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Cladistics ( ; from Ancient Greek κλάδος]] 'branch') is an approach to biological classification in which are categorized in groups ("") 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 Phenotypic trait 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 Paraphyly, 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.Columbia EncyclopediaOxford Dictionary of EnglishOxford English Dictionary
As a hypothesis, a clade can be rejected only if some groupings were explicitly excluded. It may then be found that the excluded group did actually descend from the last common ancestor of the group, and thus emerged within the group. ("Evolved from" is misleading, because in cladistics all descendants stay in the ancestral group). To keep only valid clades, upon finding that the group is paraphyletic this way, either such excluded groups should be granted to the clade, or the group should be abolished.
Branches down to the divergence to the next significant (e.g. extant) sister are considered stem-groupings of the clade, but in principle each level stands on its own, to be assigned a unique name. For a fully bifurcated tree, adding a group to a tree also adds an additional (named) clade, and a new level on that branch. Specifically, also extinct groups are always put on a side-branch, not distinguishing whether an actual ancestor of other groupings was found.
The techniques and nomenclature of cladistics have been applied to disciplines other than biology. (See phylogenetic nomenclature.)
Cladistics findings are posing a difficulty for taxonomy, where the rank and (genus-)naming of established groupings may turn out to be inconsistent.
Cladistics is now the most commonly used method to classify organisms.
What is now called the cladistic method appeared as early as 1901 with a work by Peter Chalmers Mitchell for birdsSchuh, Randall. 2000. Biological Systematics: Principles and Applications, p.7 (citing Nelson and Platnick, 1981). Cornell University Press (books.google)Folinsbee, Kaila et al. 2007. 5 Quantitative Approaches to Phylogenetics, p. 172. Rev. Mex. Div. 225-52 (kfolinsb.public.iastate.edu) and subsequently by Robert John Tillyard (for insects) in 1921, and W. Zimmermann (for plants) in 1943.Schuh, Randall. 2000. Biological Systematics: Principles and Applications, p.7. Cornell U. Press The term "clade" was introduced in 1958 by Julian Huxley after having been coined by Lucien Cuénot in 1940, "cladogenesis" in 1958,Webster's 9th New Collegiate Dictionary "cladistic" by Arthur Cain and Harrison in 1960, "cladist" (for an adherent of Hennig's school) by Ernst Mayr in 1965, and "cladistics" in 1966. Hennig referred to his own approach as "phylogenetic systematics". From the time of his original formulation until the end of the 1970s, cladistics competed as an analytical and philosophical approach to systematics with phenetics and so-called evolutionary taxonomy. Phenetics was championed at this time by the numerical taxonomists Peter Sneath and Robert Sokal, and evolutionary taxonomy by Ernst Mayr.
Originally conceived, if only in essence, by Willi Hennig in a book published in 1950, cladistics did not flourish until its translation into English in 1966 (Lewin 1997). Today, cladistics is the most popular method for inferring phylogenetic trees from morphological data.
In the 1990s, the development of effective polymerase chain reaction techniques allowed the application of cladistic methods to biochemical and molecular genetic traits of organisms, vastly expanding the amount of data available for phylogenetics. At the same time, cladistics rapidly became popular in evolutionary biology, because made it possible to process large quantities of data about organisms and their characteristics.
Every cladogram is based on a particular dataset analyzed with a particular method. Datasets are tables consisting of molecular, morphological, Ethology and/or other characters and a list of operational taxonomic units (OTUs), which may be genes, individuals, populations, species, or larger taxa that are presumed to be monophyletic and therefore to form, all together, one large clade; phylogenetic analysis infers the branching pattern within that clade. Different datasets and different methods, not to mention violations of the mentioned assumptions, often result in different cladograms. Only scientific investigation can show which is more likely to be correct.
Until recently, for example, cladograms like the following have generally been accepted as accurate representations of the ancestral relations among turtles, lizards, crocodilians, and birds:
If this phylogenetic hypothesis is correct, then the last common ancestor of turtles and birds, at the branch near the lived earlier than the last common ancestor of lizards and birds, near the . Most molecular evidence, however, produces cladograms more like this:
If this is accurate, then the last common ancestor of turtles and birds lived later than the last common ancestor of lizards and birds. Since the cladograms show two mutually exclusive hypotheses to describe the evolutionary history, at most one of them is correct.
The cladogram to the right represents the current universally accepted hypothesis that all , including Strepsirrhini like the and , had a common ancestor all of whose descendants are or were primates, and so form a clade; the name Primates is therefore recognized for this clade. Within the primates, all anthropoids (monkeys, apes, and humans) are hypothesized to have had a common ancestor all of whose descendants are or were anthropoids, so they form the clade called Anthropoidea. The "prosimians", on the other hand, form a paraphyletic taxon. The name Prosimii is not used in phylogenetic nomenclature, which names only clades; the "prosimians" are instead divided between the clades Strepsirrhini and Haplorhini, where the latter contains Tarsiiformes and Anthropoidea.
Lemurs and tarsiers may have looked closely related to humans, in the sense of being close on the evolutionary tree to humans. However, from the perspective of a tarsier, humans and lemurs would have looked close, in the exact same sense. Cladistics forces a neutral perspective, treating all branches (extant or extinct) in the same manner. It also forces one to try to make statements, and honestly take into account findings, about the exact historic relationships between the groups.
The terms plesiomorphy and apomorphy are relative; their application depends on the position of a group within a tree. For example, when trying to decide whether the tetrapods form a clade, an important question is whether having four limbs is a synapomorphy of the earliest taxa to be included within Tetrapoda: did all the earliest members of the Tetrapoda inherit four limbs from a common ancestor, whereas all other vertebrates did not, or at least not homologously? By contrast, for a group within the tetrapods, such as birds, having four limbs is a plesiomorphy. Using these two terms allows a greater precision in the discussion of homology, in particular allowing clear expression of the hierarchical relationships among different homologous features.
It can be difficult to decide whether a character state is in fact the same and thus can be classified as a synapomorphy, which may identify a monophyletic group, or whether it only appears to be the same and is thus a homoplasy, which cannot identify such a group. There is a danger of circular reasoning: assumptions about the shape of a phylogenetic tree are used to justify decisions about character states, which are then used as evidence for the shape of the tree.: "Synapomorphies are invoked to defend the hypothesis; the hypothesis is invoked to defend the synapomorphies." Phylogenetics uses various forms of parsimony to decide such questions; the conclusions reached often depend on the dataset and the methods. Such is the nature of empirical science, and for this reason, most cladists refer to their cladograms as hypotheses of relationship. Cladograms that are supported by a large number and variety of different kinds of characters are viewed as more robust than those based on more limited evidence.Brower, AVZ and Schuh, RT. 2021. Biological Systematics: Principles and Applications (3rd edn.). Cornell University Press, Ithaca nY
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| Holophyly, Monophyly | A clade, a monophyletic taxon, is a taxon that consists of the last common ancestor and all its descendants. | A clade is characterized by one or more apomorphies: derived character states present in the first member of the taxon, inherited by its descendants (unless secondarily lost), and not inherited by any other taxa. |
| Paraphyly | A paraphyletic assemblage is one that is constructed by taking a clade and removing one or more smaller clades.Many sources give a verbal definition of 'paraphyletic' that does not require the missing groups to be monophyletic. However, when diagrams are presented representing paraphyletic groups, these invariably show the missing groups as monophyletic. See e.g. (Removing one clade produces a singly paraphyletic assemblage, removing two produces a doubly paraphyletic assemblage, and so on.) | A paraphyletic assemblage is characterized by one or more plesiomorphies: character states inherited from ancestors but not present in all of their descendants. As a consequence, a paraphyletic assemblage is truncated, in that it excludes one or more clades from an otherwise monophyletic taxon. An alternative name is evolutionary grade, referring to an ancestral character state within the group. While paraphyletic assemblages are popular among paleontologists and evolutionary taxonomists, cladists do not recognize paraphyletic assemblages as having any formal information content – they are merely parts of clades. |
| Polyphyly | A polyphyletic assemblage is one which is neither monophyletic nor paraphyletic. | A polyphyletic assemblage is characterized by one or more Homoplasy: character states which have converged or reverted so as to be the same but which have not been inherited from a common ancestor. No systematist recognizes polyphyletic assemblages as taxonomically meaningful entities, although ecologists sometimes consider them meaningful labels for functional participants in ecological communities (e. g., primary producers, detritivores, etc.). |
Transformed cladistics arose in the late 1970s Platnick, Norman I. "Philosophy and the transformation of cladistics." Systematic Zoology 28, no. 4 (1979): 537–546. in an attempt to resolve some of these problems by removing a priori assumptions about phylogeny from cladistic analysis, but it has remained unpopular.Brower, Andrew VZ. "Fifty shades of cladism." Biology & Philosophy 33, no. 1-2 (2018): 8.
Anthropology and archaeology: Cladistic methods have been used to reconstruct the development of cultures or artifacts using groups of cultural traits or artifact features.
Comparative mythology and Folklore use cladistic methods to reconstruct the protoversion of many myths. Mythological phylogenies constructed with mythemes clearly support low horizontal transmissions (borrowings), historical (sometimes Palaeolithic) diffusions and punctuated evolution.d'Huy 2012a, b; d'Huy 2013a, b, c, d They also are a powerful way to test hypotheses about cross-cultural relationships among folktales.Ross and al. 2013Tehrani 2013
Literature: Cladistic methods have been used in the classification of the surviving manuscripts of the Canterbury Tales, and the manuscripts of the Sanskrit Charaka Samhita.
Historical linguistics: Cladistic methods have been used to reconstruct the phylogeny of languages using linguistic features. This is similar to the traditional comparative method of historical linguistics, but is more explicit in its use of parsimony and allows much faster analysis of large datasets (computational phylogenetics).
Textual criticism or stemmatics: Cladistic methods have been used to reconstruct the phylogeny of manuscripts of the same work (and reconstruct the lost original) using distinctive copying errors as apomorphies. This differs from traditional historical-comparative linguistics in enabling the editor to evaluate and place in genetic relationship large groups of manuscripts with large numbers of variants that would be impossible to handle manually. It also enables parsimony analysis of contaminated traditions of transmission that would be impossible to evaluate manually in a reasonable period of time.
Astrophysics infers the history of relationships between galaxies to create branching diagram hypotheses of galaxy diversification.
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