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, so many differing evolutionary trees can be consistent with the same 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.
30-710: Langbergia is an extinct genus of trirachodontid cynodont from the Early Triassic of South Africa . The type and only species L. modisei was named in 2006 after the farm where the holotype was found, Langberg 566. Langbergia was found in the Burgersdorp Formation in the Beaufort Group , a part of the Cynognathus Assemblage Zone . The closely related trirachodontids Trirachodon and Cricodon were found in
60-446: A t e s {\displaystyle n.states} , c i occupies a range from 1 to ( n . s t a t e s − 1 ) / ( n . t a x a − ⌈ n . t a x a / n . s t a t e s ⌉ ) {\displaystyle (n.states-1)/(n.taxa-\lceil n.taxa/n.states\rceil )} . The retention index (RI)
90-445: A metric to measure how consistent a candidate cladogram is with the data. Most cladogram algorithms use the mathematical techniques of optimization and minimization. In general, cladogram generation algorithms must be implemented as computer programs, although some algorithms can be performed manually when the data sets are modest (for example, just a few species and a couple of characteristics). Some algorithms are useful only when
120-540: A character in a phylogenetic analysis as they do not contribute anything to our understanding of relationships. However, homoplasy is often not evident from inspection of the character itself (as in DNA sequence, for example), and is then detected by its incongruence (unparsimonious distribution) on a most-parsimonious cladogram. Note that characters that are homoplastic may still contain phylogenetic signal . A well-known example of homoplasy due to convergent evolution would be
150-422: A dataset, the degree to which each character carries phylogenetic information, and the fashion in which additive characters are coded, rendering it unfit for purpose. c i occupies a range from 1 to 1/[ n.taxa /2] in binary characters with an even state distribution; its minimum value is larger when states are not evenly spread. In general, for a binary or non-binary character with n . s t
180-457: A larger clade. The incongruence length difference test (ILD) is a measurement of how the combination of different datasets (e.g. morphological and molecular, plastid and nuclear genes) contributes to a longer tree. It is measured by first calculating the total tree length of each partition and summing them. Then replicates are made by making randomly assembled partitions consisting of the original partitions. The lengths are summed. A p value of 0.01
210-425: Is a cladogram from Gao et al. (2010) showing the phylogenetic relationships of trirachodontids: Cynognathus Diademodon Trirachodon Langbergia Cricodon Beishanodon Sinognathus Traversodontidae The cladogram above shows a monophyletic Trirachodontidae, but multiple studies have found the family to be paraphyletic with respect to the family Traversodontidae . Below
240-410: Is a character state that is shared by two or more taxa due to some cause other than common ancestry. The two main types of homoplasy are convergence (evolution of the "same" character in at least two distinct lineages) and reversion (the return to an ancestral character state). Characters that are obviously homoplastic, such as white fur in different lineages of Arctic mammals, should not be included as
270-579: Is a cladogram from Hendrickx et al. (2020), who also recovered the members of the subfamily Trirachodontinae as a basal polytomy within the clade Neogomphodontia: Cynognathus Diademodon Titanogomphodon Langbergia Trirachodon Beishanodon Cricodon Sinognathus Traversodontidae Cladogram The characteristics used to create a cladogram can be roughly categorized as either morphological (synapsid skull, warm blooded, notochord , unicellular, etc.) or molecular (DNA, RNA, or other genetic information). Prior to
300-594: Is an extinct, possibly paraphyletic family of cynognathian cynodonts from the Triassic of China and southern Africa . Trirachodontids appeared during the Early Triassic soon after the Permian-Triassic extinction event and quickly spread over a wide geographic area in a comparatively brief amount of time from 250 to 237 million years ago. Trirachodontids have wide skulls and short, narrow snouts. Two large holes called temporal fenestrae run along
330-519: Is longuomesially orientated. Additionally, both upper and lower lower gomphodont postcanines of Langbergia increase tooth size up until the penultimate tooth and the medial and distal basins are deep and mesiodistally short Trirachodontids Trirachodon and Cricodon have a labial platform of the maxilla that arises lateral to the postcanine series, this is not observed in Langbergia. Langbergia has been recorded having stapes, despite how fragile
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#1732797528077360-411: Is obtained for 100 replicates if 99 replicates have longer combined tree lengths. Some measures attempt to measure the amount of homoplasy in a dataset with reference to a tree, though it is not necessarily clear precisely what property these measures aim to quantify The consistency index (CI) measures the consistency of a tree to a set of data – a measure of the minimum amount of homoplasy implied by
390-741: Is the Cynognathus Assemblage Zone, this zone covers the late early and early middle Triassic. The Cynognathus Assemblage Zone is then divided into a threefold subdivision. The uppermost subdivision of the Cynognathus Assemblage Zone is named the Lystrosaurus Assemblage Zone. The upper boundary of the Lystrosaurus Assemblage Zone is drawn at the Langbergia and the Garjainia . Trirachodontidae Trirachodontidae
420-586: Is the use of genomic retrotransposon markers , which are thought to be less prone to the problem of reversion that plagues sequence data. They are also generally assumed to have a low incidence of homoplasies because it was once thought that their integration into the genome was entirely random; this seems at least sometimes not to be the case, however. Researchers must decide which character states are "ancestral" ( plesiomorphies ) and which are derived ( synapomorphies ), because only synapomorphic character states provide evidence of grouping. This determination
450-526: Is usually done by comparison to the character states of one or more outgroups . States shared between the outgroup and some members of the in-group are symplesiomorphies; states that are present only in a subset of the in-group are synapomorphies. Note that character states unique to a single terminal (autapomorphies) do not provide evidence of grouping. The choice of an outgroup is a crucial step in cladistic analysis because different outgroups can produce trees with profoundly different topologies. A homoplasy
480-587: The advent of DNA sequencing, cladistic analysis primarily used morphological data. Behavioral data (for animals) may also be used. As DNA sequencing has become cheaper and easier, molecular systematics has become a more and more popular way to infer phylogenetic hypotheses. Using a parsimony criterion is only one of several methods to infer a phylogeny from molecular data. Approaches such as maximum likelihood , which incorporate explicit models of sequence evolution, are non-Hennigian ways to evaluate sequence data. Another powerful method of reconstructing phylogenies
510-774: The back of the head and have a uniformly large width. Trirachodontids also have two large canine teeth and smaller cusped postcanines. Most of the features that distinguish trirachodonts from other cynodonts are found in their dentition. Trirachodontids lived in semi-arid environments with seasonal rainfall. The bone structure of trirachodontids suggests that they grew quickly in seasons with high rainfall and slowly in less favorable seasons. One trirachodontid, Trirachodon , has been found in association with complex burrow systems. These burrows were probably used by many individuals to hide from predators, raise young, or stay warm. Two subfamilies of trirachodontids are recognized: Trirachodontinae from Africa and Sinognathinae from China. Below
540-486: The center of the tooth. Langbergia are small gomphodontian cynodonts. Cynodonts are a very important component of the Triassic. After the Langbergia fossil was found in 2006, new diagnostic features allowed for a new taxon, Langbergia modisei. Unlike other Trirachodontids, the upper and lower gomphodont post caninines of Langbergia are elliptical in cross section, slightly labiolingually elongated and their long axis
570-431: The character, "presence of wings". Although the wings of birds, bats , and insects serve the same function, each evolved independently, as can be seen by their anatomy . If a bird, bat, and a winged insect were scored for the character, "presence of wings", a homoplasy would be introduced into the dataset, and this could potentially confound the analysis, possibly resulting in a false hypothesis of relationships. Of course,
600-434: The characteristic data are molecular (DNA, RNA); other algorithms are useful only when the characteristic data are morphological. Other algorithms can be used when the characteristic data includes both molecular and morphological data. Algorithms for cladograms or other types of phylogenetic trees include least squares , neighbor-joining , parsimony , maximum likelihood , and Bayesian inference . Biologists sometimes use
630-691: The dataset). The rescaled consistency index (RC) is obtained by multiplying the CI by the RI; in effect this stretches the range of the CI such that its minimum theoretically attainable value is rescaled to 0, with its maximum remaining at 1. The homoplasy index (HI) is simply 1 − CI. This measures the amount of homoplasy observed on a tree relative to the maximum amount of homoplasy that could theoretically be present – 1 − (observed homoplasy excess) / (maximum homoplasy excess). A value of 1 indicates no homoplasy; 0 represents as much homoplasy as there would be in
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#1732797528077660-705: The only reason a homoplasy is recognizable in the first place is because there are other characters that imply a pattern of relationships that reveal its homoplastic distribution. A cladogram is the diagrammatic result of an analysis, which groups taxa on the basis of synapomorphies alone. There are many other phylogenetic algorithms that treat data somewhat differently, and result in phylogenetic trees that look like cladograms but are not cladograms. For example, phenetic algorithms, such as UPGMA and Neighbor-Joining, group by overall similarity, and treat both synapomorphies and symplesiomorphies as evidence of grouping, The resulting diagrams are phenograms, not cladograms, Similarly,
690-436: The program settles on a local minimum rather than the desired global minimum. To help solve this problem, many cladogram algorithms use a simulated annealing approach to increase the likelihood that the selected cladogram is the optimal one. The basal position is the direction of the base (or root) of a rooted phylogenetic tree or cladogram. A basal clade is the earliest clade (of a given taxonomic rank[a]) to branch within
720-405: The results of model-based methods (Maximum Likelihood or Bayesian approaches) that take into account both branching order and "branch length," count both synapomorphies and autapomorphies as evidence for or against grouping, The diagrams resulting from those sorts of analysis are not cladograms, either. There are several algorithms available to identify the "best" cladogram. Most algorithms use
750-413: The same area. Langbergia was discovered in the Cynognathus Assemblage Zone of the Beaufort Group of South Africa in 2006. It was named after the farm where the holotype was found (Langberg 566). Trirachodontids are distinguishable due to the shape of their postcanines ; the postcanines, distal to the canines, are transversely widened teeth with three main cusps disposed in a transverse row across
780-585: The structure is. Langbergia, like most other living in the Permian, went extinct during the end-Permian mass extinction . The Burgersdorp Formation in South Africa is known for having a substantial amount of fossiliferous rocks. The Permo-Triassic strata of the Beaufort Group has a substantial amount of therapsid fossils which are used in the biostratigraphic subdivision. The uppermost division
810-460: The term parsimony for a specific kind of cladogram generation algorithm and sometimes as an umbrella term for all phylogenetic algorithms. Algorithms that perform optimization tasks (such as building cladograms) can be sensitive to the order in which the input data (the list of species and their characteristics) is presented. Inputting the data in various orders can cause the same algorithm to produce different "best" cladograms. In these situations,
840-406: The tree. It is calculated by counting the minimum number of changes in a dataset and dividing it by the actual number of changes needed for the cladogram. A consistency index can also be calculated for an individual character i , denoted c i . Besides reflecting the amount of homoplasy, the metric also reflects the number of taxa in the dataset, (to a lesser extent) the number of characters in
870-423: The user should input the data in various orders and compare the results. Using different algorithms on a single data set can sometimes yield different "best" cladograms, because each algorithm may have a unique definition of what is "best". Because of the astronomical number of possible cladograms, algorithms cannot guarantee that the solution is the overall best solution. A nonoptimal cladogram will be selected if
900-399: Was proposed as an improvement of the CI "for certain applications" This metric also purports to measure of the amount of homoplasy, but also measures how well synapomorphies explain the tree. It is calculated taking the (maximum number of changes on a tree minus the number of changes on the tree), and dividing by the (maximum number of changes on the tree minus the minimum number of changes in
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