Phylogenetics

Phylogenetic separation into evolutionary relationships (clades), based on comparison of genomes is likely to supplant phenotypical (phenetic) taxonomies of the prokaryotes.

Phenetic system: groupings of organisms based on mutual similarity of phenotypic (physical and chemical) characteristics. Phenetic groupings may or may not correlate with evolutionary relationships.

Phylogenetic system: groups organisms based on shared evolutionary heritage. DNA and RNA sequencing techniques are considered to give the most meaningful phylogenies.

Monophyletic taxon or clade: an accurate grouping of only (opp. polyphyletic) and all (opp. paraphyletic) descendents of a shared common ancestor. A monopyletic group is genetically homogeneous and reflects evolutionary relationships.

Paraphyletic taxon or clade: a monophyletic group that excludes one or more discrete groups descended from the most recent common ancestral species of the entire group. Other descendent species of the most recent common ancestor have been excluded from the paraphyletic taxon, usually because of morphologic distinctiveness.

Polyphyletic taxon: opposite to monophyletic taxon: A polyphyletic group is mistakenly or improperly erected on the basis of homoplasy.—characteristics that have arisen despite not sharing a common ancestor. Homoplasy arises because of convergent evolution, parallelism, evolutionary reversals, horizontal gene transfer, or gene duplications. Polyphyletic taxa are genetically heterogeneous because members do not share a common ancestor.