The abstracts linked to by Dr.Caporale deal with the potential difficutlis in phylogenetic analyses due to non-random mutations and other occurrances that can obscure 'true' phylogentic reconstruction. The abstracts, however, iindicate that while there are
potential problems, sufficiently large datasets and programs that take such possibilities into account can compensate.
That is, it "non-random mutation" is only aproblem for phylogeny if one does not take it into account. Unfortunately for Borger, who claims that NRM essentially falsify all phylogenetic reconstructions, it is at best a minor problem.