Codificación de las inserciones-deleciones en el análisis filogenético de secuencias génicas

The general concept of phylogenetic homology visualizes that a character is any aspect of the phenotype or genotype that varies inside a group. In gene sequences each position corresponds to a hypothesis of transformational or taxic homology depending if the nucleotides vary or not in each position. It is theoretically difficult to designate a proper code to an indel. This is because an indel can be interpreted as an artifact or as phylogenetic information (taxic or transformational homology). A review of the distinct codes employed for the analysis of the indels shows that the six codes used are: ( 1) missing, (2) excluded, (3) fifth state, ( 4) presence/absence, (5) different length /several states and (6) different length /several characters. Each code was evaluated in the phylogenetic hypotheses of the phytopathogenic fungi Rhizoctonia solani with a matrix of 20 sequences of the ribosomal ARN genes. The effects of the distinct codes were measured in changes of homoplasy, topology, resolution and tree number. The effects differ depending on the code used. The most radical effect was caused by the coding of the indels as different length/several characters. The cladistic analyses with gene sequences should include an evaluation of the effects of the different codes for the indels, since they may be potentially informative.