Phylogenetic 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 method, by 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 regulated currently by the International Code of Phylogenetic Nomenclature (PhyloCode).
Phylogenetic nomenclature associates names with clades, groups consisting of an ancestor and all its descendants. Such groups are said to be monophyletic. There are slightly different methods 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 taxon named. Listing all these organisms (i.e. providing a full circumscription) requires the complete phylogenetic tree to be known. In practice, there are almost always one or more hypotheses as to the correct relationship. Different hypotheses result in different organisms being thought to be included in the named taxon, but application to the name in the context of various phylogenies generally remains unambiguous. Possible exceptions occur for apomorphy-based definitions, when optimization of the defining apomorphy is ambiguous. [2]
Phylogenetic nomenclature assigns 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 methods 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:
Several other alternatives are provided in the PhyloCode, [4] (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 methods of specifying the Neornithes (modern birds), for example, is:
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.
For 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 based on species or specimens. [5] For example, assuming Mammalia and Aves (birds) are defined in this manner, Amniotes 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 be defined similarly as the sum of multiple clades. [5]
Using 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 associated explicitly with a rank cannot be named formally, because the application of a name to a taxon is based on both a type and a rank. Thus for example the "family" Hominidae uses the genus Homo as its type; its rank (family) is indicated by the suffix -idae (see discussion below). 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.[ citation needed ]
The current codes 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 suffix for family using the zoological code. Wiley considered it to be at the rank of "tribe", and so gave it the name "Hominini", "-ini" being the suffix for tribe. Wiley's tribe Hominini formed only part of a family which he termed "Hominidae". Thus, using 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).
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 with 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) [7] 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) [8] suggested nine new ranks between family and superfamily in order to be able to classify a clade of herrings, and McKenna and Bell (1997) [9] introduced a large array of new ranks in order to cope with the diversity of Mammalia; these have not been adopted widely. For botany, the Angiosperm Phylogeny Group, responsible for the currently most widely used classification of flowering plants, chose a different method. They retained the traditional ranks of family and order, considering them to be of value for teaching and studying relationships between taxa, but also introduced named clades without formal ranks. [10]
For phylogenetic nomenclature, ranks have no bearing on the spelling of taxon names (see e.g. Gauthier (1994) [11] and the PhyloCode ). Ranks are, however, not altogether forbidden for 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. [12] [13] [14]
The principles of traditional rank-based nomenclature are incompatible logically with all taxa being strictly monophyletic. [12] [15] 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. For rank-based nomenclature, however, classes must include genera, not the other way around.[ citation needed ]
The conflict between phylogenetic and traditional nomenclature represents differing opinions of the metaphysics and epistemology of taxa. For the advocates of phylogenetic nomenclature, a taxon is an individual entity, an entity that may gain and lose attributes as time passes. [16] 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 of sex, so a taxon remains the same entity whatever characteristics are gained or lost. [17] Given the metaphysical claims regarding unobservable entities made by advocates of phylogenetic nomenclature, critics have referred to their method as origin essentialism. [18] [19]
For any individual, there has to be something that associates its temporal stages with each other by virtue of which it remains the same entity. For a person, the spatiotemporal continuity of the body provides the relevant conceptual continuity; from infancy to old age, the body traces a continuous path through the world and it is this continuity, rather than any characteristics of the individual, that associates the baby with the octogenarian. [20] This is similar to the well-known philosophical problem of the Ship of Theseus. For a taxon, IF characteristics are not relevant, THEN it can only be ancestral relations that associate the Devonian Rhyniognatha hirsti with the modern monarch butterfly as representatives, separated by 400 million years, of the taxon Insecta. [17] The opposing opinion questions the premise of that syllogism, and argues, from an epistemological perspective, that members of taxa are only recognizable empirically on the basis of their observable characteristics, and hypotheses of common ancestry are results of theoretical systematics, not a priori premises. If there are no characteristics that allow scientists to recognize a fossil as belonging to a taxonomic group, then it is just an unclassifiable piece of rock. [21]
If ancestry is sufficient for the continuity of a taxon, 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. Again, while not disagreeing with the notion that only monophyletic groups should be named, empiricist systematists counter this ancestry essentialism by pointing out that pelycosaurs are recognized as paraphyletic precisely because they exhibit a combination of synapomorphies and symplesiomorphies indicating that some of them are more closely related to mammals than they are to other pelycosaurs. The material existence of an assemblage of fossils and its status as a clade are not the same issue. Monophyletic groups are worthy of attention and naming because they share properties of interest -- synapomorphies -- that are the evidence that allows inference of common ancestry. [22]
Phylogenetic nomenclature is a semantic extension of the general acceptance of the idea of branching during the course of evolution, represented in the diagrams of Jean-Baptiste Lamarck and later writers like Charles Darwin and Ernst Haeckel. [24] [25] In 1866, Haeckel for the first time constructed a single relational diagram of all life based on the existing classification of life accepted at the time. This classification was rank-based, 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").[ citation needed ]
Ever since, it has been debated in which ways and to what extent the understanding of the phylogeny of life should be used as a basis for its classification, with opinions including "numerical taxonomy" (phenetics), "evolutionary taxonomy" (gradistics), and "phylogenetic systematics". From the 1960s onwards, rankless classifications were occasionally proposed, but in general the principles and common language of traditional nomenclature have been used by all three schools of thought.[ citation needed ]
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 [26] interpreted the name Sauropsida, defined 40 years earlier by Thomas Henry Huxley, to include the birds (Aves) as well as part of Reptilia, and invented the new name Theropsida to include the mammals as well as another part of Reptilia. As these taxa were separate from traditional zoological nomenclature, Goodrich did not emphasize ranks, but he clearly discussed the diagnostic features necessary to recognize and classify fossils belonging to the various groups. For example, in regard to the fifth metatarsal of the hind leg, he said "the facts support our view, for these early reptiles have normal metatarsals like their Amphibian ancestors. It is clear, then, that we have here a valuable corroborative character to help us to decide whether a given species belongs to the Theropsidan or the Sauropsidan line of evolution." Goodrich concluded his paper: "The possession of these characters shows that all living Reptilia belong to the Sauropsidan group, while the structure of the foot enables us to determine the affinities of many incompletely known fossil genera, and to conclude that only certain extinct orders can belong to the Theropsidan branch." Goodrich opined that the name Reptilia should be abandoned once the phylogeny of the reptiles was better known.[ citation needed ]
The principle that only clades should be named formally became popular among some researchers during 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 [27] of his earlier proposal to define ranks as geological age classes. [28] [29]
The first use of phylogenetic nomenclature in a publication can be dated to 1986. [30] 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 among the systematics 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". [31] The premise of names in traditional nomenclature is based, ultimately, on type specimens, and the circumscription of groups is considered a taxonomic choice made by the systematists working on particular groups, rather than a nomenclatural decision made based on a priori rules of the Codes on Nomenclature. [32] The desire to subsume taxonomic circumscriptions within nomenclatural definitions caused Kevin de Queiroz and the botanist Philip Cantino to start drafting their own code of nomenclature, the PhyloCode , to regulate phylogenetic nomenclature.[ citation needed ]
Willi Hennig's pioneering work provoked a controversy [33] about the relative merits of phylogenetic nomenclature versus Linnaean taxonomy, or the related method of evolutionary taxonomy, which has continued to the present. [34] Some of the controversies with which the cladists were engaged had been happening since the 19th century. [35] While Hennig insisted that different classification schemes were useful for different purposes, [36] he gave primacy to his own, claiming that the categories of his system had "individuality and reality" in contrast to the "timeless abstractions" of classifications based on overall similarity. [37]
Formal classifications based on cladistic reasoning are said to emphasize ancestry at the expense of descriptive characteristics. Nonetheless, most taxonomists presently avoid paraphyletic groups whenever they think it is possible within Linnaean taxonomy; polyphyletic taxa have long been unfashionable. Many cladists claim that the traditional Codes of Zoological and Botanical Nomenclature are fully compatible with cladistic methods, and that there is no need to reinvent a system of names that has functioned well for 250 years, [38] [39] [40] but others argue that this system is not as effective as it should be and that it is time to adopt nomenclatural principles that represent divergent evolution as a mechanism that explains much of the known biodiversity. [41] [42] In fact, calls to reform biological nomenclature were made even before phylogenetic nomenclature was developed. [43]
The ICPN, or PhyloCode, is a code of rules and recommendations for phylogenetic nomenclature.
The number of supporters for widespread adoption of the PhyloCode is still small, and it is uncertain how widely it will be followed.
Cladistics is an approach to biological classification in which organisms are categorized in groups ("clades") based on hypotheses of most recent common ancestry. The evidence for hypothesized relationships is typically shared derived characteristics (synapomorphies) that are not present in more distant groups and ancestors. However, from an empirical perspective, common ancestors are inferences based on a cladistic hypothesis of relationships of taxa whose character states can be observed. Theoretically, a last common ancestor and all its descendants constitute a (minimal) clade. Importantly, all descendants stay in their overarching ancestral clade. For example, if the terms worms or fishes were used within a strict cladistic framework, these terms would include humans. Many of these terms are normally used paraphyletically, outside of cladistics, e.g. as a 'grade', which are fruitless to precisely delineate, especially when including extinct species. Radiation results in the generation of new subclades by bifurcation, but in practice sexual hybridization may blur very closely related groupings.
In biological phylogenetics, a clade, also known as a monophyletic group or natural group, is a grouping of organisms that are monophyletic – that is, composed of a common ancestor and all its lineal descendants – on a phylogenetic tree. In the taxonomical literature, sometimes the Latin form cladus is used rather than the English form. Clades are the fundamental unit of cladistics, a modern approach to taxonomy adopted by most biological fields.
Linnaean taxonomy can mean either of two related concepts:
In biological cladistics for the classification of organisms, monophyly is the condition of a taxonomic grouping being a clade – that is, a grouping of taxa which meets these criteria:
In biology, taxonomy is the scientific study of naming, defining (circumscribing) and classifying groups of biological organisms based on shared characteristics. Organisms are grouped into taxa and these groups are given a taxonomic rank; groups of a given rank can be aggregated to form a more inclusive group of higher rank, thus creating a taxonomic hierarchy. The principal ranks in modern use are domain, kingdom, phylum, class, order, family, genus, and species. The Swedish botanist Carl Linnaeus is regarded as the founder of the current system of taxonomy, as he developed a ranked system known as Linnaean taxonomy for categorizing organisms and binomial nomenclature for naming organisms.
In biology, a taxon 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 very common, however, for taxonomists to remain at odds over what belongs to a taxon and the criteria used for inclusion, especially in the context of rank-based ("Linnaean") nomenclature. 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.
Sauropsida is a clade of amniotes, broadly equivalent to the class Reptilia, though typically used in a broader sense to also include extinct stem-group relatives of modern reptiles and birds. The most popular definition states that Sauropsida is the sibling taxon to Synapsida, the other clade of amniotes which includes mammals as its only modern representatives. Although early synapsids have historically been referred to as "mammal-like reptiles", all synapsids are more closely related to mammals than to any modern reptile. Sauropsids, on the other hand, include all amniotes more closely related to modern reptiles than to mammals. This includes Aves (birds), which are recognized as a subgroup of archosaurian reptiles despite originally being named as a separate class in Linnaean taxonomy.
The International Code of Phylogenetic Nomenclature, known as the PhyloCode for short, is 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.
Thyreophora is a group of armored ornithischian dinosaurs that lived from the Early Jurassic until the end of the Cretaceous.
Evolutionary taxonomy, evolutionary systematics or Darwinian classification is a branch of biological classification that seeks to classify organisms using a combination of phylogenetic relationship, progenitor-descendant relationship, 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.
Ornithopoda is a clade of ornithischian dinosaurs, called ornithopods. They represent one of the most successful groups of herbivorous dinosaurs during the Cretaceous. The most primitive members of the group were bipedal and relatively small-sized, while advanced members of the subgroup Iguanodontia became quadrupedal and developed large body size. Their major evolutionary advantage was the progressive development of a chewing apparatus that became the most sophisticated ever developed by a non-avian dinosaur, rivaling that of modern mammals such as the domestic cow. They reached their apex of diversity and ecological dominance in the hadrosaurids, before they were wiped out by the Cretaceous–Paleogene extinction event along with all other non-avian dinosaurs. Members are known worldwide.
Archosauriformes is a clade of diapsid reptiles encompassing archosaurs and some of their close relatives. It was defined by Jacques Gauthier (1994) as the clade stemming from the last common ancestor of Proterosuchidae and Archosauria. Phil Senter (2005) defined it as the most exclusive clade containing Proterosuchus and Archosauria. Gauthier as part of the Phylonyms (2020) defined the clade as the last common ancestor and all descendants of Gallus, Alligator, and Proterosuchus. Archosauriforms are a branch of archosauromorphs which originated in the Late Permian and persist to the present day as the two surviving archosaur groups: crocodilians and birds.
Nomenclature codes or codes of nomenclature are the various rulebooks that govern the naming of living organisms. Standardizing the scientific names of biological organisms allows researchers to discuss findings.
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.
Neornithischia is a clade of the dinosaur order Ornithischia. It is the sister group of the Thyreophora within the clade Genasauria. Neornithischians are united by having a thicker layer of asymmetrical enamel on the inside of their lower teeth. The teeth wore unevenly with chewing and developed sharp ridges that allowed neornithischians to break down tougher plant food than other dinosaurs.
Jacques Armand Gauthier is an American vertebrate paleontologist, comparative morphologist, and systematist, and one of the founders of the use of cladistics in biology.
Avemetatarsalia is a clade of diapsid reptiles containing all archosaurs more closely related to birds than to crocodilians. The two most successful groups of avemetatarsalians were the dinosaurs and pterosaurs. Dinosaurs were the largest terrestrial animals for much of the Mesozoic Era, and one group of small feathered dinosaurs has survived up to the present day. Pterosaurs were the first flying vertebrates and persisted through the Mesozoic before dying out at the Cretaceous-Paleogene (K-Pg) extinction event. Both dinosaurs and pterosaurs appeared in the Triassic Period, shortly after avemetatarsalians as a whole. The name Avemetatarsalia was first established by British palaeontologist Michael Benton in 1999. An alternate name is Pan-Aves, or "all birds", in reference to its definition containing all animals, living or extinct, which are more closely related to birds than to crocodilians.
In biology, taxonomic rank is the relative or absolute level of a group of organisms in a hierarchy that reflects evolutionary relationships. Thus, the most inclusive clades have the highest ranks, whereas the least inclusive ones have the lowest ranks. Ranks can be either relative and be denoted by an indented taxonomy in which the level of indentation reflects the rank, or absolute, in which various terms, such as species, genus, family, order, class, phylum, kingdom, and domain designate rank. This page emphasizes absolute ranks and the rank-based codes require them. However, absolute ranks are not required in all nomenclatural systems for taxonomists; for instance, the PhyloCode, the code of phylogenetic nomenclature, does not require absolute ranks.
Kevin de Queiroz is a vertebrate, evolutionary, and systematic biologist. He has worked in the phylogenetics and evolutionary biology of squamate reptiles, the development of a unified species concept and of a phylogenetic approach to biological nomenclature, and the philosophy of systematic biology.
Hadrosauromorpha is a clade of iguanodontian ornithopods, defined in 2014 by David B. Norman to divide Hadrosauroidea into the basal taxa with compressed manual bones and a pollex, and the derived taxa that lack them. The clade is formally defined in the PhyloCode as "the largest clade containing Hadrosaurus foulkii, but not Probactrosaurus gobiensis". This results in different taxon inclusion depending on the analysis.
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.
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