Homoplasy, especially the type that occurs in more closely related phylogenetic groups, can make phylogenetic analysis more challenging.
Phylogenetic trees are often selected by means of
parsimony analysis. These analyses can be done with phenotypic characters, as well as DNA sequences. Using parsimony analysis, the hypothesis of relationships that requires the fewest (or least costly) character state transformations is preferred over alternative hypotheses. Evaluation of these trees may become a challenge when clouded by the occurrence of homoplasy in the characters used for the analysis. The most important approach to overcoming these challenges is to increase the number of independent (non-
pleiotropic, non-
linked) characteristics used in the phylogenetic analysis. Along with parsimony analysis, one could perform a
likelihood analysis, where the most likely tree, given a particular model of evolution, is selected, and branch lengths are inferred. According to the
cladistic interpretation, homoplasy is invoked when the distribution of a character state cannot be explained parsimoniously (without extra inferred character state transformations between the terminals and their ancestral node) on a preferred phylogenetic hypothesis - that is, the feature in question arises (or disappears) at more than one point on the tree. In the case of DNA sequences, homoplasy is very common due to the redundancy of the genetic code. An observed homoplasy may simply be the result of
random nucleotide substitutions accumulating over time, and thus may not need an
adaptationist evolutionary explanation. == Examples and applications of homoplasy ==