Character state coding

Ptychomnion cygnisetum is a nanandrous species hence character state coding of characters 1-25 refers to female plants only. Ramification type of P. cygnisetum could not be determined with certainty. Ramification seems to be monopodial, but in the material examined the older parts of the (female) plants are usually damaged or not collected. Occasionally, ramification shows some resemblance with sympodial branching. Hattaway s (1984) description of ramification is, unfortunately, inconclusive. Hence, the state of character 1 is coded as unknown for this species. 

See Kruijer (2002) for an explanation of the method of character state coding and the sources used, and for an evaluation of the choices in character state coding that have been made for other species. 

Stevens, P.F., On characters and character states do overlapping and non-overlapping variation, morphology and molecules all yield data of the same value., in Homology and Systematics Coding Characters for Phylogenetic Analysis, Scotland, R.W. and Pennington, T., Eds., Taylor and Francis, London, 2000, pp. 81-105. 

In addition to binary, or "yes-no" answers (a "1" is a positive character state, a "0" is negative), it is possible to enter numerical information associated with a feature. As shown in Fig. 3, the columns required to hold the numbers are covered by the letter "N." In the example given, the first two features (025212 and 025215) are defined as numerical questions by the "N" columns following the features. Questions which are answered by numerical values can be searched as either numerical or binary information (e.g., a delayed reaction could be coded for the day it became positive and searched for as a delayed reaction or simply as a positive attribute). Users access binary data as features 025212 and 025215 but access numeric data as features 525212 and 525215. As a convenience to the user, system programs automatically convert numerical data into... 

List of coded characters and character states used in cladistic analysis. 

Table 26.1 Character by taxon matrix. Question marks represent either not applicable or unknown states. Last character (in parentheses) codes the stratigraphic range of the entire suborder (see Table 26.2 for list of characters and character states). See Williams et al. (2000) for the outline of brachiopod classification used...

Albert, V. A., Chase, M. W. and Mishler, B. D. (1993) Character-state weighting for cladistic analysis of protein-coding DNA seqnences. Annals of the Missouri Botanical Garden, 80 752-766. 

Definition of Morphological Characters and Coding of Character States, after Kruijer (2002)... 

Axial cavities in the basal and middle parts of the stem (the stipe and the basal and middle parts of the rachis) absent state 1 central state 2 cortical state 3. Species for which the character state of this character is coded as state 2 or 3... 

Axial cavities in ultimate branches absent slate 1 present state 2. This character state is coded as unknown for species lacking ultimate branches, viz. for species lacking any ramification, fa species usually lacking ramification in which the rare branches are similar to the main axis or show indeterminate growth, and for species with indeterminate growth... 

As mentioned above. Discrete can analyse only binary characters and any multistate character has to be either excluded from the analyses or transformed into binary ones. For some of the characters used in the present analyses, multistate codings are possible. For instance, the presence of dwarf males (character 1 state 1) can be coded as simple and unbranched, as for Garovaglia, or larger and branched, as for Euptychium, Glyphothecium and Cladomnion. It is therefore possible that the uncertainties in ancestral character state reconstructions might be an artifact of the binary... 

The primary objective of most applications carried out so far was to assess the performance of the PPP-VB method for diverse alternant and nonaltemant -electron systems of aromatic, nonaromatic or antiaromatic character, both electrically neutral and charged. The main emphasis was on ground states of different spin multiplicity, even though some preliminary calculations were also carried out for excited states. The PPP-VB codes were also employed to provide the approximate three- and four-body connected cluster components for the so-called VB-corrected coupled cluster (CC) approach [71]. In the following, we briefly point out the most important aspects of the PPP-VB method and illustrate them with a few typical results. 

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