Molecular evolutionary processes modify DNA over time, creating both newly 
derived substitutions shared by related descendant lineages (phylogenetic 
signal) and "false" similarities which confound phylogenetic reconstruction 
(homoplasy). However, some types of DNA regions, for example those containing 
tandem duplicate repeats, are preferentially subject to homoplasy-inducing 
processes such as sporadically occurring concerted evolution and DNA 
insertion/deletion. This added level of homoplasic "noise" can make DNA regions 
with repeats less reliable in phylogenetic reconstruction than those without 
repeats. Most molecular datasets which distinguish among African hominoids 
support a human-chimpanzee clade; the most notable exception is from the 
involucrin gene. However, phylogenetic resolution supporting a 
chimpanzee-gorilla clade is based entirely on involucrin DNA repeat regions. 
This is problematic because (1) involucrin repeats are difficult to align, and 
published alignments are contradictory; (2) involucrin repeats are subject to 
DNA insertion/deletion; (3) gorillas are polymorphic in that some do not have 
repeats reported to be synapomorphies linking chimpanzees and gorillas. Gene 
tree/species tree conflicts can occur due to the sorting of ancestrally 
polymorphic alleles during speciation. Because hominoid females transfer between 
groups, mitochondrial and nuclear gene flow occur to the same extent, and the 
probability of conflict between mitochondrial and nuclear gene trees is 
theoretically low. When hominoid intraspecific mitochondrial variability is 
taken into account [based on cytochrome oxidase subunit II (COII) gene 
sequences], humans and chimpanzees are most closely related, showing the same 
relative degree of separation from gorillas as when single individuals 
representing species are analyzed. Conflicting molecular phylogenies can be 
explained in terms of molecular evolutionary processes and sorting of ancient 
polymorphisms. This perspective can enhance our understanding of hominoid 
molecular phylogenies.