Estimating Phylogenetic Trees from Distance Matrices

TLDR: The distance Wagner procedure is applicable to data matrices of immunological distance, such as that of Sarich (1969a), in which between-OTU comparisons are evaluated but for which no attributes of the OTUs themselves are directly observable.

Abstract: 1. The distance Wagner procedure, presented here, is a modification of the original Wagner algorithm of Kluge and Farris (1969). Unlike previous techniques for calculating most parsimonious trees, it does not require a character-state matrix for the OTUs, but depends only upon an OTU × OTU matrix of phenetic differences. For this reason, the distance Wagner procedure is applicable to data matrices of immunological distance, such as that of Sarich (1969a), in which between-OTU comparisons are evaluated but for which no attributes of the OTUs themselves are directly observable. The distance Wagner procedure has the advantage over other available techniques for processing such data that it is free of the assumption of homogeneity of evolutionary rates over phyletic lines. 2. The estimated evolutionary trees produced by the distance Wagner procedure are undirected. Their roots may be estimated either by assuming the evolutionary rates of the two most divergent phyletic lines on the tree to be equal, or by con...