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Cladistics

Cladistics

Overview
Cladistics is a method of classifying species of organisms into groups called clade
Clade
A clade is a group consisting of a species and all its descendants. In the terms of biological systematics, a clade is a single "branch" on the "tree of life". The idea that such a "natural group" of organisms should be grouped together and given a taxonomic name is central to biological...

s
, which consist of an ancestor organism and all its descendants (and nothing else). For example, birds, dinosaurs, crocodiles, and all descendants (living or extinct) of their most recent common ancestor form a clade. In the terms of biological systematics
Systematics
Biological systematics is the study of the diversification of terrestrial life, both past and present, and the relationships among living things through time. Relationships are visualized as evolutionary trees...

, a clade is a single "branch" on the "tree of life
Tree of life (science)
Charles Darwin proposed that phylogeny, the evolutionary relatedness among species through time, was expressible as a metaphor he termed the Tree of Life...

", a monophyletic group.

Cladistics can be distinguished from other taxonomic systems, such as morphology-based phenetics
Phenetics
In biology, phenetics, also known as taximetrics, is an attempt to classify organisms based on overall similarity, usually in morphology or other observable traits, regardless of their phylogeny or evolutionary relation. It is closely related to numerical taxonomy which is concerned with the use of...

, by its focus on shared derived characters (synapomorphies
Synapomorphy
In cladistics, a synapomorphy or synapomorphic character is a trait that is shared by two or more taxa and their most recent common ancestor, whose ancestor in turn does not possess the trait. A synapomorphy is thus an apomorphy visible in multiple taxa, where the trait in question originates in...

).
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Encyclopedia
Cladistics is a method of classifying species of organisms into groups called clade
Clade
A clade is a group consisting of a species and all its descendants. In the terms of biological systematics, a clade is a single "branch" on the "tree of life". The idea that such a "natural group" of organisms should be grouped together and given a taxonomic name is central to biological...

s
, which consist of an ancestor organism and all its descendants (and nothing else). For example, birds, dinosaurs, crocodiles, and all descendants (living or extinct) of their most recent common ancestor form a clade. In the terms of biological systematics
Systematics
Biological systematics is the study of the diversification of terrestrial life, both past and present, and the relationships among living things through time. Relationships are visualized as evolutionary trees...

, a clade is a single "branch" on the "tree of life
Tree of life (science)
Charles Darwin proposed that phylogeny, the evolutionary relatedness among species through time, was expressible as a metaphor he termed the Tree of Life...

", a monophyletic group.

Cladistics can be distinguished from other taxonomic systems, such as morphology-based phenetics
Phenetics
In biology, phenetics, also known as taximetrics, is an attempt to classify organisms based on overall similarity, usually in morphology or other observable traits, regardless of their phylogeny or evolutionary relation. It is closely related to numerical taxonomy which is concerned with the use of...

, by its focus on shared derived characters (synapomorphies
Synapomorphy
In cladistics, a synapomorphy or synapomorphic character is a trait that is shared by two or more taxa and their most recent common ancestor, whose ancestor in turn does not possess the trait. A synapomorphy is thus an apomorphy visible in multiple taxa, where the trait in question originates in...

). Systems developed earlier usually employed overall morphological similarity to group species into genera, families and other higher level groups (taxa
Taxon
|thumb|270px|[[African elephants]] form a widely-accepted taxon, the [[genus]] LoxodontaA taxon is a group of organisms, which a taxonomist adjudges to be a unit. Usually a taxon is given a name and a rank, although neither is a requirement...

); cladistic classifications (usually in the form of trees called cladogram
Cladogram
A cladogram is a diagram used in cladistics which shows ancestral relations between organisms, to represent the evolutionary tree of life. Although traditionally such cladograms were generated largely on the basis of morphological characters, DNA and RNA sequencing data and computational...

s) are intended to reflect the relative recency of common ancestry or the sharing of homologous
Homology (biology)
Homology forms the basis of organization for comparative biology. In 1843, Richard Owen defined homology as "the same organ in different animals under every variety of form and function". Organs as different as a bat's wing, a seal's flipper, a cat's paw and a human hand have a common underlying...

 features. Cladistics is also distinguished by an emphasis on parsimony
Maximum parsimony
Parsimony is a non-parametric statistical method commonly used in computational phylogenetics for estimating phylogenies. Under parsimony, the preferred phylogenetic tree is the tree that requires the least evolutionary change to explain some observed data....

 and hypothesis testing (particularly falsificationism), leading to a claim that cladistics is more objective than systems which rely on subjective judgements of relationship based on similarity.

Cladistics originated in the work of the German entomologist Willi Hennig
Willi Hennig
Emil Hans Willi Hennig was a German biologist who is considered the founder of phylogenetic systematics, also known as cladistics. With his works on evolution and systematics he revolutionised the view of the natural order of beings...

, who referred to it as "phylogenetic systematics" (also the name of his 1966 book); the use of the terms "cladistics" and "clade" was popularized by other researchers. The technique and sometimes the name have been successfully applied in other disciplines: for example, to determine the relationships between the surviving manuscripts of the Canterbury Tales.

Cladists use cladogram
Cladogram
A cladogram is a diagram used in cladistics which shows ancestral relations between organisms, to represent the evolutionary tree of life. Although traditionally such cladograms were generated largely on the basis of morphological characters, DNA and RNA sequencing data and computational...

s
– diagrams which show ancestral relations between species – to represent the monophyletic relationships of species, termed sister-group relationships. This is interpreted as representing phylogeny, or evolutionary relationships. Although traditionally such cladograms were generated largely on the basis of morphological characters, genetic sequencing
Genetic sequencing
Genetic Sequencing may refer to:* DNA sequencing* Full genome sequencing...

 data and computational phylogenetics
Computational phylogenetics
Computational phylogenetics is the application of computational algorithms, methods and programs to phylogenetic analyses. The goal is to assemble a phylogenetic tree representing a hypothesis about the evolutionary ancestry of a set of genes, species, or other taxa...

 are now very commonly used in the generation of cladograms.

Cladistics, either generally or in specific applications, has been criticized from its beginnings. A decision as to whether a particular character is a synapomorphy or not may be challenged as involving subjective judgements, raising the issue of whether cladistics as actually practised is as objective as has been claimed. Formal classifications based on cladistic reasoning are said to emphasize ancestry at the expense of descriptive characteristics, and thus ignore biologically sensible, clearly defined groups which do not fall into clades (e.g. reptiles as traditionally defined or prokaryotes).

History of cladistics


The term clade
Clade
A clade is a group consisting of a species and all its descendants. In the terms of biological systematics, a clade is a single "branch" on the "tree of life". The idea that such a "natural group" of organisms should be grouped together and given a taxonomic name is central to biological...

was introduced in 1958 by Julian Huxley
Julian Huxley
Sir Julian Sorell Huxley FRS was an English evolutionary biologist, humanist and internationalist. He was a proponent of natural selection, and a leading figure in the mid-twentieth century evolutionary synthesis...

, cladistic by Cain and Harrison in 1960, and cladist (for an adherent of Hennig's school) by Mayr in 1965. Hennig referred to his own approach as phylogenetic systematics. From the time of his original formulation until the end of the 1980s cladistics remained a minority approach to classification. However, in the 1990s it rapidly became the dominant method of classification in evolutionary biology. Computer
Computer
A computer is a programmable machine designed to sequentially and automatically carry out a sequence of arithmetic or logical operations. The particular sequence of operations can be changed readily, allowing the computer to solve more than one kind of problem...

s made it possible to process large quantities of data about organisms and their characteristics. At about the same time the development of effective polymerase chain reaction
Polymerase chain reaction
The polymerase chain reaction is a scientific technique in molecular biology to amplify a single or a few copies of a piece of DNA across several orders of magnitude, generating thousands to millions of copies of a particular DNA sequence....

 techniques made it possible to apply cladistic methods of analysis to biochemical and molecular genetic
Molecular genetics
Molecular genetics is the field of biology and genetics that studies the structure and function of genes at a molecular level. The field studies how the genes are transferred from generation to generation. Molecular genetics employs the methods of genetics and molecular biology...

 features of organisms as well as to anatomical ones.

Cladistics as a successor to phenetics


For some decades in the mid to late twentieth century, a commonly used methodology was phenetics
Phenetics
In biology, phenetics, also known as taximetrics, is an attempt to classify organisms based on overall similarity, usually in morphology or other observable traits, regardless of their phylogeny or evolutionary relation. It is closely related to numerical taxonomy which is concerned with the use of...

 ("numerical taxonomy"). This can be seen as a predecessor to some methods of today's cladistics (namely distance matrix
Distance matrices in phylogeny
Distance matrices are used in phylogeny asnon-parametric distance methods were originally applied to phenetic data using a matrix of pairwise distances. These distances are then reconciled to produce a tree...

 methods such as neighbor-joining
Neighbor-joining
In bioinformatics, neighbor joining is a bottom-up clustering method for the creation of phenetic trees , created by Naruya Saitou and Masatoshi Nei...

), but made no attempt to resolve phylogeny, only similarities.

Clades


A clade is a group of taxa
Taxon
|thumb|270px|[[African elephants]] form a widely-accepted taxon, the [[genus]] LoxodontaA taxon is a group of organisms, which a taxonomist adjudges to be a unit. Usually a taxon is given a name and a rank, although neither is a requirement...

 consisting only of an ancestor taxon and all of its descendant taxa. In the diagram provided (a cladogram), it is hypothesized that all vertebrates, including ray-finned fishes (Actinopterygii
Actinopterygii
The Actinopterygii or ray-finned fishes constitute a class or sub-class of the bony fishes.The ray-finned fishes are so called because they possess lepidotrichia or "fin rays", their fins being webs of skin supported by bony or horny spines , as opposed to the fleshy, lobed fins that characterize...

), had a common ancestor all of whose descendants were vertebrates, and so form a clade. Within the vertebrates, all tetrapods, including amphibians, mammals, reptiles (as traditionally defined) and birds are hypothesized to have had a common ancestor all of whose descendants were tetrapods, and so also form a clade. The tetrapod ancestor was a descendant of the original vertebrate ancestor, but is not an ancestor of any ray-finned fish living today.

An important caution is that any cladogram is a provisional hypothesis
Hypothesis
A hypothesis is a proposed explanation for a phenomenon. The term derives from the Greek, ὑποτιθέναι – hypotithenai meaning "to put under" or "to suppose". For a hypothesis to be put forward as a scientific hypothesis, the scientific method requires that one can test it...

. There is genetic evidence, for example, that Testudines
Turtle
Turtles are reptiles of the order Testudines , characterised by a special bony or cartilaginous shell developed from their ribs that acts as a shield...

, Aves
Bird
Birds are feathered, winged, bipedal, endothermic , egg-laying, vertebrate animals. Around 10,000 living species and 188 families makes them the most speciose class of tetrapod vertebrates. They inhabit ecosystems across the globe, from the Arctic to the Antarctic. Extant birds range in size from...

, and Crocodylia
Crocodilia
Crocodilia is an order of large reptiles that appeared about 84 million years ago in the late Cretaceous Period . They are the closest living relatives of birds, as the two groups are the only known survivors of the Archosauria...

 share a common ancestor that was not an ancestor of the Lepidosauria
Lepidosauria
The Lepidosauria are reptiles with overlapping scales. This subclass includes Squamata and Sphenodontidae. It is a monophyletic group and therefore contains all descendents of a common ancestor. The squamata includes snakes, lizards, tuataras, and amphisbaenia. Lepidosauria is the sister taxon...

. This has led some researchers to propose a cladogram at variance with the one presented here, showing a clade that does not include Lepidosauria but does contain the other three groups.

The relationship between clades can be described in several ways:
  • A clade is basal
    Basal (phylogenetics)
    In phylogenetics, a basal clade is the earliest clade to branch in a larger clade; it appears at the base of a cladogram.A basal group forms an outgroup to the rest of the clade, such as in the following example:...

    to another clade if it contains that other clade as a subset within it. In the example, the vertebrate clade is basal to the tetrapod and ray-finned fish clades. (Some authors have used "basal" differently to mean a clade that is less species-rich than a sister clade, with such a deficit being taken as an indication of 'primitiveness'. Others consider this usage to be incorrect.)
  • A clade located within a clade is said to be nested within that clade. In the diagram, the tetrapod clade is nested within the vertebrate clade.
  • Two clades are sisters if they have an immediate common ancestor. In the diagram, crocodiles and birds are sister clades, as are modern amphibians
    Lissamphibia
    The subclass Lissamphibia includes all recent amphibians and means smooth amphibia.Extant amphibians fall into one of three orders — the Anura , the Caudata or Urodela , and the Gymnophiona or Apoda .Although the ancestry of each group is still unclear, all share certain common characteristics,...

     and amniotes.

Terminology for characters


The following terms are used to identify shared or distinct characters among groups:
Plesiomorphy ("close form") or ancestral state, also symplesiomorphy ("shared plesiomorphy", i.e. "shared close form"), is a characteristic that is present at the base of a tree (cladogram). Since a plesiomorphy that is inherited from the common ancestor may appear anywhere in a tree, its presence provides no evidence of relationships within the tree. The traditional definition of reptiles (the blue group in the diagram) includes being cold-blooded (i.e. not maintaining a constant high body temperature), whereas birds are warm-blooded. Since cold-bloodedness is a plesiomorphy, inherited from the common ancestor of traditional reptiles and birds, it should not be used to define a group in a system based on cladistics. Apomorphy ("separate form") or derived state is a characteristic believed to have evolved within the tree. It can thus be used to separate one group in the tree from the rest. Within the group which shares the apomorphy it is a synapomorphy
Synapomorphy
In cladistics, a synapomorphy or synapomorphic character is a trait that is shared by two or more taxa and their most recent common ancestor, whose ancestor in turn does not possess the trait. A synapomorphy is thus an apomorphy visible in multiple taxa, where the trait in question originates in...

("shared apomorphy", i.e. "shared separate form"). For example, within the vertebrates, all tetrapods (and only tetrapods) have four limbs; thus, having four limbs is a synapomorphy for tetrapods. All the tetrapods can legitimately be grouped together because they have four limbs.
  • Homoplasy is a characteristic shared by members of a tree but not present in their common ancestor. It arises by convergence or reversion. Both mammals and birds are able to maintain a high constant body temperature (i.e. they are 'warm-blooded'). However, the ancestors of each group did not share this character, so it must have evolved independently. Mammals and birds should not be grouped together on the basis that they are warm-blooded.


The terms (sym)plesiomorphy and (syn)apomorphy are relative and their application depends on the position of a group within a tree. An apomorphy of one clade is a plesiomorphy of another contained within it. For example, when trying to decide whether tetrapods should form a clade, an important question is whether having four limbs is a synapomorphy of all the taxa to be included within Tetrapoda: did all the possible members of the Tetrapoda inherit four limbs from a common ancestor, whereas all other vertebrates did not? By contrast, for a group within the tetrapods, such as birds, having four limbs is a plesiomorphy. The fact that ostriches and rheas both have four limbs does not provide any support for putting them into a separate group of 'flightless birds'. Using these two terms allows a greater precision in the discussion of homology
Homology (biology)
Homology forms the basis of organization for comparative biology. In 1843, Richard Owen defined homology as "the same organ in different animals under every variety of form and function". Organs as different as a bat's wing, a seal's flipper, a cat's paw and a human hand have a common underlying...

, in particular allowing clear expression of the hierarchical relationships among different homologies.

It can be difficult to decide whether a character is in fact the same, and thus can be classified as a synapomorphy which may identify a group, or whether it only appears to be the same, and is thus a homoplasy which cannot identify a group. There is a danger of circular reasoning: assumptions about the shape of a phylogenetic tree are used to justify decisions about characters, which are then used as evidence for the shape of the tree.

Terminology for groups


Three main types of group can be identified on the basis of their relationships in cladograms. The three can be defined in two different but related ways, as shown in the table below. The first is in terms of the shape of a set of nodes taken from a cladogram. In this approach, an 'ancestor node' is simply a branching point in the diagram; it may or may not correspond to an actual ancestor. The second is in terms of the characters of the taxa being classified and how these characters have been inherited. In this approach, an ancestor is an actual taxon, whether currently known or not.
Term Node-based definition Character-based definition
Monophyly A monophyletic group of nodes in a tree is one which includes all the nodes descended from their most recent common ancestor node, plus the most recent common ancestor node, but no other nodes. A monophyletic group of taxa is characterized by one or more synapomorphies
Synapomorphy
In cladistics, a synapomorphy or synapomorphic character is a trait that is shared by two or more taxa and their most recent common ancestor, whose ancestor in turn does not possess the trait. A synapomorphy is thus an apomorphy visible in multiple taxa, where the trait in question originates in...

: derived characters inherited by all members of the group from ancestors and not inherited by any other taxa. A monophyletic group is a 'clade
Clade
A clade is a group consisting of a species and all its descendants. In the terms of biological systematics, a clade is a single "branch" on the "tree of life". The idea that such a "natural group" of organisms should be grouped together and given a taxonomic name is central to biological...

'. A 'crown group
Crown group
A crown group is a group consisting of living representatives, their ancestors back to the most recent common ancestor of that group, and all of that ancestor's descendants. The name was given by Willi Hennig, the formulator of phylogenetic systematics, as a way of classifying living organisms...

' is an example of a monophyletic group.
Paraphyly A paraphyletic group of nodes in a tree is one which is constructed by taking a monophyletic group and removing one or more smaller monophyletic groups. (Removing one group produces a singly paraphyletic group, removing two a doubly paraphylectic group, and so on.) A paraphyletic group is necessarily non-monophyletic. A paraphyletic group of taxa is characterized by one or more (sym)plesiomorphies
Symplesiomorphy
In cladistics, a symplesiomorphy or symplesiomorphic character is a trait which is shared between two or more taxa, but which is also shared with other taxa which have an earlier last common ancestor with the taxa under consideration...

: characters inherited from ancestors but not present in all of their descendants. As a consequence, a paraphyletic group is truncated, in that it excludes one or more monophyletic taxa from an initially monophyletic group. An alternative name is an 'evolutionary grade
Evolutionary grade
In alpha taxonomy, a grade refers to a taxon united by a level of morphological or physiological complexity. The term was coined by British biologist Julian Huxley, to contrast with clade, a strictly phylogenetic unit.-Definition:...

', referring to the ancestral character state within the group. A 'stem group' is an example of a paraphyletic group.
Polyphyly A polyphyletic group of nodes in a tree is one which is neither monophyletic nor paraphyletic. A polyphyletic group of taxa is characterized by one or more homoplasies: characters which have converged or reverted so as to appear to be the same but which have not been inherited from common ancestors. As a consequence, polyphyletic groups of taxa are totally artificial.

Phylogenetic definitions of a clade



The node-based definition of a monophyletic group (i.e. a clade) given above regards the lines in the cladogram only as a way of showing connections between taxa. This is appropriate when considering only living (extant) taxa; however, when extinct taxa are to be included in a cladogram, lines correspond to sequences of ancestors. There are two alternative ways of defining a clade
Clade
A clade is a group consisting of a species and all its descendants. In the terms of biological systematics, a clade is a single "branch" on the "tree of life". The idea that such a "natural group" of organisms should be grouped together and given a taxonomic name is central to biological...

 which explicitly take into account the line below the branching point at the base of a clade. These definitions are most notably set out in the PhyloCode
PhyloCode
The International Code of Phylogenetic Nomenclature, known as the PhyloCode for short, is a developing draft for a formal set of rules governing phylogenetic nomenclature...

.

Consider how a clade combining A and B in the diagram can be defined.
  • Node-based: The node-based definition specifies A+B as the last common ancestor of A and B, and all descendants of that ancestor. It thus excludes from the clade the line below the junction of A and B. Crown group
    Crown group
    A crown group is a group consisting of living representatives, their ancestors back to the most recent common ancestor of that group, and all of that ancestor's descendants. The name was given by Willi Hennig, the formulator of phylogenetic systematics, as a way of classifying living organisms...

    s are a type of node-based clade.
  • Branch-based: A branch-based definition specifies A+B as the first ancestor of A which is not also an ancestor of C, and all descendants of that ancestor. It thus includes in the clade the line below the junction of A and B. (Many taxonomists use the term "stem-based" instead of "branch-based.") Total groups are a type of branch-based clade.
  • Apomorphy-based: An apomorphy-based definition specifies A+B as the first ancestor of A to possess derived trait M homologously
    Homology (biology)
    Homology forms the basis of organization for comparative biology. In 1843, Richard Owen defined homology as "the same organ in different animals under every variety of form and function". Organs as different as a bat's wing, a seal's flipper, a cat's paw and a human hand have a common underlying...

     (that is, synapomorphically
    Synapomorphy
    In cladistics, a synapomorphy or synapomorphic character is a trait that is shared by two or more taxa and their most recent common ancestor, whose ancestor in turn does not possess the trait. A synapomorphy is thus an apomorphy visible in multiple taxa, where the trait in question originates in...

    ) with that trait in A, and all descendants of that ancestor. It thus includes in the clade only that part of the line below the junction of A and B which corresponds to ancestors possessing the apomorphy. The process of identifying and naming groups based on apomorphies is the method that most resembles classical systematics, with the proviso that cladistic taxa always denote a clade.


Note that these alternative definitions do not alter the classification of the tips of the tree, and so are equivalent if only living (extant) taxa are being considered.

Cladograms



Cladists use cladograms, diagrams which show ancestral relations between taxa, to represent the evolutionary tree of life
Tree of life (science)
Charles Darwin proposed that phylogeny, the evolutionary relatedness among species through time, was expressible as a metaphor he termed the Tree of Life...

. Although traditionally such cladograms were generated largely on the basis of morphological characters, molecular sequencing
Sequencing
In genetics and biochemistry, sequencing means to determine the primary structure of an unbranched biopolymer...

 data and computational phylogenetics
Computational phylogenetics
Computational phylogenetics is the application of computational algorithms, methods and programs to phylogenetic analyses. The goal is to assemble a phylogenetic tree representing a hypothesis about the evolutionary ancestry of a set of genes, species, or other taxa...

 are now very commonly used in the generation of 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-like
Tree (graph theory)
In mathematics, more specifically graph theory, a tree is an undirected graph in which any two vertices are connected by exactly one simple path. In other words, any connected graph without cycles is a tree...

 relationship diagram called a cladogram
Cladogram
A cladogram is a diagram used in cladistics which shows ancestral relations between organisms, to represent the evolutionary tree of life. Although traditionally such cladograms were generated largely on the basis of morphological characters, DNA and RNA sequencing data and computational...

, or sometimes a dendrogram (Greek for "tree drawing"). The cladogram graphically represents a hypothetical evolutionary process. Cladograms are subject to revision as additional data become available.

The terms "evolutionary tree", and sometimes "phylogenetic tree
Phylogenetic tree
A phylogenetic tree or evolutionary tree is a branching diagram or "tree" showing the inferred evolutionary relationships among various biological species or other entities based upon similarities and differences in their physical and/or genetic characteristics...

" are often used synonymously with cladogram but others treat phylogenetic tree as a broader term that includes trees generated with a nonevolutionary emphasis. In cladograms, all species lie at the leaves. The two taxa
Taxon
|thumb|270px|[[African elephants]] form a widely-accepted taxon, the [[genus]] LoxodontaA taxon is a group of organisms, which a taxonomist adjudges to be a unit. Usually a taxon is given a name and a rank, although neither is a requirement...

 on either side of a split, with a common ancestor and no additional descendents, are called "sister taxa" or "sister groups". Each subtree, whether it contains only two or a hundred thousand items, is called a "clade
Clade
A clade is a group consisting of a species and all its descendants. In the terms of biological systematics, a clade is a single "branch" on the "tree of life". The idea that such a "natural group" of organisms should be grouped together and given a taxonomic name is central to biological...

". Many cladists require that all forks in a cladogram be 2-way forks. Some cladograms include 3-way or 4-way forks when there are insufficient data to resolve the forking to a higher level of detail (see under phylogenetic tree
Phylogenetic tree
A phylogenetic tree or evolutionary tree is a branching diagram or "tree" showing the inferred evolutionary relationships among various biological species or other entities based upon similarities and differences in their physical and/or genetic characteristics...

).

For a given set of taxa, the number of distinct cladograms that can be drawn (ignoring which cladogram best matches the taxon characteristics) is:
Number of taxa 2 3 4 5 6 7 8 9 10 N
Number of rooted cladograms 1 3 15 105 945 10,395 135,135 2,027,025 34,459,425 1*3*5*7*...*(2N-3)


This superexponential growth of the number of possible cladograms explains why manual creation of cladograms becomes very difficult when the number of taxa is large.
If a cladogram represents N taxa, 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
Deer
Deer are the ruminant mammals forming the family Cervidae. Species in the Cervidae family include white-tailed deer, elk, moose, red deer, reindeer, fallow deer, roe deer and chital. Male deer of all species and female reindeer grow and shed new antlers each year...

, a cladogram representing deer could be around 5 levels deep (because 25 = 32), although this is really just the lower limit. A cladogram representing the complete tree of life, with about 10 million species, could be about 23 levels deep. This formula gives a lower limit, with the actual depth generally 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.

A 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. Such cladograms are called scaled cladograms. Many cladograms are not of this type, for a variety of reasons:
  • They 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 are 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
  • 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 makes no distinction between extinct and extant 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, especially morphological characteristics that are preserved in fossils, are more likely to include extinct species.

Phylogenetic nomenclature contrasted with traditional taxonomy


Most taxonomists have used the traditional approaches of Linnaean taxonomy
Linnaean taxonomy
Linnaean taxonomy can mean either of two related concepts:# the particular form of biological classification set up by Carl Linnaeus, as set forth in his Systema Naturæ and subsequent works...

 and later Evolutionary taxonomy
Evolutionary taxonomy
Evolutionary taxonomy, evolutionary systematics or Darwinian classification is a branch of biological classification that seeks to classify organisms using a combination of phylogenetic relationship and overall similarity. This type of taxonomy considers taxa rather than single species, so that...

 to organize life forms. These approaches use several fixed levels of a hierarchy, such as kingdom
Kingdom (biology)
In biology, kingdom is a taxonomic rank, which is either the highest rank or in the more recent three-domain system, the rank below domain. Kingdoms are divided into smaller groups called phyla or divisions in botany...

, phylum
Phylum
In biology, a phylum The term was coined by Georges Cuvier from Greek φῦλον phylon, "race, stock," related to φυλή phyle, "tribe, clan." is a taxonomic rank below kingdom and above class. "Phylum" is equivalent to the botanical term division....

, class
Class (biology)
In biological classification, class is* a taxonomic rank. Other well-known ranks are life, domain, kingdom, phylum, order, family, genus, and species, with class fitting between phylum and order...

, order
Order (biology)
In scientific classification used in biology, the order is# a taxonomic rank used in the classification of organisms. Other well-known ranks are life, domain, kingdom, phylum, class, family, genus, and species, with order fitting in between class and family...

, and family
Family (biology)
In biological classification, family is* a taxonomic rank. Other well-known ranks are life, domain, kingdom, phylum, class, order, genus, and species, with family fitting between order and genus. As for the other well-known ranks, there is the option of an immediately lower rank, indicated by the...

. Phylogenetic nomenclature does not feature those terms, because 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 phylogenies
Phylogenetics
In biology, phylogenetics is the study of evolutionary relatedness among groups of organisms , which is discovered through molecular sequencing data and morphological data matrices...

. In contrast, Linnaean taxonomy allows both monophyletic and paraphyletic groups as taxa. Since the early 20th century, Linnaean taxonomists have generally attempted to make at least family
Family (biology)
In biological classification, family is* a taxonomic rank. Other well-known ranks are life, domain, kingdom, phylum, class, order, genus, and species, with family fitting between order and genus. As for the other well-known ranks, there is the option of an immediately lower rank, indicated by the...

- and lower-level taxa (i.e. those regulated by the codes of nomenclature) monophyletic. Ernst Mayr
Ernst Mayr
Ernst Walter Mayr was one of the 20th century's leading evolutionary biologists. He was also a renowned taxonomist, tropical explorer, ornithologist, historian of science, and naturalist...

 in 1985 drew a distinction between the terms cladistics and phylogeny: "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 Darwin
Charles Darwin
Charles Robert Darwin FRS was an English naturalist. He established that all species of life have descended over time from common ancestry, and proposed the scientific theory that this branching pattern of evolution resulted from a process that he called natural selection.He published his theory...

 and adopted by most students of phylogeny in the ensuing 90 years. The concept of phylogeny as mere genealogy
Genealogy
Genealogy is the study of families and the tracing of their lineages and history. Genealogists use oral traditions, historical records, genetic analysis, and other records to obtain information about a family and to demonstrate kinship and pedigrees of its members...

 should be terminologically distinguished as cladistics. To lump the two concepts together terminologically could not help but produce harmful equivocation."

Willi Hennig
Willi Hennig
Emil Hans Willi Hennig was a German biologist who is considered the founder of phylogenetic systematics, also known as cladistics. With his works on evolution and systematics he revolutionised the view of the natural order of beings...

's pioneering work provoked a spirited debate about the relative merits of phylogenetic nomenclature versus Linnaean or evolutionary taxonomy, which has continued down to the present; however Hennig did not advocate abandoning the Linnaean nomenclatural system. Some of the debates in which the cladists were engaged had been running since the 19th century, but they were renewed fervor, as can be seen from the Foreword to Hennig (1979) by Rosen, Nelson, and Patterson:
"Encumbered with vague and slippery ideas about adaptation, fitness, biological species and natural selection, neo-Darwinism (summed up in the "evolutionary" systematics of Mayr
Ernst Mayr
Ernst Walter Mayr was one of the 20th century's leading evolutionary biologists. He was also a renowned taxonomist, tropical explorer, ornithologist, historian of science, and naturalist...

 and Simpson) not only lacked a definable investigatory method, but came to depend, both for evolutionary interpretation and classification, on consensus or authority."


Phylogenetic nomenclature strictly and exclusively follows phylogeny and has arbitrarily deep trees with binary branching: each taxon corresponds to a clade. Linnaean taxonomy, while since the advent of evolutionary theory following phylogeny, also may subjectively consider similarity and has a fixed hierarchy of taxonomic rank
Taxonomic rank
In biological classification, rank is the level in a taxonomic hierarchy. Examples of taxonomic ranks are species, genus, family, and class. Each rank subsumes under it a number of less general categories...

s, and its taxa are not required to correspond to clades.

Paraphyletic groups discouraged


Many cladists discourage the use of paraphyletic groups in classification of organisms, 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
Hominidae
The Hominidae or include them .), as the term is used here, form a taxonomic family, including four extant genera: chimpanzees , gorillas , humans , and orangutans ....

 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.

Complexity of the Tree of Life


The cladistic tree of life
Tree of life
The concept of a tree of life, a many-branched tree illustrating the idea that all life on earth is related, has been used in science , religion, philosophy, mythology, and other areas...

 is a fractal
Fractal
A fractal has been defined as "a rough or fragmented geometric shape that can be split into parts, each of which is a reduced-size copy of the whole," a property called self-similarity...

:
"The tree of life is inherently fractal-like in its complexity, .... Look closely at the 'lineage' of a phylogeny ... and it dissolves into many smaller lineages, and so on, down to a very fine scale."

The overall shape of a dichotomous (bifurcating) tree is recursive
Recursion
Recursion is the process of repeating items in a self-similar way. For instance, when the surfaces of two mirrors are exactly parallel with each other the nested images that occur are a form of infinite recursion. The term has a variety of meanings specific to a variety of disciplines ranging from...

; as a viewpoint zooms into the tree of life, the same type of tree appears no matter what the scale. When extinct species are considered (both known and unknown), the complexity and depth of the tree can be very large. Moreover the tree continues to recreate itself by bifurcation, a series of events called fractal evolution. Every single speciation event, including all the species that are now extinct, represents an additional fork on the hypothetical, complete cladogram of the tree of life.

The tree of life is a quasi-self-similar fractal; that is, the deep reconstruction is not as regular as the shallow reconstruction. By shallow Mishler means the most recent branching toward and at the tips, and by deep the more ancient branches further back, which are harder to reconstruct and are missing unknown extinct lines. In the shallow part of the tree, branching events are relatively regular; it is often possible to estimate the times between them. In the deep part of the tree, "homology assessments" are "difficult" and the times vary widely. At this level Eldredge's and Gould's punctuated equilibrium
Punctuated equilibrium
Punctuated equilibrium is a theory in evolutionary biology which proposes that most species will exhibit little net evolutionary change for most of their geological history, remaining in an extended state called stasis...

 applies, which hypothesizes long periods of stability followed by punctuations of rapid speciation, based on the fossil record.

PhyloCode approach to naming species


A formal code of phylogenetic nomenclature, the PhyloCode
PhyloCode
The International Code of Phylogenetic Nomenclature, known as the PhyloCode for short, is a developing draft for a formal set of rules governing phylogenetic nomenclature...

, is currently under development. 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
Hesperornithes
Hesperornithes is an extinct and highly specialized clade of Cretaceous toothed birds. Hesperornithine birds, apparently limited to former aquatic habitats in the Northern Hemisphere, include genera such as Hesperornis, Parahesperornis, Baptornis, Enaliornis, and probably Potamornis, all...

) it has been employed to clarify uncertainties in Linnaean systematics so that in combination they yield a taxonomy that unambiguously places problematic groups in the evolutionary tree in a way that is consistent with current knowledge.

Example


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, and divides into the classes
Class (biology)
In biological classification, class is* a taxonomic rank. Other well-known ranks are life, domain, kingdom, phylum, order, family, genus, and species, with class fitting between phylum and order...

 Amphibia, Reptilia, Aves, Mammalia.

Phylogenetic nomenclature also contains the taxon Tetrapoda (see the diagram under Clades above), 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 snake). This definition gives us the Crown group
Crown group
A crown group is a group consisting of living representatives, their ancestors back to the most recent common ancestor of that group, and all of that ancestor's descendants. The name was given by Willi Hennig, the formulator of phylogenetic systematics, as a way of classifying living organisms...

 tetrapods (or Crown-Tetrapoda). A few primitive four legged ancestors (the Ichthyostegalia) fall outside Crown-Tetrapoda. An alternative is to define tetrapoda as all animals more closely related to mammals than to lungfish
Lungfish
Lungfish are freshwater fish belonging to the Subclass Dipnoi. Lungfish are best known for retaining characteristics primitive within the Osteichthyes, including the ability to breathe air, and structures primitive within Sarcopterygii, including the presence of lobed fins with a well-developed...

 (our nearest living non-tetrapod relatives). In this definition, the ichthyostegalians are included, together with a host of fossil animals usually classed as crossopterygian fish. This wider definition is termed Pan-Tetrapoda. A third option is to define Tetrapoda according to their apomorphy (their unique trait, i.e. having feet with toes rather than fins), a definition that yield the same group as the Linnaean taxon.

None of the phylogenetic taxa as described above have a rank, and neither do its subtaxa. All the subclades are contained within one another. The clades are not divided into several non-overlapping taxa (as in traditional taxonomy), rather the clade is split into two clades at the first branching, a process repeated throughout. With regards to the traditional classes, Aves and Mammalia are subclades, contained in the subclade Amniota, while Reptilia and Amphibia are paraphyletic taxa, not clades. Instead of classifying non-mammalian, non-avian amniotes as reptiles, Amniota is divided into the two clades Sauropsida
Sauropsida
Sauropsida is a group of amniotes that includes all existing reptiles and birds and their fossil ancestors, including the dinosaurs, the immediate ancestors of birds...

 (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 can be split into the Batrachomorpha
Batrachomorpha
‫‬‭‮‪‫‬‭‮Batrachomorpha is a name traditionally given to recent and extinct amphibians that are not related to reptiles. It most often includes the extinct groups Temnospondyli and Lepospondyli.-Origin of the term:...

 (fossil amphibians more closely related to modern amphibians
Lissamphibia
The subclass Lissamphibia includes all recent amphibians and means smooth amphibia.Extant amphibians fall into one of three orders — the Anura , the Caudata or Urodela , and the Gymnophiona or Apoda .Although the ancestry of each group is still unclear, all share certain common characteristics,...

) and Reptiliomorpha
Reptiliomorpha
Reptiliomorpha refers to an order or subclass of reptile-like amphibians, which gave rise to the amniotes in the Carboniferous. Under phylogenetic nomenclature, the Reptiliomorpha includes their amniote descendants though, even in phylogenetic nomenclature, the name is mostly used when referring to...

, the latter of which the amiotes is a sub-clade. Ichthyostegalians and other Stem-tetrapods represent sister groups from splits predating the Batrachomorpha/Reptilopmorpha split.

Summary of advantages of phylogenetic nomenclature


Proponents of phylogenetic nomenclature enumerate key distinctions between phylogenetic nomenclature and Linnaean taxonomy as follows:
Phylogenetic Nomenclature Linnaean Taxonomy
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
Clade
A clade is a group consisting of a species and all its descendants. In the terms of biological systematics, a clade is a single "branch" on the "tree of life". The idea that such a "natural group" of organisms should be grouped together and given a taxonomic name is central to biological...

Acceptable to name and use paraphyletic
Clade
A clade is a group consisting of a species and all its descendants. In the terms of biological systematics, a clade is a single "branch" on the "tree of life". The idea that such a "natural group" of organisms should be grouped together and given a taxonomic name is central to biological...

 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 renaming or releveling of Classes, Orders, and Kingdoms

Summary of criticisms of phylogenetic nomenclature


Critics of phylogenetic nomenclature include Ashlock, Mayr, and Williams. Some of their criticisms include:
Phylogenetic Nomenclature 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
Clade definitions emphasize ancestry at the expense of descriptive 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
Horizontal gene transfer
Horizontal gene transfer , also lateral gene transfer , is any process in which an organism incorporates genetic material from another organism without being the offspring of that organism...

Applicable to all organisms, regardless of evolutionary mechanism

Application to other disciplines



The comparisons used to acquire data on which cladograms can be based are not limited to the field of biology. Any group of individuals or classes, hypothesized to have a common ancestor, and to which a set of common characteristics may or may not apply, can be compared pairwise. Cladograms can be used to depict the hypothetical descent relationships within groups of items in many different academic realms. The only requirement is that the items have characteristics that can be identified and measured.

Recent attempts to use cladistic methods outside of biology address the reconstruction of lineages in:
  • Anthropology
    Cultural anthropology
    Cultural anthropology is a branch of anthropology focused on the study of cultural variation among humans, collecting data about the impact of global economic and political processes on local cultural realities. Anthropologists use a variety of methods, including participant observation,...

     and archeology. Compares cultures or artifacts using groups of cultural traits or artifact features.
  • Linguistics
    Historical linguistics
    Historical linguistics is the study of language change. It has five main concerns:* to describe and account for observed changes in particular languages...

    . Compares languages using groups of linguistic features.
  • Textual criticism
    Textual criticism
    Textual criticism is a branch of literary criticism that is concerned with the identification and removal of transcription errors in the texts of manuscripts...

     or Stemmatics. Compares manuscripts of the same work (original lost) using groups of distinctive copying errors.
  • Ethology
    Ethology
    Ethology is the scientific study of animal behavior, and a sub-topic of zoology....

    . Compares animal species using behavioral traits presumed hereditary.
  • Astrophysics
    Astrophysics
    Astrophysics is the branch of astronomy that deals with the physics of the universe, including the physical properties of celestial objects, as well as their interactions and behavior...

    . Infers the history of relationships between galaxies to create branching diagram hypotheses of galaxy diversification.

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