A METHOD FOR DETERMINING THE POSITION AND SIZE OF OPTIMAL SEQUENCE REGIONS FOR PHYLOGENETIC ANALYSIS

The availability of fast and accurate sequencing procedures along with the use of PCR has led to a proliferation of studies of variability a t the molecular level in populations, Nevertheless, it is often imprac tical to examine long genomic stretches and a large number of individu als at the same time. In order to optimize this kind of study, we sugg est a heuristic procedure for detection of the shortest region whose i nformational content can be considered sufficient for significant phyl ogenetic reconstruction. The method is based on the comparison of the pairwise genetic distances obtained from a set of sequences of referen ce to those obtained for different windows of variable size and positi on by means of a simple index. We also present an approach for testing whether the informative content in the stretches selected in this way is significantly different from the corresponding content shown by th e larger genomic regions used as reference, Application of this test t o the analysis of the VP1 protein gene of foot-and-mouth-disease type C virus allowed us to define optimal stretches whose informative conte nt is not significantly different from that displayed by the complete VP1 sequence. We showed that the predictions made for type C sequences are valid for type O sequences, indicating that the results of the pr ocedure are consistent.