Testing character correlation using pairwise comparisons on a phylogeny

In comparative biology, pairwise comparisons of species or genes (terminal taxa) are used to detect character associations. For instance, if pairs of species contrasting in the state of a particular character are examined, th e member of a pair with a particular state might be more likely than the ot her member to show a particular state in a second character. Pairs are chos en so as to be phylogenetically separate, that is, the path between members of a pair, along the branches of the tree, does not touch the path of any other pair. On a given phylogenetic tree, pairs must be chosen carefully to achieve the maximum possible number of pairs while maintaining phylogeneti c separation. Many alternative sets of pairs may have this maximum number. Algorithms are developed that find all taxon pairings that maximize the num ber of pairs without constraint, or with the constraint that members of eac h pair have contrasting states in a binary character, or that they have con trasting states in two binary characters. The comparisons chosen by these a lgorithms, although phylogenetically separate on the tree, are not necessar ily statistically independent. (C) 2000 Academic Press.