question: How homoplasy affects phylogenetic reconstruction?
answer: Evolutionary processes create both newly derived characteristics shared by related descendant lineages (homology) and "false" similarities which confound phylogenetic reconstruction (homoplasy). Homology arises by divergent evolution from a common ancestor and provides us with a phylogenetic signal, while homoplasy arises by convergent evolution or random coincidence. Homoplastic characters do not allows branch points and clade membership to be accurately estimated, as they may group unrelated taxa together. Such characters add "noise" in phylogenetic analysis and are not informative for the population genetics and the phylogenetic reconstruction of closely related taxa. In phylogenetic reconstruction, homoplasy leads to inaccurate conclusions about phylogenetic relationships among operational taxonomic units, and characters with high degree of homoplasy result in incongruences of cladistic relationships.