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{{BioPsy}}
[[Image:cladogram-example1.png|200px|thumb|right|This cladogram shows the relationship among various insect groups.]]
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{{evolution3}}
[[Image:cladogram-example2.png|200px|thumb|right|Cladograms are [[Tree (graph theory)|tree-like]] relationship- diagrams.]]
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'''Cladistics''' is the hierarchical classification of species based on evolutionary ancestry. Cladistics is distinguished from other [[taxonomic]] classification systems because it focuses on [[evolution]] (rather than focusing on similarities between species), and because it places heavy emphasis on objective, quantitative analysis. Cladistics generates diagrams called ''cladograms'' that represent the evolutionary [[tree of life (science)|tree of life]]. [[DNA]] and [[RNA]] sequencing data are used in many important cladistic efforts. [[Computer programs]] are widely used in cladistics, due to the highly complex nature of [[computational phylogenetics|cladogram-generation procedures]]. A major contributor to cladistics was the German entomologist [[Willi Hennig]], who referred to it as ''phylogenetic systematics''.<ref>''Phylogenetic Systematics'' is the title of Hennig's 1966 book</ref> The term ''[[phylogenetics]]'' is often used synonymously with ''cladistics''. Cladistics originated in the field of [[biology]] but in recent years has found application in other disciplines. The word ''cladistics'' is derived from the [[ancient Greek]] ''{{Polytonic|κλάδος}}'', ''klados'', or "branch."
'''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, 1979). The word ''cladistics'' is derived from the [[ancient Greek]] ''{{Polytonic|κλάδος}}'', ''klados'', "branch."
 
   
As the end result of a cladistic analysis, [[Tree (graph theory)|tree-like]] relationship-diagrams called "cladograms" are drawn up to show hypothesized relationships. 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 [[Morphology (biology)|morphological]] data.
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== Cladograms ==
   
In a cladogram, all organisms lie at the leaves, and each inner node is ideally binary (two-way). The two [[taxon|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 set off by a series 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 [[synapomorphy|synapomorphies]] (shared, derived characters). For instance, hardened front [[insect wing|wings]] ([[elytron|elytra]]) are a synapomorphy of [[beetle]]s, while [[Vernation|circinate vernation]], or the unrolling of new fronds, is a synapomorphy of [[fern]]s.
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[[Image:cladogram-example1.svg|200px|thumb|right|This cladogram shows the evolutionary relationship among various insect groups inferred from a dataset.]]
   
==Definitions==
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[[Image:cladogram-example2.svg|200px|thumb|right|Cladograms are [[Tree (graph theory)|trees]] in the [[Graph theory|graph theoretic]] sense.]]
A character state (see below) that is present in both the outgroups (the nearest relatives of the group that are not part of the group itself) 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 present. For example, when considering birds and mammals together, neither is basal to the other: both have many derived characters.
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[[Image:Neomuratree.svg|thumb|220px|A cladogram showing how Eukaryota and Archaea are more closely related to each other than to [[Bacteria]]. Note the 3-way fork in the middle of the cladogram.]]
   
A clade or species located within another clade can be described as '''nested''' within that clade.
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The starting point of cladistic analysis is a group of species and molecular, morphological, or other data characterizing those species. The end result is a [[Tree (graph theory)|tree-like]] relationship-diagram called a ''cladogram''.<ref>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.</ref> The cladogram graphically represents a hypothetical evolutionary process. Cladograms are subject to revision as additional data becomes available.
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'''Synonyms''' — The term ''[[evolutionary tree]]'' is often used synonymously with ''cladogram''. The term ''[[phylogenetic tree]]'' is sometimes used synonymously with cladogram,<ref>
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{{cite book|
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last= Singh| first=Gurcharan |
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title=Plant Systematics: An Integrated Approach |
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publisher=Science|
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pages=203-4 |
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year=2004 |
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isbn=1578083516
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}}
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</ref> but others treat ''phylogenetic tree'' as a broader term that includes trees generated with a non-evolutionary emphasis.
   
==Cladistics as a break with the past==
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'''Subtrees are Clades''' — In a cladogram, all organisms lie at the leaves.<ref name=Albert>{{cite book |last=Albert|first=Victor|year=2006|page=3-55 |title=Parsimony, Phylogeny, and Genomics |publisher=Oxford University Press|isbn=0199297304}}</ref> The two [[taxon|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]]''.
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:
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<blockquote>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).</blockquote>
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'''2-Way versus 3-Way Forks''' Many cladists require that all forks in a cladogram be 2-way forks. Some cladograms include 3-way or 4-way forks when the data is insufficient to resolve the forking to a higher level of detail, but nodes with more than two branches are discouraged by many cladists. See ''[[phylogenetic tree]]'' for more information about forking choices in trees.
   
==Cladistic methods==
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'''Depth of a Cladogram''' — If a cladogram represents N species, the number of levels (the "depth") in the cladogram is on the order of log<sub>2</sub>(N).<ref>{{Citation
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."
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| last1 = Aldous| first1 = David
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| contribution = Probability Distributions on Cladograms
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| title = Random Discrete Structures
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| publisher = Springer
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| page = 13
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| year = 1996 }}</ref> For example, if there are 32 species of [[deer]], a cladogram representing deer will be around 5 levels deep (because 2<sup>5</sup>=32). A cladogram representing the complete tree of life, with about 10 million species, would be about 23 levels deep. This formula gives a lower limit: in most cases the actual depth will be a larger value because the various branches of the cladogram will not be uniformly deep. Conversely, the depth may be shallower if forks larger than 2-way forks are permitted.
   
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.
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'''Number of Distinct Cladograms''' For a given set of species, the number of distinct rooted cladograms that can be drawn (ignoring which cladogram best matches the species characteristics) is:<ref name=Lowe>{{cite book |last=Lowe|first=Andrew |authorlink=Andrew Lowe |year=2004|page=164 |title=Ecological Genetics: Design, Analysis, and Application|publisher=Blackwell Publishing|isbn=1405100338}}</ref>
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{| border="1" cellpadding="1"
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|-valign="top"
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|width="14%"|'''Number of Species'''
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|width="5%"|'''2'''
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|width="5%"|'''3'''
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|width="5%"|'''4'''
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|width="5%"|'''5'''
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|width="5%"|'''6'''
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|width="5%"|'''7'''
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|width="5%"|'''8'''
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|width="5%"|'''9'''
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|width="5%"|'''10'''
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|width="10%"|'''N'''
   
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 is the character wings. Though the wings of birds and insects may superficially resemble one another and serve the same function, each evolved independently. If a bird and an insect are both accidentally scored "POSITIVE" for the character "presence of wings", a homoplasy would be introduced into the dataset, and this gives a false picture of evolution.
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|-valign="top" cellpadding="1"
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|'''Number of Cladograms'''
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|1
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|3
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|15
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|105
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|945
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|10,395
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|135,135
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|2,027,025
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|34,459,425
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|1*3*5*7*...*(2N-3)
   
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 we tentatively accept (see [[Occam's razor]] for more on the principle of parsimony). 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 [[List of phylogenetics software|PAUP*]] allow the statistical evaluation of the confidence we have in the veracity of the nodes of a cladogram.
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|}
   
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 Marker|retrotransposon markers]], which are thought to be less prone to the reversion and convergence that plagues sequence data.
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This exponential growth of the number of possible cladograms explains why manual creation of cladograms becomes very difficult when the number of species is large.
   
Ideally, morphological, molecular and possibly other (behavioral etc.) phylogenies should be combined: none of the methods is "superior", but 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 are more common in the latter (see [[long branch attraction]]).
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'''Extinct Species in Cladograms''' — Cladistics makes no distinction between extinct and non-extinct species,<ref>{{cite book |last=Scott-Ram|first=N. R.|year=1990|page=83 |title=Transformed Cladistics, Taxonomy and Evolution |publisher=Cambridge University Press|isbn=0521340861}}</ref> and it is appropriate to include extinct species in the group of organisms being analyzed. Cladograms that are based on DNA/RNA generally do not include extinct species because DNA/RNA samples from extinct species are rare. Cladograms based on morphology, especially morphological characteristics that are preserved in fossils, are more likely to include extinct species.
   
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]].
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'''Time Scale of a Cladogram''' A cladogram tree has an implicit time axis,<ref>{{cite book |last=Freeman|first=Scott|year=1998|page=380 |title=Evolutionary Analysis|publisher=Prentice Hall|isbn=0135680239}}</ref> with time running forward from the base of the tree to the leaves of the tree. If the approximate date (for example, expressed as millions of years ago) of all the evolutionary forks were known, those dates could be captured in the cladogram. Thus, the time axis of the cladogram could be assigned a time scale (e.g. 1 cm = 1 million years), and the forks of the tree could be graphically located along the time axis. Such cladograms are called ''scaled cladograms''. Many cladograms are not scaled along the time axis, for a variety of reasons:
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* Many cladograms are built from species characteristics that cannot be readily dated (e.g. morpohological data in the absence of fossils or other dating information)
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* When the characteristic data is DNA/RNA sequences, it is feasible to use sequence differences to establish the ''relative'' ages of the forks, but converting those ages into actual ''years'' requires a significant approximation of the rate of change<ref>
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{{cite book|
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page=80|
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last=Carrol | first=Robert|
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year=1997|
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title=Patterns and Processes of Vertebrate Evolution |
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publisher=Cambridge University Press|
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isbn=052147809X
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}}
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</ref>
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* Even when the dating information is available, positioning the cladogram's forks along the time axis in proportion to their dates may cause the cladogram to become difficult to understand or hard to fit within a human-readable format
   
==Cladistic classification==
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==Cladistics compared with Linnaean taxonomy==
[[Image:Clade types.png|framed|Three ways to define a clade for use in a cladistic taxonomy.<br/>'''Node-based''': the most recent common ancestor of A and B and all its descendants.<br/>'''Stem-based''': all descendants of the oldest common ancestor of A and B that is not also an ancestor of Z.<br/>'''Apomorphy-based''': the most recent common ancestor of A and B possessing a certain [[Cladistics#Definitions|apomorphy]] (derived character), and all its descendants.]]
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[[Image:iTOL Tree of life.jpg|thumb|260px|A highly resolved, automatically generated [[Tree of life (science)|tree of life]] based on completely sequenced genomes<ref>{{cite journal | last = Letunic | first = I | year = 2007 | title = Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. | journal = Bioinformatics | volume = 23(1) | pages = 127-8 | url = http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=17050570 | format = [[Pubmed]] }}</ref>]]
   
A recent trend in biology since the 1960s, called '''cladism''' or '''cladistic taxonomy''', requires taxa to be clades. In other words, cladists argue that the classification system should be reformed to eliminate all non-clades. In contrast, other [[evolutionary taxonomy|taxonomists]] insist that groups reflect [[phylogeny|phylogenies]] and often make use of cladistic techniques, but allow both [[monophyletic]] and [[paraphyletic]] groups as [[taxa]].
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Prior to the advent of cladistics, most taxonomists used [[Linnaean taxonomy]] to organizing lifeforms. That traditional approach used several fixed levels of a hierarchy, such as Kingdom, [[Phylum]], [[Class (biology)|Class]], [[Order (biology)|Order]], and [[Family (biology)|Family]]. Cladistics does not use those terms, because one of the fundamental premises of cladistics is that the evolutionary tree is very deep and very complex, and it is not meaningful to use a fixed number of levels.
   
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.
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Linnaean taxonomy insists that groups reflect [[phylogeny|phylogenies]], but in contrast to cladistics allows both [[monophyletic]] and [[paraphyletic]] groups as [[taxa]]. Since the early 20th century, Linnaean taxonomists have generally attempted to make [[genus]]- and lower-level taxa monophyletic.
   
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 [[convergent evolution|convergence]] or other [[homoplasy]] was misinterpreted as [[homology (biology)|homology]].
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Cladistics originated in the work of Willi Hennig, and since that time, there has been a spirited debate<ref>
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{{cite book|
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title=Species Concepts and Phylogenetic Theory: A Debate |
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last=Wheeler|first=Quentin|
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isbn=0231101430|
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publisher=Columbia University Press|
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year=2000
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}}</ref> about the relative merits of cladistics versus Linnaean classification.<ref>{{cite journal |author=Benton, M.|title=Stems, nodes, crown clades, and rank-free lists: is Linnaeus dead? |journal=Biological Reviews|volume=75|issue=4 |pages=633-648 |year=2000}}</ref> 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,<ref name=Hull>{{cite book |last=Hull|first=David|authorlink=David Hull|year=1988|page=232-276 |title=Science as a Process|publisher=University of Chicago Press|isbn=0226360512}}</ref> as can be learned from the ''Foreword'' to Hennig (1979) in which Rosen, Nelson, and Patterson wrote the following:
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<blockquote>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)</blockquote>
   
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.
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Proponents of cladistics enumerate key distinctions between cladistics and Linnaean taxonomy as follows:<ref>{{cite journal | last=Hennig | first=Willi | authorlink=Willi_Hennig | date=1975 | title='Cladistic analysis or cladistic classification': a reply to Ernst Mayr | journal=Systematic Zoology | volume=24 | pages=244-256 }}</ref>
   
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 [[gradualism|gradualist]] near-equilibria are [[punctuated equilibria|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.
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{| border="1" cellpadding="2"
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|-valign="top"
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|width="40%" style="background:#ffcd9c;" |'''Cladistics'''
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|width="40%" style="background:#ddffdd;" |'''Linnaean Taxonomy'''
   
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 [[synapomorph]]ies - 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 (biology)|class]], although the latter are a highly derived offshoot of some forms of the former which themselves were already quite advanced.
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|-valign="top"
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|bgcolor="#ffefbe"|Treats all levels of the tree as equivalent.
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|bgcolor="#eeffee"|Treats each tree level uniquely. Uses special names (such as Family, Class, Order) for each level.
   
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.
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|-valign="top"
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|bgcolor="#ffefbe" |Handles arbitrarily-deep trees.
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|bgcolor="#eeffee" |Often must invent new level-names (such as superorder, suborder, infraorder, parvorder, magnorder) to accommodate new discoveries. Biased towards trees about 4 to 12 levels deep.
   
==See also==
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|-valign="top"
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|bgcolor="#ffefbe" |Discourages naming or use of groups that are not [[monophyletic]]
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|bgcolor="#eeffee" |Acceptable to name and use [[paraphyletic]] groups
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|-valign="top"
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|bgcolor="#ffefbe"|Primary goal is to reflect actual process of evolution
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|bgcolor="#eeffee"|Primary goal is to group species based on morphological similarities
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|-valign="top"
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|bgcolor="#ffefbe"|Assumes that the shape of the tree will change frequently, with new discoveries
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|bgcolor="#eeffee"|New discoveries often require re-naming or re-levelling of Classes, Orders, and Kingdoms
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|-valign="top"
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|bgcolor="#ffefbe"|Definitions of taxa are objective, hence free from personal interpretation
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|bgcolor="#eeffee"|Definitions of taxa require individuals to make subjective decisions. For example, various taxonomists suggest that the number of Kingdoms is two, three, four, five, or six (see [[Kingdom (biology)|Kingdom]]).
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|-valign="top"
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|bgcolor="#ffefbe"|Taxa, once defined, are permanent (e.g. "taxon X comprises the most recent common ancestor of species A and B along with its descendants")
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|bgcolor="#eeffee"|Taxa can be renamed and eliminated (e.g. [[Insectivora]] is one of many taxa in the Linnaean system that have been eliminated).
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|}
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Proponents of Linnaean taxonomy contend that it has some advantages over cladistics, such as:<ref>{{cite book | last=Mayr | first=Ernst | authorlink=Ernst Mayr | title=Evolution and the diversity of life (Selected essays) | date=1976 |publisher=Harvard Univ. Press | location=Cambridge, MA | isbn=0-674-27105-X }}</ref>
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{| border="1" cellpadding="2"
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|-valign="top"
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|width="40%" style="background:#ffcd9c;" |'''Cladistics'''
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|width="40%" style="background:#ddffdd;" |'''Linnaean Taxonomy'''
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|-valign="top"
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|bgcolor="#ffefbe"|Limited to entities related by evolution or ancestry
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|bgcolor="#eeffee"|Supports groupings without reference to evolution or ancestry
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|-valign="top"
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|bgcolor="#ffefbe"|Does not include a process for naming species
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|bgcolor="#eeffee"|Includes a process for giving unique names to species
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|-valign="top"
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|bgcolor="#ffefbe"|Difficult to understand the essence of a clade, because clade definitions emphasize ancestry at the expense of meaningful characteristics
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|bgcolor="#eeffee"|Taxa definitions based on tangible characteristics
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|-valign="top"
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|bgcolor="#ffefbe"|Ignores sensible, clearly-defined paraphyletic groups such as [[reptiles]]
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|bgcolor="#eeffee"|Permits clearly-defined groups such as [[reptiles]]
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|-valign="top"
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|bgcolor="#ffefbe"|Difficult to determine if a given species is in a clade or not (e.g. if clade X is defined as "most recent common ancestor of A and B along with its descendants", then the only way to determine if species Y is in the clade is to perform a complex evolutionary analysis)
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|bgcolor="#eeffee"|Straightforward process to determine if a given species is in a taxon or not
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|-valign="top"
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|bgcolor="#ffefbe"|Limited to organisms that evolved by inherited traits; not applicable to organisms that evolved via complex gene-sharing or lateral transfer
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|bgcolor="#eeffee"|Applicable to all organisms, regardless of evolutionary mechanism
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|}
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== Cladistics compared to phenetics==
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For some decades in the mid-late 20th century, a commonly used methodology was [[phenetics]] ("numerical taxonomy"). This can be seen as a precedessor<ref>{{cite book | last=Mayr | first=Ernst | authorlink=Ernst Mayr | title=The growth of biological thought: diversity, evolution and inheritance | page=221|date=1982 |publisher=Harvard Univ. Press | location=Cambridge, MA | isbn=0-674-36446-5 }}</ref> to some methods of today's cladistics (namely [[Distance matrices in phylogeny|distance matrix]] methods like [[neighbor-joining]]), but made no attempt to resolve [[phylogeny]], only similarities. Considered cutting-edge at its time as they were among the first [[bioinformatics]] applications, phenetic methods are today superseded by cladistic analyses{{Fact|date=November 2007}} due to their inability of phenetics to provide an [[evolution|evolutionary]] hypothesis, except by chance.
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== Monophyletic groups encouraged ==
  +
  +
Many cladists discourage the use of paraphyletic groups because they detract from cladisitcs' emphasis on clades (monophyletic groups). In contrast, proponents of the use of paraphyletic groups argue that any dividing line in a cladogram creates both a monophyletic section above and a paraphyletic section below. They also contend that 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 paraphyletic groups and clades are valuable notions with separate purposes.
  +
  +
==Simplified step by step procedure==
  +
[[Image:MyosinUnrootedTree.jpg|thumb|280px|right|Unrooted cladogram of the myosin supergene family<ref name=Hodge_2000>{{cite journal |author=Hodge T, Cope M |title=A myosin family tree |journal=J Cell Sci |volume=113 Pt 19 |issue= |pages=3353-4 |year=2000 |url=http://jcs.biologists.org/cgi/content/full/113/19/3353 |id=PMID 10984423}}</ref> ]]
  +
A simplified procedure for generating a cladogram is:<ref name=DeSalle>{{cite book |last=DeSalle|first=Rob|authorlink|year=2002 |title=Techniques in Molecular Systematics and Evolution |publisher=Birkhauser|isbn=376436257X}}</ref>
  +
# Gather and organize data
  +
# Consider possible cladograms
  +
# Select best cladogram
  +
  +
===Step 1: Gather and organize data===
  +
A cladistic analysis begins with the following data:
  +
*a list of species to be organized
  +
*a list of characteristics to be compared
  +
*for each species, the value of each of the listed characteristics or ''character states''
  +
  +
For example, if analyzing 20 species of birds, the data might be:
  +
*the list of 20 species
  +
*characteristics such as genome sequence, skeletal anatomy, biochemical processes, and feather coloration
  +
*for each of the 20 species, its particular genome sequence, skeletal anatomy, biochemical processes, and feather coloration
  +
  +
====Molecular versus morphological data====
  +
  +
The characteristics used to create a cladogram can be roughly categorized as either morphological (synapsid skull, warm-blooded, notochord, unicellular, etc.) or molecular (DNA, RNA, or other genetic information).<ref name=DeSalle/> Prior to the advent of DNA sequencing, all cladistic analysis used morphological data.
  +
  +
As [[DNA sequencing]] has become cheaper and easier, [[molecular systematics]] has become a more and more popular way to reconstruct phylogenies.<ref>{{cite book |last=Hillis|first=David|authorlink|year=1996|title=Molecular Systematics |year=1996 |publisher=Sinaur|isbn=0878932828}}</ref> 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 marker]]s, which are thought to be less prone to the problem of [[reversion (genetics)|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 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.
  +
  +
====Plesiomorphies and synapomorphies====
  +
  +
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''. 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.
  +
  +
====Avoid homoplasies====
  +
  +
A [[homoplasy]] is a character that is shared by multiple species due to some cause ''other'' than common ancestry.<ref>{{cite book | last=West-Eberhard| first=Mary| title=Developmental Plasticity and Evolution |pages=353-376| date=2003 |publisher=Oxford Univ. Press | isbn=0195122356 }}</ref> Typically, homoplasies occur due to convergent evolution. Use of homoplasies when building a cladogram is sometimes unavoidable but is to be avoided when possible.
  +
  +
A well-known example of homoplasy due to convergent evolution would be a character "presence of wings". Though the wings of birds, bats, and insects serve the same function, each evolved independently, as can be seen by their [[anatomy]]. If a bird, bat, 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 evolutionary scenario.
  +
  +
Homoplasies can often be avoided outright in morphological datasets by defining characters more precisely and increasing their number. In the example above, utilizing "wings supported by bony [[endoskeleton]]" and "wings supported by [[chitin]]ous [[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 imprecise, 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 or character set, no method of evaluation is likely to produce a phylogeny representing the evolutionary reality.
  +
  +
===Step 2: Consider possible cladograms===
  +
  +
[[Image:Simple cladistics.svg|thumb|right|300px]]
  +
{{main|Computational phylogenetics}}
  +
When there are just a few species being organized, it is possible to do this step manually, but most cases require a computer program. There are scores of computer programs available to support cladistics.<ref>
  +
{{cite web|
  +
url=http://evolution.genetics.washington.edu/phylip/software.pars.html|
  +
title=List of Cladistics Software Programs
  +
}}
  +
</ref> See ''[[phylogenetic tree]]'' for more information about tree-generating computer programs.
  +
  +
Because the total number of possible cladograms grows exponentially with the number of species, it is impractical for a computer program to evaluate every individual cladogram. A typical cladistic program begins by using [[heuristic]] techniques to identify a small number of candidate cladograms. Many cladistic programs then continue the search with the following repetitive steps:
  +
  +
# Evaluate the candidate cladograms by comparing them to the characteristic data
  +
# Identify the best candidates that are most consistent with the characteristic data
  +
# Create additional candidates by creating several variants of each of the best candidates from the prior step
  +
# Use heuristics to create several new candidate cladograms unrelated to the prior candidates
  +
# Repeat these steps until the cladograms stop getting better
  +
  +
Computer programs that generate cladograms use algorithms that are very computationally intensive,<ref name=Hodkinson>{{cite book |last=Hodkinson|first=Trevor|year=2006|page=61-128 |title=Reconstructing the Tree of Life: Taxonomy and Systematics of Species Rich Taxa |publisher=CRC Press|isbn=0849395798}}</ref> because the cladogram algorithm is [[NP-hard]].
  +
  +
===Step 3: Select the best cladogram===
  +
  +
There are several [[algorithms]] available to identify the "best" cladogram.<ref>
  +
{{cite book|
  +
title=Cladistics: The Theory and Practice of Parsimony Analysis |
  +
last=Kitching | first=Ian|
  +
isbn=0198501382|
  +
year=1998|
  +
publisher=Oxford University Press
  +
}}
  +
</ref> Most algorithms use a [[Metric (mathematics)|metric]] to measure how consistent a candidate cladogram is with the data. Most cladogram algorithms use the mathematical techniques of [[Optimization (mathematics)|optimization]] and [[minimization]].
  +
  +
In general, cladogram-generation algorithms must be implemented as computer programs, although some algorithms can be performed manually when the data sets are trivial (for example, just a few species and a couple of characteristics).
  +
  +
Some algorithms are useful only when the characteristic data is molecular (DNA, RNA) data. Other algorithms are useful only when the characteristic data is morphological data. Other algorithms can be used when the characteristic data includes both molecular and morphological data.
  +
  +
Algorithms for cladograms include [[least squares]], [[neighbor-joining]], [[parsimony]], [[maximum likelihood]], and [[Bayesian inference]].
  +
  +
Biologists sometimes use the term [[parsimony]] for a specific kind of cladogram-generation algorithm and sometimes as an umbrella term for all cladogram algorithms.<ref>
  +
{{cite journal|
  +
author=Stewart, Caro-Beth|
  +
journal=Nature|
  +
title=The Powers and Pitfalls of Parsimony|
  +
year=1993|
  +
volume=361|
  +
pages=603-607
  +
}}</ref>
  +
  +
Algorithms that perform optimization tasks (such as building cladograms) can be sensitive to the order in which the input data (the list of species and their characteristics) is presented. Inputting the data in various orders can cause the same algorithm to produce different "best" cladograms. In these situations, the user should input the data in various orders and compare the results.
  +
  +
Using different algorithms on a single data set can sometimes yield different "best" cladograms, because each algorithm may have a unique definition of what is "best".
  +
  +
Because of the astronomical number of possible cladograms, algorithms cannot guarantee that the solution is the overall best solution. A non-optimal cladogram will be selected if the program settles on a local minimum rather than the desired global minimum.<ref>
  +
{{cite book |
  +
last=Foley |
  +
first=Peter|
  +
title=Cladistics: A Practical Course in Systematics |
  +
year=1993|
  +
page=66|
  +
publisher=Oxford Univ. Press|
  +
isbn=0198577664
  +
}}</ref> To help solve this problem, many cladogram algorithms use a [[simulated annealing]] approach to increase the likelihood that the selected cladogram is the optimal one.<ref>
  +
{{cite journal|
  +
author=Nixon K. C.|
  +
journal=Cladistics|
  +
title=The Parsimony Ratchet: a new method for rapid parsimony analysis |
  +
year=1999|
  +
volume=15|
  +
pages=407-414
  +
}}</ref>
  +
  +
==How complex is the Tree of Life?==
  +
  +
One of the arguments in favor of cladistics is that it supports arbitrarily complex, arbitrarily deep trees. Especially when extinct species are considered (both known and unknown), the complexity and depth of the tree can be very large. Every single speciation event, including all the species that are now extinct, represents an additional fork on the hypothetical, complete cladogram representing the full tree of life. Fractals can be used to represent this notion of increasing detail: as a viewpoint zooms into the tree of life, the complexity remains virtually constant<ref>
  +
{{cite book|
  +
title = The Hierarchical Genome and Differentiation Waves|
  +
last = Gordon | first=Richard|
  +
isbn=9810222688|
  +
year=1999|
  +
publisher=World Scientific|
  +
page=632
  +
}}
  +
</ref>. This great complexity of the tree, and the uncertainty associated with the complexity, is one of the reasons that cladists cite for the attractiveness of cladistics over traditional taxonomy.
  +
  +
Proponents of non-cladistic approaches to taxonomy point to puncuated equilibrium to bolster the case that the tree-of-life has a finite depth and finite complexity. If the number of species currently alive is finite, and the number of extinct species that we will ever know about is finite, then the depth and complexity of the tree of life is bounded, and there is no need to handle arbitrarily deep trees.
  +
  +
==Phylocode approach to naming species==
  +
  +
A formal code of phylogenetic nomenclature, the [[PhyloCode]]<ref>{{cite journal |author=Pennisi, E. |title=Evolutionary Biology: Preparing the Ground for a Modern 'Tree of Life' |journal=Science|volume=293 |pages=1979-1980 |year=2001}}</ref>, 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.
  +
  +
==Terminology==
  +
[[Image:Phylogenetic-Groups.svg|thumb|250px|right|The yellow group ([[sauropsids]]) is [[Monophyly|monophyletic]], the blue group ([[reptiles]]) is [[Paraphyly|paraphyletic]], and the red group (warm-blooded animals) is [[Polyphyly|polyphyletic]].]]
  +
{{main|Phylogenetic nomenclature}}
  +
* A ''[[clade]]'' is an ancestor species and all of its decencents
  +
* A ''[[monophyletic]]'' group is a clade
  +
* A ''[[paraphyletic]]'' group is a monophyletic group that excludes some of the descendants (e.g. reptiles are sauropsids excluding birds). Most cladists discourage the use of paraphyletic groups.
  +
* A ''[[polyphyletic]]'' group is a group consisting of members from two non-overlapping monophyletic groups (e.g. flying animals). Most cladists discourage the use of polyphyletic groups.
  +
* An ''outgroup'' is an organism that is considered not to be part of the group in question, but is closely related to the group.
  +
* A characteristic that is present in both the outgroups and in the ancestors is called a ''plesiomorphy'' (meaning "close form", also called an ancestral state).
  +
* A characteristic that occurs only in later descendants is called an ''apomorphy'' (meaning "separate form", also called a "derived" state) for that group. Note: 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.
  +
* A species or clade is ''[[Basal (phylogenetics)|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 taxon|extant]]. For example, palaeodicots are basal to flowering plants.
  +
* A clade or species located within another clade is said to be ''nested'' within that clade.
  +
  +
====Origin of the term "cladistics"====
  +
  +
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. A review paper by Dupuis 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.<ref>{{cite journal | last=Dupuis | first=Claude | date=1984 | title=Willi Hennig's impact on taxonomic thought | journal=Annual Review of Ecology and Systematics | volume=15 | pages=1-24 | issn=0066-4162 }}</ref>
  +
  +
[[Image:Clade types.png|framed]]
  +
  +
====Three definitions of clade====
  +
  +
There are three ways to define a clade for use in a cladistic taxonomy.<ref>{{cite journal |author=de Queiroz, K. and J. Gauthier|title=Toward a phylogenetic system of biological nomenclature |journal=Trends in Research in Ecology and Evolution |volume=9|issue=1 |pages=27-31 |year=1994}}</ref>
  +
  +
*''Node-based'': the most recent common ancestor of A and B along with all of 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, along with all of its descendants, possessing a certain derived character. This definition is generally discouraged by most cladists.
  +
  +
==Applying Cladistics to other disciplines==
  +
  +
The processes used to generate cladograms are not limited to the field of biology<ref>{{
  +
cite book |
  +
last=Mace| first= Ruth|
  +
date=2005 |
  +
title=The Evolution of Cultural Diversity: A Phylogenetic Approach |
  +
publisher=Routledge Cavendish |
  +
isbn=1844720993
  +
}}</ref>. The generic nature of cladistics means that cladistics can be used to organize groups of items in many different realms. The only requirement is that the items have chararacteristics that can be identified and measured.
  +
  +
For example, one could take a group of 200 spoken languages, measure various characteristics of each language (vocabulary, phonemes, rhythms, accents, dynamics, etc) and then apply a cladogram algorithm to the data. The result will be a tree that may shed light on how, and in what order, the languages came into existence.
  +
  +
Thus, cladistic methods have recently been usefully applied to non-biological systems, including determining [[language families]] in [[historical linguistics]], culture, history<ref>{{
  +
cite book |
  +
last=Lipo| first= Carl|
  +
date=2005 |
  +
title=Mapping Our Ancestors: Phylogenetic Approaches in Anthropology and Prehistory |
  +
publisher=Aldine Transaction |
  +
isbn=0202307514
  +
}}
  +
</ref>,
  +
and filiation of manuscripts in [[textual criticism]].
  +
  +
==Footnotes==
  +
  +
{{reflist}}
  +
  +
== See also ==
  +
{| width=100%
  +
| valign=top width=33% |
  +
*[[Bauplan]]
  +
*[[Bioinformatics]]
  +
*[[Biomathematics]]
  +
*[[Clade]]
  +
*[[Coalescent theory]]
  +
*[[Dendrogram]]
  +
*[[Evolution of Mollusca]] for a cladistic illustration
  +
| valign=top width=34% |
 
*[[Evolutionary tree]]
 
*[[Evolutionary tree]]
*[[List of publications in biology#Phylogenetics|Important publications in cladistics]]
+
*[[Last common ancestor]]
*[[Evolution of Mollusca]]
+
*[[List of publications in biology#Phylogenetics|Important publications in phylogenetics]]
  +
*[[Language family]]
  +
*[[Maximum parsimony]]
  +
*[[Molecular phylogeny]]
 
*[[PhyloCode]]
 
*[[PhyloCode]]
  +
| valign=top width=33% |
  +
*[[Phylogenetics]]
 
*[[Phylogenetic tree]]
 
*[[Phylogenetic tree]]
*[[Scientific classification]]
+
*[[Phylogenetic network]]
  +
*[[List of phylogenetics software|Phylogenetics software]]
  +
*[[Phylogeography]]
  +
*[[Phylogenetic comparative methods]]
  +
*[[Scientific Classification]]
  +
*[[Systematics]]
  +
|}
   
==References==<!-- ZoolScripta33:293 -->
+
==References==<!-- Systematics and Biodiversity4: 137–147
  +
doi:10.1017/S1477200005001830; ZoolScripta33:293 -->
 
<div class="references-small">
 
<div class="references-small">
* {{cite journal | author=Ashlock, Peter D. | date=1974 | title=The uses of cladistics | journal=Annual Review of Ecology and Systematics | volume=5 | pages=81-99 }}
+
* {{cite journal | last=Ashlock | first=Peter D. | date=1974 | title=The uses of cladistics | journal=Annual Review of Ecology and Systematics | issn=0066-4162 | volume=5 | pages=81-99 }}
* {{cite journal | author=de Queiroz, Kevin; and Jacques A. Gauthier | date=1992 | title= Phylogenetic taxonomy | journal=Annual Review of Ecology and Systematics | volume=23 | pages= 449–480 }}
+
* {{cite journal | last=Cuénot | first=Lucien | authorlink=Lucien Cuénot | date=1940 | title=Remarques sur un essai d'arbre généalogique du règne animal | journal=Comptes Rendus de l'Académie des Sciences de Paris | volume=210 | pages=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'.
* {{cite journal | author=Dupuis, Claude | date=1984 | title=Willi Hennig's impact on taxonomic thought | journal=Annual Review of Ecology and Systematics | volume=15 | pages=1-24 | id={{ISSN|0066-4162}} }}
+
* {{cite journal
* {{cite book | author=Felsenstein, Joseph | date=2004 | title=Inferring phylogenies | publisher=Sinauer Associates | location=Sunderland, MA | isbn=0-87893-177-5 }}
+
|author=[[L.L. Cavalli-Sforza|Cavalli-Sforza, L.L.]] and [[A.W.F. Edwards]]
* {{cite journal | author=Hamdi, Hamdi; Hitomi Nishio, Rita Zielinski and Achilles Dugaiczyk | date=1999 | title=Origin and phylogenetic distribution of ''Alu'' DNA repeats: irreversible events in the evolution of primates | journal=Journal of Molecular Biology | volume=289 | pages=861–871 | id=PMID 10369767}}
+
|month=Sep.,
* {{cite book | author=Hennig, Willi | title=Grundzüge einer Theorie der Phylogenetischen Systematik | publisher=Deutscher Zentralverlag | location=Berlin | date=1950 }}.
+
|year=1967
* {{cite book | author=Hennig, Willi | title=Phylogenetische Systematik (ed. Wolfgang Hennig) | publisher=Blackwell Wissenschaft | location=Berlin | date=1982 | id=ISBN 3-8263-2841-8 }}
+
|title=Phylogenetic analysis: Models and estimation procedures
* {{cite journal | author=Hennig, Willi | date=1975 | title='Cladistic analysis or cladistic classification': a reply to Ernst Mayr | journal=Systematic Zoology | volume=24 | pages=244-256 }}
+
|journal=Evol.
* {{cite book | author=Hennig, Willi | date=1979 | title=Phylogenetic systematics (tr. D. Dwight Davis and Rainer Zangerl) | publisher=Univ. of Illinois Press (reprinted 1999) | location=Urbana, IL | id=ISBN 0-252-06814-9 }}
+
|volume=21
* {{cite journal | author=Hull, David L. | date=1979 | title=The limits of cladism | journal=Systematic Zoology | volume=28 | pages=416-440 }}
+
|issue=3
* {{cite book | author=Kitching, Ian J.; Peter L. Forey, Christopher J. Humphries and David M. Williams | date=1998 | title=Cladistics: Theory and practice of parsimony analysis, 2nd ed. | publisher=Oxford University Press | id=ISBN 0-19-850138-2 }}
+
|pages=550-570
* {{cite book | author=Luria, Salvador; Stephen Jay Gould and Sam Singer | date=1981 | title=A view of life | publisher=Benjamin/Cummings | location=Menlo Park, CA | isbn=0-8053-6648-2 }}
+
|url=http://links.jstor.org/sici?sici=0014-3820%28196709%2921%3A3%3C550%3APAMAEP%3E2.0.CO%3B2-I
* {{cite book | author=Mayr, Ernst | title=The growth of biological thought: diversity, evolution and inheritance | date=1982 |publisher=Harvard Univ. Press | location=Cambridge, MA | id=ISBN 0-674-36446-5 }}
+
}}
* {{cite conference| author=Patterson, Colin | date=1982 | title=Morphological characters and homology | editor=Joysey, Kenneth A; A. E. Friday (editors) | booktitle=Problems in Phylogenetic Reconstruction | publisher=Academic Press | location=London | id=ISBN 0-12-391250-4}}
+
* {{cite journal | last=de Queiroz | first=Kevin | authors=and Jacques A. Gauthier | date=1992 | title= Phylogenetic taxonomy | journal=Annual Review of Ecology and Systematics | issn=0066-4162 | volume=23 | pages= 449–480 }}
  +
* {{cite journal | last=Dupuis | first=Claude | date=1984 | title=Willi Hennig's impact on taxonomic thought | journal=Annual Review of Ecology and Systematics | volume=15 | pages=1-24 | issn=0066-4162 }}
  +
* {{cite book | last=Felsenstein | first=Joseph | date=2004 | title=Inferring phylogenies | publisher=Sinauer Associates | location=Sunderland, MA | isbn=0-87893-177-5 }}
  +
* {{cite journal | last=Hamdi | first= Hamdi | coauthors=Hitomi Nishio, Rita Zielinski and Achilles Dugaiczyk | date=1999 | title=Origin and phylogenetic distribution of ''Alu'' DNA repeats: irreversible events in the evolution of primates | journal=Journal of Molecular Biology | volume=289 | pages=861–871 | pmid=10369767}}
  +
* {{cite book | last=Hennig | first=Willi | authorlink=Willi_Hennig | title=Grundzüge einer Theorie der Phylogenetischen Systematik | publisher=Deutscher Zentralverlag | location=Berlin | date=1950 }}.
  +
* {{cite book | last=Hennig | first=Willi | authorlink=Willi_Hennig | title=Phylogenetische Systematik (ed. Wolfgang Hennig) | publisher=Blackwell Wissenschaft | location=Berlin | date=1982 | isbn=3-8263-2841-8 }}
  +
* {{cite journal | last=Hennig | first=Willi | authorlink=Willi_Hennig | date=1975 | title='Cladistic analysis or cladistic classification': a reply to Ernst Mayr | journal=Systematic Zoology | volume=24 | pages=244-256 }} The paper he was responding to is reprinted in Mayr (1976).
  +
* {{cite book | last=Hennig | first= Willi | authorlink=Willi_Hennig | date=1966 | title=Phylogenetic systematics (tr. D. Dwight Davis and Rainer Zangerl) | publisher=Univ. of Illinois Press (reprinted 1979 and 1999) | location=Urbana, IL | isbn=0-252-06814-9 }}
  +
* {{cite book | last=Hennig | first= Willi | authorlink=Willi_Hennig | date=1979 | title=Phylogenetic systematics (3rd edition of 1966 book) | isbn=0-252-06814-9 }}Translated from manuscript and so never published in German.
  +
* {{cite journal | last=Hull | first=David L. | date=1979 | title=The limits of cladism | journal=Systematic Zoology | volume=28 | pages=416-440 }}
  +
* {{cite book | last=Kitching | first=Ian J. | coauthors=Peter L. Forey, Christopher J. Humphries and David M. Williams | date=1998 | title=Cladistics: Theory and practice of parsimony analysis | edition=2nd ed. | publisher=Oxford University Press | isbn=0-19-850138-2 }}
  +
* {{cite book | last=Luria | first= Salvador | coauthors=Stephen Jay Gould and Sam Singer | date=1981 | title=A view of life | publisher=Benjamin/Cummings | location=Menlo Park, CA | isbn=0-8053-6648-2 }}
  +
* {{cite book | last=Mayr | first=Ernst | authorlink=Ernst Mayr | title=The growth of biological thought: diversity, evolution and inheritance | date=1982 |publisher=Harvard Univ. Press | location=Cambridge, MA | isbn=0-674-36446-5 }}
  +
* {{cite book | last=Mayr | first=Ernst | authorlink=Ernst Mayr | title=Evolution and the diversity of life (Selected essays) | date=1976 |publisher=Harvard Univ. Press | location=Cambridge, MA | 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.
  +
* {{cite conference | last=Patterson | first=Colin | date=1982 | title=Morphological characters and homology | editor=Joysey, Kenneth A; A. E. Friday (editors) | booktitle=Problems in Phylogenetic Reconstruction | publisher=Academic Press | location=London | isbn=0-12-391250-4}}
 
* Rosen, Donn; Gareth Nelson and Colin Patterson (1979), Foreword ''provided for Hennig (1979)''
 
* Rosen, Donn; Gareth Nelson and Colin Patterson (1979), Foreword ''provided for Hennig (1979)''
* {{cite journal | author=Shedlock, Andrew M; Norihiro Okada | date=2000 | title=SINE insertions: Powerful tools for molecular systematics | journal=Bioessays | volume=22 | pages=148–160 | id=PMID 10655034 }}
+
* {{cite journal | last=Shedlock | first=Andrew M | coauthors=Norihiro Okada | date=2000 | title=SINE insertions: Powerful tools for molecular systematics | journal=Bioessays | issn=0039-7989 |volume=22 | pages=148–160 | pmid=10655034 }}
* {{cite journal | author=Sokal, Robert R. | date=1975 | title=Mayr on cladism -- and his critics | journal=Systematic Zoology | volume=24 | pages=257-262 }}
+
* {{cite journal | last=Sokal | first=Robert R. | date=1975 | title=Mayr on cladism -- and his critics | journal=Systematic Zoology | volume=24 | pages=257-262 }}
* {{cite conference| author=Swofford, David L; G. J. Olsen, P. J. Waddell and David M. Hillis | date=1996 | title=Phylogenetic inference | editor=Hillis, David M; C. Moritz and B. K. Mable (editors)| booktitle=Molecular Systematics | location=Sunderland, MA | publisher=Sinauer Associates | id=ISBN 0-87893-282-8}}
+
* {{cite book| last=Swofford | first=David L. | coauthors=G. J. Olsen, P. J. Waddell and David M. Hillis | date=1996 | chapter=Phylogenetic inference | editor=Hillis, David M; C. Moritz and B. K. Mable (editors)| title=Molecular Systematics | edition=2. ed. | location=Sunderland, MA | publisher=Sinauer Associates | isbn=0-87893-282-8}}
* {{cite book | author=Wiley, Edward O. | date=1981 | title=Phylogenetics: The Theory and Practice of Phylogenetic Systematics | publisher=Wiley Interscience | location=New York | isbn=0-471-05975-7}}
+
* {{cite book | last=Wiley | first=Edward O. | date=1981 | title=Phylogenetics: The Theory and Practice of Phylogenetic Systematics | publisher=Wiley Interscience | location=New York | isbn=0-471-05975-7}}
  +
*{{cite journal |author=Zwickl DJ, Hillis DM |title=Increased taxon sampling greatly reduces phylogenetic error |journal=Systematic Biology |volume=51 |pages=588-598 |year=2002}}
 
</div>
 
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{{Spoken Wikipedia|Cladistics.ogg|2005-04-30}}
 
{{Spoken Wikipedia|Cladistics.ogg|2005-04-30}}
 
* [http://www.amnh.org/learn/pd/fish_2/pdf/compleat_cladist.pdf The Compleat Cladist (pdf)]
 
* [http://www.amnh.org/learn/pd/fish_2/pdf/compleat_cladist.pdf The Compleat Cladist (pdf)]
  +
* [http://tellapallet.com/tree_of_life.htm Tree of Life illustration] - A high-level cladogram showing the complete tree of life.
 
* [http://rjohara.net/darwin/files/bmcr Example of cladistics used in textual criticism]
 
* [http://rjohara.net/darwin/files/bmcr Example of cladistics used in textual criticism]
 
* [http://www.ucmp.berkeley.edu/clad/clad4.html Journey into Phylogenetic Systematics]
 
* [http://www.ucmp.berkeley.edu/clad/clad4.html Journey into Phylogenetic Systematics]
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* [http://www.blackwellpublishing.com/journal.asp?ref=0748-3007 Cladistics: The International Journal of the Willi Hennig Society] <small>({{ISSN|0748-3007}})</small>
 
* [http://www.blackwellpublishing.com/journal.asp?ref=0748-3007 Cladistics: The International Journal of the Willi Hennig Society] <small>({{ISSN|0748-3007}})</small>
 
* [http://www.trex.uqam.ca Phylogenetic inferring on the T-REX server]
 
* [http://www.trex.uqam.ca Phylogenetic inferring on the T-REX server]
  +
* [http://evolution.genetics.washington.edu/phylip/software.pars.html A list of cladogram-generating programs]
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* For a cladistic approach to animal classification: [http://anthro.palomar.edu/animal/default.htm Classification of living things]
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Cladistics is the hierarchical classification of species based on evolutionary ancestry. Cladistics is distinguished from other taxonomic classification systems because it focuses on evolution (rather than focusing on similarities between species), and because it places heavy emphasis on objective, quantitative analysis. Cladistics generates diagrams called cladograms that represent the evolutionary tree of life. DNA and RNA sequencing data are used in many important cladistic efforts. Computer programs are widely used in cladistics, due to the highly complex nature of cladogram-generation procedures. A major contributor to cladistics was the German entomologist Willi Hennig, who referred to it as phylogenetic systematics.[1] The term phylogenetics is often used synonymously with cladistics. Cladistics originated in the field of biology but in recent years has found application in other disciplines. The word cladistics is derived from the ancient Greek κλάδος, klados, or "branch."

Cladograms Edit

File:Cladogram-example1.svg
File:Cladogram-example2.svg
File:Neomuratree.svg

The starting point of cladistic analysis is a group of species and molecular, morphological, or other data characterizing those species. The end result is a tree-like relationship-diagram called a cladogram.[2] The cladogram graphically represents a hypothetical evolutionary process. Cladograms are subject to revision as additional data becomes available.

Synonyms — The term evolutionary tree is often used synonymously with cladogram. The term phylogenetic tree is sometimes used synonymously with cladogram,[3] but others treat phylogenetic tree as a broader term that includes trees generated with a non-evolutionary emphasis.

Subtrees are Clades — In a cladogram, all organisms lie at the leaves.[4] 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.

2-Way versus 3-Way Forks — Many cladists require that all forks in a cladogram be 2-way forks. Some cladograms include 3-way or 4-way forks when the data is insufficient to resolve the forking to a higher level of detail, but nodes with more than two branches are discouraged by many cladists. See phylogenetic tree for more information about forking choices in trees.

Depth of a Cladogram — If a cladogram represents N species, the number of levels (the "depth") in the cladogram is on the order of log2(N).[5] For example, if there are 32 species of deer, a cladogram representing deer will be around 5 levels deep (because 25=32). A cladogram representing the complete tree of life, with about 10 million species, would be about 23 levels deep. This formula gives a lower limit: in most cases the actual depth will be a larger value because the various branches of the cladogram will not be uniformly deep. Conversely, the depth may be shallower if forks larger than 2-way forks are permitted.

Number of Distinct Cladograms — For a given set of species, the number of distinct rooted cladograms that can be drawn (ignoring which cladogram best matches the species characteristics) is:[6]

Number of Species 2 3 4 5 6 7 8 9 10 N
Number of Cladograms 1 3 15 105 945 10,395 135,135 2,027,025 34,459,425 1*3*5*7*...*(2N-3)

This exponential growth of the number of possible cladograms explains why manual creation of cladograms becomes very difficult when the number of species is large.

Extinct Species in Cladograms — Cladistics makes no distinction between extinct and non-extinct species,[7] and it is appropriate to include extinct species in the group of organisms being analyzed. Cladograms that are based on DNA/RNA generally do not include extinct species because DNA/RNA samples from extinct species are rare. Cladograms based on morphology, especially morphological characteristics that are preserved in fossils, are more likely to include extinct species.

Time Scale of a Cladogram — A cladogram tree has an implicit time axis,[8] with time running forward from the base of the tree to the leaves of the tree. If the approximate date (for example, expressed as millions of years ago) of all the evolutionary forks were known, those dates could be captured in the cladogram. Thus, the time axis of the cladogram could be assigned a time scale (e.g. 1 cm = 1 million years), and the forks of the tree could be graphically located along the time axis. Such cladograms are called scaled cladograms. Many cladograms are not scaled along the time axis, for a variety of reasons:

  • Many cladograms are built from species characteristics that cannot be readily dated (e.g. morpohological data in the absence of fossils or other dating information)
  • When the characteristic data is DNA/RNA sequences, it is feasible to use sequence differences to establish the relative ages of the forks, but converting those ages into actual years requires a significant approximation of the rate of change[9]
  • Even when the dating information is available, positioning the cladogram's forks along the time axis in proportion to their dates may cause the cladogram to become difficult to understand or hard to fit within a human-readable format

Cladistics compared with Linnaean taxonomyEdit

File:ITOL Tree of life.jpg

Prior to the advent of cladistics, most taxonomists used Linnaean taxonomy to organizing lifeforms. That traditional approach used several fixed levels of a hierarchy, such as Kingdom, Phylum, Class, Order, and Family. Cladistics does not use those terms, because one of the fundamental premises of cladistics is that the evolutionary tree is very deep and very complex, and it is not meaningful to use a fixed number of levels.

Linnaean taxonomy insists that groups reflect phylogenies, but in contrast to cladistics allows both monophyletic and paraphyletic groups as taxa. Since the early 20th century, Linnaean taxonomists have generally attempted to make genus- and lower-level taxa monophyletic.

Cladistics originated in the work of Willi Hennig, and since that time, there has been a spirited debate[11] about the relative merits of cladistics versus Linnaean classification.[12] 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,[13] 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)

Proponents of cladistics enumerate key distinctions between cladistics and Linnaean taxonomy as follows:[14]

Cladistics Linnaean Taxonomy
Treats all levels of the tree as equivalent. Treats each tree level uniquely. Uses special names (such as Family, Class, Order) for each level.
Handles arbitrarily-deep trees. Often must invent new level-names (such as superorder, suborder, infraorder, parvorder, magnorder) to accommodate new discoveries. Biased towards trees about 4 to 12 levels deep.
Discourages naming or use of groups that are not monophyletic Acceptable to name and use paraphyletic groups
Primary goal is to reflect actual process of evolution Primary goal is to group species based on morphological similarities
Assumes that the shape of the tree will change frequently, with new discoveries New discoveries often require re-naming or re-levelling of Classes, Orders, and Kingdoms
Definitions of taxa are objective, hence free from personal interpretation Definitions of taxa require individuals to make subjective decisions. For example, various taxonomists suggest that the number of Kingdoms is two, three, four, five, or six (see Kingdom).
Taxa, once defined, are permanent (e.g. "taxon X comprises the most recent common ancestor of species A and B along with its descendants") Taxa can be renamed and eliminated (e.g. Insectivora is one of many taxa in the Linnaean system that have been eliminated).

Proponents of Linnaean taxonomy contend that it has some advantages over cladistics, such as:[15]

Cladistics Linnaean Taxonomy
Limited to entities related by evolution or ancestry Supports groupings without reference to evolution or ancestry
Does not include a process for naming species Includes a process for giving unique names to species
Difficult to understand the essence of a clade, because clade definitions emphasize ancestry at the expense of meaningful characteristics Taxa definitions based on tangible characteristics
Ignores sensible, clearly-defined paraphyletic groups such as reptiles Permits clearly-defined groups such as reptiles
Difficult to determine if a given species is in a clade or not (e.g. if clade X is defined as "most recent common ancestor of A and B along with its descendants", then the only way to determine if species Y is in the clade is to perform a complex evolutionary analysis) Straightforward process to determine if a given species is in a taxon or not
Limited to organisms that evolved by inherited traits; not applicable to organisms that evolved via complex gene-sharing or lateral transfer Applicable to all organisms, regardless of evolutionary mechanism

Cladistics compared to pheneticsEdit

For some decades in the mid-late 20th century, a commonly used methodology was phenetics ("numerical taxonomy"). This can be seen as a precedessor[16] to some methods of today's cladistics (namely distance matrix methods like neighbor-joining), but made no attempt to resolve phylogeny, only similarities. Considered cutting-edge at its time as they were among the first bioinformatics applications, phenetic methods are today superseded by cladistic analyses[How to reference and link to summary or text] due to their inability of phenetics to provide an evolutionary hypothesis, except by chance.

Monophyletic groups encouraged Edit

Many cladists discourage the use of paraphyletic groups because they detract from cladisitcs' emphasis on clades (monophyletic groups). In contrast, proponents of the use of paraphyletic groups argue that any dividing line in a cladogram creates both a monophyletic section above and a paraphyletic section below. They also contend that 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 paraphyletic groups and clades are valuable notions with separate purposes.

Simplified step by step procedureEdit

MyosinUnrootedTree

Unrooted cladogram of the myosin supergene family[17]

A simplified procedure for generating a cladogram is:[18]

  1. Gather and organize data
  2. Consider possible cladograms
  3. Select best cladogram

Step 1: Gather and organize dataEdit

A cladistic analysis begins with the following data:

  • a list of species to be organized
  • a list of characteristics to be compared
  • for each species, the value of each of the listed characteristics or character states

For example, if analyzing 20 species of birds, the data might be:

  • the list of 20 species
  • characteristics such as genome sequence, skeletal anatomy, biochemical processes, and feather coloration
  • for each of the 20 species, its particular genome sequence, skeletal anatomy, biochemical processes, and feather coloration

Molecular versus morphological dataEdit

The characteristics used to create a cladogram can be roughly categorized as either morphological (synapsid skull, warm-blooded, notochord, unicellular, etc.) or molecular (DNA, RNA, or other genetic information).[18] Prior to the advent of DNA sequencing, all cladistic analysis used morphological data.

As DNA sequencing has become cheaper and easier, molecular systematics has become a more and more popular way to reconstruct phylogenies.[19] 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 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.

Plesiomorphies and synapomorphiesEdit

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. 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.

Avoid homoplasiesEdit

A homoplasy is a character that is shared by multiple species due to some cause other than common ancestry.[20] Typically, homoplasies occur due to convergent evolution. Use of homoplasies when building a cladogram is sometimes unavoidable but is to be avoided when possible.

A well-known example of homoplasy due to convergent evolution would be a character "presence of wings". Though the wings of birds, bats, and insects serve the same function, each evolved independently, as can be seen by their anatomy. If a bird, bat, 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 evolutionary scenario.

Homoplasies can often be avoided outright in morphological datasets by defining characters more precisely and increasing their number. In the example above, 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 imprecise, 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 or character set, no method of evaluation is likely to produce a phylogeny representing the evolutionary reality.

Step 2: Consider possible cladogramsEdit

File:Simple cladistics.svg
Main article: Computational phylogenetics

When there are just a few species being organized, it is possible to do this step manually, but most cases require a computer program. There are scores of computer programs available to support cladistics.[21] See phylogenetic tree for more information about tree-generating computer programs.

Because the total number of possible cladograms grows exponentially with the number of species, it is impractical for a computer program to evaluate every individual cladogram. A typical cladistic program begins by using heuristic techniques to identify a small number of candidate cladograms. Many cladistic programs then continue the search with the following repetitive steps:

  1. Evaluate the candidate cladograms by comparing them to the characteristic data
  2. Identify the best candidates that are most consistent with the characteristic data
  3. Create additional candidates by creating several variants of each of the best candidates from the prior step
  4. Use heuristics to create several new candidate cladograms unrelated to the prior candidates
  5. Repeat these steps until the cladograms stop getting better

Computer programs that generate cladograms use algorithms that are very computationally intensive,[22] because the cladogram algorithm is NP-hard.

Step 3: Select the best cladogramEdit

There are several algorithms available to identify the "best" cladogram.[23] Most algorithms use a metric to measure how consistent a candidate cladogram is with the data. Most cladogram algorithms use the mathematical techniques of optimization and minimization.

In general, cladogram-generation algorithms must be implemented as computer programs, although some algorithms can be performed manually when the data sets are trivial (for example, just a few species and a couple of characteristics).

Some algorithms are useful only when the characteristic data is molecular (DNA, RNA) data. Other algorithms are useful only when the characteristic data is morphological data. Other algorithms can be used when the characteristic data includes both molecular and morphological data.

Algorithms for cladograms include least squares, neighbor-joining, parsimony, maximum likelihood, and Bayesian inference.

Biologists sometimes use the term parsimony for a specific kind of cladogram-generation algorithm and sometimes as an umbrella term for all cladogram algorithms.[24]

Algorithms that perform optimization tasks (such as building cladograms) can be sensitive to the order in which the input data (the list of species and their characteristics) is presented. Inputting the data in various orders can cause the same algorithm to produce different "best" cladograms. In these situations, the user should input the data in various orders and compare the results.

Using different algorithms on a single data set can sometimes yield different "best" cladograms, because each algorithm may have a unique definition of what is "best".

Because of the astronomical number of possible cladograms, algorithms cannot guarantee that the solution is the overall best solution. A non-optimal cladogram will be selected if the program settles on a local minimum rather than the desired global minimum.[25] To help solve this problem, many cladogram algorithms use a simulated annealing approach to increase the likelihood that the selected cladogram is the optimal one.[26]

How complex is the Tree of Life?Edit

One of the arguments in favor of cladistics is that it supports arbitrarily complex, arbitrarily deep trees. Especially when extinct species are considered (both known and unknown), the complexity and depth of the tree can be very large. Every single speciation event, including all the species that are now extinct, represents an additional fork on the hypothetical, complete cladogram representing the full tree of life. Fractals can be used to represent this notion of increasing detail: as a viewpoint zooms into the tree of life, the complexity remains virtually constant[27]. This great complexity of the tree, and the uncertainty associated with the complexity, is one of the reasons that cladists cite for the attractiveness of cladistics over traditional taxonomy.

Proponents of non-cladistic approaches to taxonomy point to puncuated equilibrium to bolster the case that the tree-of-life has a finite depth and finite complexity. If the number of species currently alive is finite, and the number of extinct species that we will ever know about is finite, then the depth and complexity of the tree of life is bounded, and there is no need to handle arbitrarily deep trees.

Phylocode approach to naming speciesEdit

A formal code of phylogenetic nomenclature, the PhyloCode[28], 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.

TerminologyEdit

File:Phylogenetic-Groups.svg
Main article: Phylogenetic nomenclature
  • A clade is an ancestor species and all of its decencents
  • A monophyletic group is a clade
  • A paraphyletic group is a monophyletic group that excludes some of the descendants (e.g. reptiles are sauropsids excluding birds). Most cladists discourage the use of paraphyletic groups.
  • A polyphyletic group is a group consisting of members from two non-overlapping monophyletic groups (e.g. flying animals). Most cladists discourage the use of polyphyletic groups.
  • An outgroup is an organism that is considered not to be part of the group in question, but is closely related to the group.
  • A characteristic that is present in both the outgroups and in the ancestors is called a plesiomorphy (meaning "close form", also called an ancestral state).
  • A characteristic that occurs only in later descendants is called an apomorphy (meaning "separate form", also called a "derived" state) for that group. Note: 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.
  • 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, palaeodicots are basal to flowering plants.
  • A clade or species located within another clade is said to be nested within that clade.

Origin of the term "cladistics"Edit

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. A review paper by Dupuis 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.[29]

Clade types

Three definitions of cladeEdit

There are three ways to define a clade for use in a cladistic taxonomy.[30]

  • Node-based: the most recent common ancestor of A and B along with all of 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, along with all of its descendants, possessing a certain derived character. This definition is generally discouraged by most cladists.

Applying Cladistics to other disciplinesEdit

The processes used to generate cladograms are not limited to the field of biology[31]. The generic nature of cladistics means that cladistics can be used to organize groups of items in many different realms. The only requirement is that the items have chararacteristics that can be identified and measured.

For example, one could take a group of 200 spoken languages, measure various characteristics of each language (vocabulary, phonemes, rhythms, accents, dynamics, etc) and then apply a cladogram algorithm to the data. The result will be a tree that may shed light on how, and in what order, the languages came into existence.

Thus, cladistic methods have recently been usefully applied to non-biological systems, including determining language families in historical linguistics, culture, history[32], and filiation of manuscripts in textual criticism.

FootnotesEdit

  1. Phylogenetic Systematics is the title of Hennig's 1966 book
  2. 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.
  3. Singh, Gurcharan (2004). Plant Systematics: An Integrated Approach, 203-4, Science.
  4. Albert, Victor (2006). Parsimony, Phylogeny, and Genomics, Oxford University Press.
  5. Aldous, David (1996), "Probability Distributions on Cladograms", Random Discrete Structures, Springer, p. 13 
  6. Lowe, Andrew (2004). Ecological Genetics: Design, Analysis, and Application, Blackwell Publishing.
  7. Scott-Ram, N. R. (1990). Transformed Cladistics, Taxonomy and Evolution, Cambridge University Press.
  8. Freeman, Scott (1998). Evolutionary Analysis, Prentice Hall.
  9. Carrol, Robert (1997). Patterns and Processes of Vertebrate Evolution, Cambridge University Press.
  10. Letunic, I (2007). Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation.. Bioinformatics 23(1): 127-8.
  11. Wheeler, Quentin (2000). Species Concepts and Phylogenetic Theory: A Debate, Columbia University Press.
  12. Benton, M. (2000). Stems, nodes, crown clades, and rank-free lists: is Linnaeus dead?. Biological Reviews 75 (4): 633-648.
  13. Hull, David (1988). Science as a Process, University of Chicago Press.
  14. Hennig, Willi (1975). 'Cladistic analysis or cladistic classification': a reply to Ernst Mayr. Systematic Zoology 24: 244-256.
  15. Mayr, Ernst (1976). Evolution and the diversity of life (Selected essays), Cambridge, MA: Harvard Univ. Press.
  16. Mayr, Ernst (1982). The growth of biological thought: diversity, evolution and inheritance, Cambridge, MA: Harvard Univ. Press.
  17. Hodge T, Cope M (2000). A myosin family tree. J Cell Sci 113 Pt 19: 3353-4. PMID 10984423.
  18. 18.0 18.1 DeSalle, Rob (2002). Techniques in Molecular Systematics and Evolution, Birkhauser.
  19. Hillis, David (1996). Molecular Systematics, Sinaur.
  20. West-Eberhard, Mary (2003). Developmental Plasticity and Evolution, 353-376, Oxford Univ. Press.
  21. List of Cladistics Software Programs.
  22. Hodkinson, Trevor (2006). Reconstructing the Tree of Life: Taxonomy and Systematics of Species Rich Taxa, CRC Press.
  23. Kitching, Ian (1998). Cladistics: The Theory and Practice of Parsimony Analysis, Oxford University Press.
  24. Stewart, Caro-Beth (1993). The Powers and Pitfalls of Parsimony. Nature 361: 603-607.
  25. Foley, Peter (1993). Cladistics: A Practical Course in Systematics, Oxford Univ. Press.
  26. Nixon K. C. (1999). The Parsimony Ratchet: a new method for rapid parsimony analysis. Cladistics 15: 407-414.
  27. Gordon, Richard (1999). The Hierarchical Genome and Differentiation Waves, World Scientific.
  28. Pennisi, E. (2001). Evolutionary Biology: Preparing the Ground for a Modern 'Tree of Life'. Science 293: 1979-1980.
  29. Dupuis, Claude (1984). Willi Hennig's impact on taxonomic thought. Annual Review of Ecology and Systematics 15: 1-24.
  30. de Queiroz, K. and J. Gauthier (1994). Toward a phylogenetic system of biological nomenclature. Trends in Research in Ecology and Evolution 9 (1): 27-31.
  31. Mace, Ruth (2005). The Evolution of Cultural Diversity: A Phylogenetic Approach, Routledge Cavendish.
  32. Lipo, Carl (2005). Mapping Our Ancestors: Phylogenetic Approaches in Anthropology and Prehistory, Aldine Transaction.

See also Edit

ReferencesEdit

  • Ashlock, Peter D. (1974). The uses of cladistics. Annual Review of Ecology and Systematics 5: 81-99.
  • 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'.
  • Cavalli-Sforza, L.L. and A.W.F. Edwards (Sep., 1967). Phylogenetic analysis: Models and estimation procedures. Evol. 21 (3): 550-570.
  • de Queiroz, Kevin (1992). Phylogenetic taxonomy. Annual Review of Ecology and Systematics 23: 449–480.
  • Dupuis, Claude (1984). Willi Hennig's impact on taxonomic thought. Annual Review of Ecology and Systematics 15: 1-24.
  • Felsenstein, Joseph (2004). Inferring phylogenies, Sunderland, MA: Sinauer Associates.
  • 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.
  • Hennig, Willi (1950). Grundzüge einer Theorie der Phylogenetischen Systematik, Berlin: Deutscher Zentralverlag..
  • Hennig, Willi (1982). Phylogenetische Systematik (ed. Wolfgang Hennig), Berlin: Blackwell Wissenschaft.
  • 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).
  • Hennig, Willi (1979). Phylogenetic systematics (3rd edition of 1966 book).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.
  • Luria, Salvador; Stephen Jay Gould and Sam Singer (1981). A view of life, Menlo Park, CA: Benjamin/Cummings.
  • Mayr, Ernst (1982). The growth of biological thought: diversity, evolution and inheritance, Cambridge, MA: Harvard Univ. Press.
  • Mayr, Ernst (1976). Evolution and the diversity of life (Selected essays), Cambridge, MA: Harvard Univ. Press. 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.
  • 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" Hillis, David M; C. Moritz and B. K. Mable (editors) Molecular Systematics, 2. ed., Sunderland, MA: Sinauer Associates.
  • Wiley, Edward O. (1981). Phylogenetics: The Theory and Practice of Phylogenetic Systematics, New York: Wiley Interscience.
  • Zwickl DJ, Hillis DM (2002). Increased taxon sampling greatly reduces phylogenetic error. Systematic Biology 51: 588-598.

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