Cladistics

For the scientific journal, see Cladistics (journal). For phylogenetic nomenclature, often called "cladistic nomenclature" or "cladistic terminology", see Phylogenetic nomenclature.

Cladistics (from Greek κλάδος, klados, i.e. "branch")[1] is an approach to biological classification in which organisms are grouped together based on whether or not they have one or more shared unique characteristics that come from the group's last common ancestor and are not present in more distant ancestors. Therefore, members of the same group are thought to share a common history and are considered to be more closely related.[2][3][4][5]

The original methods used in cladistic analysis and the school of taxonomy derived from it originated in 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 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.[6]

The techniques of cladistics, and sometimes the terminology, have been successfully applied to other disciplines: for example, to determine the relationships between the surviving manuscripts of the Canterbury Tales,[7] or also between 53 manuscripts of the Sanskrit Charaka Samhita.[8]

History

What is now called the cladistic method appeared as early as 1901 with a work by Peter Chalmers Mitchell (for birds)[9][10] and subsequently by Robert John Tillyard (for insects) in 1921,[10] and W. Zimmermann (for plants) in 1943.[11] The term "clade" was introduced in 1958 by Julian Huxley after having been coined by Lucien Cuénot in 1940,[12] "cladogenesis" in 1958,[13] "cladistic" by Cain and Harrison in 1960,[14] "cladist" (for an adherent of Hennig's school) by Mayr in 1965,[15] and "cladistics" in 1966.[13] Hennig referred to his own approach as "phylogenetic systematics". From the time of his original formulation until the end of the 1970s, cladistics competed as an analytical and philosophical approach to phylogenetic inference with phenetics and so-called evolutionary taxonomy. Phenetics was championed at this time by the numerical taxonomists Peter Sneath and Robert Sokal and the evolutionary taxonomist Ernst Mayr.

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). Today, cladistics is the most popular method for constructing phylogenies not only from morphological data but also from molecular. Unlike phenetics, cladistics is specifically aimed at reconstructing evolutionary histories.

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, as well as to anatomical ones, vastly expanding the amount of data available for phylogenetics. At the same time, cladistics rapidly became the dominant set of methods of phylogenetics in evolutionary biology, because computers made it possible to process large quantities of data about organisms and their characteristics.

The way for computational phylogenetics was paved by phenetics,[16] a set of methods commonly used from the 1950s to 1980s and to some degree later. Phenetics did not try to reconstruct phylogenetic trees; rather, it tried to build dendrograms from similarity data; its algorithms required less computer power than phylogenetic ones.

Methodology

Main articles: Phylogenetics and Cladogram

The cladistic method interprets each character state transformation implied by the distribution of shared character states among taxa (or other terminals) as a potential piece of evidence for grouping. The outcome of a cladistic analysis is a cladogram – a tree-shaped diagram (dendrogram)[17] that is interpreted to represent the best hypothesis of phylogenetic relationships. Although traditionally such cladograms were generated largely on the basis of morphological characters and originally calculated by hand, genetic sequencing data and computational phylogenetics are now commonly used in phylogenetic analyses, and the parsimony criterion has been abandoned by many phylogeneticists in favor of more "sophisticated" but less parsimonious evolutionary models of character state transformation. Cladists contend that these models are unjustified.

Every cladogram is based on a particular dataset analyzed with a particular method. Datasets are tables consisting of molecular, morphological, ethological[18] and/or other characters and a list of operational taxonomic units (OTUs), which may be genes, individuals, populations, species, or larger taxa that are presumed to be monophyletic and therefore to form, all together, one large clade; phylogenetic analysis infers the branching pattern within that clade. Different datasets and different methods, not to mention violations of the mentioned assumptions, often result in different cladograms. Only scientific investigation can show which is more likely to be correct.

Until recently, for example, cladograms like the following have generally been accepted as accurate representations of the ancestral relations among turtles, lizards, crocodilians, and birds:[19]

  ▼
Testudines  

turtles


Diapsida   ♦
Lepidosauria  

lizards


Archosauria
Crocodylomorpha  

crocodilians


Dinosauria

birds





If this phylogenetic hypothesis is correct, then the last common ancestor of turtles and birds, at the ⊣ connection near the ▼ (a ⊤ in some browsers) lived earlier than the last common ancestor of lizards and birds, near the ♦. Most molecular evidence, however, produces cladograms more like this:[20]

Diapsida   ♦
Lepidosauria  

lizards


Lepidosauria▼
Testudines  

turtles


Archosauria  
Crocodylomorpha  

crocodilians


Dinosauria

birds





If this is accurate, then the last common ancestor of turtles and birds lived later than the last common ancestor of lizards and birds. Since the cladograms provide competing accounts of real events, at most one of them is correct.

Cladogram of the primates, showing a monophyletic taxon (a clade: the simians or Anthropoidea, in yellow), a paraphyletic taxon (the prosimians, in blue, including the red patch), and a polyphyletic taxon (the nocturnal primates – the lorises and the tarsiers – in red)

The cladogram to the right represents the current universally accepted hypothesis that all primates, including strepsirrhines like the lemurs and lorises, had a common ancestor all of whose descendants were primates, and so form a clade; the name Primates is therefore recognized for this clade. Within the primates, all anthropoids (monkeys, apes and humans) are hypothesized to have had a common ancestor all of whose descendants were anthropoids, so they form the clade called Anthropoidea. The "prosimians", on the other hand, form a paraphyletic taxon. The name Prosimii is not used in phylogenetic nomenclature, which names only clades; the "prosimians" are instead divided between the clades Strepsirhini and Haplorhini, where the latter contains Tarsiiformes and Anthropoidea.

Terminology for character states

The following terms, coined by Hennig, are used to identify shared or distinct character states among groups:[21][22][23]

The terms plesiomorphy and apomorphy are relative; their application depends on the position of a group within a tree. For example, when trying to decide whether the tetrapods form a clade, an important question is whether having four limbs is a synapomorphy of the earliest taxa to be included within Tetrapoda: did all the earliest members of the Tetrapoda inherit four limbs from a common ancestor, whereas all other vertebrates did not, or at least not homologously? By contrast, for a group within the tetrapods, such as birds, having four limbs is a plesiomorphy. Using these two terms allows a greater precision in the discussion of homology, in particular allowing clear expression of the hierarchical relationships among different homologous features.

It can be difficult to decide whether a character state is in fact the same and thus can be classified as a synapomorphy, which may identify a monophyletic group, or whether it only appears to be the same and is thus a homoplasy, which cannot identify such a group. There is a danger of circular reasoning: assumptions about the shape of a phylogenetic tree are used to justify decisions about character states, which are then used as evidence for the shape of the tree.[26] Phylogenetics uses various forms of parsimony to decide such questions; the conclusions reached often depend on the dataset and the methods. Such is the nature of empirical science, and for this reason, most cladists refer to their cladograms as hypotheses of relationship. Cladograms that are supported by a large number and variety of different kinds of characters are viewed as more robust than those based on more limited evidence.

Terminology for taxa

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.[22][23][27] These are compared in the table below.

Term Node-based definition Character-based definition
Monophyly A clade, a monophyletic taxon, is a taxon that includes all descendants of an inferred ancestor. 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.
Paraphyly A paraphyletic assemblage is one that is constructed by taking a clade and removing one or more smaller clades.[28] (Removing one clade produces a singly paraphyletic assemblage, removing two produces a doubly paraphylectic assemblage, and so on.)[29] 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.
Polyphyly A polyphyletic assemblage is one which is neither monophyletic nor paraphyletic. 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.).

Criticism

Cladistics, either generally or in specific applications, has been criticized from its beginnings. 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.[30] Transformed cladistics arose in the late 1970s in an attempt to resolve some of these problems by removing phylogeny from cladistic analysis, however it has remained unpopular.

However, homology is usually determined from analysis of the results that are evaluated with homology measures, mainly the CI (consistency index) and RI (retention index), which, it has been claimed, makes the process objective. Also, homology can be equated to synapomorphy, which is what Patterson has done.[31]

In disciplines other than biology

The comparisons used to acquire data on which cladograms can be based are not limited to the field of biology.[32] 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. 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. Cladistic methods outside of biology address the reconstruction of lineages in a variety of ways.

Anthropology and archaeology:[33] Cladistic methods have been used to reconstruct the development of cultures or artifacts using groups of cultural traits or artifact features.

Comparative mythology and folktale use cladistic methods to reconstruct the protoversion of many myths. Mythological phylogenies constructed with mythemes clearly support low horizontal transmissions (borrowings), historical (sometimes Palaeolithic) diffusions and punctuated evolution.[34] They also are a powerful way to test hypotheses about cross-cultural relationships among folktales.[35][36]

Historical linguistics:[37] Cladistic methods have been used to reconstruct the phylogeny of languages using linguistic features. 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).

Textual criticism or stemmatics:[8][38] 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. 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. It also enables parsimony analysis of contaminated traditions of transmission that would be impossible to evaluate manually in a reasonable period of time.

Astrophysics[39] infers the history of relationships between galaxies to create branching diagram hypotheses of galaxy diversification.

See also

Notes and references

  1. ↑ "clade". Online Etymology Dictionary.
  2. ↑ Columbia Encyclopedia
  3. ↑ "Introduction to Cladistics". Ucmp.berkeley.edu. Retrieved 2014-01-06.
  4. ↑ Oxford Dictionary of English
  5. ↑ Oxford English Dictionary
  6. ↑ Brinkman & Leipe 2001, p. 323
  7. ↑ "Canterbury Tales Project". Retrieved 4 July 2009.
  8. ↑ 8.0 8.1 Maas 2010
  9. ↑ Schuh, Randall. 2000. Biological Systematics: Principles and Applications, p.7 (citing Nelson and Platnick, 1981). Cornell University Press (books.google)
  10. ↑ 10.0 10.1 Folinsbee, Kaila et al. 2007. 5 Quantitative Approaches to Phylogenetics, p. 172. Rev. Mex. Div. 225-52 (kfolinsb.public.iastate.edu)
  11. ↑ Schuh, Randall. 2000. Biological Systematics: Principles and Applications, p.7. Cornell U. Press
  12. ↑ Cuénot 1940
  13. ↑ 13.0 13.1 Webster's 9th New Collegiate Dictionary
  14. ↑ Cain & Harrison 1960
  15. ↑ Dupuis 1984
  16. ↑ Mayr 1982, p. 221
  17. ↑ Weygoldt 1998
  18. ↑ Jerison 2003, p. 254
  19. ↑ Benton, Michael J. (2005), Vertebrate Palaeontology, Blackwell, pp. 214, 233, ISBN 978-0-632-05637-8
  20. ↑ Lyson, Tyler; Gilbert, Scott F. (2009), "Turtles all the way down: loggerheads at the root of the chelonian tree" (PDF), Evolution & Development 11 (2): 133–135, doi:10.1111/j.1525-142X.2009.00325.x
  21. ↑ Patterson 1982, pp. 21–74
  22. ↑ 22.0 22.1 Patterson 1988
  23. ↑ 23.0 23.1 de Pinna 1991
  24. ↑ Laurin & Anderson 2004
  25. ↑ Hennig 1966
  26. ↑ James & Pourtless IV 2009, p. 25: "Synapomorphies are invoked to defend the hypothesis; the hypothesis is invoked to defend the synapomorphies."
  27. ↑ Patterson 1982
  28. ↑ Many sources give a verbal definition of 'paraphyletic' that does not require the missing groups to be monophyletic. However, when diagrams are presented representing paraphyletic groups, these invariably show the missing groups as monophyletic. See e.g.Wiley et al. 1991, p. 4
  29. ↑ Taylor 2003
  30. ↑ Adrain, Edgecombe & Lieberman 2002, pp. 56–57
  31. ↑ Forey, Peter et al. 1992. Cladistics,1st ed., p. 9, Oxford U. Press.
  32. ↑ Mace, Clare & Shennan 2005, p. 1
  33. ↑ Lipo et al. 2006
  34. ↑ d'Huy 2012a, b; d'Huy 2013a, b, c, d
  35. ↑ Ross and al. 2013
  36. ↑ Tehrani 2013
  37. ↑ Oppenheimer 2006, pp. 290–300, 340–56
  38. ↑ Robinson & O’Hara 1996
  39. ↑ Fraix-Burnet et al. 2006

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