Cladistics
"You will observe with concern how long a useful truth may be known, and exist, before it is generally received and practiced on. - Benjamin Franklin" 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. As a hypothesis, a clade can only be rejected 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). 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. Testifying to human focus, bias and perhaps exceptionalism, humans have never been placed in a paraphyletic group, whereas most other organisms have been. 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 potentially a new level. 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. 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 (also the title of his 1966 book); 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 (for insects) in 1921, and W. Zimmermann (for plants) 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" (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 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 (shared, derived character states) are viewed as evidence of grouping, while symplesiomorphies (shared ancestral character states) are not. The outcome of a cladistic analysis is a cladogram – a tree-shaped diagram (dendrogram) 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 sets Every 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 (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 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 (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 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 (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. Terminology for character states. The following terms, coined by Hennig, are used to identify shared  or distinct character states among 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. 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. Terminology for taxa. Mono-, para- and polyphyletic taxa can be understood based on the shape of the tree (as done  above), as well as based on their character states. These are compared in the table below. Criticism. Cladistics, either generally or in specific applications, has been criticized from its beginnings. Decisions as to whether particular character states are homologous, a precondition of their being synapomorphies, have been challenged as involving circular reasoning and subjective judgements. Of course, the potential unreliability of evidence is a problem for any systematic method, or for that matter, for any empirical scientific endeavor at all. Transformed cladistics arose in the late 1970s in an attempt to resolve some of these problems by removing a priori  assumptions about phylogeny from cladistic analysis, but it has remained unpopular. Issues. Ancestors. The cladistic method does not identify fossil species as actual ancestors of a clade. Instead, fossil taxa are identified as belonging to separate extinct branches. While a fossil species could be the actual ancestor of a clade, there is no way to know that. Therefore, a more conservative hypothesis is that the fossil taxon is related to other fossil and extant taxa, as implied by the pattern of shared apomorphic features. Extinction status. An otherwise extinct group with any extant descendants, is not considered (literally) extinct, and  for instance does not have a date of extinction. Hybridization, interbreeding Anything having to do with biology and sex is complicated and messy, and cladistics is no exception. Many species reproduce sexually, and are capable of interbreeding for millions of years. Worse, during such a period, many branches may have radiated, and it may take hundreds of millions of years for them to have whittled down to just two. Only then one can theoretically assign proper last common ancestors of groupings which do not inadvertently include earlier branches. The process of true cladistic bifurcation can thus take a much more  extended time than one is usually aware of. In practice, for recent radiations, cladistically guided findings only give a coarse impression of the complexity. A more detailed account will give details about fractions of introgressions between groupings, and even geographic variations thereof. Horizontal gene transfer There are several processes in nature which can cause horizontal gene transfer. This does typically not directly interfere with ancestry of the organism, but can complicate the determination of that ancestry. On another level, one can map the horizontal gene transfer processes, by determining the phylogeny of the individual genes using cladistics. In disciplines other  than biology. The comparisons used to acquire data on which cladograms can be based are not limited to the field of biology. Any group of individuals or classes that are hypothesized to have a common ancestor, and to which a set of common characteristics may or may not apply, can be compared pairwise. Cladograms can be used to depict the hypothetical descent relationships within groups of items in many different academic realms. The only requirement is that the items have characteristics that can be identified and measured. 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 folktale 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. They also are a powerful way to test hypotheses about cross-cultural relationships among folktales. 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.