Cladistics

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For the scientific journal, see Cladistics (journal). Cladistics_sentence_0

For phylogenetic nomenclature, often called "cladistic nomenclature" or "cladistic terminology", see Phylogenetic nomenclature. Cladistics_sentence_1

Cladistics (/kləˈdɪstɪks/, from Greek κλάδος, kládos, "branch") is an approach to biological classification in which organisms are categorized in groups ("clades") based on the most recent common ancestor. Cladistics_sentence_2

Hypothesized relationships are typically based on shared derived characteristics (synapomorphies) that can be traced to the most recent common ancestor and are not present in more distant groups and ancestors. Cladistics_sentence_3

A key feature of a clade is that a common ancestor and all its descendants are part of the clade. Cladistics_sentence_4

Importantly, all descendants stay in their overarching ancestral clade. Cladistics_sentence_5

For example, if within a strict cladistic framework the terms animals, bilateria/worms, fishes/vertebrata, or monkeys/anthropoidea were used, these terms would include humans. Cladistics_sentence_6

Many of these terms are normally used paraphyletically, outside of cladistics, e.g. as a 'grade'. Cladistics_sentence_7

Radiation results in the generation of new subclades by bifurcation, but in practice sexual hybridization may blur very closely related groupings. Cladistics_sentence_8

The techniques and nomenclature of cladistics have been applied to disciplines other than biology. Cladistics_sentence_9

(See phylogenetic nomenclature.) Cladistics_sentence_10

Cladistics is now the most commonly used method to classify organisms. Cladistics_sentence_11

History Cladistics_section_0

The original methods used in cladistic analysis and the school of taxonomy derived from the work of the German entomologist Willi Hennig, who referred to it as phylogenetic systematics (also the title of his 1966 book); the terms "cladistics" and "clade" were popularized by other researchers. Cladistics_sentence_12

Cladistics in the original sense refers to a particular set of methods used in phylogenetic analysis, although it is now sometimes used to refer to the whole field. Cladistics_sentence_13

What is now called the cladistic method appeared as early as 1901 with a work by Peter Chalmers Mitchell for birds and subsequently by Robert John Tillyard (for insects) in 1921, and W. Cladistics_sentence_14 Zimmermann (for plants) in 1943. Cladistics_sentence_15

The term "clade" was introduced in 1958 by Julian Huxley after having been coined by Lucien Cuénot in 1940, "cladogenesis" in 1958, "cladistic" by Arthur Cain and Harrison in 1960, "cladist" (for an adherent of Hennig's school) by Ernst Mayr in 1965, and "cladistics" in 1966. Cladistics_sentence_16

Hennig referred to his own approach as "phylogenetic systematics". Cladistics_sentence_17

From the time of his original formulation until the end of the 1970s, cladistics competed as an analytical and philosophical approach to systematics with phenetics and so-called evolutionary taxonomy. Cladistics_sentence_18

Phenetics was championed at this time by the numerical taxonomists Peter Sneath and Robert Sokal, and evolutionary taxonomy by Ernst Mayr. Cladistics_sentence_19

Originally conceived, if only in essence, by Willi Hennig in a book published in 1950, cladistics did not flourish until its translation into English in 1966 (Lewin 1997). Cladistics_sentence_20

Today, cladistics is the most popular method for constructing phylogenies from morphological data. Cladistics_sentence_21

In the 1990s, the development of effective polymerase chain reaction techniques allowed the application of cladistic methods to biochemical and molecular genetic traits of organisms, vastly expanding the amount of data available for phylogenetics. Cladistics_sentence_22

At the same time, cladistics rapidly became popular in evolutionary biology, because computers made it possible to process large quantities of data about organisms and their characteristics. Cladistics_sentence_23

Methodology Cladistics_section_1

Main articles: Phylogenetics and Cladogram Cladistics_sentence_24

See also: Phylogenetic tree Cladistics_sentence_25

Terminology for character states Cladistics_section_2

Terminology for taxa Cladistics_section_3

Mono-, para- and polyphyletic taxa can be understood based on the shape of the tree (as done above), as well as based on their character states. Cladistics_sentence_26

These are compared in the table below. Cladistics_sentence_27

Cladistics_table_general_0

TermCladistics_header_cell_0_0_0 Node-based definitionCladistics_header_cell_0_0_1 Character-based definitionCladistics_header_cell_0_0_2
MonophylyCladistics_cell_0_1_0 A clade, a monophyletic taxon, is a taxon that includes all descendants of an inferred ancestor.Cladistics_cell_0_1_1 A clade is characterized by one or more apomorphies: derived character states present in the first member of the taxon, inherited by its descendants (unless secondarily lost), and not inherited by any other taxa.Cladistics_cell_0_1_2
ParaphylyCladistics_cell_0_2_0 A paraphyletic assemblage is one that is constructed by taking a clade and removing one or more smaller clades. (Removing one clade produces a singly paraphyletic assemblage, removing two produces a doubly paraphylectic assemblage, and so on.)Cladistics_cell_0_2_1 A paraphyletic assemblage is characterized by one or more plesiomorphies: character states inherited from ancestors but not present in all of their descendants. As a consequence, a paraphyletic assemblage is truncated, in that it excludes one or more clades from an otherwise monophyletic taxon. An alternative name is evolutionary grade, referring to an ancestral character state within the group. While paraphyletic assemblages are popular among paleontologists and evolutionary taxonomists, cladists do not recognize paraphyletic assemblages as having any formal information content – they are merely parts of clades.Cladistics_cell_0_2_2
PolyphylyCladistics_cell_0_3_0 A polyphyletic assemblage is one which is neither monophyletic nor paraphyletic.Cladistics_cell_0_3_1 A polyphyletic assemblage is characterized by one or more homoplasies: character states which have converged or reverted so as to be the same but which have not been inherited from a common ancestor. No systematist recognizes polyphyletic assemblages as taxonomically meaningful entities, although ecologists sometimes consider them meaningful labels for functional participants in ecological communities (e. g., primary producers, detritivores, etc.).Cladistics_cell_0_3_2

Criticism Cladistics_section_4

Cladistics, either generally or in specific applications, has been criticized from its beginnings. Cladistics_sentence_28

Decisions as to whether particular character states are homologous, a precondition of their being synapomorphies, have been challenged as involving circular reasoning and subjective judgements. Cladistics_sentence_29

Transformed cladistics arose in the late 1970s in an attempt to resolve some of these problems by removing phylogeny from cladistic analysis, but it has remained unpopular. Cladistics_sentence_30

However, homology is usually determined from analysis of the results that are evaluated with homology measures, mainly the consistency index (CI) and retention index (RI), which, it has been claimed, makes the process objective. Cladistics_sentence_31

Also, homology can be equated to synapomorphy, which is what Patterson has done. Cladistics_sentence_32

Issues Cladistics_section_5

In organisms with sexual reproduction, incomplete lineage sorting may result in inconsistent phylogenetic trees, depending on which genes are assessed. Cladistics_sentence_33

It is also possible that multiple surviving lineages are generated while interbreeding is still significantly occurring (polytomy). Cladistics_sentence_34

Interbreeding is possible over periods of about 10 million years. Cladistics_sentence_35

Typically speciation occurs over only about 1 million years, which makes it less likely multiple long surviving lineages developed "simultaneously". Cladistics_sentence_36

Even so, interbreeding can result in a lineage being overwhelmed and absorbed by a related more numerous lineage. Cladistics_sentence_37

Simulation studies suggest that phylogenetic trees are most accurately recovered from data that is morphologically coherent (i.e. where closely related organisms share the highest proportion of characters). Cladistics_sentence_38

This relationships is weaker in data generated under selection, potentially due to convergent evolution. Cladistics_sentence_39

The cladistic method does not typically identify fossil species as actual ancestors of a clade. Cladistics_sentence_40

Instead, they are identified as belonging to separate extinct branches. Cladistics_sentence_41

While a fossil species could be the actual ancestor of a clade, the default assumption is that they are more likely to be a related species. Cladistics_sentence_42

In disciplines other than biology Cladistics_section_6

The comparisons used to acquire data on which cladograms can be based are not limited to the field of biology. Cladistics_sentence_43

Any group of individuals or classes that are hypothesized to have a common ancestor, and to which a set of common characteristics may or may not apply, can be compared pairwise. Cladistics_sentence_44

Cladograms can be used to depict the hypothetical descent relationships within groups of items in many different academic realms. Cladistics_sentence_45

The only requirement is that the items have characteristics that can be identified and measured. Cladistics_sentence_46

Anthropology and archaeology: Cladistic methods have been used to reconstruct the development of cultures or artifacts using groups of cultural traits or artifact features. Cladistics_sentence_47

Comparative mythology and folktale use cladistic methods to reconstruct the protoversion of many myths. Cladistics_sentence_48

Mythological phylogenies constructed with mythemes clearly support low horizontal transmissions (borrowings), historical (sometimes Palaeolithic) diffusions and punctuated evolution. Cladistics_sentence_49

They also are a powerful way to test hypotheses about cross-cultural relationships among folktales. Cladistics_sentence_50

Literature: Cladistic methods have been used in the classification of the surviving manuscripts of the Canterbury Tales, and the manuscripts of the Sanskrit Charaka Samhita. Cladistics_sentence_51

Historical linguistics: Cladistic methods have been used to reconstruct the phylogeny of languages using linguistic features. Cladistics_sentence_52

This is similar to the traditional comparative method of historical linguistics, but is more explicit in its use of parsimony and allows much faster analysis of large datasets (computational phylogenetics). Cladistics_sentence_53

Textual criticism or stemmatics: Cladistic methods have been used to reconstruct the phylogeny of manuscripts of the same work (and reconstruct the lost original) using distinctive copying errors as apomorphies. Cladistics_sentence_54

This differs from traditional historical-comparative linguistics in enabling the editor to evaluate and place in genetic relationship large groups of manuscripts with large numbers of variants that would be impossible to handle manually. Cladistics_sentence_55

It also enables parsimony analysis of contaminated traditions of transmission that would be impossible to evaluate manually in a reasonable period of time. Cladistics_sentence_56

Astrophysics infers the history of relationships between galaxies to create branching diagram hypotheses of galaxy diversification. Cladistics_sentence_57

See also Cladistics_section_7

Credits to the contents of this page go to the authors of the corresponding Wikipedia page: en.wikipedia.org/wiki/Cladistics.