Cladistics
Cladistics is an approach to biological classification in which organisms are categorized in groups based on hypotheses of most recent common ancestry. The evidence for hypothesized relationships is typically shared derived characteristics 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 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.
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.. 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 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 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.
Cladistics findings are posing a difficulty for taxonomy, where the rank and naming of established groupings may turn out to be inconsistent.
Cladistics is now the most commonly used method to classify organisms.
History
The original methods used in cladistic analysis and the school of taxonomy derived from the work of the German entomologist Willi Hennig, who referred to it as phylogenetic systematics ; but the terms "cladistics" and "clade" were popularized by other researchers. Cladistics in the original sense refers to a particular set of methods used in phylogenetic analysis, although it is now sometimes used to refer to the whole field.What is now called the cladistic method appeared as early as 1901 with a work by Peter Chalmers Mitchell for birds and subsequently by Robert John Tillyard in 1921, and W. Zimmermann in 1943. The term "clade" was introduced in 1958 by Julian Huxley after having been coined by Lucien Cuénot in 1940, "cladogenesis" in 1958, "cladistic" by Arthur Cain and Harrison in 1960, "cladist" 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. 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 computers made it possible to process large quantities of data about organisms and their characteristics.
Methodology
The cladistic method interprets each shared character state transformation as a potential piece of evidence for grouping. Synapomorphies are viewed as evidence of grouping, while symplesiomorphies are not. The outcome of a cladistic analysis is a cladogram – a tree-shaped diagram that is interpreted to represent the best hypothesis of phylogenetic relationships. Although traditionally such cladograms were generated largely on the basis of morphological characters and originally calculated by hand, genetic sequencing data and computational phylogenetics are now commonly used in phylogenetic analyses, and the parsimony criterion has been abandoned by many phylogeneticists in favor of more "sophisticated" but less parsimonious evolutionary models of character state transformation. Cladists contend that these models are unjustified because there is no evidence that they recover more "true" or "correct" results from actual empirical data setsEvery cladogram is based on a particular dataset analyzed with a particular method. Datasets are tables consisting of molecular, morphological, ethological and/or other characters and a list of operational taxonomic units, 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.
File:Monophyly, paraphyly, polyphyly.svg|thumb|upright=1.8|Cladogram of the primates, showing a monophyletic taxon, a paraphyletic taxon, and a polyphyletic taxon
The cladogram to the right represents the current universally accepted hypothesis that all primates, including strepsirrhines like the lemurs and lorises, 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 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 Strepsirhini 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 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.
Terminology for character states
The following terms, coined by Hennig, are used to identify shared or distinct character states among groups:- A plesiomorphy or ancestral state is a character state that a taxon has retained from its ancestors. When two or more taxa that are not nested within each other share a plesiomorphy, it is a symplesiomorphy. Symplesiomorphies do not mean that the taxa that exhibit that character state are necessarily closely related. For example, Reptilia is traditionally characterized by being cold-blooded, whereas birds are warm-blooded. Since cold-bloodedness is a plesiomorphy, inherited from the common ancestor of traditional reptiles and birds, and thus a symplesiomorphy of turtles, snakes and crocodiles, it does not mean that turtles, snakes and crocodiles form a clade that excludes the birds.
- An apomorphy or derived state is an innovation. It can thus be used to diagnose a clade – or even to help define a clade name in phylogenetic nomenclature. Features that are derived in individual taxa are called autapomorphies. Autapomorphies express nothing about relationships among groups; clades are identified by synapomorphies. For example, the possession of digits that are homologous with those of Homo sapiens is a synapomorphy within the vertebrates. The tetrapods can be singled out as consisting of the first vertebrate with such digits homologous to those of Homo sapiens together with all descendants of this vertebrate. Importantly, snakes and other tetrapods that do not have digits are nonetheless tetrapods: other characters, such as amniotic eggs and diapsid skulls, indicate that they descended from ancestors that possessed digits which are homologous with ours.
- A character state is homoplastic or "an instance of homoplasy" if it is shared by two or more organisms but is absent from their common ancestor or from a later ancestor in the lineage leading to one of the organisms. It is therefore inferred to have evolved by convergence or reversal. Both mammals and birds are able to maintain a high constant body temperature. However, the accepted cladogram explaining their significant features indicates that their common ancestor is in a group lacking this character state, so the state must have evolved independently in the two clades. Warm-bloodedness is separately a synapomorphy of mammals and of birds, but it is not a synapomorphy of any group including both these clades. Hennig's Auxiliary Principle states that shared character states should be considered evidence of grouping unless they are contradicted by the weight of other evidence; thus, homoplasy of some feature among members of a group may only be inferred after a phylogenetic hypothesis for that group has been established.
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. 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.