Cladistics
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{{For|the scientific journal|Cladistics (journal)}}
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'''Cladistics''' is the hierarchical classification of [[species]] based on evolutionary ancestry. Cladistics is distinguished from other [[taxonomic]] systems because it focuses on [[evolution]] rather than 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]]. Cladistics originated in the work of the German [[entomologist]], [[Willi Hennig]], who himself referred to it as ''phylogenetic systematics''; the use of the terms "cladistics" and "clade" was popularized by other researchers.<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'', "branch."
== Cladograms ==
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>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 become available.
===Synonyms===
The terms ''[[evolutionary tree]]'', and sometimes ''[[phylogenetic tree]]'' are often used synonymously with ''cladogram'',<ref>
{{cite book|
last= Singh| first=Gurcharan |
title=Plant Systematics: An Integrated Approach |
publisher=Science|
pages=203-4 |
year=2004 |
isbn=1578083516
}}
</ref> but others treat ''phylogenetic tree'' as a broader term that includes trees generated with a nonevolutionary emphasis.
===Subtrees are clades===
In cladograms, 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]]''.
===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. See ''[[phylogenetic tree]]'' for more information about forking choices in trees.
===Number of distinct cladograms===
For a given set of species, the number of distinct 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>
{| border="1" cellpadding="1"
|-valign="top"
|width="14%"|'''Number of Species'''
|width="5%"|'''2'''
|width="5%"|'''3'''
|width="5%"|'''4'''
|width="5%"|'''5'''
|width="5%"|'''6'''
|width="5%"|'''7'''
|width="5%"|'''8'''
|width="5%"|'''9'''
|width="5%"|'''10'''
|width="10%"|'''N'''
|-valign="top" cellpadding="1"
|'''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===
Cladistics makes no distinction between extinct and nonextinct 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.
===Cladogram===
====Depth====
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
| last1 = Aldous| first1 = David
| contribution = Probability Distributions on Cladograms
| title = Random Discrete Structures
| publisher = Springer
| year = 1996
| pages = 13 }}</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.
====Time scale====
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:
* Many cladograms are built from species characteristics that cannot be readily dated (e.g. morphological 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<ref>
{{cite book|
page=80|
last=Carroll | first=Robert Lynn|
year=1997|
title=Patterns and Processes of Vertebrate Evolution |
publisher=Cambridge University Press|
isbn=052147809X
}}
</ref>
* 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
==Traditional taxonomy==
[[Image:Tree of life SVG.svg|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 | doi = 10.1093/bioinformatics/btl529 <!--Retrieved from Yahoo! by DOI bot-->| 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>]]
Prior to the advent of cladistics, most taxonomists used [[Linnaean taxonomy]] and later [[Evolutionary taxonomy]] to organize life forms. These traditional approaches, still in use by some researchers (especially in works intended for a more general audience<ref name=DU06b>{{cite book |last=Unwin |first=David M. |authorlink=David M. Unwin |title=The Pterosaurs: From Deep Time |year=2006 |publisher=Pi Press |location=New York |isbn=ISBN 0-13-146308-X |pages=246}}</ref>) use 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 so deep and so complex that it is inadvisable to set a fixed number of levels.
Evolutionary taxonomy insists that groups reflect [[phylogenetics|phylogenies]]. In contrast, Linnean taxonomy allows both monophyletic and paraphyletic groups as [[taxa]]. Since the early 20th century, Linnaean taxonomists have generally attempted to make [[genus]]-level and lower-level taxa monophyletic. [[Ernst Mayr]] drew a distinction between the terms cladistics and phylogeny, using the term ''cladistics'' to refer to classifications which only take into account [[genealogy]], as opposed to ''phylogeny'', which had previously been used in a broader sense to refer to the combination of genealogy and amount of divergence from an ancestor (i.e. Evolutionary taxonomy). Mayr wrote, in 1985:
{{quote|It would seem to me to be quite evident that the two concepts of phylogeny (and their role in the construction of classifications) are sufficiently different to require terminological distinction. The term ''phylogeny'' should be retained for the broad concept of phylogeny, promoted by [[Charles Darwin|Darwin]] and adopted by most students of phylogeny in the ensuing 90 years. The concept of phylogeny as mere genealogy should be terminologically distinguished as ''cladistics''. To lump the two concepts together terminologically could not help but produce harmful equivocation.|<ref name="mayr1985">Mayr, E. (1985). "Darwin and the Definition of Phylogeny." ''Systematic Zoology'', '''34'''(1): 97-98.</ref>}}
[[Willi Hennig]]'s pioneering work provoked a spirited debate<ref>
{{cite book|
title=Species Concepts and Phylogenetic Theory: A Debate |
last=Wheeler|first=Quentin|
isbn=0231101430|
publisher=Columbia University Press|
year=2000
}}</ref> about the relative merits of cladistics versus traditional taxonomy which has continued down to the present.<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 seen from the ''Foreword'' to Hennig (1979) by Rosen, Nelson, and Patterson:
{{quote|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}}
Cladistics strictly and exclusively follows [[phylogeny]], and has arbitrarily deep trees with binary branching: each taxon is a clade. Linnaean taxonomy, while following phylogeny, also subjectively considers [[morphology (biology)|morphology]], and has a fixed hierarchy, whose taxa are not always clades.
===Example===
{{details|Reptilia#History of classification}}
For example, Linnaean taxonomy contains the taxon [[Tetrapoda]], defined morphologically as [[vertebrates]] with four limbs (as well as animals with four-limbed ancestors, such as snakes), which is often given the rank of [[Superclass (biology)|superclass]], and divides into the [[class (biology)|classes]] [[Amphibia]], [[Reptilia]], [[Aves]], [[Mammalia]], and some extinct [[family (biology)|families]].
Cladistics also contains the taxon [[Tetrapoda]], whose living members can be classified phylogenically as "the clade defined by the common ancestor of amphibians and mammals", or more precisely the clade defined by the common ancestor of a specific amphibian and mammal (or bird or reptile), but whose tree is still being worked out (there are a number of extinct branches). The taxon does not have a rank, and its subtaxa are subclades: these can be contained within one another, but one does not divide the clade into several non-overlapping taxa (as in traditional taxonomy): one can split into two clades at the first branching, but that is all. With regards to the traditional classes, [[Aves]] and [[Mammalia]] are subclades, contained in the subclade [[Amniota]], but Reptilia* is a paraphyletic taxon, not a clade — "At best, the cladists suggest, we could say that the traditional Reptilia are "non-avian, non-mammalian amniotes"<ref name="tudge">{{RefTudgeVariety}}</ref> — and instead one divides Amniota into the two clades [[Sauropsida]] (which contains birds and all living amniotes other than mammals, including all living traditional reptiles) and [[Theropsida]] (mammals and the extinct "mammal-like reptiles"). Similarly, Amphibia* is a paraphyletic taxon.
===Distinctions===
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 | doi=10.2307/2412765 }}</ref>
{| border="1" cellpadding="2"
|-valign="top"
|width="40%" style="background:#ffcd9c;" |'''Cladistics'''
|width="40%" style="background:#ddffdd;" |'''Linnaean Taxonomy'''
|-valign="top"
|bgcolor="#ffefbe"|Treats all levels of the tree as equivalent.
|bgcolor="#eeffee"|Treats each tree level uniquely. Uses special names (such as Family, Class, Order) for each level.
|-valign="top"
|bgcolor="#ffefbe" |Handles arbitrarily deep trees.
|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.
|-valign="top"
|bgcolor="#ffefbe" |Discourages naming or use of groups that are not [[Clade|monophyletic]]
|bgcolor="#eeffee" |Acceptable to name and use [[Clade|paraphyletic]] groups
|-valign="top"
|bgcolor="#ffefbe"|Primary goal is to reflect actual process of evolution
|bgcolor="#eeffee"|Primary goal is to group species based on morphological similarities
|-valign="top"
|bgcolor="#ffefbe"|Assumes that the shape of the tree will change frequently, with new discoveries
|bgcolor="#eeffee"|New discoveries often require renaming or releveling of Classes, Orders, and Kingdoms
|-valign="top"
|bgcolor="#ffefbe"|Definitions of taxa are objective, hence free from personal interpretation
|bgcolor="#eeffee"|Definitions of taxa require individuals to make subjective decisions. For example, various taxonomists suggest that the number of [[Kingdom (biology)|Kingdom]]s in Biology is two, three, four, five, or six.
|-valign="top"
|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")
|bgcolor="#eeffee"|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:<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>
{| border="1" cellpadding="2"
|-valign="top"
|width="40%" style="background:#ffcd9c;" |'''Cladistics'''
|width="40%" style="background:#ddffdd;" |'''Linnaean Taxonomy'''
|-valign="top"
|bgcolor="#ffefbe"|Limited to entities related by evolution or ancestry
|bgcolor="#eeffee"|Supports groupings without reference to evolution or ancestry
|-valign="top"
|bgcolor="#ffefbe"|Does not include a process for naming species
|bgcolor="#eeffee"|Includes a process for giving unique names to species
|-valign="top"
|bgcolor="#ffefbe"|Difficult to understand the essence of a clade, because clade definitions emphasize ancestry at the expense of meaningful characteristics
|bgcolor="#eeffee"|Taxa definitions based on tangible characteristics
|-valign="top"
|bgcolor="#ffefbe"|Ignores sensible, clearly defined paraphyletic groups such as [[reptiles]]
|bgcolor="#eeffee"|Permits clearly defined groups such as [[reptiles]]
|-valign="top"
|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)
|bgcolor="#eeffee"|Straightforward process to determine if a given species is in a taxon or not
|-valign="top"
|bgcolor="#ffefbe"|Limited to organisms that evolved by inherited traits; not applicable to organisms that evolved via complex gene sharing or lateral transfer
|bgcolor="#eeffee"|Applicable to all organisms, regardless of evolutionary mechanism
|}
==Cladistics compared to phenetics==
For some decades in the mid to late 20th century, a commonly used methodology was [[phenetics]] ("numerical taxonomy"). This can be seen as a predecessor<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 in their time as they were among the first [[bioinformatics]] applications, phenetic methods are today superseded by cladistic analyses{{Fact|date=November 2007}} due to the inability of phenetics to provide an [[evolution]]ary hypothesis, except by chance: as phenetics does not distinguish between ''plesiomorphies'' (ancient common retained characters) and ''apomorphies'' (novel characters that arose after the last common ancestor), it will consider groups as "natural" even if they are only united by "primitive" (i.e., retained) characters.
Consider for example a [[cow]], a [[whale]] and a [[human]]. A cladistic analysis would recognize the whale's lack of legs as an apomorphy, whereas the presence of legs in cows and humans is plesiomorphic. It thus does not provide information on their relationships in a cladistic analysis, except that their last common ancestor had legs too. In a phenetic analysis, the presence of legs in cows and humans could be considered to indicate that they are closer relatives of each other than either is to whales. In fact, whales and cows are closer related to each other than either is to humans.
In short, phenetic analysis tend to resolve [[evolutionary grade]]s as presumably [[Clade|monophyletic]] groups.
==Monophyletic groups encouraged==
Many cladists discourage the use of paraphyletic groups because they detract from cladistics' 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==
{{howto}}
[[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 |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===
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|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 are unrecognizable 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 the character, "presence of wings". Though the wings of birds, [[bat]]s, 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 would confound 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. 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; to continue with the "wings" example, the presence of wings would be hardly be a useful character 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===
[[Image:Simple cladistics.png|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===
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|
doi=10.1038/361603a0
}}</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 nonoptimal 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|
doi=10.1111/j.1096-0031.1999.tb00277.x
}}</ref>
==Complexity of the Tree of Life==
One argument 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. [[Fractal]]s 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, are among the reasons that cladists cite for the attractiveness of cladistics over traditional taxonomy.
Proponents of noncladistic approaches to taxonomy point to [[punctuated 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' | doi = 10.1126/science.293.5537.1979 <!--Retrieved from Yahoo! by DOI bot-->|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 descendents
* 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, [[palaeodicot]]s 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====
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'', as 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|doi=10.1016/0169-5347(94)90231-3}}</ref>
*''Node based'': the most recent common ancestor of A and B, and all its descendants. See [[crown group]].
* ''Stem based'': all descendants of the oldest common ancestor of A and B that is not also an ancestor of Z. See [[total group]].
*''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.
==Application 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 academic realms. The only requirement is that the items have characteristics that can be identified and measured.
[[Image:Gldt.svg|thumb|right|A triple family tree of Linux distributions.]]
Recent attempts in the use of cladistic methods outside of biology attack problems in anthropology<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>, [[historical linguistics|languages]],
the filiation of manuscripts in [[textual criticism]]{{Fact|date=May 2008}}, and the lineage of [[Linux distros]], a class of computer [[operating system]]{{Fact|date=May 2008}}.
==Criticisms==
Critics of cladistics include Ashlock,<ref>Ashlock PD. 1971. Monophyly and associated terms. Systematic Zoology 20: 63–69.<br />Ashlock PD. 1972. Monophyly again. Systematic Zoology 21: 430–438.<br />Ashlock PD. 1974. The uses of cladistics. Annual Review of Ecology and Systematics 5: 81–89.<br />Ashlock PD. 1979. An evolutionary systematist’s view of classification. Systematic Zoology 28: 441–450.</ref> Mayr,<ref>Mayr E. 1974. Cladistic analysis or cladistic classification? Zeitschrift fűr Zoologische Systematik und Evolutionforschung 12: 94–128.<br />Mayr E. 1978. Origin and history of some terms in systematic and evolutionary biology. Systematic Zoology 27: 83–88.<br />Mayr E, Bock WJ. 2002. Classifications and other ordering systems. Journal of Zoological Systematics and Evolutionary Research 40: 169–194.</ref> Williams<ref>Williams, P.A. 1992. Confusion in cladism. Synthese 01:135-132</ref> and Envall<ref>Envall, M. 2008. On mono-, holo- and paraphyletic groups - a consistentdistinction of process and pattern. Biol. J. Linn. Soc. 94:217-220.</ref>.
==Footnotes==
{{reflist|2}}
== 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]]
*[[Last common ancestor]]
*[[List of publications in biology#Phylogenetics|Important publications in phylogenetics]]
*[[Language family]]
*[[Maximum parsimony]]
*[[Molecular phylogeny]]
*[[PhyloCode]]
| valign=top width=33% |
*[[Phylogenetics]]
*[[Phylogenetic tree]]
*[[Phylogenetic network]]
*[[List of phylogenetics software|Phylogenetics software]]
*[[Phylogeography]]
*[[Phylogenetic comparative methods]]
*[[Scientific Classification]]
*[[Systematics]]
|}
==References==<!-- Systematics and Biodiversity4: 137–147
doi:10.1017/S1477200005001830; ZoolScripta33:293 -->
<div class="references-small">
* {{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 | doi=10.1146/annurev.es.05.110174.000501 }}
* {{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=[[L.L. Cavalli-Sforza|Cavalli-Sforza, L.L.]] and [[A.W.F. Edwards]]
|month=Sep.,
|year=1967
|title=Phylogenetic analysis: Models and estimation procedures
|journal=Evol.
|volume=21
|issue=3
|pages=550–570
|url=http://links.jstor.org/sici?sici=0014-3820%28196709%2921%3A3%3C550%3APAMAEP%3E2.0.CO%3B2-I
|doi=10.2307/2406616
}}
* {{cite journal | last=de Queiroz | first=Kevin | date=1992 | title= Phylogenetic taxonomy | journal=Annual Review of Ecology and Systematics | issn=0066-4162 | volume=23 | pages= 449–480 | author=and Jacques A. Gauthier | doi= 10.1111/j.1096-3642.2006.00293.x }}
* {{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 | doi=10.1006/jmbi.1999.2797}}
* {{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 | doi=10.2307/2412765 }} 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 | doi=10.2307/2412558 }}
* {{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)''
* {{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 | doi = 10.1002/(SICI)1521-1878(200002)22:2 <!--Retrieved from PMID by DOI bot--> }}
* {{cite journal | last=Sokal | first=Robert R. | date=1975 | title=Mayr on cladism -- and his critics | journal=Systematic Zoology | volume=24 | pages=257–262 | doi=10.2307/2412766 }}
* {{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 | 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 |doi=10.1080/10635150290102339}}
</div>
==External links==
{{Spoken Wikipedia|Cladistics.ogg|2005-04-30}}
* [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://www.ucmp.berkeley.edu/clad/clad4.html Journey into Phylogenetic Systematics]
* [http://www.talkorigins.org/faqs/comdesc/phylo.html Phylogenetics Primer] from Talk.Origins
* [http://www.cladistics.org Willi Hennig Society]
* [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://evolution.genetics.washington.edu/phylip/software.pars.html A list of cladogram-generating programs]
* For a cladistic approach to animal classification: [http://anthro.palomar.edu/animal/default.htm Classification of living things]
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