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- Characters—Ontology and Epistemology
- Homology and Molecular Characters
- Morphological Characters
- Operational Aspects
- Individualization and Coding Levels
- Hierarchic Character Patterns and Implications For Coding: Examples
- Acknowledgements
As with any system in which a theoretical framework has real applications, it is important to distinguish the conceptual basis for characters (telling us what a character is) from the practical operation of finding them and to recognize that the resulting empirical units may correspond only imperfectly to the conceptual ideal. This can be due to co...
It is helpful to focus first on molecular characters to examine homology relations because the situation is at least superficially more straightforward than with morphology due to the discrete and “simple” nature of the characters. An important first point is that the way that attributes of taxa originate with respect to each other is the key to th...
Patterson (1988)described the parallels between morphological and molecular homology, but did not examine the range of morphological situations that exist, nor did he make the conceptual connection between homology relation and the distinction between characters and states. In fact, he explicitly rejected the use of character states as distinct fro...
Although the concept of a character may be easily stated, the empirical exercise of sorting orthologs into their paralogs can be a difficult one and is an integral part of the process of establishing homology hypotheses. Indeed, there have been empirical methods proposed to deal explicitly with accommodating molecular paralogs in phylogenetic analy...
Having discussed what characters are conceptually and how to distinguish them operationally, I now turn to practical aspects of their coding. Because not every distinguishable feature need be individualized with respect to transformational independence, not every one should be called a character. Particular hairs on a mammal would not be considered...
Thus far we have a character concept that can be applied at different levels within an organism. Once characters and their states have been recognized, it is necessary to code them for analysis, which means fitting these constructs into a form that is interpretable by current phylogenetic analysis software, using what are termed hereafter “matrix c...
The author thanks Allan Baker, Marymegan Daly, Jerrold Davis, Roderic Page, Kurt Pickett, Daniel Potter, Chris Randle, Mark Simmons, Peter Stevens, Günter Wagner, John Wenzel, and Mark Wilkinson for discussion of these ideas and comments on the manuscript.
- John V. Freudenstein
- 2005
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