”

“…Our analyses measure compatibility, stratigraphic compatibility, center of gravity, and morphological disparity. Compatible characters have three of four possible combinations if the characters are binary (26,27); if one or both characters have three or more states, then we first assess whether the pair is compatible (SI Appendix, Fig. S1), and then, we tally all binary breakdowns of the two characters with three of four possible pairs (SI Appendix, Figs.…”

“…Stratigraphic patterns among compatible character pairs are one example. Character pairs are compatible if there are phylogenies that do not require parallelism or convergence for either character (26,27). If both characters have two states, then at most, only three of four possible combinations evolve.…”

Exhaustion of Morphologic Character States Among Fossil Taxa

“…However, this inference assumes that homoplasy is a biologically real phenomenon. An alternative view is that homoplasy is an artifact of poor character/state interpretations (Hennig 1966;Estabrook et al 1975). An explanation that follows from this view is that apparent exhaustion simply demonstrates the poor state of comparative anatomy among paleobiologists.…”

Accuracy Estimation and Parameter Advising for Protein Multiple Sequence Alignment

“…More specifically, a pair of columns passes the four gametes test if at most three of the four possible patterns 00, 01, 10, 11 occur in the rows of these two columns. A socalled perfect phylogeny exists, in which the binary gapping pattern in each column is explained by a single insertion or deletion event on an edge of the tree, if and only if all pairs of columns pass this test (see Gusfield (1997), pages 462-463; or Estabrook et al (1975)). The Gap Compatibility feature measures the fraction of pairs of columns in the reduced binary data that pass this test, which is a rough measure of how tree-like the gapping pattern is in the alignment.…”