Cladistics

For the scientific journal, see Cladistics (journal).

This cladogram shows the evolutionary relationship among various insect groups inferred from a dataset.

Cladograms are trees in the graph theoretic sense.

Cladistics is a philosophy of classification that arranges organisms only by their order of branching in an evolutionary tree and not by their morphological similarity, in the words of Luria et al. (1981). A major contributor to this school of thought was the German entomologist Willi Hennig, who referred to it as phylogenetic systematics (Hennig, 1966). The word cladistics is derived from the ancient Greek κλάδος, klados, or "branch."

Cladograms

As the end result of a cladistic analysis, 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 morphological data.

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

3-Way forks

Cladistics dictates that all branches in a cladogram be two-way fork. Trees can be drawn with 3-way forks or 4-way forks, but they are not true cladograms and are discouraged by the principles of cladistics. 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). 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 aobut 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 caldogram will not be uniformly deep.

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:

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.

Represenation of Extinct Species in Cladograms

Cladistics makes no distinction between extinct and non-extinct species, 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, expecialy morphological characteristics that are preserved in fossils, are more likely to include extinct species.

Incorporation of Time in Cladogram

The cladogram tree has an implicit time axis, 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.

In practice, cladograms typically do not attempt to represent the time axis, for a variety of reasons. First, most cladistic methods that generate cladograms do not produce dating information (although DNA/RNA data often does provide approximate dates for the forks). Second even if the dating information were 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.

Terminology

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

A group with members from separate evolutionary lines is called polyphyletic. For instance, the once-recognized Pachydermata was found to be polyphyletic because elephants and rhinoceroses arose from non-pachyderms separately. Evolutionary taxonomists consider polyphyletic groups to be errors in classification, often occurring because convergence or other homoplasy was misinterpreted as homology. 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 character state (see below) that is present in both the outgroups (see below) and in the ancestors is called a plesiomorphy (meaning "close form", also called an ancestral state). A character state that occurs only in later descendants is called an apomorphy (meaning "separate form", also called a "derived" state) for that group. The adjectives plesiomorphic and apomorphic are used instead of "primitive" and "advanced" to avoid placing value-judgments on the evolution of the character states, since both may be advantageous in different circumstances. It is not uncommon to refer informally to a collective set of plesiomorphies as a ground plan for the clade or clades they refer to.

A species or clade is basal to another clade if it holds more plesiomorphic characters than that other clade. Usually a basal group is very species-poor as compared to a more derived group. It is not a requirement that a basal group be extant. For example, when considering birds and mammals together, neither is basal to the other: both have many derived characters.

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

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 (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.

Cladistics Compared to Alternative Taxonomic Approaches

Cladistics is just one approach to organizing organisms into a hierarchy. Other approaches include Linnaean taxonomy and phenetics.

Cladistics Compared to Linnaean Taxonomy

Before Cladistics, most taxonomists used Linnaean taxonomy (a Kingdom-based approach) to organizing lifeforms. That traditional approach used several fixed levels of a hierarchy, such as Kingdom, Phylum, Biology, 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.

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

The school of thought now known as cladistics took inspiration from the work of Willi Hennig. Some of the debates that the cladists engaged in had been running since the 19th century, but they entered these debates with a new fervor, as can be learned from the Foreword to Hennig (1979) in which Rosen, Nelson and Patterson wrote the following:

Encumbered with vague and slippery ideas about adaptation, fitness, biological species and natural selection, neo-Darwinism (summed up in the "evolutionary" systematics of Mayr and Simpson) not only lacked a definable investigatory method, but came to depend, both for evolutionary interpretation and classification, on consensus or authority. (Foreword, page ix).

The key distinctions between cladistics and Linnaean taxonomy are:

Cladistics	Linnean Taxonomy
Treats all levels of the tree as equivalent	Assigns special significance and names to various levels (Genus, Family, etc).
Requires all forks in the tree to be 2-way forks	Common to have 3-way, 4-way, or larger forks
Discourages naming or use of groups of species that are not sub-trees (monophyletic)	Acceptable to name and use groups of species that are not sub-trees (paraphyletic, polyphyletic)
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
Aims to be an objective process, free from personal interpretation	Some aspects are subjective (for example, see 3-Kingom, 5-Kingdom, 6-Kingdom schemes in Kingdom (biology)

Cladistics Compared to Phenetics

For some decades in the mid-late 20th century, the dominant methodology was phenetics ("numerical taxonomy"). This can be seen as a precedessor 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 superceded by cladistic analyses due to their inability of phenetics to provide an evolutionary hypothesis, except by chance.

Cladistic methods

Starting Point

A cladistic analysis begins with a certain set of information, usually a group of species, and a set of characteristics for each species.

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."

Step-By-Step Procedure

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.

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

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

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

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

The Final Result: A Cladogram

Many cladograms are possible for any given set of taxa, but one is chosen based on the principle of parsimony: the most compact arrangement, that is, with the fewest character state changes (synapomorphies), is the hypothesis of relationship accept here (see Occam's razor for a discussion of the principle of parsimony and possible complications).

The chosen cladogram is selected because it is optimal as defined by some metric. There are several metrics available to determine which cladogram - of all possible cladograms - best fits the raw data. Using different metrics can - in some circumstances - yield different optimal cladograms for the same data set.

Genetic vs. Morphological Data

The data used to create a cladogram can be roughly categorized as either morphological (synapsid skull, warm-blooded, notochord, unicellular, etc) or genetic (DNA, RNA, or other genetic information). 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. 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.

Use of Computer Programs for Cladistics

When the number of species under study is extremely large, or when the amount of information used is large (for instance, when using RNA for cladistics) it becomes impossible to generate a cladogram by manual methods. In these cases a computer program must be used, such as PAUP*.

Computer programs that generate Cladograms use algorithms that are very computationally intensive, since the cladogram algorithm is NP-hard. The programs that generate cladograms are trying to minimize a metric. Because of the astronomical number of possible cladograms, minimization programs 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". To help solve this problem, many cladogram programs use a simulated annealing approach to increase the likelihood that the selected cladogram is the optimal one. See Phylogenetic tree for more information about tree-generating computer programs.

Another issue faced by users computer programs is that some programs can be sensitive to the order the input data (list of species and their characteristics) is presented. Inputting the data in various ways can cause such programs to produce multiple "best" cladograms. In these cases, the users should input the data multiple times and compare the results.

Three Definitions of Clade

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

Groups of Organisms that are Not Clades

Main article: Phylogenetic nomenclature

A clade is a complete subtree of a cladogram. Some groups of organisms are not clades, for example paraphyletic groups and polyphyletic groups. A clade is also called a monophyletic group.

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

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

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

PhyloCode

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.

Application of Cladisitics to Other Fields

The processes used to generate cladograms are not limited to the field of biology. 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 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.

See also

• Clade
• Dendrogram
• Evolution of Mollusca for a cladistic illustration
• Evolutionary tree
• PhyloCode
• Phylogenetic tree
• Last common ancestor
• Important publications in cladistics
• Scientific classification

References

• Ashlock, Peter D. (1974). "The uses of cladistics". Annual Review of Ecology and Systematics. 5: 81–99. ISSN 0066-4162.
• Cuénot, Lucien (1940). "Remarques sur un essai d'arbre généalogique du règne animal". Comptes Rendus de l'Académie des Sciences de Paris. 210: 23–27. Available free online at http://gallica.bnf.fr (No direct URL). This is the paper credited by Hennig (1979) for the first use of the term 'clade'.
• de Queiroz, Kevin (1992). "Phylogenetic taxonomy". Annual Review of Ecology and Systematics. 23: 449–480. ISSN 0066-4162. {{cite journal}}: Unknown parameter |authors= ignored (help)
• Dupuis, Claude (1984). "Willi Hennig's impact on taxonomic thought". Annual Review of Ecology and Systematics. 15: 1–24. ISSN 0066-4162.
• Felsenstein, Joseph (2004). Inferring phylogenies. Sunderland, MA: Sinauer Associates. ISBN 0-87893-177-5.
• Hamdi, Hamdi (1999). "Origin and phylogenetic distribution of Alu DNA repeats: irreversible events in the evolution of primates". Journal of Molecular Biology. 289: 861–871. PMID 10369767. {{cite journal}}: Unknown parameter |coauthors= ignored (|author= suggested) (help)
• Hennig, Willi (1950). Grundzüge einer Theorie der Phylogenetischen Systematik. Berlin: Deutscher Zentralverlag..
• Hennig, Willi (1982). Phylogenetische Systematik (ed. Wolfgang Hennig). Berlin: Blackwell Wissenschaft. ISBN 3-8263-2841-8.
• Hennig, Willi (1975). "'Cladistic analysis or cladistic classification': a reply to Ernst Mayr". Systematic Zoology. 24: 244–256. The paper he was responding to is reprinted in Mayr (1976).
• Hennig, Willi (1966). Phylogenetic systematics (tr. D. Dwight Davis and Rainer Zangerl). Urbana, IL: Univ. of Illinois Press (reprinted 1979 and 1999). ISBN 0-252-06814-9.Translated from manuscript and so never published in German.
• Hull, David L. (1979). "The limits of cladism". Systematic Zoology. 28: 416–440.
• Kitching, Ian J. (1998). Cladistics: Theory and practice of parsimony analysis (2nd ed. ed.). Oxford University Press. ISBN 0-19-850138-2. {{cite book}}: |edition= has extra text (help); Unknown parameter |coauthors= ignored (|author= suggested) (help)
• Luria, Salvador (1981). A view of life. Menlo Park, CA: Benjamin/Cummings. ISBN 0-8053-6648-2. {{cite book}}: Unknown parameter |coauthors= ignored (|author= suggested) (help)
• Mayr, Ernst (1982). The growth of biological thought: diversity, evolution and inheritance. Cambridge, MA: Harvard Univ. Press. ISBN 0-674-36446-5.
• Mayr, Ernst (1976). Evolution and the diversity of life (Selected essays). Cambridge, MA: Harvard Univ. Press. ISBN 0-674-27105-X. Reissued 1997 in paperback. Includes a reprint of Mayr's 1974 anti-cladistics paper at pp. 433-476, "Cladistic analysis or cladistic classification." This is the paper to which Hennig (1975) is a response.
• Patterson, Colin (1982). "Morphological characters and homology". In Joysey, Kenneth A; A. E. Friday (editors) (ed.). Problems in Phylogenetic Reconstruction. London: Academic Press. ISBN 0-12-391250-4. {{cite conference}}: |editor= has generic name (help); Unknown parameter |booktitle= ignored (|book-title= suggested) (help)CS1 maint: multiple names: editors list (link)
• Rosen, Donn; Gareth Nelson and Colin Patterson (1979), Foreword provided for Hennig (1979)
• Shedlock, Andrew M (2000). "SINE insertions: Powerful tools for molecular systematics". Bioessays. 22: 148–160. ISSN 0039-7989. PMID 10655034. {{cite journal}}: Unknown parameter |coauthors= ignored (|author= suggested) (help)
• Sokal, Robert R. (1975). "Mayr on cladism -- and his critics". Systematic Zoology. 24: 257–262.
• Swofford, David L. (1996). "Phylogenetic inference". In Hillis, David M; C. Moritz and B. K. Mable (editors) (ed.). Molecular Systematics (2. ed. ed.). Sunderland, MA: Sinauer Associates. ISBN 0-87893-282-8. {{cite book}}: |edition= has extra text (help); |editor= has generic name (help); Unknown parameter |coauthors= ignored (|author= suggested) (help)CS1 maint: multiple names: editors list (link)
• Wiley, Edward O. (1981). Phylogenetics: The Theory and Practice of Phylogenetic Systematics. New York: Wiley Interscience. ISBN 0-471-05975-7.

External links

• The Compleat Cladist (pdf)
• Tree of Life illustration - A high-level cladogram showing the complete tree of life.
• Example of cladistics used in textual criticism
• Journey into Phylogenetic Systematics
• Phylogenetics Primer from Talk.Origins
• Willi Hennig Society
• Cladistics: The International Journal of the Willi Hennig Society (ISSN 0748-3007)
• Phylogenetic inferring on the T-REX server
• A list of cladogram-generating programs