Cladistics

Cladistics (/kləˈdɪstɪks/, from Greek κλάδος, cládos, "branch")[1] is an approach to biological classification in which organisms are categorized in groups ("clades") based on the most recent common ancestor. 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. A key feature of a clade is that a common ancestor and all its descendants are part of the clade. Importantly, all descendants stay in their overarching ancestral clade. For example, if within a strict cladistic framework the terms animals, bilateria/worms, fishes/vertebrata, or monkeys/anthropoidea would be used, these terms would include humans. Many of these terms are normally used paraphyletically, outside of cladistics, e.g. as a 'grade'. Radiation results in the generation of new subclades by bifurcation.[2][3][4][5]

The techniques and nomenclature of cladistics have been applied to other disciplines. (See phylogenetic nomenclature.)

Cladistics is now the most commonly used method to classify organisms.[6]

History

Willi Hennig2
Willi Hennig 1972
Peter Chalmers Mitchell 1920
Peter Chalmers Mitchell in 1920
CSIRO ScienceImage 2955 Robert J Tillyard 18811937
Robert John Tillyard

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 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.[7]

What is now called the cladistic method appeared as early as 1901 with a work by Peter Chalmers Mitchell for birds[8][9] 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 systematics with phenetics and so-called evolutionary taxonomy. Phenetics was championed at this time by the numerical taxonomists Peter Sneath and Robert Sokal, and evolutionary taxonomy by 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 from morphological data.

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. 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.

Methodology

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)[16] 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[17] 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:[18]

  
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 branch near the lived earlier than the last common ancestor of lizards and birds, near the . Most molecular evidence, however, produces cladograms more like this:[19]

Diapsida   
Lepidosauria  

lizards

Archosauromorpha
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.

Monophyly, paraphyly, polyphyly
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:[20][21][22]

  • A plesiomorphy ("close form") or ancestral state is a character state that a taxon has retained from its ancestors. When two or more taxa that are not nested within each other share a plesiomorphy, it is a symplesiomorphy (from syn-, "together"). Symplesiomorphies do not mean that the taxa that exhibit that character state are necessarily closely related. For example, Reptilia is traditionally characterized by (among other things) 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, and thus a symplesiomorphy of turtles, snakes and crocodiles (among others), it does not mean that turtles, snakes and crocodiles form a clade that excludes the birds.
  • An apomorphy ("separate form") or derived state is an innovation. It can thus be used to diagnose a clade – or even to help define a clade name in phylogenetic nomenclature. Features that are derived in individual taxa (a single species or a group that is represented by a single terminal in a given phylogenetic analysis) are called autapomorphies (from auto-, "self"). Autapomorphies express nothing about relationships among groups; clades are identified (or defined) by synapomorphies (from syn-, "together"). For example, the possession of digits that are homologous with those of Homo sapiens is a synapomorphy within the vertebrates. The tetrapods can be singled out as consisting of the first vertebrate with such digits homologous to those of Homo sapiens together with all descendants of this vertebrate (an apomorphy-based phylogenetic definition).[23] Importantly, snakes and other tetrapods that do not have digits are nonetheless tetrapods: other characters, such as amniotic eggs and diapsid skulls, indicate that they descended from ancestors that possessed digits which are homologous with ours.
  • A character state is homoplastic or "an instance of homoplasy" if it is shared by two or more organisms but is absent from their common ancestor or from a later ancestor in the lineage leading to one of the organisms. It is therefore inferred to have evolved by convergence or reversal. Both mammals and birds are able to maintain a high constant body temperature (i.e., they are warm-blooded). However, the accepted cladogram explaining their significant features indicates that their common ancestor is in a group lacking this character state, so the state must have evolved independently in the two clades. Warm-bloodedness is separately a synapomorphy of mammals (or a larger clade) and of birds (or a larger clade), but it is not a synapomorphy of any group including both these clades. Hennig's Auxiliary Principle [24] states that shared character states should be considered evidence of grouping unless they are contradicted by the weight of other evidence; thus, homoplasy of some feature among members of a group may only be inferred after a phylogenetic hypothesis for that group has been established.

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.[25] 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.[21][22][26] 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.[27] (Removing one clade produces a singly paraphyletic assemblage, removing two produces a doubly paraphylectic assemblage, and so on.)[28] 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.[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.

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. Also, homology can be equated to synapomorphy, which is what Patterson has done.[30]

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.[31] 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.

Anthropology and archaeology:[32] 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.[33] They also are a powerful way to test hypotheses about cross-cultural relationships among folktales.[34][35]

Literature: Cladistic methods have been used in the classification of the surviving manuscripts of the Canterbury Tales,[36] and the manuscripts of the Sanskrit Charaka Samhita.[37]

Historical linguistics:[38] 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:[37][39] 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[40] 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. ^ "The Need for Cladistics". www.ucmp.berkeley.edu. Retrieved 2018-08-12.
  7. ^ Brinkman & Leipe 2001, p. 323
  8. ^ Schuh, Randall. 2000. Biological Systematics: Principles and Applications, p.7 (citing Nelson and Platnick, 1981). Cornell University Press (books.google)
  9. ^ Folinsbee, Kaila et al. 2007. 5 Quantitative Approaches to Phylogenetics, p. 172. Rev. Mex. Div. 225-52 (kfolinsb.public.iastate.edu)
  10. ^ Craw, RC (1992). "Margins of cladistics: Identity, differences and place in the emergence of phylogenetic systematics". In Griffiths, PE. Trees of life: Essays in the philosophy of biology. Dordrecht: Kluwer Academic. pp. 65–107. ISBN 978-94-015-8038-0.
  11. ^ Schuh, Randall. 2000. Biological Systematics: Principles and Applications, p.7. Cornell U. Press
  12. ^ Cuénot 1940
  13. ^ a b Webster's 9th New Collegiate Dictionary
  14. ^ Cain & Harrison 1960
  15. ^ Dupuis 1984
  16. ^ Weygoldt 1998
  17. ^ Jerison 2003, p. 254
  18. ^ Benton, Michael J. (2005), Vertebrate Palaeontology, Blackwell, pp. 214, 233, ISBN 978-0-632-05637-8
  19. ^ Lyson, Tyler; Gilbert, Scott F. (March–April 2009), "Turtles all the way down: loggerheads at the root of the chelonian tree" (PDF), Evolution & Development, 11 (2): 133–135, CiteSeerX 10.1.1.695.4249, doi:10.1111/j.1525-142X.2009.00325.x, PMID 19245543
  20. ^ Patterson 1982, pp. 21–74
  21. ^ a b Patterson 1988
  22. ^ a b de Pinna 1991
  23. ^ Laurin & Anderson 2004
  24. ^ Hennig 1966
  25. ^ James & Pourtless IV 2009, p. 25: "Synapomorphies are invoked to defend the hypothesis; the hypothesis is invoked to defend the synapomorphies."
  26. ^ Patterson 1982
  27. ^ 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
  28. ^ Taylor 2003
  29. ^ Adrain, Edgecombe & Lieberman 2002, pp. 56–57
  30. ^ Forey, Peter et al. 1992. Cladistics,1st ed., p. 9, Oxford U. Press.
  31. ^ Mace, Clare & Shennan 2005, p. 1
  32. ^ Lipo et al. 2006
  33. ^ d'Huy 2012a, b; d'Huy 2013a, b, c, d
  34. ^ Ross and al. 2013
  35. ^ Tehrani 2013
  36. ^ "Canterbury Tales Project". Archived from the original on 7 July 2009. Retrieved 2009-07-04.
  37. ^ a b Maas 2010–2011
  38. ^ Oppenheimer 2006, pp. 290–300, 340–56
  39. ^ Robinson & O’Hara 1996
  40. ^ Fraix-Burnet et al. 2006

Bibliography

External links

Clade

A clade (from Ancient Greek: κλάδος, klados, "branch"), also known as monophyletic group, is a group of organisms that consists of a common ancestor and all its lineal descendants, and represents a single "branch" on the "tree of life".The common ancestor may be an individual, a population, a species (extinct or extant), and so on right up to a kingdom and further. Clades are nested, one in another, as each branch in turn splits into smaller branches. These splits reflect evolutionary history as populations diverged and evolved independently. Clades are termed monophyletic (Greek: "one clan") groups.

Over the last few decades, the cladistic approach has revolutionized biological classification and revealed surprising evolutionary relationships among organisms. Increasingly, taxonomists try to avoid naming taxa that are not clades; that is, taxa that are not monophyletic. Some of the relationships between organisms that the molecular biology arm of cladistics has revealed are that fungi are closer relatives to animals than they are to plants, archaea are now considered different from bacteria, and multicellular organisms may have evolved from archaea.

Cladistics (journal)

Cladistics is a bimonthly peer-reviewed scientific journal publishing research in cladistics. It is published by Wiley-Blackwell on behalf of the Willi Hennig Society. Cladistics publishes papers relevant to evolution, systematics, and integrative biology. Papers of both a conceptual or philosophical nature, discussions of methodology, empirical studies on taxonomic groups from animals to bacteria, and applications of systematics in disciplines such as genomics and paleontology are accepted. Five types of paper appear in the journal: reviews, regular papers, forum papers, letters to the editor, and book reviews. According to the Journal Citation Reports, the journal has a 2016 impact factor of 4.309, ranking it 11th out of 48 journals in the category "Evolutionary Biology". Its editor-in-chief is Dennis Stevenson.

Cladogram

A cladogram (from Greek clados "branch" and gramma "character") is a diagram used in cladistics to show relations among organisms. A cladogram is not, however, an evolutionary tree because it does not show how ancestors are related to descendants, nor does it show how much they have changed; many evolutionary trees can be inferred from a single cladogram. A cladogram uses lines that branch off in different directions ending at a clade, a group of organisms with a last common ancestor. There are many shapes of cladograms but they all have lines that branch off from other lines. The lines can be traced back to where they branch off. These branching off points represent a hypothetical ancestor (not an actual entity) which can be inferred to exhibit the traits shared among the terminal taxa above it. This hypothetical ancestor might then provide clues about the order of evolution of various features, adaptation, and other evolutionary narratives about ancestors. Although traditionally such cladograms were generated largely on the basis of morphological characters, DNA and RNA sequencing data and computational phylogenetics are now very commonly used in the generation of cladograms, either on their own or in combination with morphology.

Cochylimorpha

Cochylimorpha is a genus of moths belonging to the Tortricidae family.

Convergent evolution

Convergent evolution is the independent evolution of similar features in species of different lineages. Convergent evolution creates analogous structures that have similar form or function but were not present in the last common ancestor of those groups. The cladistic term for the same phenomenon is homoplasy. The recurrent evolution of flight is a classic example, as flying insects, birds, pterosaurs, and bats have independently evolved the useful capacity of flight. Functionally similar features that have arisen through convergent evolution are analogous, whereas homologous structures or traits have a common origin but can have dissimilar functions. Bird, bat, and pterosaur wings are analogous structures, but their forelimbs are homologous, sharing an ancestral state despite serving different functions.

The opposite of convergence is divergent evolution, where related species evolve different traits. Convergent evolution is similar to parallel evolution, which occurs when two independent species evolve in the same direction and thus independently acquire similar characteristics; for instance, gliding frogs have evolved in parallel from multiple types of tree frog.

Many instances of convergent evolution are known in plants, including the repeated development of C4 photosynthesis, seed dispersal by fleshy fruits adapted to be eaten by animals, and carnivory.

Evolutionary anthropology

Evolutionary anthropology is the interdisciplinary study of the evolution of human physiology and human behaviour and the relation between hominids and non-hominid primates. Evolutionary anthropology is based in natural science and social science. Various fields and disciplines of evolutionary anthropology are:

Human evolution and anthropogeny.

Paleoanthropology and paleontology of both human and non-human primates.

Primatology and primate ethology.

The sociocultural evolution of human behavior, including phylogenetic approaches to historical linguistics.

The evolutionary psychology and evolutionary linguistics of humans.

The archaeological study of human technology and change over time and space.

Human evolutionary genetics and changes in the human genome over time.

The neuroscience, endocrinology, and neuroanthropology of human and primate cognition, culture and actions and abilities.

Human behavioural ecology and the interaction of humans and the environment.

Studies of human anatomy, physiology, molecular biology, biochemistry, and differences and changes between species, variation between human groups, and relationships to cultural factors.Evolutionary anthropology is concerned with both biological and cultural evolution of humans, past and present. It is based on a scientific approach, and brings together fields such as archaeology, behavioral ecology, psychology, primatology, and genetics. It is a dynamic and interdisciplinary field, drawing on many lines of evidence to understand the human experience, past and present.

Studies of biological evolution generally concern the evolution of the human form. Cultural evolution involves the study of cultural change over time and space and frequently incorporate cultural transmission models. Note that cultural evolution is not the same as biological evolution, and that human culture involves the transmission of cultural information, which behaves in ways quite distinct from human biology and genetics. The study of cultural change is increasingly performed through cladistics and genetic models.

Evolutionary grade

In alpha taxonomy, a grade is 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.

Homology (biology)

In biology, homology is the existence of shared ancestry between a pair of structures, or genes, in different taxa. A common example of homologous structures is the forelimbs of vertebrates, where the wings of bats, the arms of primates, the front flippers of whales and the forelegs of dogs and horses are all derived from the same ancestral tetrapod structure. Evolutionary biology explains homologous structures adapted to different purposes as the result of descent with modification from a common ancestor. The term was first applied to biology in a non-evolutionary context by the anatomist Richard Owen in 1843. Homology was later explained by Charles Darwin's theory of evolution in 1859, but had been observed before this, from Aristotle onwards, and it was explicitly analysed by Pierre Belon in 1555.

In developmental biology, organs that developed in the embryo in the same manner and from similar origins, such as from matching primordia in successive segments of the same animal, are serially homologous. Examples include the legs of a centipede, the maxillary palp and labial palp of an insect, and the spinous processes of successive vertebrae in a vertebral column. Male and female reproductive organs are homologous if they develop from the same embryonic tissue, as do the ovaries and testicles of mammals including humans.

Sequence homology between protein or DNA sequences is similarly defined in terms of shared ancestry. Two segments of DNA can have shared ancestry because of either a speciation event (orthologs) or a duplication event (paralogs). Homology among proteins or DNA is inferred from their sequence similarity. Significant similarity is strong evidence that two sequences are related by divergent evolution from a common ancestor. Alignments of multiple sequences are used to discover the homologous regions.

Homology remains controversial in animal behaviour, but there is suggestive evidence that, for example, dominance hierarchies are homologous across the primates.

Monophyly

In cladistics, a monophyletic group, or clade, is a group of organisms that consists of all the descendants of a common ancestor. Monophyletic groups are typically characterised by shared derived characteristics (synapomorphies), which distinguish organisms in the clade from other organisms. The arrangement of the members of a monophyletic group is called a monophyly.

Monophyly is contrasted with paraphyly and polyphyly as shown in the second diagram. A paraphyletic group consists of all of the descendants of a common ancestor minus one or more monophyletic groups. A polyphyletic group is characterized by convergent features or habits of scientific interest (for example, night-active primates, fruit trees, aquatic insects). The features by which a polyphyletic group is differentiated from others are not inherited from a common ancestor.

These definitions have taken some time to be accepted. When the cladistics school of thought became mainstream in the 1960s, several alternative definitions were in use. Indeed, taxonomists sometimes used terms without defining them, leading to confusion in the early literature, a confusion which persists.The first diagram shows a phylogenetic tree with two monophyletic groups. The several groups and subgroups are particularly situated as branches of the tree to indicate ordered lineal relationships between all the organisms shown. Further, any group may (or may not) be considered a taxon by modern systematics, depending upon the selection of its members in relation to their common ancestor(s); see second and third diagrams.

Neontology

Neontology is a part of biology that, in contrast to paleontology, deals with living (or, more generally, recent) organisms. It is the study of extant taxa (singular: extant taxon): taxa (such as species, genera and families) with members still alive, as opposed to (all) being extinct. For example:

The moose (Alces alces) is an extant species, and the dodo is an extinct species.

In the group of molluscs known as the cephalopods, as of 1987 there were approximately 600 extant species and 7,500 extinct species.A taxon can be classified as extinct if it is broadly agreed or certified that no members of the group are still alive. Conversely, an extinct taxon can be reclassified as extant if there are new discoveries of extant species ("Lazarus species"), or if previously-known extant species are reclassified as members of the taxon.

Most biologists, zoologists, and botanists are in practice neontologists, and the term neontologist is used largely by paleontologists referring to non-paleontologists. Stephen Jay Gould said of neontology:

All professions maintain their parochialisms, and I trust that nonpaleontological readers will forgive our major manifestation. We are paleontologists, so we need a name to contrast ourselves with all you folks who study modern organisms in human or ecological time. You therefore become neontologists. We do recognize the unbalanced and parochial nature of this dichotomous division.

Neontological evolutionary biology has a temporal perspective between 100 to 1000 years. Neontology's fundamental basis relies on models of natural selection as well as speciation. Neontology's methods, when compared to evolutionary paleontology, has a greater emphasis on experiments. There are more frequent discontinuities present in paleontology than in neontology, because paleontology involves extinct taxa. Neontology has organisms actually present and available to sample and perform research on. Neontology's research method uses cladistics to examine morphologies and genetics. Neontology data has more emphasis on genetic data and the population structure than paleontology does.

Outgroup (cladistics)

In cladistics or phylogenetics, an outgroup is a more distantly related group of organisms that serves as a reference group when determining the evolutionary relationships of the ingroup, the set of organisms under study, and is distinct from sociological outgroups. The outgroup is used as a point of comparison for the ingroup and specifically allows for the phylogeny to be rooted. Because the polarity (direction) of character change can be determined only on a rooted phylogeny, the choice of outgroup is essential for understanding the evolution of traits along a phylogeny.

Paraphyly

In taxonomy, a group is paraphyletic if it consists of the group's last common ancestor and all descendants of that ancestor excluding a few—typically only one or two—monophyletic subgroups. The group is said to be paraphyletic with respect to the excluded subgroups. The arrangement of the members of a paraphyletic group is called a paraphyly. The term is commonly used in phylogenetics (a subfield of biology) and in linguistics.

The term was coined to apply to well-known taxa like Reptilia (reptiles) which, as commonly named and traditionally defined, is paraphyletic with respect to mammals and birds. Reptilia contains the last common ancestor of reptiles and all descendants of that ancestor—including all extant reptiles as well as the extinct synapsids—except for mammals and birds. Other commonly recognized paraphyletic groups include fish, monkeys, and lizards.If many subgroups are missing from the named group, it is said to be polyparaphyletic. A paraphyletic group cannot be a clade, or monophyletic group, which is any group of species that includes only a common ancestor and all of its descendants. Formally, a paraphyletic group is the relative complement of one or more subclades within a clade: removing one or more subclades leaves a paraphyletic group.

Phenetics

In biology, phenetics (Greek: phainein - to appear) , 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 methods for taxonomic classification. Many people contributed to the development of phenetics, but the most influential were Peter Sneath and Robert R. Sokal. Their books are still primary references for this sub-discipline, although now out of print.Phenetics has largely been superseded by cladistics for research into evolutionary relationships among species. However, certain phenetic methods, such as neighbor-joining, have found their way into phylogenetics, as a reasonable approximation of phylogeny when more advanced methods (such as Bayesian inference) are too computationally expensive.

Phenetic techniques include various forms of clustering and ordination. These are sophisticated ways of reducing the variation displayed by organisms to a manageable level. In practice this means measuring dozens of variables, and then presenting them as two- or three-dimensional graphs. Much of the technical challenge in phenetics revolves around balancing the loss of information in such a reduction against the ease of interpreting the resulting graphs.

The method can be traced back to 1763 and Michel Adanson (in his Familles des plantes) because of two shared basic principles — overall similarity and equal weighting — and modern pheneticists are sometimes called neo-Adansonians.

Phylogenesis

Phylogenesis (from Greek φῦλον phylon "tribe" + γένεσις genesis "origin") is the biological process by which a taxon (of any rank) appears. The science that studies these processes is called phylogenetics.These terms may be confused with the term phylogenetics, the application of molecular - analytical methods (i.e. molecular biology and genomics), in the explanation of phylogeny and its research.

Phylogenetic relationships are discovered through phylogenetic inference methods that evaluate observed heritable traits, such as DNA sequences or overall morpho-anatomical, ethological, and other characteristics.

Phylogenetics

In biology, phylogenetics (Greek: φυλή, φῦλον – phylé, phylon = tribe, clan, race + γενετικός – genetikós = origin, source, birth) is the study of the evolutionary history and relationships among individuals or groups of organisms (e.g. species, or populations). These relationships are discovered through phylogenetic inference methods that evaluate observed heritable traits, such as DNA sequences or morphology under a model of evolution of these traits. The result of these analyses is a phylogeny (also known as a phylogenetic tree) – a diagrammatic hypothesis about the history of the evolutionary relationships of a group of organisms. The tips of a phylogenetic tree can be living organisms or fossils, and represent the "end", or the present, in an evolutionary lineage. Phylogenetic analyses have become central to understanding biodiversity, evolution, ecology, and genomes.

Taxonomy is the identification, naming and classification of organisms. It is usually richly informed by phylogenetics, but remains a methodologically and logically distinct discipline. The degree to which taxonomies depend on phylogenies (or classification depends on evolutionary development) differs depending on the school of taxonomy: phenetics ignores phylogeny altogether, trying to represent the similarity between organisms instead; cladistics (phylogenetic systematics) tries to reproduce phylogeny in its classification without loss of information; evolutionary taxonomy tries to find a compromise between them.

Sauropsida

Sauropsida ("lizard faces") is a taxonomic clade that includes both reptiles and birds. All Tetrapoda except Amphibia are Amniota, and all Amniota except Synapsida, including Mammalia, are Sauropsida. This clade includes Parareptilia and other extinct clades. All living sauropsids are members of the subgroup Diapsida, the Parareptilia having died out 200 million years ago. The term originated in 1864 with Thomas Henry Huxley, who grouped birds with reptiles based on fossil evidence.

Strisores

Strisores ( STRY-sorz; STRY-zorz; STREE-sorz) is a clade of birds. It includes the living families and orders Caprimulgidae (nightjars, nighthawks and allies), Nyctibiidae (potoos), Steatornithidae (oilbirds), Podargidae (frogmouths), Apodiformes (swifts and hummingbirds), as well as the Aegotheliformes (owlet-nightjars) whose distinctness was only recently realized. The Apodiformes (which include the "Trochiliformes" of the Sibley-Ahlquist taxonomy) and the Aegotheliformes form the Daedalornithes.

Toxicofera

Toxicofera (Greek for "those who bear toxins") is a proposed clade of scaled reptiles (squamates) that includes the Serpentes (snakes), Anguimorpha (monitor lizards, gila monster, and alligator lizards) and Iguania (iguanas, agamas, and chameleons). Toxicofera contains about 4,600 species, (nearly 60%) of extant squamata. It encompasses all venomous reptile species, as well as numerous related non-venomous species. There is little morphological evidence to support this grouping, however it has been recovered by all recent molecular analyses.

Willi Hennig

Emil Hans Willi Hennig (April 20, 1913 – November 5, 1976) was a German biologist who is considered the founder of phylogenetic systematics, also known as cladistics. In 1945 as a prisoner of war, Hennig began work on his theory of cladistics, which he published in 1950. With his works on evolution and systematics he revolutionised the view of the natural order of beings. As a taxonomist, he specialised in dipterans (ordinary flies and mosquitoes).

He is remembered, among other things, for Hennig's progression rule in cladistics, which argues controversially that the most primitive species are found in the earliest, central part of a group's area.

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