Phylogenetic nomenclature

Phylogenetic nomenclature, often called cladistic nomenclature, is a method of nomenclature for taxa in biology that uses phylogenetic definitions for taxon names as explained below. This contrasts with the traditional approach, in which taxon names are defined by a type, which can be a specimen or a taxon of lower rank, and a description in words.[1] Phylogenetic nomenclature is currently not regulated, but the International Code of Phylogenetic Nomenclature (PhyloCode) is intended to regulate it once it is ratified.

Definitions

Clade names and phylogenetic hypotheses
The clade shown by the dashed lines in each figure is specified by the ancestor X. Under the hypothesis that the relationships are as in the left tree, the clade includes X, A, B and C. Under the hypothesis that the relationships are as in the right tree, the clade includes X, A and B.

Phylogenetic nomenclature ties names to clades, groups consisting of an ancestor and all its descendants. These groups can equivalently be called monophyletic. There are slightly different ways of specifying the ancestor, which are discussed below. Once the ancestor is specified, the meaning of the name is fixed: the ancestor and all organisms which are its descendants are included in the named taxon. Listing all these organisms (i.e. providing a full circumscription) requires the full phylogenetic tree to be known. In practice, there are only one or more hypotheses as to the correct tree. Different hypotheses lead to different organisms being thought to be included in the named taxon, but do not affect what organisms the name actually applies to. In this sense the name is independent of theory revision.

Phylogenetic definitions of clade names

Phylogenetic nomenclature ties names to clades, groups consisting solely of an ancestor and all its descendants. All that is needed to specify a clade, therefore, is to designate the ancestor. There are a number of ways of doing this. Commonly, the ancestor is indicated by its relation to two or more specifiers (species, specimens, or traits) that are mentioned explicitly. The diagram shows three common ways of doing this. For previously defined clades A, B, and C, the clade X can be defined as:

Clade types
The three most common ways to define the name of a clade: node-based, branch-based and apomorphy-based definition. The tree represents a phylogenetic hypothesis on the relations of A, B and C.
  • A node-based definition could read: "the last common ancestor of A and B, and all descendants of that ancestor". Thus, the entire line below the junction of A and B does not belong to the clade to which the name with this definition refers.
Example: The sauropod dinosaurs consist of the last common ancestor of Vulcanodon (A) and Apatosaurus (B)[2] and all of that ancestor's descendants. This ancestor was the first sauropod. C could include other dinosaurs like Stegosaurus.
  • A branch-based definition, often called a stem-based definition, could read: "the first ancestor of A which is not also an ancestor of C, and all descendants of that ancestor". Thus, the entire line below the junction of A and B (other than the bottommost point) does belong to the clade to which the name with this definition refers.
Example: The rodents consist of the first ancestor of the house mouse (A) that is not also an ancestor of the eastern cottontail rabbit (C) together with all descendants of that ancestor. Here, the ancestor is the very first rodent. B is some other descendant, perhaps the red squirrel.
  • An apomorphy-based definition could read: "the first ancestor of A to possess trait M that is inherited by A, and all descendants of that ancestor". In the diagram, M evolves at the intersection of the horizontal line with the tree. Thus, the clade to which the name with this definition refers contains that part of the line below the last common ancestor of A and B which corresponds to ancestors possessing the apomorphy M. The lower part of the line is excluded. It is not required that B have trait M; it may have disappeared in the lineage leading to B.
Example: the tetrapods consist of the first ancestor of humans (A) from which humans inherited limbs with fingers or toes (M) and all descendants of that ancestor. These descendants include snakes (B), which do not have limbs.

Several other alternatives are provided in the PhyloCode,[3] (see below) though there is no attempt to be exhaustive.

Phylogenetic nomenclature allows the use, not only of ancestral relations, but also of the property of being extant. One of the many ways of specifying the Neornithes (modern birds), for example, is:

The Neornithes consist of the last common ancestor of the extant members of the most inclusive clade containing the cockatoo Cacatua galerita but not the dinosaur Stegosaurus armatus as well as all descendants of that ancestor.

Neornithes is a crown clade, a clade for which the last common ancestor of its extant members is also the last common ancestor of all its members.

Node names

  • Crown node: Most recent common ancestor of the sampled species of the clade of interest
  • Stem node: Most recent common ancestor of the clade of interest and its sister clade

Ancestry-based definitions of the names of paraphyletic and polyphyletic taxa

In the PhyloCode, only a clade can receive a "phylogenetic definition", and this restriction is observed in the present article. However, it is also possible to create definitions for the names of other groups that are phylogenetic in the sense that they use only ancestral relations anchored on species or specimens.[4] For example, assuming Mammalia and Aves (birds) are defined in this manner, Reptilia could be defined as "the most recent common ancestor of Mammalia and Aves and all its descendants except Mammalia and Aves". This is an example of a paraphyletic group, a clade minus one or more subordinate clades. Names of polyphyletic groups, characterized by a trait that evolved convergently in two or more subgroups, can similarly be defined as the sum of multiple clades.[4]

Ranks

Under the traditional nomenclature codes, such as the International Code of Zoological Nomenclature and the International Code of Nomenclature for algae, fungi, and plants, taxa that are not explicitly associated with a rank cannot be formally named, because the application of a name to a taxon is based on both a type and a rank. The requirement for a rank is a major difference between traditional and phylogenetic nomenclature. It has several consequences: it limits the number of nested levels at which names can be applied; it causes the endings of names to change if a group has its rank changed, even if it has precisely the same members (i.e. the same circumscription); and it is logically inconsistent with all taxa being monophyletic.

Especially in recent decades (due to advances in phylogenetics), taxonomists have named many "nested" taxa (i.e. taxa which are contained inside other taxa). No system of nomenclature attempts to name every clade; this would be particularly difficult in traditional nomenclature since every named taxon must be given a lower rank than any named taxon in which it is nested, so the number of names that can be assigned in a nested set of taxa can be no greater than the number of generally recognized ranks. Gauthier et al. (1988)[5] suggested that, if Reptilia is assigned its traditional rank of class, then a phylogenetic classification has to assign the rank of genus to Aves.[6] In such a classification, all ~12,000 known species of extant and extinct birds would then have to be incorporated into this genus.

Various solutions have been proposed while keeping the rank-based nomenclature codes. Patterson and Rosen (1977)[7] suggested nine new ranks between family and superfamily in order to be able to classify a clade of herrings, and McKenna and Bell (1997)[8] introduced a large array of new ranks in order to cope with the diversity of Mammalia; these have not been widely adopted. In botany, the Angiosperm Phylogeny Group, responsible for the currently most widely used classification of flowering plants, chose a different approach. They retained the traditional ranks of family and order, considering them to be of value in teaching and in studying relationships between taxa, but also introduced named clades without formal ranks.[9]

The current codes also have rules stating that names must have certain endings depending on the rank of the taxa to which they are applied. When a group has a different rank in different classifications, its name must have a different suffix. Ereshefsky (1997:512)[6] gave an example. He noted that Simpson in 1963 and Wiley in 1981 agreed that the same group of genera, which included the genus Homo, should be placed together in a taxon. Simpson treated this taxon as a family, and so gave it the name "Hominidae": "Homin-" from "Homo" and "-idae" as the family ending under the zoological code. Wiley considered it to be at the rank of tribe, and so gave it the name "Hominini", "-ini" being the tribe ending. Wiley's tribe Hominini formed only part of a family which he called "Hominidae". Thus, under the zoological code, two groups with precisely the same circumscription were given different names (Simpson's Hominidae and Wiley's Hominini) and two groups with the same name had different circumscriptions (Simpson's Hominidae and Wiley's Hominidae).

In phylogenetic nomenclature, ranks have no bearing on the spelling of taxon names (see e.g. Gauthier (1994)[10] and the PhyloCode). Ranks are, however, not altogether forbidden in phylogenetic nomenclature. They are merely decoupled from nomenclature: they do not influence which names can be used, which taxa are associated with which names, and which names can refer to nested taxa.[11][12][13]

The principles of traditional rank-based nomenclature are logically incompatible with all taxa being strictly monophyletic.[11][14] Every organism must belong to a genus, for example, so there would have to be a genus for every common ancestor of the mammals and the birds. For such a genus to be monophyletic, it would have to include both the class Mammalia and the class Aves. In rank-based nomenclature, however, classes must include genera, not the other way around.

Philosophy

The conflict between phylogenetic and traditional nomenclature reflects differing views of the metaphysics of taxa. For the advocates of phylogenetic nomenclature, a taxon is an individual, an entity that gains and loses attributes as time passes.[15] Just as a person does not become somebody else when his or her properties change through maturation, senility, or more radical changes like amnesia, the loss of a limb, or a change in sex, so a taxon remains the same entity whatever characteristics are gained or lost.[16]

For any individual, there has to be something that connects its temporal stages in virtue of which it remains the same thing. For a person, the spatiotemporal continuity of the body provides the relevant connection; from infancy to old age, the body traces a continuous path through the world and it is this path, rather than any characteristics of the individual, that connects the baby and the octogenarian.[17] For a taxon, if characteristics are not relevant, it can only be ancestral relations that connect the Devonian Rhyniognatha hirsti with the modern monarch butterfly as representatives, separated by 400 million years, of the taxon Insecta.[16]

If ancestry is sufficient for the continuity of a taxon, however, then all descendants of a taxon member will also be included in the taxon, so all bona fide taxa are monophyletic; the names of paraphyletic groups do not merit formal recognition. As "Pelycosauria" refers to a paraphyletic group that includes some Permian tetrapods but not their extant descendants, it cannot be admitted as a valid taxon name.

To the adherent of traditional nomenclature, on the other hand, taxa are sets or classes.[15] Unlike individuals, they are constituted by similarities, characteristics shared among their members.[18] Monophyletic groups are particularly worthy of attention and naming primarily because they often share properties of interest. Since many paraphyletic groups also share such properties, plesiomorphies in their case, providing them with names is also conducive to productive research. Such naming is strongly defended by some scientists; in a 2005 letter to the editors of the journal Taxon, 150 biologists from around the world joined in defense of paraphyletic taxa.[19] For Darwin, they pointed out, evolution involved descent and modification, not just descent. Taxa, for them, are sets of organisms united by similarity; when the similarity is too weak, descendants are not in all of their ancestors' taxa.

History

Haeckel arbol bn
"Monophyletic phylogenetic tree of organisms".[20]

Phylogenetic nomenclature is a result of the general acceptance of branching in the course of evolution, represented in the diagrams of Jean-Baptiste Lamarck and later writers like Charles Darwin and Ernst Haeckel.[21] In 1866, Haeckel for the first time constructed a single tree of all life and immediately proceeded to translate it into a classification. This classification was rank-based, as was usual at the time, but did not contain taxa that Haeckel considered polyphyletic. In it, Haeckel introduced the rank of phylum which carries a connotation of monophyly in its name (literally meaning "stem").

Ever since, it has been debated in which ways and to what extent the phylogeny of life should be used as a basis for its classification, with views ranging from "numerical taxonomy" (phenetics) over "evolutionary taxonomy" (gradistics) to "phylogenetic systematics". From the 1960s onwards, rankless classifications were occasionally proposed, but in general the principles of rank-based nomenclature were used by all three schools of thought.

Most of the basic tenets of phylogenetic nomenclature (lack of obligatory ranks, and something close to phylogenetic definitions) can, however, be traced to 1916, when Edwin Goodrich[22] interpreted the name Sauropsida, erected 40 years earlier by T. H. Huxley, to include the birds (Aves) as well as part of Reptilia, and coined the new name Theropsida to include the mammals as well as another part of Reptilia. Goodrich did not give them ranks, and treated them exactly as if they had phylogenetic definitions, using neither contents nor diagnostic characters to decide whether a given animal should belong to Theropsida, Sauropsida, or something else once its phylogenetic position was agreed upon. Goodrich also opined that the name Reptilia should be abandoned once the phylogeny of the reptiles would be better known.

The principle that only clades should be formally named became popular in some circles in the second half of the 20th century. It spread together with the methods for discovering clades (cladistics) and is an integral part of phylogenetic systematics (see above). At the same time, it became apparent that the obligatory ranks that are part of the traditional systems of nomenclature produced problems. Some authors suggested abandoning them altogether, starting with Willi Hennig's abandonment[23] of his earlier proposal to define ranks as geological age classes.[24][25]

The first use of phylogenetic nomenclature in a publication can be dated to 1986.[26] Theoretical papers outlining the principles of phylogenetic nomenclature, as well as further publications containing applications of phylogenetic nomenclature (mostly to vertebrates), soon followed (see Literature section).

In an attempt to avoid a schism in the biologist community, "Gauthier suggested to two members of the ICZN to apply formal taxonomic names ruled by the zoological code only to clades (at least for supraspecific taxa) and to abandon Linnean ranks, but these two members promptly rejected these ideas" (Laurin, 2008: 224).[27] This led Kevin de Queiroz and the botanist Philip Cantino to start drafting their own code of nomenclature, the PhyloCode, for regulating phylogenetic nomenclature.

Controversy

Willi Hennig's pioneering work provoked a spirited debate[28] about the relative merits of phylogenetic nomenclature versus Linnaean taxonomy, or the related approach of evolutionary taxonomy, which has continued down to the present.[29] Some of the debates in which the cladists were engaged had been running since the 19th century.[30] While Hennig insisted that different classification schemes were useful for different purposes,[31] he gave primacy to his own, claiming that the categories of his system had "individuality and reality" in contrast to the "timeless abstractions" of morphology-based classifications.[32]

Formal classifications based on cladistic reasoning are said to emphasize ancestry at the expense of descriptive characteristics. Nonetheless, most taxonomists today avoid paraphyletic groups whenever they think it is possible within Linnaean taxonomy; polyphyletic taxa have long fallen out of fashion.

The International Code of Phylogenetic Nomenclature

The ICPN, or PhyloCode, is a draft code of rules and recommendations for phylogenetic nomenclature.

  • The ICPN will only regulate clade names. Names for para- or polyphyletic taxa, and names for species (which may or may not be clades), will not be considered, at least not at first. This means that the regulation of species names will be left, for the time being, to the rank-based codes of nomenclature.
  • The Principle of Priority will be introduced for names and for definitions. The starting point for priority will be the publication date of the ICPN.
  • Definitions for existing names, and new names along with their definitions, will have to be published in peer-reviewed works (on or after the starting date) and will have to be registered in an online database in order to be valid.

The number of supporters for widespread adoption of the PhyloCode is still small, and it is uncertain (as of August 2019) when the code will be implemented and how widely it will be followed.

References

  1. ^ International Commission on Zoological Nomenclature (1999). "Glossary". International Code of Zoological Nomenclature (4th ed.). ISBN 978-0-85301-006-7
  2. ^ Benton, Michael J. (2005). Vertebrate Palaeontology. Blackwell. p. 214. ISBN 978-0-632-05637-8.
  3. ^ Cantino, Philip D. & de Queiroz, Kevin (2010). "International Code of Phylogenetic Nomenclature, Version 4c". note 9.3.1 |contribution= ignored (help).
  4. ^ a b de Queiroz, K.; Gauthier, J. (1990). "Phylogeny as a central principle in taxonomy: phylogenetic definitions of taxon names". Systematic Zoology. 39 (4): 307–322. doi:10.2307/2992353. JSTOR 2992353.
  5. ^ Gauthier, J., Estes, R. & de Queiroz, K. 1988. A Phylogenetic Analysis of Lepidosauromorpha. Pp. 15–98 in R. Estes & G. Pregill (eds): Phylogenetic Relationships of the Lizard Families: Essays Commemorating Charles L. Camp. Stanford University Press. ISBN 978-0-8047-1435-8
  6. ^ a b Ereshefsky, M. (1997). "The Evolution of the Linnaean Hierarchy". Biology and Philosophy. 12 (4): 493–519. doi:10.1023/A:1006556627052.
  7. ^ Patterson, C. & Rosen, D. 1977 Review of ichthyodectiform and other Mesozoic teleost fishes and the theory and practice of classifying fossils. Bulletin of the American Museum of Natural History 158: 81–172.
  8. ^ McKenna, M. C. & Bell, S. K. 1997. Classification of Mammals Above the Species Level. Columbia University Press. ISBN 0-231-11012-X
  9. ^ Angiosperm Phylogeny Group (1998). "An ordinal classification for the families of flowering plants". Annals of the Missouri Botanical Garden. 85 (4): 531–553. doi:10.2307/2992015. JSTOR 2992015
  10. ^ Gauthier, J. A. 1994. The diversification of the amniotes. Pp. 129–159 in: D. R. Prothero & Rainer R. Schoch (eds): Major features of vertebrate evolution. Paleontological Society.
  11. ^ a b de Queiroz, K.; Gauthier, J. (1992). "Phylogenetic taxonomy [sic]". Annu. Rev. Ecol. Syst. 23: 449–480.
  12. ^ Cantino, P. D. (2000). "Phylogenetic nomenclature: addressing some concerns". Taxon. 49 (1): 85–93. doi:10.2307/1223935. JSTOR 1223935.
  13. ^ Bryant, H. N.; Cantino, P. D. (2002). "A review of criticisms of phylogenetic nomenclature: is taxonomic freedom the fundamental issue?". Biol. Rev. 77 (1): 39–55. doi:10.1017/S1464793101005802. PMID 11911373.
  14. ^ Kazlev, M. A. "Cladistic and Linnaean systems — incompatible or complementary?". (palaeos.com). Retrieved September 30, 2012.
  15. ^ a b Assis, L. C. S.; Brigandt, I. (2009). "Homology: Homeostatic Property Cluster Kinds in Systematics and Evolution" (PDF). Evolutionary Biology. 36 (2): 248–255. doi:10.1007/s11692-009-9054-y
  16. ^ a b Rowe, Timothy (1988). "Definition, diagnosis, and origin of Mammalia" (PDF). Journal of Vertebrate Paleontology. 8 (3): 241–264. doi:10.1080/02724634.1988.10011708
  17. ^ Wiggins, David (1967). Identity and Spatio-temporal Continuity. Oxford University Press. ISBN 978-0631103707
  18. ^ Entry for "taxon" in: International Commission on Zoological Nomenclature (1999). "Glossary". International Code of Zoological Nomenclature (4th ed.). ISBN 978-0-85301-006-7
  19. ^ Nordal, Inger & Stedje, Brita, coordinators (2005). "Paraphyletic taxa should be accepted". Taxon. 54 (1): 5–8. doi:10.2307/25065296. JSTOR 25065296CS1 maint: Multiple names: authors list (link)
  20. ^ Haeckel, E. H. Ph. A. 1866. Generelle Morphologie der Organismen. Georg Reimer.
  21. ^ Ragan, Mark A. (2009). "Trees and networks before and after Darwin". Biology Direct. 4 (43): 43. doi:10.1186/1745-6150-4-43. PMC 2793248. PMID 19917100
  22. ^ Goodrich, E. S. (1916). "On the classification of the Reptilia". Proceedings of the Royal Society B. 89 (615): 261–276. doi:10.1098/rspb.1916.0012.
  23. ^ Hennig, W. 1969. Die Stammesgeschichte der Insekten. Waldemar Kramer.
  24. ^ Hennig, W. 1950. Grundzüge einer Theorie der phylogenetischen Systematik. Deutscher Zentralverlag.
  25. ^ Hennig, W. (1965). "Phylogenetic Systematics". Annual Review of Entomology. 10: 97–116. doi:10.1146/annurev.en.10.010165.000525.
  26. ^ Gauthier, J. 1986. Saurischian Monophyly and the Origin of Birds. Pp. 1–55 in K. Padian (ed.): The Origin of Birds and the Evolution of Flight. Memoir 8 of the California Academy of Sciences.
  27. ^ Laurin, M. (2008). "The splendid isolation of biological nomenclature". Zoologica Scripta. 37 (2): 223–233. doi:10.1111/j.1463-6409.2007.00318.x.
  28. ^ Wheeler, Quentin (2000). Species Concepts and Phylogenetic Theory: A Debate. Columbia University Press. ISBN 978-0-231-10143-1
  29. ^ Benton, M. J. (2000). "Stems, nodes, crown clades, and rank-free lists: is Linnaeus dead?" (PDF). Biological Reviews. 75 (4): 633–648. CiteSeerX 10.1.1.573.4518. doi:10.1111/j.1469-185X.2000.tb00055.x. PMID 11117201
  30. ^ Hull, David (1988). Science as a Process. University of Chicago Press. pp. 232–276. ISBN 978-0-226-36051-5
  31. ^ Hennig, Willi (1966). Phylogenetic systematics (tr. D. Dwight Davis and Rainer Zangerl). Urbana, IL: Univ. of Illinois Press (reprinted 1979 and 1999). p. 9. ISBN 978-0-252-06814-0
  32. ^ Hennig 1966, p. 81

Further reading

A few publications not cited in the references are cited here. An exhaustive list of publications about phylogenetic nomenclature can be found on the website of the International Society for Phylogenetic Nomenclature.

  • Bryant, Harold N. (1994). "Comments on the phylogenetic definition of taxon names and conventions regarding the naming of crown clades". Syst. Biol. 43: 124–129. doi:10.1093/sysbio/43.1.124.
  • Cantino, Philip D.; Olmstead, Richard G. (2008). "Application of phylogenetically defined names does not require that every specifier be present on a tree". Syst. Biol. 57 (1): 157–160. doi:10.1080/10635150701883873. PMID 18300028.
  • de Queiroz, Kevin (1992). Phylogenetic definitions and taxonomic philosophy. Biol. Philos. 7:295–313.
  • Gauthier, Jacques A., Arnold G. Kluge, and Timothy Rowe (1988). The early evolution of the Amniota. Pages 103–155 in Michael J. Benton (ed.): The Phylogeny and Classification of the Tetrapods, Volume 1: Amphibians, Reptiles, Birds. Syst. Ass. Spec. Vol. 35A. Clarendon Press, Oxford.
  • Gauthier, Jacques, David Cannatella, Kevin de Queiroz, Arnold G. Kluge, and Timothy Rowe (1989). Tetrapod phylogeny. Pages 337–353 in B. Fernholm, K. Bremer, and H. Jörnvall (eds.): The Hierarchy of Life. Elsevier Science B. V. (Biomedical Division), New York.
  • Ghiselin, M. T. (1984). "Definition," "character," and other equivocal terms". Syst. Zool. 33 (1): 104–110. doi:10.2307/2413135. JSTOR 2413135.
  • Keesey, T. Michael (2007). "A mathematical approach to defining clade names, with potential applications to computer storage and processing". Zool. Scr. 36 (6): 607–621. doi:10.1111/j.1463-6409.2007.00302.x.
  • Laurin, Michel (2005). The advantages of phylogenetic nomenclature over Linnean nomenclature. Pages 67–97 in A. Minelli, G. Ortalli, and G. Sanga (eds): Animal Names. Instituto Veneto di Scienze, Lettere ed Arti; Venice.
  • Lee, Michael S. Y. (2005). "Choosing reference taxa in phylogenetic nomenclature". Zool. Scr. 34 (3): 329–331. doi:10.1111/j.1463-6409.2005.00196.x.
  • Rowe, Timothy (1987). "Definition and diagnosis in the phylogenetic system". Syst. Zool. 36 (2): 208–211. doi:10.2307/2413270. JSTOR 2413270.
  • Rowe, Timothy; Gauthier, Jacques (1992). "Ancestry, paleontology and definition of the name Mammalia". Syst. Biol. 41 (3): 372–378. doi:10.1093/sysbio/41.3.372.
  • Sereno, Paul C. (1998). "A rationale for phylogenetic definitions, with application to the higher-level taxonomy of Dinosauria". N. Jb. Geol. Paläont. Abh. 210: 41–83. doi:10.1127/njgpa/210/1998/41.
  • Sereno, Paul C. (1999). "Definitions in phylogenetic taxonomy: critique and rationale". Syst. Biol. 48 (2): 329–351. doi:10.1080/106351599260328. PMID 12066711.
  • Sereno, Paul C. (2005). "The Logical Basis of Phylogenetic Taxonomy [sic]". Syst. Biol. 54 (4): 595–619. doi:10.1080/106351591007453. PMID 16109704.
  • Taylor, Michael P. (2007). "Phylogenetic definitions in the pre-PhyloCode era; implications for naming clades under the PhyloCode". PaleoBios. 27: 1–6.
  • Wilkinson, Mark (2006). "Identifying stable reference taxa for phylogenetic nomenclature". Zool. Scr. 35: 109–112. doi:10.1111/j.1463-6409.2005.00213.x.
  • Wyss, A. R.; Meng, J. (1996). "Application of phylogenetic taxonomy to poorly resolved crown clades: a stem-modified node-based definition of Rodentia". Syst. Biol. 45 (4): 559–568. doi:10.1093/sysbio/45.4.559.
Apiales

The Apiales are an order of flowering plants. The families are those recognized in the APG III system. This is typical of the newer classifications, though there is some slight variation and in particular, the Torriceliaceae may be divided.Under this definition, well-known members include carrots, celery, parsley, and Hedera helix (English ivy).

The order Apiales is placed within the asterid group of eudicots as circumscribed by the APG III system. Within the asterids, Apiales belongs to an unranked group called the campanulids, and within the campanulids, it belongs to a clade known in phylogenetic nomenclature as Apiidae. In 2010, a subclade of Apiidae named Dipsapiidae was defined to consist of the three orders: Apiales, Paracryphiales, and Dipsacales.

Carnivoramorpha

Carnivoramorpha are a clade of mammals that includes the modern order Carnivora.

Clade

A clade (from Ancient Greek: κλάδος, klados, "branch"), also known as monophyletic group, is a group of organisms that consists of a common ancestor and all its lineal descendants, and represents a single "branch" on the "tree of life". Rather than the English term, the equivalent Latin term cladus (plural cladi) is often used in taxonomical literature.

The common ancestor may be an individual, a population, a species (extinct or extant), and so on right up to a kingdom and further. Clades are nested, one in another, as each branch in turn splits into smaller branches. These splits reflect evolutionary history as populations diverged and evolved independently. Clades are termed monophyletic (Greek: "one clan") groups.

Over the last few decades, the cladistic approach has revolutionized biological classification and revealed surprising evolutionary relationships among organisms. Increasingly, taxonomists try to avoid naming taxa that are not clades; that is, taxa that are not monophyletic. Some of the relationships between organisms that the molecular biology arm of cladistics has revealed are that fungi are closer relatives to animals than they are to plants, archaea are now considered different from bacteria, and multicellular organisms may have evolved from archaea.

Cladistics

Cladistics (, from Greek κλάδος, kládos, "branch") is an approach to biological classification in which organisms are categorized in groups ("clades") based on the most recent common ancestor. Hypothesized relationships are typically based on shared derived characteristics (synapomorphies) that can be traced to the most recent common ancestor and are not present in more distant groups and ancestors. A key feature of a clade is that a common ancestor and all its descendants are part of the clade. Importantly, all descendants stay in their overarching ancestral clade. For example, if within a strict cladistic framework the terms animals, bilateria/worms, fishes/vertebrata, or monkeys/anthropoidea were used, these terms would include humans. Many of these terms are normally used paraphyletically, outside of cladistics, e.g. as a 'grade'. Radiation results in the generation of new subclades by bifurcation.The techniques and nomenclature of cladistics have been applied to other disciplines. (See phylogenetic nomenclature.)

Cladistics is now the most commonly used method to classify organisms.

Evolutionary grade

In alpha taxonomy, a grade is a taxon united by a level of morphological or physiological complexity. The term was coined by British biologist Julian Huxley, to contrast with clade, a strictly phylogenetic unit.

Evolutionary taxonomy

Evolutionary taxonomy, evolutionary systematics or Darwinian classification is a branch of biological classification that seeks to classify organisms using a combination of phylogenetic relationship (shared descent), progenitor-descendant relationship (serial descent), and degree of evolutionary change. This type of taxonomy may consider whole taxa rather than single species, so that groups of species can be inferred as giving rise to new groups. The concept found its most well-known form in the modern evolutionary synthesis of the early 1940s.

Evolutionary taxonomy differs from strict pre-Darwinian Linnaean taxonomy (producing orderly lists only), in that it builds evolutionary trees. While in phylogenetic nomenclature each taxon must consist of a single ancestral node and all its descendants, evolutionary taxonomy allows for groups to be excluded from their parent taxa (e.g. dinosaurs are not considered to include birds, but to have given rise to them), thus permitting paraphyletic taxa.

Heteroptera

The Heteroptera are a group of about 40,000 species of insects in the order Hemiptera. They are sometimes called "true bugs", though that name more commonly refers to the Hemiptera as a whole. "Typical bugs" might be used as a more unequivocal alternative, since the heteropterans are most consistently and universally termed "bugs" among the Hemiptera. "Heteroptera" is Greek for "different wings": most species have forewings with both membranous and hardened portions (called hemelytra); members of the primitive sub-group Enicocephalomorpha have completely membranous wings.

The name "Heteroptera" is used in two very different ways in modern classifications. In Linnean nomenclature, it commonly appears as a suborder within the order Hemiptera, where it can be paraphyletic or monophyletic depending on its delimitation. In phylogenetic nomenclature, it is used as an unranked clade within the Prosorrhyncha clade, which in turn is in the Hemiptera clade. This results from the realization that the Coleorrhyncha are just "living fossil" relatives of the traditional Heteroptera, close enough to them to be united with that group.

The Gerromorpha and Nepomorpha contain most of the aquatic and semiaquatic members of the Heteroptera, while nearly all of the remaining groups that are common and familiar are in the Cimicomorpha and Pentatomomorpha.

International Society for Phylogenetic Nomenclature

The International Society for Phylogenetic Nomenclature was established to encourage and facilitate the development and use of, and communication about, phylogenetic nomenclature. It was established in the first international phylogenetic nomenclature meeting, which convened in the Muséum national d'histoire naturelle, in Paris, in July 6–9, 2004. It organizes periodic scientific meetings and is overseeing the completion and implementation of the PhyloCode. In the second meeting, rules concerning the choice of name for crown clades were discussed, along with rules to clarify the use of binomial species names in the context of phylogenetic nomenclature and to enhance the information content of these names (regarding the monophyly or paraphyly of the genus name, considered a prenomen, in the context of the PhyloCode). It was also decided then to expand the CPN (Committee on Phylogenetic Nomenclature) from nine to twelve members. The third meeting convened at Dalhousie University in Halifax, from July 20 to 22. The editors of the Companion Volume presented a progress report, and a demonstration of the RegNum on-line registration database was given. Both of these are important to the society because they are required to implement the PhyloCode. Other discussions at the meeting covered the problem of hybrids in rank-based and phylogenetic nomenclature, phyloinformatics, and teaching phylogenetic nomenclature.

Mammaliaformes

Mammaliaformes ("mammal-shaped") is a clade that contains the crown group mammals and their closest extinct relatives; the group radiated from earlier probainognathian cynodonts. It is defined as the clade originating from the most recent common ancestor of Morganucodonta and the crown group mammals; the latter is the clade originating with the most recent common ancestor of extant Monotremata, Marsupialia, and Placentalia. Besides Morganucodonta and the crown group mammals, Mammaliaformes includes Docodonta and Hadrocodium as well as the Triassic Tikitherium, the earliest known member of the group.Mammaliaformes is a term of phylogenetic nomenclature. In contrast, the assignment of organisms to Mammalia has traditionally been founded on traits and, on this basis, Mammalia is slightly more inclusive than Mammaliaformes. In particular, trait-based taxonomy generally includes Adelobasileus and Sinoconodon in Mammalia, though they fall outside the Mammaliaformes definition. These genera are included in the broader clade Mammaliamorpha, defined phylogenetically as the clade originating with the last common ancestor of Tritylodontidae and the crown group mammals. This wider group includes some families that trait-based taxonomy does not include in Mammalia, in particular Tritylodontidae and Brasilodontidae.

Animals in the Mammaliaformes clade are often called mammaliaforms, without the e. Sometimes, the spelling mammaliforms is used. The origin of true mammals (Mammalia) extends back to the Jurassic, with extensive findings in the Late Jurassic outcrops of Portugal and China.

Mesangiospermae

Mesangiospermae (core angiosperms) is a group of flowering plants (angiosperms), informally called "mesangiosperms". They are one of two main clades of angiosperms. It is a name created under the rules of the PhyloCode system of phylogenetic nomenclature. There are about 350,000 species of mesangiosperms. The mesangiosperms contain about 99.95% of the flowering plants, assuming that there are about 175 species not in this group and about 350,000 that are. While such a clade with a similar circumscription exists in the APG III system, it was not given a name.

Michel Laurin

Michel Laurin is a Canadian-born French a vertebrate paleontologist whose specialities include the emergence of a land-based lifestyle among vertebrates, the evolution of body size and the origin and phylogeny of lissamphibians. He has also made important contributions to the literature on phylogenetic nomenclature.

As an undergraduate, he worked in the laboratory of Robert L. Carroll and earned his Ph.D. at the University of Toronto under the direction of Robert R. Reisz; his thesis concerned the osteology of seymouriamorphs. His 1991 review of diapsid phylogeny provided the broadest review of the subject up to that date. In 1995, Laurin and Reisz coauthored a widely cited article providing evidence that the synapsids are the sister group of all other amniotes. He later worked on untangling the phylogeny of the Stegocephalia, a group with a notoriously difficult phylogeny. He later moved to France; since 1998, he has been a CNRS researcher at the Muséum National d'Histoire Naturelle.He is an editor-in-chief of Comptes Rendus Palevol, a journal in the Comptes Rendus de l'Académie des Sciences family, as well as being a reviewing editor for the Journal of Evolutionary Biology. He has been a key contributor to the International Society for Phylogenetic Nomenclature, where he served as president 2008–2009 and as secretary 2010–2011.

PhyloCode

The International Code of Phylogenetic Nomenclature, known as the PhyloCode for short, is a developing draft for a formal set of rules governing phylogenetic nomenclature. Its current version is specifically designed to regulate the naming of clades, leaving the governance of species names up to the rank-based Nomenclature codes (ICN, ICZN, ICNB, ICTV).

The PhyloCode is associated with the International Society for Phylogenetic Nomenclature (ISPN). Its companion volume, Phylonyms, will establish the first taxon names under PhyloCode, serving as examples for those unfamiliar with the code. RegNum is an associated online database for Phylogenic names.The PhyloCode proposes to regulate phylogenetic nomenclature by providing rules for how to decide which associations of names and definitions will be considered established, which of those will be considered homonyms or synonyms, and which one of a set of synonyms or homonyms will be considered accepted (generally the one registered first; see below). The PhyloCode will only allow the naming of clades, not of paraphyletic or polyphyletic groups, and will only allow the use of specimens, species, and apomorphies as specifiers (anchors).

Pleurodonta

Pleurodonta (from Greek lateral teeth, in reference to the position of the teeth on the jaw) is one of the two subdivisions of Iguania, the other being Acrodonta (teeth on the top [of the jaw]). Pleurodonta includes all families previously split from Iguanidae sensu lato (Corytophanidae, Crotaphytidae, Hoplocercidae, Opluridae, Polychrotidae, etc.), whereas Acrodonta includes Agamidae and Chamaeleonidae. The name Pleurodonta was first used by paleontologist and herpetologist Edward Drinker Cope in 1864, although he used it in a different sense than it is used today. Because of this difference, the name Iguanoidea has been proposed as a replacement for Pleurodonta in phylogenetic nomenclature.Pleurodonta is also a synonym of gastropod genus Pleurodonte.

Sauriurae

Sauriurae (meaning "lizard tails" in Greek) is a now-deprecated subclass of birds created by Ernst Haeckel in 1866. It was intended to include Archaeopteryx and distinguish it from all other birds then known, which he grouped in the sister-group Ornithurae ("bird tails"). The distinction Haeckel referred to in this name is that Archaeopteryx possesses a long, reptile-like tail, while all other birds known to him had short tails with few vertebrae, fused at the end into a pygostyle. The unit was not much referred to, and when Hans Friedrich Gadow in 1893 erected Archaeornithes for basically the same fossils, this became the common name for the early reptile-like grade of birds.

Ji Qiang and Larry Martin have continued to refer to the Sauriurae as a valid natural group. However, researchers like Jacques Gauthier (2001) and Julia Clarke (2002) have found that fossils found after Haeckel's time have bridged the gap between long and short-tailed Avialae. In their view, any grouping of avialans with long tails must exclude some of their descendants—making Sauriurae a paraphyletic and, thus, an invalid group under current systems of phylogenetic nomenclature.

Sauropsida

Sauropsida ("lizard faces") is a taxonomic clade that consists of reptiles, birds, and the extinct Parareptilia. All living sauropsids are members of the subgroup Diapsida, the Parareptilia having died out 200 million years ago. The term originated in 1864 with Thomas Henry Huxley, who grouped birds with reptiles based on fossil evidence. Sauropsids are the sister taxon to synapsids, or "mammal-like reptiles", some of which later evolved into mammals.

Stegocephalia

Stegocephalia is a name used for four-limbed stem-tetrapods, and their amphibian-grade descendants, and in phylogenetic nomenclature for all tetrapods. The term was coined in 1868 by American paleontologist Edward Drinker Cope and comes from Greek στεγοκεφαλια - "roofed head", and refer to the copious amounts of dermal armour some of the larger primitive forms evidently had. Canadian paleontologist Michel Laurin gave the group its first formal phylogenetic definition, roughly including all vertebrates with digits rather than fins, except where secondarily lost.

Stem tetrapoda

The Stem Tetrapoda are a cladistically defined group, consisting of all animals more closely related to extant four-legged vertebrates than to their closest extant relatives (the lungfish), but excluding the crown group Tetrapoda. They are thus paraphyletic, though acceptable in phylogenetic nomenclature as the group is defined by strict reference to phylogeny rather than to traits as in traditional systematics. Sarcopterygian fish are considered to be stem tetrapods.

Taxon

In biology, a taxon (plural taxa; back-formation from taxonomy) is a group of one or more populations of an organism or organisms seen by taxonomists to form a unit. Although neither is required, a taxon is usually known by a particular name and given a particular ranking, especially if and when it is accepted or becomes established. It is not uncommon, however, for taxonomists to remain at odds over what belongs to a taxon and the criteria used for inclusion. If a taxon is given a formal scientific name, its use is then governed by one of the nomenclature codes specifying which scientific name is correct for a particular grouping.

Initial attempts at classifying and ordering organisms (plants and animals) were set forth in Linnaeus's system in Systema Naturae, 10th edition, (1758) as well as an unpublished work by Bernard and Antoine Laurent de Jussieu. The idea of a unit-based system of biological classification was first made widely available in 1805 in the introduction of Jean-Baptiste Lamarck's Flore françoise, of Augustin Pyramus de Candolle's Principes élémentaires de botanique. Lamarck set out a system for the "natural classification" of plants. Since then, systematists continue to construct accurate classifications encompassing the diversity of life; today, a "good" or "useful" taxon is commonly taken to be one that reflects evolutionary relationships.Many modern systematists, such as advocates of phylogenetic nomenclature, use cladistic methods that require taxa to be monophyletic (all descendants of some ancestor). Their basic unit, therefore, is the clade rather than the taxon. Similarly, among those contemporary taxonomists working with the traditional Linnean (binomial) nomenclature, few propose taxa they know to be paraphyletic. An example of a well-established taxon that is not also a clade is the class Reptilia, the reptiles; birds are descendants of reptiles but are not included in the Reptilia.

Vertebrate Paleontology and Evolution

Vertebrate Paleontology and Evolution is an advanced textbook on vertebrate paleontology by Robert L. Carroll, published in 1988 by WH Freeman. It provides a very detailed technical account of various groups of living and fossil vertebrates.

The book, which is written in the style of Alfred Sherwood Romer's Vertebrate Paleontology, presented more recent overall coverage of the subject. At the rear of the book is a 53-page Classification list which lists every genus known at the time of publication, along with locality and stratigraphic range.

Vertebrate Paleontology and Evolution appeared in print in 1988, just before the cladistic taxonomy became popular in vertebrate paleontology. The books thus uses the classical systematic scheme, including a number of paraphyletic taxa that are not recognised under phylogenetic nomenclature.

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