Particularities and conflicts of phylogenetic analysis

Systematics has been a discipline that over the years has undergone changes both in its philosophy and in its concepts and methods. In particular, I believe it should be started by explaining what the objectives of this discipline have been over the years. The main ones are usually to describe the kinship relations between the different groups, understand the processes or causal factors of these relationships, and even to propose hypotheses of historical relationships and the evolution of the different groups (Gould, 1977).

But how to classify the different groups? According to Farris (1983) are classified from genealogical relationships, which are evidenced from synapomorphies, the latter being the one that provides evidence of these evolutionary relationships. Patterson (1982) proposes that the term synapomorphy is synonymous with homology, however, this has been much debated. Hennig (1966) proposes that both the term synapomorphy and symplesiomorphy are types of homologies. Likewise, Ritcher (2016) proposes that the two terms should not be considered as synonyms because although they both respond to the same phenomenon, they consider it from different perspectives. That is, homology does not imply a direction in the transformation, contrary to synapomorphy, which implies a character "derived" from that symplesiomorphy or "primitive" character.

Due to all this, it is important to try to define the concept of homology, which according to Farris et al, (1970) and De Pinna (1991) is the one that pass the first homology test proposed by Patterson (1988) which corresponds to similarity , which could lead to think that a character is homologous if and only if it is that which makes a group monophilic, which according to Donoghue (1994) that is not true, because this character must be considered as a synapomorphy to be considered later as homology. If this initial character does not behave like synapomorphy, it becomes a homoplasic character. This is why De Pinna (1991) proposes primary homology as a conjecture of homology and secondary homology as supported by phylogenetic hypotheses.

Given the above, what happens when the character is the absence of it? According to Hennig (1966) it is erroneous to consider the absence of a character as a homology, because the term homology applies only to structures that are present, for which Richter (2016) suggests the term "synapomorphy" which can also apply to those characters where a state represents the absence of the structure or organ.

All these differences of opinion and others that are still to be mentioned, have long been debated, however, it is important to consider each and every one of them in order to define a good phylogenetic analysis according to the researcher.

References:

- De Pinna, M.C.C., 1991. Concepts and tests of homology in the cladistic paradigm. Cladistics 7, 367–394.

- Donoghue, M. (1994) Complexity and homology in plants. Department of Organismic and Evolutionary Biology. Harvard University, Cambridge.

- Farris, J.S., Kluge, A.G., Eckhardt, M.J., 1970. A numerical approach to phylogenetic systematics. Syst. Zool. 19, 172–191.

- Farris, J. (1983) The Logical Basis of Phylogenetic Analysis. Disponible en http://www.reocities.com/Hollywood/makeup/5023/Farris1983.pdf.

- Gould, Stephen J, (1977). Ontogeny and Phylogeny. Cambridge: Harvard University Press. https://books.google.com.co/books (Accessed 10 Dec 2017).

- Hennig, W., 1966. Phylogenetic Systematics. University of Illinois Press, Urbana.

- Patterson, C. (1988) Homology in Classical and Molecular Biology. Mol. Biol. Evol. 5(6):603-625.

- Ritcher, S. (2016) Homology and synapomorphy-symplesiomorphy—neither synonymous nor equivalent but different perspectives on the same phenomenon. Cladistics 0, 1–5

- Sereno, P. (2005) The Logical Basis of Phylogenetic Taxonomy. Syst. Biol. 54(4):595–619