||This article needs additional citations for verification. (January 2010)|
Paraphyly is a characteristic of some groups of organisms and families of languages. In phylogenetics (a subfield of biology) and in linguistics, a group is said to be paraphyletic if it consists of all the descendants of the last common ancestor of the group's members minus a small number of monophyletic groups of descendants, typically just one or two such groups. For example, the group of reptiles, as traditionally defined, is paraphyletic: it contains the last common ancestor of the reptiles—including the extant reptiles as well as the extinct mammal-like reptiles—along with all descendants of that ancestor except for mammals and birds.
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. Ereshefsky has argued that that paraphyletic taxa are the result of anagenesis.
A taxon that is not paraphyletic or monophyletic is 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).
Examples of paraphyletic groups 
Many of the older classifications contain paraphyletic groups, including the traditional 2–6 kingdom systems and the classic division of the vertebrates. Examples of well-known paraphyletic groups include:
- In the flowering plants, dicotyledons, in the traditional sense, because they exclude monocotyledons. The former name has not been used as an ICBN classification for decades, but is allowed as a synonym of Magnoliopsida.[note 1] The former angiosperms (Magnoliophyta), or flowering plants, comprised both. Phylogenetic analysis, however, indicates that the monocots are a development from a dicot ancestor. Excluding them from the dicots makes the latter a paraphyletic group.
- The order Artiodactyla (even-toed ungulates), because it excludes Cetaceans (whales, dolphins, etc.). In the ICZN Code, the two taxa are orders of equal rank. Molecular studies, however, have shown that the Cetacea descend from the Artiodactyl ancestors, although the precise phylogeny within the order remains uncertain. Without the Cetacean descendants the Artiodactyls must be paraphyletic.
- The class Reptilia as traditionally defined, because it excludes birds (class Aves) and mammals (class Mammalia). In the ICZN Code, the three taxa are classes of equal rank. However, mammals hail from the mammal-like reptiles and birds are descended from the dinosaurs (a group of Diapsida), both of which are classified as reptiles.
- The prokaryotes (single-celled life forms without cell nuclei), because they exclude the eukaryotes, a descendant group. Bacteria and Archaea are prokaryotes, but archaea and eukaryotes share a common ancestor that is not ancestral to the bacteria. The prokaryote/eukaryote distinction was proposed by Edouard Chatton in 1937 and was generally accepted after being adopted by Roger Stanier and C.B. van Niel in 1962. The botanical code (the ICBN, now the ICN) abandoned consideration of bacterial nomenclature in 1975; currently, prokaryotic nomenclature is regulated under the ICNB with a starting date of January 1, 1980 (in contrast to a 1753 start date under the ICBN/ICN).
- 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.
The following table shows some paraphyletic groups.
|Paraphyletic Taxon||Excluded Clades||Corresponding Monophyletic Taxon|
|Reptiles||Mammalia, Aves (Birds)||Amniota|
Uses for paraphyletic groups 
When the appearance of significant traits has led a subclade on an evolutionary path very divergent from that of a more inclusive clade, it often makes sense to study the paraphyletic group that remains without considering the larger clade. For example, the Neogene evolution of the Artiodactyla (even-toed ungulates, like deer) has taken place in an environment so different from that of the Cetacea (whales, dolphins, and porpoises) that the Artiodactyla are often studied in isolation even though the cetaceans are a descendent group. The prokaryote group is another example; it is paraphyletic because it excludes many of its descendent organisms (the eukaryotes), but it is very useful because it has a clearly defined and significant distinction (no cell nucleus) from its excluded descendants.
Also, paraphyletic groups are involved in evolutionary transitions, the development of the first tetrapods from their ancestors for example. Any name given to these ancestors to distinguish them from tetrapods—"fish", for example—necessarily picks out a paraphyletic group, since the descendent tetrapods are not included.
Paraphyly cannot be based on independently evolved traits 
Vivipary, the production of offspring without the involvement of a fertilized egg, developed independently in the lineages that led to humans (Homo sapiens) and southern water skinks (Eulampus tympanum, a kind of lizard). Put another way, at least one of the lineages that led to these species from their last common ancestor contains nonviviparous animals, the pelycosaurs ancestral to humans for example; vivipary appeared subsequently in the human lineage.
Independently-developed traits like these cannot be used to distinguish paraphyletic groups since paraphyly requires the excluded groups to be monophyletic. Pelycosaurs were descended from the last common ancestor of skinks and humans, so vivipary could be paraphyletic only if the pelycosaurs were part of an excluded monophyletic group. Since this group is monophyletic, it contains all descendents of the pelycosaurs; since it is excluded, it contains no viviparous animals. This doesn't work, since humans are among these descendents. Vivipary in a group that includes humans and skinks cannot be paraphyletic.
Though the last common ancestor of skinks and humans was not viviparous, this is not essential to the argument. The last common ancestor of porpoises and sharks, like these extant animals, probably had a dorsal fin on its back, but the Mesozoic ancestors of porpoises (a mammal group) did not have the fin, so it does not define a paraphyly. The presence of a trait in a last common ancestor is not sufficient for paraphyly.
Not Paraphyly 
- Amphibious fish are not a paraphyletic group because although they appear similar several different groups of amphibious fishes evolved independently, see Convergent evolution.
- Flightless birds are also not paraphyletic because their flightless charasteristics evolved independently.
- Quadrupedal archosaurs are not a paraphyletic group. Bipedal dinosaurs like Eoraptor, ancestral to quadrupedal ones, were descendents of the last common ancestor of quadrupedal dinosaurs and other quadrupedal archosaurs like the crocodilians.
The concept of paraphyly has also been applied to historical linguistics, where the methods of cladistics have found some utility in comparing languages. For instance, the Formosan languages form a paraphyletic group of the Austronesian languages as the term refers to the nine branches of the Austronesian family that are not Malayo-Polynesian and restricted to the island of Taiwan.
- The history of flowering plant classification can be found under History of the classification of flowering plants.
- Simpson 2006, pp. 139–140. "It is now thought that the possession of two cotyledons is an ancestral feature for the taxa of the flowering plants and not an apomorphy for any group within. The 'dicots' ... are paraphyletic ...."
- O'Leary, Maureen A. (2001). "The phylogenetic position of cetaceans: further combined data analyses, comparisons with the stratigraphic record and a discussion of character optimization". American Zoologist 41 (3): 487–506. doi:10.1093/icb/41.3.487.
- Romer, A. S. & Parsons, T. S. (1985): The Vertebrate Body. (6th ed.) Saunders, Philadelphia.
- Sapp, Jan (June 2005). "The prokaryote–eukaryote dichotomy: meanings and mythology". Microbiology and Molecular Biology Reviews 69 (2): 292–305. doi:10.1128/MMBR.69.2.292-305.2005. PMC 1197417. PMID 15944457.
- Stackebrabdt, E.; Tindell, B.; Ludwig, W.; Goodfellow, M. (1999). "Prokaryotic Diversity and Systematics". In Lengeler, Joseph W.; Drews, Gerhart; Schlegel, Hans Günter. Biology of the prokaryotes. Stuttgart: Georg Thieme Verlag. p. 679
- A Tree of Life
- O'Leary, Maureen A. (2001). "The Phylogenetic Position of Cetaceans: Further Combined Data Analyses, Comparisons with the Stratigraphic Record and a Discussion of Character Optimization". American Zoologist 41 (3): 487–506. doi:10.1093/icb/41.3.487.
- Savage, R. J. G. & Long, M. R. (1986). Mammal Evolution: an illustrated guide. New York: Facts on File. p. 208. ISBN 0-8160-1194-X.
- Tudge, Colin (2000). The Variety of Life. Oxford University Press. ISBN 0198604262.
- Berg, Linda (2008). Introductory Botany: Plants, People, and the Environment (2nd ed.). Belmont CA: Thomson Corporation. p. 360. ISBN 0-03-075453-4.
- Kielan-Jaworowska, Z. and Hurum, J. (2001). "Phylogeny and Systematics of Multituberculate Animals". Palaeontology 44 (3): 389–429.
- David R. Andrew (2011). "A new view of insect–crustacean relationships II. Inferences from expressed sequence tags and comparisons with neural cladistics". Arthropod Structure & Development 40: 289–302. doi:10.1016/j.asd.2011.02.001.
- Bjoern M. von Reumont, Ronald A. Jenner, Matthew A. Wills, Emiliano Dell'Ampio, Günther Pass, Ingo Ebersberger, Benjamin Meyer, Stefan Koenemann, Thomas M. Iliffe, Alexandros Stamatakis, Oliver Niehuis, Karen Meusemann & Bernhard Misof (2012). "Pancrustacean phylogeny in the light of new phylogenomic data: support for Remipedia as the possible sister group of Hexapoda" (PDF proofs). Molecular Phylogenetics and Evolution 29 (3): 1031–1045. doi:10.1093/molbev/msr270. PMID 22049065.
- Kazlev, M.A. and White, T. "Amphibians, Systematics, and Cladistics". Palaeos website. Retrieved 16 August 2012.
- Dawkins, Richard (2004). "Mammal-like Reptiles". The Ancestor's Tale, A Pilgrimage to the Dawn of Life. Boston: Houghton Mifflin Company. ISBN 0-618-00583-8.
- Greenhill, Simon J. and Russell D. Gray. (2009.) "Austronesian Language and Phylogenies: Myths and Misconceptions About Bayesian Computational Methods," in Austronesian Historical Linguistics and Culture History: a Festschrift for Robert Blust, edited by Alexander Adelaar and Andrew Pawley. Canberra: Pacific Linguistics, Research School of Pacific and Asian Studies, The Australian National University.
- Simpson, Michael George (2006). Plant systematics. Burlington; San Diego; London: Elsevier Academic Press. ISBN 0-12-644460-9.
|Look up paraphyletic in Wiktionary, the free dictionary.|
- Funk, D. J.; Omland, K. E. (2003). "Species-level paraphyly and polyphyly: Frequency, cause and consequences, with insights from animal mitochondrial DNA". Annual Review of Ecology, Evolution and Systematics 34: 397–423. doi:10.1146/annurev.ecolsys.34.011802.132421.