In the maximum parsimony problem, one produces an ancestral branching arrangement (phylogenetic tree, dendrogram) and ancestral messenger RNA sequences which account for contemporary amino acid sequences with the fewest number of nucleotide replacements consistent with the genetic code. This parsimony approach is not likely to capture the full extent of mutational change on branches of the tree which are represented by relatively few contemporary species, either due to inadequate data or extinction. A computer algorithm introduced by Goodman, Moore, Barnabas & Matsuda (1974) seeks to equalize this disparity by propagating mutational information from pairs of points in the dendrogram with many intervening links to pairs of points with few intervening links. Two pairs of points are assumed to be comparable if the number of aligned, non-matching nucleotides for one pair of points equals that for the other pair. This paper demonstrates mathematically that the Goodman et al. (1974) algorithm adds the minimum possible new mutations to the tree, consistent with such a propagation procedure.
ASJC Scopus subject areas
- Agricultural and Biological Sciences(all)