Recent mathematical approaches to reconstruct phylogenies: A chemosystematist's and botanist's view

Some basic problems of mathematical phylogenetics are discussed. While algorithms regularly depend on the principle of parsimony, some features of phylogenesis interfere with that principle. Nonrandomness of the distribution of mutations as well as the inconstancy of the molecular clock in time and within a given sequence can bias the calculated relationships of closely related taxa. True comparability of sequences is difficult to establish, since this requires defining of homology of positions and of functions of amino acids as well. Parallelism and convergence can give rise to errors in establishing homology. Furthermore, they are difficult to be integrated into a consistent mathematical …