63-531: Old classification The superkingdom Metakaryota was defined by Thomas Cavalier-Smith as advanced eukaryotes resulting from the endosymbiosis of a proteobacterium , giving rise to the mitochondrion , by an archezoan eukaryote. However, with the collapse of the Archezoa hypothesis (that amitochondriate eukaryotes were basal), this grouping was abandoned in later schemes. In 2023, using molecular phylogenetic analysis of 186 taxa, Al Jewari and Baldauf proposed
126-421: 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 inferring phylogenetic trees 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
189-413: A cladistic analysis is a cladogram – a tree -shaped diagram ( dendrogram ) 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
252-422: A coarse impression of the complexity. A more detailed account will give details about fractions of introgressions between groupings, and even geographic variations thereof. This has been used as an argument for the use of paraphyletic groupings, but typically other reasons are quoted. Horizontal gene transfer is the mobility of genetic info between different organisms that can have immediate or delayed effects for
315-460: A hypothesis, a clade can be rejected only if some groupings were explicitly excluded. It may then be found that the excluded group did actually descend from the last common ancestor of the group, and thus emerged within the group. ("Evolved from" is misleading, because in cladistics all descendants stay in the ancestral group). To keep only valid clades, upon finding that the group is paraphyletic this way, either such excluded groups should be granted to
378-453: A large body of work which is well regarded. Still, he is controversial in a way that is a bit difficult to describe. The issue may be one of writing style. Cavalier-Smith has a tendency to make pronouncements where others would use declarative sentences, to use declarative sentences where others would express an opinion, and to express opinions where angels would fear to tread. In addition, he can sound arrogant, reactionary, and even perverse. On
441-489: A large number and variety of different kinds of characters are viewed as more robust than those based on more limited evidence. 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. These are compared in the table below. Cladistics, either generally or in specific applications, has been criticized from its beginnings. Decisions as to whether particular character states are homologous ,
504-473: A lot of possible trees. Assigning names to each possible clade may not be prudent. Furthermore, established names are discarded in cladistics, or alternatively carry connotations which may no longer hold, such as when additional groups are found to have emerged in them. Naming changes are the direct result of changes in the recognition of mutual relationships, which often is still in flux, especially for extinct species. Hanging on to older naming and/or connotations
567-475: A particular method. Datasets are tables consisting of molecular , morphological, ethological 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
630-720: A particular set of methods used in phylogenetic analysis, although it is now sometimes used to refer to the whole field. 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. Zimmermann (for plants) in 1943. 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. Hennig referred to his own approach as "phylogenetic systematics". From
693-457: A period, many branches may have radiated, and it may take hundreds of millions of years for them to have whittled down to just two. Only then one can theoretically assign proper last common ancestors of groupings which do not inadvertently include earlier branches. The process of true cladistic bifurcation can thus take a much more extended time than one is usually aware of. In practice, for recent radiations, cladistically guided findings only give
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#1732772230343756-444: A phylogenetic tree are used to justify decisions about character states, which are then used as evidence for the shape of the tree. 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
819-809: A phylogenetic tree with the metamonad Parabasalia as basal Eukaryotes. Discoba and the rest of the Eukaryota appear to have emerged as sister taxon to the Preaxostyla, incorporating a single alphaproteobacterium as mitochondria by endosymbiosis. Thus the Fornicata are more closely related to e.g. animals than to Parabasalia. The rest of the Eukaryotes emerged within the Excavata as sister of the Discoba. Caesar al Jewari and Sandra Baldauf argue instead that
882-553: A powerful way to test hypotheses about cross-cultural relationships among folktales. 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 . Historical linguistics : Cladistic methods have been used to reconstruct the phylogeny of languages using linguistic features. This
945-400: A precondition of their being synapomorphies, have been challenged as involving circular reasoning and subjective judgements. Of course, the potential unreliability of evidence is a problem for any systematic method, or for that matter, for any empirical scientific endeavor at all. Transformed cladistics arose in the late 1970s in an attempt to resolve some of these problems by removing
1008-406: A priori assumptions about phylogeny from cladistic analysis, but it has remained unpopular. The cladistic method does not identify fossil species as actual ancestors of a clade. Instead, fossil taxa are identified as belonging to separate extinct branches. While a fossil species could be the actual ancestor of a clade, there is no way to know that. Therefore, a more conservative hypothesis is that
1071-401: A side-branch, not distinguishing whether an actual ancestor of other groupings was found. The techniques and nomenclature of cladistics have been applied to disciplines other than biology. (See phylogenetic nomenclature .) Cladistics findings are posing a difficulty for taxonomy , where the rank and (genus-)naming of established groupings may turn out to be inconsistent. Cladistics is now
1134-561: A total of 23 animal phyla. Cavalier-Smith's 2003 classification scheme: Cavalier-Smith and his collaborators revised the classification in 2015, and published it in PLOS ONE . In this scheme they reintroduced the division of prokaryotes into two kingdoms, Bacteria (previously 'Eubacteria') and Archaea (previously 'Archebacteria'). This is based on the consensus in the Taxonomic Outline of Bacteria and Archaea (TOBA) and
1197-695: A variety of major taxonomic groups, such as the Chromista , Chromalveolata , Opisthokonta , Rhizaria , and Excavata . He was known for his systems of classification of all organisms . Cavalier-Smith was born on 21 October 1942 in London. His parents were Mary Maude (née Bratt) and Alan Hailes Spencer Cavalier Smith. He was educated at Norwich School , Gonville and Caius College, Cambridge (MA) in Biology and King's College London (PhD) in Zoology. He
1260-535: Is a stub . You can help Misplaced Pages by expanding it . Thomas Cavalier-Smith Thomas ( Tom ) Cavalier-Smith , FRS , FRSC , NERC Professorial Fellow (21 October 1942 – 19 March 2021 ), was a professor of evolutionary biology in the Department of Zoology, at the University of Oxford . His research has led to discovery of a number of unicellular organisms ( protists ) and advocated for
1323-565: 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
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#17327722303431386-440: 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: lizards turtles crocodilians 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
1449-578: Is counter-productive, as they typically do not reflect actual mutual relationships precisely at all. E.g. Archaea, Asgard archaea, protists, slime molds, worms, invertebrata, fishes, reptilia, monkeys, Ardipithecus , Australopithecus , Homo erectus all contain Homo sapiens cladistically, in their sensu lato meaning. For originally extinct stem groups, sensu lato generally means generously keeping previously included groups, which then may come to include even living species. A pruned sensu stricto meaning
1512-500: Is often adopted instead, but the group would need to be restricted to a single branch on the stem. Other branches then get their own name and level. This is commensurate to the fact that more senior stem branches are in fact closer related to the resulting group than the more basal stem branches; that those stem branches only may have lived for a short time does not affect that assessment in cladistics. The comparisons used to acquire data on which cladograms can be based are not limited to
1575-504: 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 : 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
1638-474: Is typically shared derived characteristics ( synapomorphies ) that are not present in more distant groups and ancestors. However, from an empirical perspective, common ancestors are inferences based on a cladistic hypothesis of relationships of taxa whose character states can be observed. Theoretically, a last common ancestor and all its descendants constitute a (minimal) clade. Importantly, all descendants stay in their overarching ancestral clade. For example, if
1701-795: The Canadian Institute for Advanced Research (CIFAR) in 1988, the Royal Society of Canada (FRSC) in 1997, and the Royal Society of London (FRS) in 1998. He received the International Prize for Biology from the Emperor of Japan in 2004, and the Linnean Medal for Zoology in 2007. He was appointed Fellow of the Canadian Institute for Advanced Research (CIFAR) between 1998 and 2007, and Advisor of
1764-590: The Catalogue of Life . In 2006, Cavalier-Smith proposed that the last universal common ancestor to all life was a non-flagellate Gram-negative bacterium ("negibacterium") with two membranes (also known as diderm bacterium ). Cavalier-Smith was elected Fellow of the Linnean Society of London (FLS) in 1980, the Institute of Biology (FIBiol) in 1983, the Royal Society of Arts (FRSA) in 1987,
1827-409: 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 because there is no evidence that they recover more "true" or "correct" results from actual empirical data sets Every cladogram is based on a particular dataset analyzed with
1890-488: The scientific community . His taxonomic revisions often influenced the overall classification of all life forms. Cavalier-Smith's first major classification system was the division of all organisms into eight kingdoms. In 1981, he proposed that by completely revising Robert Whittaker's Five Kingdom system, there could be eight kingdoms: Bacteria, Eufungi, Ciliofungi, Animalia, Biliphyta, Viridiplantae, Cryptophyta, and Euglenozoa. In 1983, he revised his system particularly in
1953-636: The Eukaryotes possibly started with an endosymbiosis event of a deltaproteobacterium or gammaproteobacterium, accounting for the otherwise unexplained presence of anaerobic bacterial enzymes in metamonada in this scenario. The sister of the Preaxostyla within Metamonada represents the rest of the Eukaryotes which acquired a alphaproteobacterium. Hodarchaeales Parabasalia Fornicata Preaxostyla Jakobida Heterolobosea Euglenozoa and allies Amorphea (inc. animals, fungi) SAR Archaeplastida (inc. plants) This biology article
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2016-634: The Integrated Microbial Biodiversity of CIFAR. He won the 2007 Frink Medal of the Zoological Society of London . Cladistic Cladistics ( / k l ə ˈ d ɪ s t ɪ k s / klə- DIST -iks ; from Ancient Greek κλάδος kládos 'branch') is an approach to biological classification in which organisms are categorized in groups (" clades ") based on hypotheses of most recent common ancestry . The evidence for hypothesized relationships
2079-539: 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. The cladistic method interprets each shared character state transformation as a potential piece of evidence for grouping. Synapomorphies (shared, derived character states) are viewed as evidence of grouping, while symplesiomorphies (shared ancestral character states) are not. The outcome of
2142-422: The clade, or the group should be abolished. Branches down to the divergence to the next significant (e.g. extant) sister are considered stem-groupings of the clade, but in principle each level stands on its own, to be assigned a unique name. For a fully bifurcated tree, adding a group to a tree also adds an additional (named) clade, and a new level on that branch. Specifically, also extinct groups are always put on
2205-443: The cladograms show two mutually exclusive hypotheses to describe the evolutionary history, at most one of them is correct. 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 are or were primates, and so form a clade; the name Primates is therefore recognized for this clade. Within
2268-402: 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. They also are
2331-410: The exact historic relationships between the groups. The following terms, coined by Hennig, are used to identify shared or distinct character states among groups: 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
2394-512: The field of biology. 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 : Cladistic methods have been used to reconstruct
2457-455: The following scheme: The kingdom Animalia was divided into four subkingdoms: Radiata (phyla Porifera , Cnidaria , Placozoa , and Ctenophora ), Myxozoa , Mesozoa , and Bilateria (all other animal phyla). He created three new animal phyla: Acanthognatha ( rotifers , acanthocephalans , gastrotrichs , and gnathostomulids ), Brachiozoa ( brachiopods and phoronids ), and Lobopoda ( onychophorans and tardigrades ) and recognised
2520-481: The fossil taxon is related to other fossil and extant taxa, as implied by the pattern of shared apomorphic features. An otherwise extinct group with any extant descendants, is not considered (literally) extinct, and for instance does not have a date of extinction. Anything having to do with biology and sex is complicated and messy, and cladistics is no exception. Many species reproduce sexually, and are capable of interbreeding for millions of years. Worse, during such
2583-418: The goals of cladification and classification were different; his approach was similar to that of many others' broad-based treatments of protists. The scope of Cavalier-Smith's taxonomic propositions was grand, but the numbers and composition of the components (taxa), and, often, their relations were not stable. Propositions were often ambiguous and short-lived; he frequently amended taxa without any change in
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2646-407: 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
2709-435: The ideas to be easily grasped. Some such diagrams made their way into publications, where careful scrutiny was possible, and where the conjectural nature of some assertions was evident. The richness of his ideas, their continuing evolution, and the transition into taxonomies that gave Cavalier-Smith's investigations into evolutionary paths ( phylogeny ) and the resulting classifications, its distinctive character. Cavalier-Smith
2772-464: The kingdom Archezoa to the phylum Amoebozoa . By 1998, Cavalier-Smith had reduced the total number of kingdoms from eight to six: Animalia , Protozoa , Fungi , Plantae (including Glaucophyte, red and green algae ), Chromista , and Bacteria. Nevertheless, he had already presented this simplified scheme for the first time on his 1981 paper and endorsed it in 1983. Five of Cavalier-Smith's kingdoms are classified as eukaryotes as shown in
2835-487: The latter contains Tarsiiformes and Anthropoidea. Lemurs and tarsiers may have looked closely related to humans, in the sense of being close on the evolutionary tree to humans. However, from the perspective of a tarsier, humans and lemurs would have looked close, in the exact same sense. Cladistics forces a neutral perspective, treating all branches (extant or extinct) in the same manner. It also forces one to try to make statements, and honestly take into account findings, about
2898-404: The light of growing evidence that Archaebacteria were a separate group from Bacteria, to include an array of lineages that had been excluded from his 1981 treatment, to deal with issues of polyphyly, and to promote new ideas of relationships. In addition, some protists lacking mitochondria were discovered. As mitochondria were known to be the result of the endosymbiosis of a proteobacterium , it
2961-419: 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: turtles lizards crocodilians birds If this phylogenetic hypothesis
3024-455: The most commonly used method to classify organisms. 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); but the terms "cladistics" and "clade" were popularized by other researchers. Cladistics in the original sense refers to
3087-525: The name. His approach was not universally accepted: Others attempted to underpin taxonomy of protists with a nested series of atomised, falsifiable propositions, following the philosophy of transformed cladistics. However, this approach is no longer considered defensible. Cavalier-Smith's ideas that led to the taxonomic structures were usually first presented in the form of tables and complex, annotated diagrams . When presented at scientific meetings, they were sometimes too rich, and often written too small, for
3150-505: The other [hand], he has a long history of being right when everyone else was wrong. To our way of thinking, all of this is overshadowed by one incomparable virtue: the fact that he will grapple with the details. This makes for very long, very complex papers and causes all manner of dark murmuring, tearing of hair, and gnashing of teeth among those tasked with trying to explain his views of early life. See, [for example], Zrzavý (2001) [and] Patterson (1999). Nevertheless, he deals with all of
3213-444: The primates, all anthropoids (monkeys, apes, and humans) are hypothesized to have had a common ancestor all of whose descendants are or 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
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#17327722303433276-432: The reciprocal host. There are several processes in nature which can cause horizontal gene transfer . This does typically not directly interfere with ancestry of the organism, but can complicate the determination of that ancestry. On another level, one can map the horizontal gene transfer processes, by determining the phylogeny of the individual genes using cladistics. If there is unclarity in mutual relationships, there are
3339-650: The relevant facts. Cavalier-Smith wrote extensively on the taxonomy and classification of all life forms, but especially protists . One of his major contributions to biology was his proposal of a new kingdom of life: the Chromista , even though it is not widely accepted to be monophyletic (see above). He also introduced new taxonomic groupings group for eukaryotes such as the Chromalveolata (1981), Opisthokonta (1987), Rhizaria (2002), and Excavata (2002). Though well known, many of his claims have been controversial and have not gained widespread acceptance in
3402-552: The scope of taxa a taxonomic name was applied to. Cavalier-Smith also reused familiar names (such as Protozoa) for innovative taxonomic concepts. This created confusion because Protozoa was and still is used in its old sense, alongside its use in the newer senses. Because of Cavalier-Smith's tendency to publish rapidly and to change his narratives and taxonomic summaries frequently, his approach and claims were frequently debated. Palaeos .com described his writing style as follows: Prof. Cavalier-Smith of Oxford University has produced
3465-500: The taxonomic relationships among living organisms. He was prolific, drawing on a near-unparalleled wealth of information to suggest novel relationships. In 1989 he was appointed Professor of Botany at the University of British Columbia . In 1999, he joined the University of Oxford , becoming Professor of evolutionary biology in 2000. Thomas Cavalier-Smith died in March ;2021 following the development of cancer. Cavalier-Smith
3528-461: The terms worms or fishes were used within a strict cladistic framework, these terms would include humans. Many of these terms are normally used paraphyletically , outside of cladistics, e.g. as a ' grade ', which are fruitless to precisely delineate, especially when including extinct species. Radiation results in the generation of new subclades by bifurcation, but in practice sexual hybridization may blur very closely related groupings. As
3591-410: 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
3654-484: Was a prolific taxonomist, drawing on a near-unparalleled wealth of information to suggest novel relationships. His suggestions were translated into taxonomic concepts and classifications with which he associated new names, or in some cases, reused old names. Cavalier-Smith did not follow or espouse an explicit taxonomic philosophy but his approach was closest to evolutionary taxonomy. He and several other colleagues were opposed to cladistic approaches to taxonomy arguing that
3717-485: Was a single endosymbiotic event by which chlorophyll a c containing plastids were acquired by a common ancestor of all three groups, and that the differences (such as cytological components and their arrangements) among the groups were the result of subsequent evolutionary changes. This interpretation that chromists were monophyletic also required that the heterotrophic ( protozoan ) members of all three groups had arisen from ancestors with plastids. The alternative hypothesis
3780-435: Was courageous in his adherence to the earlier traditionalist style characterized by Charles Darwin , that of relying on narratives. One example was his advocacy for the Chromista that united lineages that had plastids with chlorophylls a and c (primarily chrysophytes and other stramenopiles , cryptophytes, and haptophytes) despite clear evidence that the group corresponded to a clade. It was Cavalier-Smith's claim that there
3843-709: Was that the three chromophytic lineages were not closely related (to the exclusion of other lineages) (i.e. were polyphyletic), likely that all were ancestrally without plastids, and that separate symbiotic events established the chlorophyll a/c plastids stramenopiles, cryptomonads and haptophytes. The polyphyly of the chromists has been re-asserted in subsequent studies. Cavalier-Smith's lack of an objective and reproducible methodology that would translate evolutionary insights into taxa and hierarchical schemes, were often confusing to those who did not follow his publications closely. Many of his taxa requiring his frequent adjustment, as illustrated below. In turn this led to confusion as to
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#17327722303433906-673: Was thought that these amitochondriate eukaryotes were primitively so, marking an important step in eukaryogenesis . As a result, these amitochondriate protists were given special status as a protozan subkingdom Archezoa , that he later elevated to kingdom status. This was later referred to as the Archezoa hypothesis . In 1993, the eight kingdoms became: Eubacteria, Archaebacteria, Archezoa, Protozoa, Chromista, Plantae, Fungi, and Animalia. The kingdom Archezoa went through many compositional changes due to evidence of polyphyly and paraphyly before being abandoned. He assigned some former members of
3969-474: Was under the supervision of Sir John Randall for his PhD thesis between 1964 and 1967; his thesis was entitled " Organelle Development in Chlamydomonas reinhardii". From 1967 to 1969, Cavalier-Smith was a guest investigator at Rockefeller University . He became Lecturer of biophysics at King's College London in 1969. He was promoted to Reader in 1982. From the early 1980s, Smith promoted views about
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