Paraphyly

A cladogram showing a hypothetical descent from an ancestor species of the clade vertebrata.^[1] Note that cladograms do not necessarily correspond to taxonomic classifications. In this one, Sauropsida are a paraphyletic group. It can be made monophyletic by including the birds (Aves).

Comparison of phylogenetic groups, showing a monophyly (all descendants of the first reptiles), a paraphyly (descendants of reptiles, minus birds), and a polyphyly (warm-blooded animals: mammals and birds)

A group of taxa is said to be paraphyletic if the group consists of all the descendants of a hypothetical closest common ancestor minus one or more monophyletic groups of descendants (typically one such group). This term is used in both phylogenetics^{[note 1]} and linguistics.

Phylogenetics

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 is neither monophyletic nor paraphyletic 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).

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 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 2]} 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.^[2]

• 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.^[3]

• 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 (see the illustration above).^[4] Reptiles would be monophyletic if they were defined to include Mammalia and Aves.^[5]

• The Prokaryotes (single-celled life forms without cell nuclei), because the Archaea descend from a common ancestor with the Eukaryotes. The Prokaryote/Eukaryote distinction was proposed by Edouard Chatton in 1937^[6] and was generally accepted after being adopted by Roger Stanier and C.B. van Niel in 1962. It was never adopted by any code because by that time the inappropriateness of the ICBN code and the ICZN Code for classifying life forms that are neither plant nor animal was also generally recognized and the ICNB code did not appear until 1975. It did recognize Prokaryotic taxa beginning in 1980.^[7] Chatton's system became known as the two-empire system but the latter was replaced by Carl Woese's three-domain system published in 1990. The former Prokaryotes became the Bacteria and the Archaea, while the third domain remained the Eukaryotes. Subsequent phylogenetic analysis led to a conclusion that the Archaea and the Eukaryotes share a common ancestor.^[8]

• Agnatha, jawless fish, because of its two significant animal groups, hagfish and lampreys, the lampreys descend from the stem of the Gnathostomes. In 1806 Duméril united the hagfish with the lampreys under Cyclostomi, which Cope in 1889 made into Agnatha, as opposed to Gnathostome, the jawed fish. These two taxa became classes or superclasses in the ICZN Code. In the late 20th century phylogenetic analysis using dozens of characters (features) indicated the lampreys came from gnathostome ancestors, but the original agnatha/gnathostome ancestor did not have a jaw. The removal of the lampreys from the Agnatha downgraded the latter to a paraphyletic group.^[9]

• 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.^[10]

• Porifera are now divided into siliceous sponges and calcareous sponges, which together are not monophyletic.^{[citation needed]}

• Recently Crustaceans has been defined as paraphyletic group by molecular phylogenetic study, so Hexapods would be evolved from a subfamily of this group.^{[citation needed]}

Cladistics generally discourages 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 organisms, 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, in cladistics 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. Ereshefsky notes that paraphyletic taxa are the result of anagenesis.

For instance, the Prokaryote group is paraphyletic because it excludes many of its descendent organisms (the 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.^[11]

Linguistics

Main article: Tree model

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.^[12]

Notes

1. ^ A paraphyletic group is defined in terms of a clade; that is, the group is the same as the equivalent clade, except that it lacks one or more of the clade's full complement. The concept of the last common ancestor is the same, but it has been expanded to be node-based, branch-based and apomorphy-based. Those terms are defined under Phylogenetic nomenclature.
2. ^ The history of flowering plant classification can be found under History of the classification of flowering plants.

References

1. ^ Laurin, Michel; Gauthier, Jacques A. (1996). "Amniota". Tree of Life Web Project. http://tolweb.org/amniota. Retrieved 25 January 2010. 
2. ^ 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 ...."
3. ^ 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. http://icb.oxfordjournals.org/cgi/content/full/41/3/487. 
4. ^ Romer, A. S. & Parsons, T. S. (1985): The Vertebrate Body. (6th ed.) Saunders, Philadelphia.
5. ^ Tudge, Colin (2000). The Variety of Life. Oxford University Press. ISBN 0198604262. 
6. ^ 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. http://mmbr.asm.org/cgi/content/full/69/2/292?ijkey=9c01f67410bfc780c9d62495284c6efd50dc4f46#THE_TALE_OF_EDOUARD_CHATTON. 
7. ^ 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 
8. ^ Berg, Linda (2008). Introductory Botany: Plants, People, and the Environment (2nd ed.). Belmont CA: Thomson Corporation. p. 360. ISBN 0030754534. 
9. ^ Janvier, Philippe (2002) [1996]. Early Vertebrates. Oxford Monographs in Geology. Oxford: Oxford University Press. p. 44. ISBN 0198540477. 
10. ^ A Tree of Life
11. ^ 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. 
12. ^ 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.

Bibliography

• Simpson, Michael George (2006). Plant systematics. Burlington; San Diego; London: Elsevier Academic Press. ISBN 0126444609. 

• Tudge, Colin (2000). The Variety of Life. Oxford University Press. ISBN 0198604262. 

External links

• 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. http://www.umbc.edu/biosci/Faculty/OmlandLabWebpage/NewPages/papers/FunkOmlandARev.pdf.