DNA hybridization is a "distance method" for phylogenetic reconstruction and, as 
such, shares a set of assumptions, advantages, and problems with other 
techniques that do not directly employ character data. The technique purports to 
measure the average percent mismatch of homologous nucleotide sequences between 
the single-copy genomes of species. This measurement, as any other, is subject 
to considerations of accuracy and precision. While replicate measurements and 
technical modifications can improve precision, the accuracy of such measurements 
is limited by the equivalence of genomes under comparison. Such routine events 
in genome evolution as gene duplication and deletion may complicate the 
interpretation of DNA hybridization distances. Beyond measurement limitations, 
the most serious potential distortions of distances are due to biased sequence 
sampling and homoplasy. These problems, however, do not necessarily preclude 
phylogenetic reconstruction, and their effects may be mitigated by numerical 
corrections. Homoplasy, in particular, is a difficulty faced by all methods of 
phylogenetic inference. If such distortions can be eliminated, mitigated by 
correction, or shown to be trivial, pairwise tree-construction strategies should 
provide reliable estimates of phylogeny.