INCONSISTENCY OF THE MAXIMUM PARSIMONY METHOD WHEN THE RATE OF NUCLEOTIDE SUBSTITUTION IS CONSTANT

The inconsistency of the maximum parsimony method is known to occur ev en when the rate of nucleotide substitution is constant. To understand why this inconsistency occurs, a mathematical study was conducted for the cases of five, six, and seven sequences. The results obtained ind icate that this inconsistency occurs because the probability of occurr ence of nucleotide configurations generated by one substitution on a s hort interior branch is often lower than that of configurations genera ted by more substitutions on other longer branches. The chance of occu rrence of this event-or, the inconsistency of the maximum parsimony me thod-apparently increases as the number of sequences increases. The in consistency may occur even when the extent of sequence divergence is r elatively small.