HistoryThe original methods used in cladistic analysis and the school of taxonomy derived from the work of the German entomologist , 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 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 birdsFolinsbee, 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. The term " " 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 taxonomy, 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 genetics, 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.
MethodologyThe 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 (graph theory), 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, DNA sequencing, genetic sequencing data and computational phylogenetics are now commonly used in phylogenetic analyses, and the Maximum parsimony (phylogenetics), 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 phylogenetics, molecular, morphological, Ethology, 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:
Terminology for character statesThe following terms, coined by Hennig, are used to identify shared or distinct character states among groups: * A plesiomorphy ("close form") 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 (from ''syn-'', "together"). Symplesiomorphies do not mean that the taxa that exhibit that character state are necessarily closely related. For example, Reptilia is traditionally characterized by (among other things) being Poikilotherm, cold-blooded (i.e., not maintaining a constant high body temperature), whereas birds are Homeothermy, 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 (among others), it does not mean that turtles, snakes and crocodiles form a clade that excludes the birds. * An apomorphy ("separate form") 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 (a single species or a group that is represented by a single terminal in a given phylogenetic analysis) are called autapomorphies (from ''auto-'', "self"). Autapomorphies express nothing about relationships among groups; clades are identified (or defined) by synapomorphies (from ''syn-'', "together"). For example, the possession of Digit (anatomy), digits that are Homology (biology), 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 (an apomorphy-based Phylogenetic nomenclature, phylogenetic definition). 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 (i.e., they are warm-blooded). 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 (or a larger clade) and of birds (or a larger clade), 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. 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 Maximum parsimony (phylogenetics), 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 taxaMono-, 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.
CriticismCladistics, either generally or in specific applications, has been criticized from its beginnings. Decisions as to whether particular character states are Homology (biology), 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.
IssuesThe 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.
In disciplines other than biologyThe 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. Cultural anthropology, 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, 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 (linguistics), comparative method of historical linguistics, but is more explicit in its use of Occam's razor, 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 Maximum parsimony (phylogenetics), 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.
See also* Bioinformatics * Biomathematics * Coalescent theory * Common descent * Glossary of scientific naming * Language family * Patrocladogram * Phylogenetic network * Scientific classification * Stratocladistics * Subclade * Systematics * Three-taxon analysis * Tree model * Tree structure
Notes and references
Bibliography* * * * * * * Available free online a