On the different concepts of homology
Homology is a central concept in biology, and it refers to the correspondence of morphological or molecular attributes due to common ancestry. It is generally useful to sort and evaluate relationships among organisms (Pinna 1991), depending on the field of study (Brigandt 2003). In comparative biology, it allows for effective descriptions across species and unified morphological knowledge, which provides comparisons that could be finely used for classifications. In other branches of biology such as evolutionary biology and phylogenetic systematics, it serves to explain the adaptive modifications of characters and to characterize taxa, respectively (Brigandt 2003). Given its diverse extents, there is also a set of criteria to infer it, among them, the similarity in molecular, structural detail and histology, the connectivity to adjacent structures, correspondence of the developmental origin (Patterson 1982; Patterson 1988) , and step-counting.
Regarding the concepts of homology, (De Pinna 1991) made a distinction between “primary” and “secondary” homology, treating the first as an untested supposition that two parts are equivalent by inheritance -definition that (Agnarsson & Coddington 2007) pondered as the prior of a logical analysis or the background knowledge that is not concerned to morphological data- , and the second as the hypothesis that has passed the congruence test and thus can be treated as a synapomorphy. A large discussion has been taken upon this latter concept, as for authors like (De Queiroz 1985) it does not equal homology, for he argued that homology applies to instantaneous morphologies, while synapomorphy applies to ontogenetic transformations that characterize monophyletic groups. On the other hand, like (Eldredge, N, Cracraft 1980), like (De Pinna 1991), considered these concepts as a single one. However, (Patterson 1982) and (Rieppel 1980) assigned a certain hierarchical organization of homologies, distinguishing between taxic (the feature of a monophyletic group) and transformational (the change of a structure into another) homology. Taking this into context, the radula of molluscs or the radular teeth constitute a taxic homology, and the classic example of the incus and the quadrate are a transformational homology (Zelditch M.L., Fink W.L. 1995).
A main question that can be asked is how do we recognize a character as homologous? One of the most outstanding processes was proposed by Patterson (Patterson 1982), and it is an evaluation that compresses three tests that a character needs to pass to be considered as an homology in a phylogenetic analysis. These tests are: similarity, which refers to the resemblance between structures that could share a common ancestor and thus it is a first “candidate” of homology; conjunction which evaluates that two different states of a character can not be present within the same organism (angels are definitely not an useful species to be included in an analysis using this test); and congruence that is the final test that shows whether a character most probably represents an homology.
Choosing criteria of evaluation
A question that arises when it comes to the evaluation of homology is what test or what methodology to use. In theory, parsimony or other criteria, could guide choice among competing homology hypotheses before assessing their fit to a tree (Agnarsson & Coddington 2007). Testing the fit of data to trees using various optimality criteria has been widely studied. However, the evaluation of the initial criteria of similarity in the formation of homology hypotheses, such as whether two structures should be considered homologous, remains a key point of attention. The authors proposed an index to make this initial assessment, weighting topology, function and similarity equally, so that multiple points of comparison within each criterion allow them to be averaged or down-weighted. Thence it took each criterion into a comparable unit.
Although morphological data present several points of special attention (Patterson 1982), molecular data is a powerful source that definitely has to be carefully analyzed. Mainly because it passes through a test of similarity that could render wrong assumptions and results. Taking into account that homologous sequences can be orthologous -as divergent from a common ancestor- or paralogous -as product of gene duplication-, as well as other mechanisms or variations -like xenology- (Fitch 2000) we can not be sure that a result from a similarity test will not come up as a convergence.
Another issue to consider is the character optimization and analysis, which basically have two different arguments: one that supports sequence alignment as a crucial step (Simmons and Freudenstein, 2003), and another that has proved that aligning base positions is not that fundamental and the optimization can be directly done (Wheeler 2001; Wheeler 2006). Wheeler introduced the concept of dynamic homology, which states that nucleotide homologies are topology specific and can be identified by optimization processes that determine nucleotide correspondence and transformation via a specific criterion. This method does not rely on a prior alignment, but analyses the variation, rendering likely cladograms.
Overall, it is evident that homology is a wide concept and its assessment is rather complex. There are several types of potential information and methods to analyze it properly. However, it is always necessary to bring the evolutionary histology and biology principles into the discussion, so one could be a little more positive about the obtained phylogenies, which at the end, are hypotheses that should constantly be evaluated until the phylogenetic relationships within a group are considered to be clear. As (Patterson 1982) stated, homology can be seen as a probability, as a result of any of the three tests, interpreting them is always a delicate task assigned to biologists.
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Rieppel, O., 1980. Homology, a deductive concept? Journal of Zoological Systematics and Evolutionary Research, 18(4), pp.315–319.
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Wheeler, W.C., 2006. Cladistics Dynamic homology and the likelihood criterion. , 22, pp.157–170.
Zelditch M.L., Fink W.L., S.D.L., 1995. Morphometrics, Homology, and Phylogenetics: Quantified Characters as Synapomorphies. Syst Biol, 44(2), pp.179–189.