cladistic

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This cladogram shows the evolutionary relationship among various insect groups inferred from a dataset.
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Cladograms are trees in the graph theoretic sense.
Cladistics is a philosophy of classification that arranges organisms only by their order of branching in an evolutionary tree and not by their morphological similarity, in the words of Luria et al. (1981). A major contributor to this school of thought was the German entomologist Willi Hennig, who referred to it as phylogenetic systematics (Hennig, 1966). The word cladistics is derived from the ancient Greek κλάδος, klados, or "branch."

As the end result of a cladistic analysis, tree-like relationship-diagrams called "cladograms" are drawn up to show hypothesized relationships. [1] A cladistic analysis can be based on as much or as little information as the researcher selects. Modern systematic research is likely to be based on a wide variety of information, including DNA-sequences (so-called "molecular data"), biochemical data and morphological data.

In a cladogram, all organisms lie at the leaves, and each inner node is ideally binary (two-way). The two taxa on either side of a split are called sister taxa or sister groups. Each subtree, whether it contains one item or a hundred thousand items, is called a clade. A natural group has all the organisms contained in any one clade that share a unique ancestor (one which they do not share with any other organisms on the diagram) for that clade. Each clade is distinguished by a set of characteristics that appear in its members, but not in the other forms from which it diverged. These identifying characteristics of a clade are called synapomorphies (shared, derived characters). For instance, hardened front wings (elytra) are a synapomorphy of beetles, while circinate vernation, or the unrolling of new fronds, is a synapomorphy of ferns.

Definitions

A character state (see below) that is present in both the outgroups (see below) and in the ancestors is called a plesiomorphy (meaning "close form", also called an ancestral state). A character state that occurs only in later descendants is called an apomorphy (meaning "separate form", also called a "derived" state) for that group. The adjectives plesiomorphic and apomorphic are used instead of "primitive" and "advanced" to avoid placing value-judgments on the evolution of the character states, since both may be advantageous in different circumstances. It is not uncommon to refer informally to a collective set of plesiomorphies as a ground plan for the clade or clades they refer to.

Several more terms are defined for the description of cladograms and the positions of items within them. A species or clade is basal to another clade if it holds more plesiomorphic characters than that other clade. Usually a basal group is very species-poor as compared to a more derived group. It is not a requirement that a basal group be extant. For example, when considering birds and mammals together, neither is basal to the other: both have many derived characters.

A clade or species located within another clade can be described as nested within that clade.

Cladistics as a break with the past

The school of thought now known as cladistics took inspiration from the work of Willi Hennig. But Hennig's major book, even the 1979 version, does not contain the term 'cladistics' in the index. He referred to his own approach as phylogenetic systematics, implied by the book's title (Hennig, 1979). A review paper by Dupuis (1984) observes that the term 'clade' was introduced in 1958 by Julian Huxley, 'cladistic' by Cain and Harrison in 1960 and 'cladist' (for an adherent of Hennig's school) by Mayr in 1965. Some of the debates that the cladists engaged in had been running since the 19th century, but they entered these debates with a new fervor, as can be learned from the Foreword to Hennig (1979) in which Rosen, Nelson and Patterson wrote the following:
Encumbered with vague and slippery ideas about adaptation, fitness, biological species and natural selection, neo-Darwinism (summed up in the "evolutionary" systematics of Mayr and Simpson) not only lacked a definable investigatory method, but came to depend, both for evolutionary interpretation and classification, on consensus or authority. (Foreword, page ix).

Cladistic methods

A cladistic analysis is applied to a certain set of information. To organize this information a distinction is made between characters, and character states. Consider the color of feathers, this may be blue in one species but red in another. Thus, "red feathers" and "blue feathers" are two character states of the character "feather-color."

The researcher decides which character states were present before the last common ancestor of the species group (plesiomorphies) and which were present in the last common ancestor (synapomorphies) by considering one or more outgroups. An outgroup is an organism that is considered not to be part of the group in question, but is closely related to the group. This makes the choice of an outgroup an important task, since this choice can profoundly change the topology of a tree. Note that only synapomorphies are of use in characterising clades.

Next, different possible cladograms are drawn up and evaluated. Clades ideally have many "agreeing" synapomorphies. Ideally there is a sufficient number of true synapomorphies to overwhelm homoplasies caused by convergent evolution (i.e. characters that resemble each other because of environmental conditions or function, not because of common ancestry). A well-known example of homoplasy due to convergent evolution would be a character "presence of wings". Though the wings of birds and insects serve the same function, each evolved independently, as can be seen by their anatomy. If a bird and a winged insect were scored for the character "presence of wings", a homoplasy would be introduced into the dataset, and this confounds the analysis, possibly resulting in a false picture of evolution.

Homoplasies can often be avoided outright in morphological datasets by defining characters more precisely and increasing their number: in the example above, e.g. utilizing "wings supported by bony endoskeleton" and "wings supported by chitinous exoskeleton" as characters would avoid the homoplasy. When analyzing "supertrees" (datasets incorporating as many taxa of a suspected clade as possible), it may become unavoidable to introduce character definitions that are unprecise, as otherwise the characters might not apply at all to a large number of taxa. The "wings" example would be hardly useful if attempting a phylogeny of all Metazoa as most of these don't have wings at all. Cautious choice and definition of characters thus is another important element in cladistic analyses. With a faulty outgroup and/or character set, no method of evaluation is likely to produce a phylogeny representing the evolutionary reality.

Many cladograms are possible for any given set of taxa, but one is chosen based on the principle of parsimony: the most compact arrangement, that is, with the fewest character state changes (synapomorphies), is the hypothesis of relationship accept here (see Occam's razor for a discussion of the principle of parsimony and possible complications). Though at one time this analysis was done by hand, computers are now used to evaluate much larger data sets. Sophisticated software packages such as PAUP* allow the statistical evaluation of the confidence we can put in the veracity of the nodes of a cladogram.

It is important to note that the nodes of cladograms do not usually represent divergences of evolutionary lineages, but divergences of character states that are found between such lineages. DNA sequence characters can only diverge after gene flow between (sub)populations has been reduced below some threshold, whereas comprehensive morphological alterations, usually being epistatic (the product of interactions of several genes), usually occur only after lineages have already evolved separately for quite some time: Biological subspecies can usually be distinguished genetically but not for example by internal anatomy

As DNA sequencing has become cheaper and easier, molecular systematics has become a more and more popular way to reconstruct phylogenies. Using a parsimony criterion is only one of several methods to infer a phylogeny from molecular data; maximum likelihood and Bayesian inference, which incorporate explicit models of sequence evolution, are non-Hennigian ways to evaluate sequence data. Another powerful method of reconstructing phylogenies is the use of genomic retrotransposon markers, which are thought to be less prone to the problem of reversion that plagues sequence data. They are also generally assumed to have a low incidence of homoplasies because it was once thought that their integration into the genome was entirely random; this seems at least sometimes not to be the case however.

Ideally, morphological, molecular and possibly other (behavioral etc.) phylogenies should be combined into an analysis of total evidence: all have different intrinsic sources of error. For example, character convergence (homoplasy) is much more common in morphological data than in molecular sequence data, but character reversions that cannot be noticed as such are more common in the latter (see long branch attraction). Morphological homoplasies can usually be recognized as such if character states are defined with enough attention to detail.

Cladistics does not assume any particular theory of evolution, only the background knowledge of descent with modification. Thus, cladistic methods can be, and recently have been, usefully applied to non-biological systems, including determining language families in historical linguistics and the filiation of manuscripts in textual criticism.

Classification using cladistics

Three ways to define a clade for use in a cladistic taxonomy.
Node-based: the most recent common ancestor of A and B and all its descendants.
Stem-based: all descendants of the oldest common ancestor of A and B that is not also an ancestor of Z.
Apomorphy-based: the most recent common ancestor of A and B possessing a certain apomorphy (derived character), and all its descendants.


A recent trend in biology since the 1960s, called phylogenetic nomenclature, attempts to use cladistic trees as the basis for scientific classification, requiring taxa to be clades. In other words, cladists argue that the classification system should be reformed to eliminate all non-clades. In contrast, other taxonomists insist that groups reflect phylogenies and often make use of cladistic techniques, but allow both monophyletic and paraphyletic groups as taxa. In effect, already since the early 20th century at latest, it was generally attempted to make genus- and lower-level taxa monophyletic (even though the word might not have been used). Class- and higher-level taxa proved to be more difficult.

A monophyletic group is a clade, comprising an ancestral form and all of its descendants, and so forming one (and only one) evolutionary group. A paraphyletic group is similar, but excludes some of the descendants that have undergone significant changes. For instance, the traditional class Reptilia excludes birds even though they evolved from the ancestral reptile. Similarly, the traditional Invertebrates are paraphyletic because Vertebrates are excluded, although the latter evolved from an Invertebrate.

A group with members from separate evolutionary lines is called polyphyletic. For instance, the once-recognized Pachydermata was found to be polyphyletic because elephants and rhinoceroses arose from non-pachyderms separately. Evolutionary taxonomists consider polyphyletic groups to be errors in classification, often occurring because convergence or other homoplasy was misinterpreted as homology.

Following Hennig, cladists argue that paraphyly is as harmful as polyphyly. The idea is that monophyletic groups can be defined objectively, in terms of common ancestors or the presence of synapomorphies. In contrast, paraphyletic and polyphyletic groups are both defined based on key characters, and the decision of which characters are of taxonomic import is inherently subjective. Many argue that they lead to "gradistic" thinking, where groups advance from "lowly" grades to "advanced" grades, which can in turn lead to teleology. In evolutionary studies, teleology is usually avoided because it implies a plan that cannot be empirically demonstrated.

Going further, some cladists argue that ranks for groups above species are too subjective to present any meaningful information, and so argue that they should be abandoned. Thus they have moved away from Linnaean taxonomy towards a simple hierarchy of clades. The validity of this argument hinges crucially on how often in evolution gradualist near-equilibria are punctuated. A quasi-stable state will result in phylogenies, which may be all but unmappable onto the Linnaean hierarchy, whereas a punctuation event that balances a taxon out of its ecological equilibrium is likely to lead to a split between clades that occurs in comparatively short time and thus lends itself readily for classification according to the Linnaean system.

Other evolutionary systematists argue that all taxa are inherently subjective, even when they reflect evolutionary relationships, since living things form an essentially continuous tree. Any dividing line is artificial, and creates both a monophyletic section above and a paraphyletic section below. Paraphyletic taxa are necessary for classifying earlier sections of the tree – for instance, the early vertebrates that would someday evolve into the family Hominidae cannot be placed in any other monophyletic family. They also argue that paraphyletic taxa provide information about significant changes in organisms' morphology, ecology, or life history – in short, that both taxa and clades are valuable but distinct notions, with separate purposes. Many use the term monophyly in its older sense, where it includes paraphyly, and use the alternate term holophyly to describe clades (monophyly in Hennig's sense). As an unscientific rule of thumb, if a distinct lineage that renders the containing clade paraphyletic has undergone marked adaptive radiation and collected many synapomorphies - especially ones that are radical and/or unprecedented -, the paraphyly is usually not considered a sufficient argument to prevent recognition of the lineage as distinct under the Linnaean system (but it is by definition sufficient in phylogenetic nomenclature). For example, as touched upon briefly above, the Sauropsida ("reptiles") and the Aves (birds) are both ranked as a Linnaean class, although the latter are a highly derived offshoot of some forms of the former which themselves were already quite advanced.

A formal code of phylogenetic nomenclature, the PhyloCode, is currently under development for cladistic taxonomy. It is intended for use by both those who would like to abandon Linnaean taxonomy and those who would like to use taxa and clades side by side. In several instances (see for example Hesperornithes) it has been employed to clarify uncertainties in Linnaean systematics so that in combination they yield a taxonomy that is unambiguously placing the group in the evolutionary tree in a way that is consistent with current knowledge.

Footnotes

1. ^ See, for example, pp. 45, 78 and 555 of Joel Cracraft and Michael J. Donaghue, eds. (2004). Assembling the Tree of Life. Oxford, England: Oxford University Press.

See also

References

  • Ashlock, Peter D. (1974). "The uses of cladistics". Annual Review of Ecology and Systematics 5: 81-99. ISSN 0066-4162. 
  • Cuénot, Lucien (1940). "Remarques sur un essai d'arbre généalogique du règne animal". Comptes Rendus de l'Académie des Sciences de Paris 210: 23-27.  Available free online at http://gallica.bnf.fr (No direct URL). This is the paper credited by Hennig (1979) for the first use of the term 'clade'.
  • de Queiroz, Kevin (1992). "Phylogenetic taxonomy". Annual Review of Ecology and Systematics 23: 449–480. ISSN 0066-4162. 
  • Dupuis, Claude (1984). "Willi Hennig's impact on taxonomic thought". Annual Review of Ecology and Systematics 15: 1-24. ISSN 0066-4162. 
  • Felsenstein, Joseph (2004). Inferring phylogenies. Sunderland, MA: Sinauer Associates. ISBN 0-87893-177-5. 
  • Hamdi, Hamdi; Hitomi Nishio, Rita Zielinski and Achilles Dugaiczyk (1999). "Origin and phylogenetic distribution of Alu DNA repeats: irreversible events in the evolution of primates". Journal of Molecular Biology 289: 861–871. PMID 10369767. 
  • Hennig, Willi (1950). Grundzüge einer Theorie der Phylogenetischen Systematik. Berlin: Deutscher Zentralverlag. .
  • Hennig, Willi (1982). Phylogenetische Systematik (ed. Wolfgang Hennig). Berlin: Blackwell Wissenschaft. ISBN 3-8263-2841-8. 
  • Hennig, Willi (1975). "'Cladistic analysis or cladistic classification': a reply to Ernst Mayr". Systematic Zoology 24: 244-256.  The paper he was responding to is reprinted in Mayr (1976).
  • Hennig, Willi (1966). Phylogenetic systematics (tr. D. Dwight Davis and Rainer Zangerl). Urbana, IL: Univ. of Illinois Press (reprinted 1979 and 1999). ISBN 0-252-06814-9. Translated from manuscript and so never published in German.
  • Hull, David L. (1979). "The limits of cladism". Systematic Zoology 28: 416-440. 
  • Kitching, Ian J.; Peter L. Forey, Christopher J. Humphries and David M. Williams (1998). Cladistics: Theory and practice of parsimony analysis, 2nd ed., Oxford University Press. ISBN 0-19-850138-2. 
  • Luria, Salvador; Stephen Jay Gould and Sam Singer (1981). A view of life. Menlo Park, CA: Benjamin/Cummings. ISBN 0-8053-6648-2. 
  • Mayr, Ernst (1982). The growth of biological thought: diversity, evolution and inheritance. Cambridge, MA: Harvard Univ. Press. ISBN 0-674-36446-5. 
  • Mayr, Ernst (1976). Evolution and the diversity of life (Selected essays). Cambridge, MA: Harvard Univ. Press. ISBN 0-674-27105-X.  Reissued 1997 in paperback. Includes a reprint of Mayr's 1974 anti-cladistics paper at pp. 433-476, "Cladistic analysis or cladistic classification." This is the paper to which Hennig (1975) is a response.
  • Patterson, Colin (1982). "Morphological characters and homology". Joysey, Kenneth A; A. E. Friday (editors) Problems in Phylogenetic Reconstruction, London: Academic Press. 
  • Rosen, Donn; Gareth Nelson and Colin Patterson (1979), Foreword provided for Hennig (1979)
  • Shedlock, Andrew M; Norihiro Okada (2000). "SINE insertions: Powerful tools for molecular systematics". Bioessays 22: 148–160. ISSN 0039-7989. PMID 10655034. 
  • Sokal, Robert R. (1975). "Mayr on cladism -- and his critics". Systematic Zoology 24: 257-262. 
  • Swofford, David L.; G. J. Olsen, P. J. Waddell and David M. Hillis (1996). "Phylogenetic inference", in Hillis, David M; C. Moritz and B. K. Mable (editors): Molecular Systematics, 2. ed., Sunderland, MA: Sinauer Associates. ISBN 0-87893-282-8. 
  • Wiley, Edward O. (1981). Phylogenetics: The Theory and Practice of Phylogenetic Systematics. New York: Wiley Interscience. ISBN 0-471-05975-7. 

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Emil Hans Willi Hennig (April 20, 1913 in Dürrhennersdorf/Oberlausitz – November 5, 1976 in Ludwigsburg) was a German biologist who is considered the founder of phylogenetic systematics, also known as cladistics.
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phylogenetics (Greek: phyle = tribe, race and genetikos = relative to birth, from genesis = birth) is the study of evolutionary relatedness among various groups of organisms (e.g., species, populations).
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Biological systematics is the study of the diversity of life on the planet Earth, both past and present, and the relationships among living things through time. Relationships are visualized as evolutionary trees (synonyms: phylogenic trees, phylogenies).
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Ancient Greek refers to the second stage in the history of the Greek language[1] as it existed during the Archaic (9th–6th centuries BC) and Classical (5th–4th centuries BC) periods in Greece.
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In graph theory, a tree is a graph in which any two vertices are connected by exactly one path. Alternatively, any connected graph with no cycles is a tree. A forest is a disjoint union of trees.
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The term morphology in biology refers to the outward appearance (shape, structure, color, pattern) of an organism or taxon and its component parts. This is in contrast to physiology, which deals primarily with function.
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A taxon (plural taxa), or taxonomic unit, is a name designating an organism or group of organisms. A taxon is assigned a rank and can be placed at a particular level in a systematic hierarchy reflecting evolutionary
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In evolutionary biology, a synapomorphy is a derived character state shared by two or more terminal groups (taxa included in a cladistic analysis as further indivisible units) and inherited from their most recent common ancestor.
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Insect wings are outgrowths of the insect exoskeleton that enable insects to fly. They are found on the second and third thoracic segments (the mesothorax and metathorax), and the two pairs are often referred to as the forewings and hindwings
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elytron (plural: elytra) is a modified, hardened forewing of certain insect orders, notably beetles (Coleoptera) and true bugs (Hemiptera). An elytron is sometimes also referred to as a shard.
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Vernation (from vernal, since that is when leaves "spring forth" in Temperate regions) is the formation of new leaves or fronds. In plant anatomy, it is the arrangement of leaves in a bud.

In pine trees, new leaves are short and encased in sheaths.
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In phylogenetics, basal members of a group diverged earlier than a subgroup of others (or vice versa). It is often used in opposition to the word derived. The following are example usages of the term basal:....
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Extant is a term commonly used to refer to taxa, species, genera or families that are still in existence (living). For example, Brandt's Cormorant is an extant species, while the Spectacled Cormorant is an extinct species.
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In evolutionary biology, convergent evolution is the process whereby organisms not closely related (not monophyletic), independently evolve similar traits as a result of having to adapt to similar environments or ecological niches[1].
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Anatomy (from the Greek ἀνατομία anatomia, from ἀνατέμνειν
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An endoskeleton is an internal support structure of an animal. In three phyla and one subclass of animals, endoskeletons of various complexity are found: Chordata, Echinodermata, Porifera and Coleoidea.
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Chitin (C8H13O5N)n (IPA: [ˈkaɪtn̩]) is a long-chain polymer of beta-glucose that forms a hard, semitransparent material found throughout the natural world.
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An exoskeleton is an external anatomical feature that supports and protects an animal's body, in contrast to the internal endoskeleton of, for example, a human. Whilst many many other invertebrate animals (such as shelled mollusks) have exoskeletons in the sense of external hard
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Parsimony is a 'less is better' concept of frugality/economy/stinginess or caution in arriving at a hypothesis or course of action. The word derives from Middle English parcimony, from Latin parsimonia, from parsus, past participle of parcere:
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This list of phylogenetics software is a compilation of computational phylogenetics software used to produce phylogenetic trees. Such tools are commonly used in comparative genomics, cladistics, and bioinformatics.
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In population genetics, gene flow (also known as gene migration) is the transfer of alleles of genes from one population to another.
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Epistasis is the interaction between genes. Epistasis takes place when the action of one gene is modified by one or several other genes, which are sometimes called modifier genes.
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