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; nevertheless, 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.
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 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 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 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 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 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 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, 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, 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 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 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 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, 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 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 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 is obtained for 100 replicates if 99 replicates have longer combined tree lengths.
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 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 ci.
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 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.
ci 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 , ci occupies a range from 1 to .
The retention index (RI) 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 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 a fully random dataset, and negative values indicate more homoplasy still (and tend only to occur in contrived examples). The HER is presented as the best measure of homoplasy currently available.
Afroaves is a clade of birds, consisting of the kingfishers and kin (Coraciiformes), woodpeckers and kin (Piciformes), hornbills and kin (Bucerotiformes), trogons (Trogoniformes), cuckoo roller (Leptosomatiformes), mousebirds (Coliiformes), owls (Strigiformes), raptors (Accipitriformes) and New World vultures (Cathartiformes). The most basal clades are predatory, suggesting the last common ancestor of the group was also.
Cladogram of Afroaves relationships based on Prum, R.O. et al. (2015) with some clade names after Yury, T. et al. (2013) and Kimball et al. 2013.Australaves
Australaves is a recently defined clade of birds, consisting of the Eufalconimorphae (passerines, parrots and falcons) as well as the Cariamiformes (including seriemas and the extinct "terror birds"). They appear to be the sister group of Afroaves. As in the case of Afroaves, the most basal clades have predatory extant members, suggesting this was the ancestral lifestyle; however, some researchers like Darren Naish are skeptical of this assessment, since some extinct representatives such as the herbivorous Strigogyps lead other lifestyles. Basal parrots and falcons are at any rate vaguely crow-like and probably omnivorous.
Cladogram of Telluraves relationships based on Prum, R.O. et al. (2015).Basal (phylogenetics)
In phylogenetics, basal is the direction of the base (or root) of a rooted phylogenetic tree or cladogram. The term may be more strictly applied only to nodes adjacent to the root, or more loosely applied to nodes regarded as being close to the root. Each node in the tree corresponds to a clade; i.e., clade C may be described as basal within a larger clade D if its root is directly linked to the root of D. The terms deep-branching or early-branching are similar in meaning.
While there must always be two or more equally basal clades sprouting from the root of every cladogram, those clades may differ widely in taxonomic rank and/or species diversity. If C is a basal clade within D that has the lowest rank of all basal clades within D, C may be described as the basal taxon of that rank within D. Greater diversification may be associated with more evolutionary innovation, but ancestral characters should not be imputed to the members of a less species-rich basal clade without additional evidence, as there can be no assurance such an assumption is valid.In general, clade A is more basal than clade B if B is a subgroup of the sister group of A. Within large groups, "basal" may be used loosely to mean 'closer to the root than the great majority of', and in this context terminology such as "very basal" may arise. A 'core clade' is a clade representing all but the basal clade(s) of lowest rank within a larger clade; e.g., core eudicots.Boreoeutheria
Boreoeutheria (synonymous with Boreotheria) (from Greek Βορέας, Boreas "the greek god of north wind", εὐ-, eu- "good, right" and θηρίον, thēríon "beast" hence "northern true beasts") is a clade (magnorder) of placental mammals which is composed of the sister taxa Laurasiatheria (most hoofed mammals, most pawed carnivores, and several other groups) and Euarchontoglires (Supraprimates). It is now well supported by DNA sequence analyses, as well as retrotransposon presence or absence data. Placental mammals outside of this clade are the clades Xenarthra (sloths and their close relatives) and Afrotheria (elephants and their close relatives).
The earliest known fossils belonging to this group date to about 65 million years ago, shortly after the K-Pg extinction event, though molecular data suggest they may have originated earlier, during the Cretaceous period.With a few exceptions male animals in the clade have a scrotum which serves the function of cooling the testicles to improve the production of sperm. The sub-clade Scrotifera was named after this feature.Gastrodontoidea
Gastrodontoidea is a taxonomic superfamily of air-breathing land snails, terrestrial pulmonate gastropod mollusks in the limacoid clade.Helicarionoidea
Helicarionoidea is a superfamily of air-breathing land snails and semi-slugs, terrestrial pulmonate gastropod mollusks in the limacoid clade.Limacoid clade
The limacoid clade is a taxonomic clade of air-breathing land snails, semislugs and slugs, terrestrial pulmonate gastropod molluscs in the informal group Sigmurethra.Mikko's Phylogeny Archive
Mikko's Phylogeny Archive is an amateur paleontology website maintained by Mikko Haaramo, a student at the University of Helsinki's Department of Geology, Division of Geology and Palaeontology.The project is aimed at collecting phylogenetic trees of all organisms. Each page presents a cladogram that is hyperlinked to its parent and daughter cladograms, plus a section for references. Taxa of uncertain relationship are indicated by a question mark. No indication is given for what part of the cladogram is based on which specific references.
The site was originally simply named "Life as We Know It", and with the Dinosauricon it was the first web-site to use an ascii text-based format for showing cladograms.
Although the Archive has been hosted by the Finnish Museum of the Natural History and now the University of Helsinki's servers, the museum has no formal affiliation with it. Haaramo points out that the site is a private project, is not peer-reviewed, and should not be used as a scientific reference. Together with Palaeos and the Paleobiology Database it provides a near comprehensive listing of many groups, genera and species of extinct organisms, along with recent taxa.Neodiapsida
Neodiapsida is a clade, or major branch, of the reptilian family tree and includes all diapsids apart from some early primitive types known as the araeoscelidians.
In phylogenetic systematics, they are variously defined as the common ancestor and all its descendants of Younginiforms and "crown diapsids" (the common ancestor of lizards, crocodilians and birds, and all their descendants) [Callaway 1997], or all diapsids that are more closely related to Sauria than to Araeoscelidia (Laurin and Gauthier 2000).
Early or basal Permian neodiaspids were lizard-like, but already include specialised forms for swimming (Claudiosaurus) and gliding (Coelurosauravidae), as well as more conventional lizard-like forms (Youngina etc.). Before the end of the Permian, the neodiapsids give rise to the main branches of the diapsid evolutionary tree, the lepidosaurs and archosaurs.Pancrustacea
Pancrustacea is a clade, comprising all crustaceans and hexapods. This grouping is contrary to the Atelocerata hypothesis, in which Myriapoda and Hexapoda are sister taxa, and Crustacea are only more distantly related. As of 2010, the Pancrustacea taxon is considered well-accepted. The clade has also been called Tetraconata, referring to the square ommatidia of many of its members. That name is preferred by some scientists as a means of avoiding confusion with the use of "pan-" to indicate a clade that includes a crown group and all of its stem group representatives.Panpulmonata
Panpulmonata is a taxonomic clade of snails and slugs in the clade Heterobranchia within the clade Euthyneura.Panpulmonata was established as a new taxon by Jörger et al. in October 2010.The older name "Pulmonata" referred to a group of gastropods which were considered to be "air-breathers". This meaning certainly does not apply to the panpulmonate groups Acochlidia, Sacoglossa and Pyramidelloidea, and also was inaccurate when applied to some of the more traditional pulmonate taxa such as Siphonarioidea or Hygrophila, most members of which lack permanently air-filled lungs. However, the term Panpulmonata was chosen by Jörger et al. (2010) to provide some continuity in the terminology.
Panpulmonata consists of following taxa:
Acochlidiacea (mentioned as Acochlidia)
Eupulmonata: Stylommatophora, Systellommatophora, Ellobioidea, Otinoidea, Trimusculoidea.Plateosauria
Plateosauria is a clade of sauropodomorph dinosaurs which lived during the Late Triassic to the Late Cretaceous. The name Plateosauria was first coined by Gustav Tornier in 1913. The name afterwards fell out of use until the 1980s.
Plateosauria is a node-based taxon. In 1998, Paul Sereno defined Plateosauria as the last common ancestor of Plateosaurus engelhardti and Massospondylus carinatus, and its descendants. Peter Galton and Paul Upchurch in 2004 used a different definition: the last common ancestor of Plateosaurus engelhardti and Jingshanosaurus xinwaensis, and its descendants. In their cladistic analysis the Plateosauria belonged to the Prosauropoda, and included the Plateosauridae subgroup. In Galton's and Upchurch's study also Coloradisaurus, Euskelosaurus, Jingshanosaurus, Massospondylus, Mussaurus, Sellosaurus, and Yunnanosaurus proved to be plateosaurians.However, recent cladistic analyses suggest that the Prosauropoda as traditionally defined is paraphyletic to sauropods. Prosauropoda, as currently defined, is a synonym of Plateosauridae as both contain the same taxa by definition.
The following cladogram simplified after an analysis presented by Apaldetti and colleagues in 2011.
The following cladogram simplified after an analysis presented by Blair McPhee and colleagues in 2014.Polysporangiophyte
Polysporangiophytes, also called polysporangiates or formally Polysporangiophyta, are plants in which the spore-bearing generation (sporophyte) has branching stems (axes) that terminate in sporangia. The name literally means many sporangia plant. The clade includes all land plants (embryophytes) except for the bryophytes (liverworts, mosses and hornworts) whose sporophytes are normally unbranched, even if a few exceptional cases occur. While the definition is independent of the presence of vascular tissue, all living polysporangiophytes also have vascular tissue, i.e., are vascular plants or tracheophytes. Fossil polysporangiophytes are known that have no vascular tissue, and so are not tracheophytes.Rafetus
Rafetus is a genus of highly endangered softshell turtles in the family Trionychidae. It is a genus of large turtles which are found in freshwater habitats in Asia.Romeriida
Romeriida is a clade of reptiles that consists of diapsids and the extinct protorothyridid genus Paleothyris, if not the entire family Protorothyrididae. It is phylogenetically defined by Laurin & Reisz (1995) as the last common ancestor of Paleothyris and diapsids, and all its descendants. It is named after Alfred Romer, a prominent vertebrate paleontologist of the twentieth century.Protorothyridids were once placed in the family Romeriidae along with the captorhinid Romeria. Because Romeria is now considered to be a captorhinid, and Captorhinidae is placed outside Romeriida, the genus is excluded from the clade. Protorothyridids were once the collective term for several romeriid genera of uncertain classification. However, more recent studies have proposed that Protorothyrididae is a paraphyletic taxon. Therefore, it is possible that many protorothyridids do not lie within the clade Romeriida.
Several synapomorphies characterize the romeriids. These include the separation of the tabular bone from the opisthotic bone, ventrally keeled anterior pleurocentra, long and slender carpi and tarsi, and overlapping metapodials.Below is a cladogram showing the placement of Romeriida within Amniota, modified from Hill, 2005:
Cladogram after Müller & Reisz, 2006:
Polyphyletic ProtorothyrididaeSynapomorphy and apomorphy
In phylogenetics, apomorphy and synapomorphy refer to derived characters of a clade: characters or traits that are derived from ancestral characters over evolutionary history. An apomorphy is a character that is different from the form found in an ancestor, i.e., an innovation, that sets the clade apart from other clades. A synapomorphy is a shared apomorphy that distinguishes a clade from other organisms. In other words, it is an apomorphy shared by members of a monophyletic group, and thus assumed to be present in their most recent common ancestor.Telluraves
Telluraves (also called land birds or core landbirds) is a recently defined clade of birds with controversial content. Based on most recent genetic studies, the clade unites a variety of bird groups, including the australavians (passerines, parrots, seriamas, and falcons) as well as the afroavians (including the Accipitrimorphae – eagles, hawks, buzzards, vultures etc. – owls and woodpeckers, among others). They appear to be the sister group of a newly defined clade centered on Aequornithes.Given that the most basal extant members of both Afroaves (Accipitrimorphae, Strigiformes) and Australaves (Cariamiformes, Falconiformes) are carnivorous, it has been suggested that the last common ancestor of all Telluraves was probably a predator. Other researchers are skeptical of this assessment, citing the herbivorous cariamiform Strigogyps as evidence to the contrary.
Cladogram of Telluraves relationships based on Prum, R.O. et al. (2015) with some clade names after Yury, T. et al. (2013) and Kimball et al. 2013.