On Homology

Introduction
The importance of homology has been discused by several authors (Patterson, 1988; Wagner, 1989; de Pinna, 1991; Rieppel & Kearney, 2002; Agnarsson & Coddington, 2007). So, homology is a crucial basis in the Systematics. The most simple meaning of homology is equivalence of parts (de Pinna, 1991). In 1982, Patterson states that homology is equal to synapomorphy. So, the synapomorphic characters must be homologous. Nevertheless, the symplesiomorphic characters could be homologous (homologies at a higher level).
There are two kinds of homologies; the primary homology - conjectures or hypothesis about common origin of characters -, and the secondary homology - the tested hypothesis – (de Pinna, 1991).

Pattern or process
A question about homology is the significance of evolutionary process in the identification of homologous characters. Implicitly, the evolutionary events are bounded to the analysis of characters (Lee, 2002). However, Brower (2000) stated that “the similarities - homologies - between taxa represent the only necessary ontological foundation for the construction of cladograms and hypotheses of taxonomic grouping”. So, the evolutionary asumptions are not necessary in the identification of homologies; but the homologous characters can be explained by evolutionary process (Rieppel & Kearney, 2002).
Equally, some authors claims that the phenomenon of circularity in homology (need of a priori topology) is undesirable because the recognition of homologous characters is conditionated to mapping of them in a initial topology. Nevertheless, the circularity is not a “big” problem, because the tested homologies (mapped hypothesis of homologies) are “tested hypothesis” attached to new set of analysis (new tests).

Coding
An inherent point in the identification of homologous characters is the character's coding. A inadequate definition of characters produces bias in the identification of homology. Some author claims that the real problem in homology is the character's coding. So, for example, there is the belief that the character's coding is linked to knowledge of researcher about taxon. So, the “eyes” of an experienced researcher would discriminate and describe “best” characters and character's states that an non-experienced researcher.
A approach used in the the character's coding was the morphometric analysis (biometry). However, the biometry is not useful in homology because the complexity of the biological estrucures and its incompatibility with the statistical multivariate analysis (Bookstein, 1994).

Tests
The three tests of homology (similarity, conjuction, and congruence) are secuencial in the identification of homology. Nevertheless, the similarity is not a test (in Popperian sense), similarity is a conjecture of homologous characters - primary homology – (de Pinna, 1991) . The conjuction and congruence (agreement in supporting the same phylogenetics relationships) are the “hard” tests of homology – the secondary homology from de Pinna - (Rieppel and Kearney, 2002). Although there is interdependece among them (tests), it not means that the three tests will be one only. So, the result is a hypothesis of homology corroborated, but they is not definitive (“true homology”).

Molecular homology
The identification of homology in molecular characters (nucleotide sequences) presents problems not found in other kinds of character data. For example, although each base position presents one of four identical states (A, C, G or T), the number of these positions is likely to vary, that is homologous nucleotide sequences may differ in length (Wheeler, 1996). Further, Patterson (1988) claims that the tests of homology in molecular characters are equal to morphological characters. However, the significance of tests (similarity, conjuction, and congruence) is different because the similarity is the most crucial test, while in morphological characters is test of congruence.
A point of discussion in the identification of homologies in molecular sequences is the need of an alignment to determine sites or homologous fragment. However, this way is considered inadequate because alignment is generated using a priori costs and asumptions. Wheeler (2003) proposes a synapomorphic-based alignment methods - Implied alignment – (IA) that identifies homologies in the topology using Direct Optimization (DO). So, Implied alignment generating all posibles alignments and all posibles homologies are analized. This method may be efficient to identify homologies. Nevertheless, the a priori asumptions are inherent to alignments.

Bibliography

• Agnarsson, I., & Coddington, J. A. (2007). Quantitative tests of primary homology. Cladistics, 23, 1-11.

• Brower, A. V. Z. (2000). Evolution is not an assumption of cladistics. Cladistics, 16, 143–154.

• de Pinna, M. C. C. (1991) Concepts and tests of homology in the cladistic paradigm. Cladistics, 7, 367-394.

• Lee, M. S. Y. (2002). Divergent evolution, hierarchy, and cladistics. Zoologica Scripta, 31, 217–219.

• Patterson, C. (1988). Homology in classical and molecular biology. Molecular Biology and Evolution, 5, 603-625.

• Rieppel, O., & Kearney, M. (2002) Similarity. Biological Journal of the Linnean Society, 75, 59-82.

• Wagner, G. P. (1989) The biological homology concept. Annual Reviews of Ecology and Systematics. 20, 51-69.

• Wheeler, W. C. (1996). Optimization alignment: the end of multiple sequence alignment in phylogenetics?. Cladistics, 12, 1-9.

• Wheeler, W. C. (2003) Implied alignment: a synapomorphic-based multiple alignment method and its use in cladogram search. Cladistics, 19, 261-268.