NUCLEIC ACID SEQUENCE PHYLOGENY AND RANDOM OUTGROUPS

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Abstract
When divergent taxa are used to root networks, it is assumed that the character states in the outgroup have historical similarity to those in the ingroup. Yet, if the data are nucleic acid sequences the character states shared by a divergent outgroup may be based not on history but on random similarity. A simple procedure is proposed to test this possibility. In the absence of an appropriate outgroup, root position can be estimated with the use of an asymmetrical character transformation matrix. If the matrix is sufficently biased, it can supply the polarity information usually derived from an outgroup. This outgroup test and rooting procedure are demonstrated with ADH sequences from the genus Drosophila.