RECONSTRUCTION OF ANCESTRAL SEQUENCES BY THE INFERENTIAL METHOD, A TOOL FOR PROTEIN ENGINEERING STUDIES

This paper describes the inferential method, an approach for reconstru cting protein and nucleotide sequences of ancestral species, starting from known, homologous, contemporary sequences. The method requires kn owledge of the topology of the phylogenetic tree, whose nodes are the species to whom the reconstructed sequences belong. The method has bee n tested by computer simulation of speciation and nucleotide substitut ions, starting from a single ancestral sequence, and by subsequent rec onstruction of nodal sequences. Results have shown that reconstruction s obtained by the inferential method are affected by limited error fre quencies, which (1) are proportional to the squares of nucleotide subs titution rates and of internodal distances, and (2) are little influen ced by non-uniformity of transformation rates of nucleotides. Furtherm ore, good agreement of the results has been obtained by comparing prot ein-sequence reconstructions carried out with the inferential method w ith those obtained using the maximum parsimony method in two different cases: e.g., a reconstruction of simulated sequences and a reconstruc tion of mammalian ribonuclease sequences.