Paraphyly

In phylogenetics, a group of organisms is said to be paraphyletic if the group contains its most recent common ancestor but does not contain all the descendants of that ancestor.

Relation to monophyletic groups
Groups that do include all the descendants of the most recent common ancestor are said to be monophyletic. A paraphyletic group is a monophyletic group from which one or more of the clades is excluded to form a separate group (as in the paradigmatic example of reptiles and birds, shown in the picture).

A group that does not contain the most recent common ancestor of its members is said to be polyphyletic (Greek πολύς (polys), "many").

These terms were developed during the debates of the 1960s and 70s accompanying the rise of cladistics (a clade is a term for a monophyletic group). Before that period the distinction between mono- and polyphyletic groups was based on the inclusion or exclusion of the most recent common ancestor. It was shown, however, that the inclusion of ancestors in the classification leads to unavoidable logical inconsistencies, and, in some schools of taxonomy, the phylogenetic pattern is described exclusively in terms of nested patterns of the sister group relationships between the known representatives of taxa without referring to the ancestor-descendant relationships.

Examples of paraphyletic groups
Many of the older classifications contain paraphyletic groups, especially the traditional 2–6 kingdom systems and the classic division of the vertebrates. Paraphyletic groups are often erected on the basis of (sym)-plesiomorphies (ancestral similarities) instead of (syn)apomorphies (derived similarities). Examples of well-known paraphyletic groups includes:


 * In the flowering plants, Dicotyledonae, in the traditional sense, because they exclude Monocotyledonae.


 * The order Artiodactyla (Even-toed ungulates), because it excludes Cetaceans (whales, dolphins, etc).


 * The class Reptilia as traditionally defined is paraphyletic because that class excludes birds (class Aves), which are descended from reptiles (see the illustration above). Reptiles would be monophyletic if Reptiles were defined to include Aves.


 * The Prokaryotes (organisms without cell nuclei) consisting of bacteria and archaea, which is paraphyletic, because the clade containing the prokaryotes also includes all eukaryotes (organisms with cell nuclei). This is because the root of the tree of life, the last universal common ancestor (LUCA), is believed to lie between Archaea and Bacteria.  Archaea and Eukaryota are thought to share a more recent common ancestor.


 * Agnatha, jawless fish. This group contains two significant animal groups, hagfish and lampreys.  Their nearest common ancestor is the ancestor of all vertebrates, so Agnatha is paraphyletic.


 * Osteichthyes, bony fish, are paraphyletic because they include Actinopterygii (ray-finned fish) and Sarcopterygii (lungfish, etc). However, tetrapods are descendants of the nearest common ancestor of Actinopterygii and Sarcopterygii, and tetrapods are not in Osteichthyes, hence Osteichthyes is paraphyletic.


 * Porifera - Now divided into Siliceous Sponges and Calcareous sponges, which together are not monophyletic.


 * Invertebrates are defined as all animals other than vertebrates, although vertebrates are derived from this larger group.


 * Recently Crustaceans has been defined as paraphyletic group by molecular phylogenetic study, so Hexapods would be evolved from a subfamily of this group.

The term paraphyly may be used in any system in which genetic descent modeled by trees is useful. For instance, in linguistics, the Formosan languages form a paraphyletic group of the Austronesian languages as the term refers to the nine branches of the Autronesian family that are not Malayo-Polynesian and restricted to the island of Taiwan.

Cladistics generally discourage paraphyletic groups
In most cladistics-based schools of taxonomy, the existence of paraphyletic groups (as well as polyphyletic groups) in a classification is discouraged. Monophyletic groups (that is, clades) are considered by these schools of thought to be the most important grouping of organisims, for the following reasons:


 * Clades are simple to define: a typical clade definition is "All descendants of the nearest common ancestor of species X and Y".  On the other hand, polyphyletic and paraphyletic groups are always defined in terms of clades, for example "reptiles are the Sauropsid clade, minus the Aves clade".   Or "Warm-blooded animals are the Aves clade plus the Mammals clade".   Because polyphyletic and paraphyletic groups are defined in terms of clades, they are considered less important than clades.


 * For a given evolutionary tree of, say, N nodes, there are exactly N clades (one per node). However, the number of paraphyletic groups and polyphyletic groups is exponentially larger than that, on the order of $$2^N$$.  Yet only a small fraction of the paraphyletic groups are given names or discussed.


 * Paraphyletic groups often have their origin in traditional taxonomy, based on similar morphological characteristics. The original perception may have been that the group was entirely descended from a single ancestor.   If such a group is later discovered (for instance, due to convergent evolution) to be paraphyletic, rather than monophyletic, then such a group  loses its original significance.

Uses for paraphyletic groups
Others argue that paraphyletic groups are necessary for a comprehensive classification including extinct groups, since each species, genus, and so forth necessarily originates from part of another.

For instance, the Prokaryote group is paraphyletic because it excludes many of its descendent organisms (such as Eukaryotes), yet the Prokaryote group is very useful because it has a clearly-defined and significant distinction (no cell nucleus) from its excluded descendants. So, even though Prokaryotes are not a clade, the term is still useful.

It has been suggested that paraphyletic groups be clearly marked to distinguish them from clades, for instance with asterisks: Reptilia*. The term evolutionary grade is sometimes used for such groups.