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34-453: Zingiberineae Heliconiaceae Strelitziineae Musaceae They form a Suborder Zingiberineae Kress in taxonomic classification, with the following phylogeny , the four families being grouped into two superfamilies. Zingiberaceae Costaceae Cannaceae Marantaceae This Zingiberales -related article is a stub . You can help Misplaced Pages by expanding it . Phylogeny A phylogenetic tree , phylogeny or evolutionary tree

68-506: A binary tree ), and an unrooted bifurcating tree takes the form of an unrooted binary tree , a free tree with exactly three neighbors at each internal node. In contrast, a rooted multifurcating tree may have more than two children at some nodes and an unrooted multifurcating tree may have more than three neighbors at some nodes. Both rooted and unrooted trees can be either labeled or unlabeled. A labeled tree has specific values assigned to its leaves, while an unlabeled tree, sometimes called

102-480: A rooted phylogenetic tree, each node with descendants represents the inferred most recent common ancestor of those descendants, and the edge lengths in some trees may be interpreted as time estimates. Each node is called a taxonomic unit. Internal nodes are generally called hypothetical taxonomic units, as they cannot be directly observed. Trees are useful in fields of biology such as bioinformatics , systematics , and phylogenetics . Unrooted trees illustrate only

136-409: A clear outgroup. Another method is midpoint rooting, or a tree can also be rooted by using a non-stationary substitution model . Unrooted trees illustrate the relatedness of the leaf nodes without making assumptions about ancestry. They do not require the ancestral root to be known or inferred. Unrooted trees can always be generated from rooted ones by simply omitting the root. By contrast, inferring

170-814: A combination of genes that come from different genomic sources (e.g., from mitochondrial or plastid vs. nuclear genomes), or genes that would be expected to evolve under different selective regimes, so that homoplasy (false homology ) would be unlikely to result from natural selection. When extinct species are included as terminal nodes in an analysis (rather than, for example, to constrain internal nodes), they are considered not to represent direct ancestors of any extant species. Extinct species do not typically contain high-quality DNA . The range of useful DNA materials has expanded with advances in extraction and sequencing technologies. Development of technologies able to infer sequences from smaller fragments, or from spatial patterns of DNA degradation products, would further expand

204-427: A function of the number of tips. For 10 tips, there are more than 34 × 10 6 {\displaystyle 34\times 10^{6}} possible bifurcating trees, and the number of multifurcating trees rises faster, with ca. 7 times as many of the latter as of the former. A dendrogram is a general name for a tree, whether phylogenetic or not, and hence also for the diagrammatic representation of

238-399: A more reticulate evolutionary history of the organisms sampled. 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

272-609: A more suitable metaphor than the tree . Indeed, phylogenetic corals are useful for portraying past and present life, and they have some advantages over trees ( anastomoses allowed, etc.). Phylogenetic trees composed with a nontrivial number of input sequences are constructed using computational phylogenetics methods. Distance-matrix methods such as neighbor-joining or UPGMA , which calculate genetic distance from multiple sequence alignments , are simplest to implement, but do not invoke an evolutionary model. Many sequence alignment methods such as ClustalW also create trees by using

306-536: A number of different formats, all of which must represent the nested structure of a tree. They may or may not encode branch lengths and other features. Standardized formats are critical for distributing and sharing trees without relying on graphics output that is hard to import into existing software. Commonly used formats are Although phylogenetic trees produced on the basis of sequenced genes or genomic data in different species can provide evolutionary insight, these analyses have important limitations. Most importantly,

340-441: A phylogenetic tree. A cladogram only represents a branching pattern; i.e., its branch lengths do not represent time or relative amount of character change, and its internal nodes do not represent ancestors. A phylogram is a phylogenetic tree that has branch lengths proportional to the amount of character change. A chronogram is a phylogenetic tree that explicitly represents time through its branch lengths. A Dahlgrenogram

374-402: 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. Although the concept of outgroups has been in use from the earliest days of cladistics, the term "outgroup"

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408-445: A tree shape, defines a topology only. Some sequence-based trees built from a small genomic locus, such as Phylotree, feature internal nodes labeled with inferred ancestral haplotypes. The number of possible trees for a given number of leaf nodes depends on the specific type of tree, but there are always more labeled than unlabeled trees, more multifurcating than bifurcating trees, and more rooted than unrooted trees. The last distinction

442-604: Is a diagram representing a cross section of a phylogenetic tree. A phylogenetic network is not strictly speaking a tree, but rather a more general graph , or a directed acyclic graph in the case of rooted networks. They are used to overcome some of the limitations inherent to trees. A spindle diagram, or bubble diagram, is often called a romerogram, after its popularisation by the American palaeontologist Alfred Romer . It represents taxonomic diversity (horizontal width) against geological time (vertical axis) in order to reflect

476-406: Is a graphical representation which shows the evolutionary history between a set of species or taxa during a specific time. In other words, it is a branching diagram or a tree showing the evolutionary relationships among various biological species or other entities based upon similarities and differences in their physical or genetic characteristics. In evolutionary biology, all life on Earth

510-506: Is most true of genetic material that is subject to lateral gene transfer and recombination , where different haplotype blocks can have different histories. In these types of analysis, the output tree of a phylogenetic analysis of a single gene is an estimate of the gene's phylogeny (i.e. a gene tree) and not the phylogeny of the taxa (i.e. species tree) from which these characters were sampled, though ideally, both should be very close. For this reason, serious phylogenetic studies generally use

544-414: Is that the outgroup species has a common ancestor with the ingroup that is older than the common ancestor of the ingroup. Choice of outgroup can change the topology of a phylogeny. Therefore, phylogeneticists typically use more than one outgroup in cladistic analysis. The use of multiple outgroups is preferable because it provides a more robust phylogeny, buffering against poor outgroup candidates and testing

578-539: Is the most biologically relevant; it arises because there are many places on an unrooted tree to put the root. For bifurcating labeled trees, the total number of rooted trees is: For bifurcating labeled trees, the total number of unrooted trees is: Among labeled bifurcating trees, the number of unrooted trees with n {\displaystyle n} leaves is equal to the number of rooted trees with n − 1 {\displaystyle n-1} leaves. The number of rooted trees grows quickly as

612-474: Is theoretically part of a single phylogenetic tree, indicating common ancestry . Phylogenetics is the study of phylogenetic trees. The main challenge is to find a phylogenetic tree representing optimal evolutionary ancestry between a set of species or taxa. Computational phylogenetics (also phylogeny inference) focuses on the algorithms involved in finding optimal phylogenetic tree in the phylogenetic landscape. Phylogenetic trees may be rooted or unrooted. In

646-476: Is thought to have been coined in the early 1970s at the American Museum of Natural History . Prior to the advent of the term, various other terms were used by evolutionary biologists, including "exgroup", "related group", and "outside groups". The chosen outgroup is hypothesized to be less closely related to the ingroup than the ingroup is related to itself. The evolutionary conclusion from these relationships

680-529: The book Elementary Geology , by Edward Hitchcock (first edition: 1840). Charles Darwin featured a diagrammatic evolutionary "tree" in his 1859 book On the Origin of Species . Over a century later, evolutionary biologists still use tree diagrams to depict evolution because such diagrams effectively convey the concept that speciation occurs through the adaptive and semirandom splitting of lineages. The term phylogenetic , or phylogeny , derives from

714-451: The evolutionary relationships of a clade within a genus—an appropriate outgroup would be a member of the sister clade. However, for deeper phylogenetic analysis, less closely related taxa can be used. For example, Jarvis et al. (2014) used humans and crocodiles as outgroups while resolving the early branches of the avian phylogeny. In molecular phylogenetics , satisfying the second requirement typically means that DNA or protein sequences from

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748-424: The ingroup's hypothesized monophyly. To qualify as an outgroup, a taxon must satisfy the following two characteristics: Therefore, an appropriate outgroup must be unambiguously outside the clade of interest in the phylogenetic study. An outgroup that is nested within the ingroup will, when used to root the phylogeny, result in incorrect conclusions about phylogenetic relationships and trait evolution. However,

782-428: The optimal level of relatedness of the outgroup to the ingroup depends on the depth of phylogenetic analysis. Choosing a closely related outgroup relative to the ingroup is more useful when looking at subtle differences, while choosing an unduly distant outgroup can result in mistaking convergent evolution for a direct evolutionary relationship due to a common ancestor . For shallow phylogenetics—for example, resolving

816-439: The optimal tree using many of these techniques is NP-hard , so heuristic search and optimization methods are used in combination with tree-scoring functions to identify a reasonably good tree that fits the data. Tree-building methods can be assessed on the basis of several criteria: Tree-building techniques have also gained the attention of mathematicians. Trees can also be built using T-theory . Trees can be encoded in

850-436: The outgroup can be successfully aligned to sequences from the ingroup. Although there are algorithmic approaches to identify the outgroups with maximum global parsimony, they are often limited by failing to reflect the continuous, quantitative nature of certain character states. Character states are traits, either ancestral or derived, that affect the construction of branching patterns in a phylogenetic tree. In each example,

884-403: The parent of all other nodes in the tree. The root is therefore a node of degree 2, while other internal nodes have a minimum degree of 3 (where "degree" here refers to the total number of incoming and outgoing edges). The most common method for rooting trees is the use of an uncontroversial outgroup —close enough to allow inference from trait data or molecular sequencing, but far enough to be

918-405: The range of DNA considered useful. Phylogenetic trees can also be inferred from a range of other data types, including morphology, the presence or absence of particular types of genes, insertion and deletion events – and any other observation thought to contain an evolutionary signal. Phylogenetic networks are used when bifurcating trees are not suitable, due to these complications which suggest

952-473: The relatedness of the leaf nodes and do not require the ancestral root to be known or inferred. The idea of a tree of life arose from ancient notions of a ladder-like progression from lower into higher forms of life (such as in the Great Chain of Being ). Early representations of "branching" phylogenetic trees include a "paleontological chart" showing the geological relationships among plants and animals in

986-574: The root of an unrooted tree requires some means of identifying ancestry. This is normally done by including an outgroup in the input data so that the root is necessarily between the outgroup and the rest of the taxa in the tree, or by introducing additional assumptions about the relative rates of evolution on each branch, such as an application of the molecular clock hypothesis . Both rooted and unrooted trees can be either bifurcating or multifurcating. A rooted bifurcating tree has exactly two descendants arising from each interior node (that is, it forms

1020-417: The simpler algorithms (i.e. those based on distance) of tree construction. Maximum parsimony is another simple method of estimating phylogenetic trees, but implies an implicit model of evolution (i.e. parsimony). More advanced methods use the optimality criterion of maximum likelihood , often within a Bayesian framework , and apply an explicit model of evolution to phylogenetic tree estimation. Identifying

1054-411: The tree before hybridisation takes place, and conserved sequences . Also, there are problems in basing an analysis on a single type of character, such as a single gene or protein or only on morphological analysis, because such trees constructed from another unrelated data source often differ from the first, and therefore great care is needed in inferring phylogenetic relationships among species. This

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1088-529: The trees that they generate are not necessarily correct – they do not necessarily accurately represent the evolutionary history of the included taxa. As with any scientific result, they are subject to falsification by further study (e.g., gathering of additional data, analyzing the existing data with improved methods). The data on which they are based may be noisy ; the analysis can be confounded by genetic recombination , horizontal gene transfer , hybridisation between species that were not nearest neighbors on

1122-422: The two ancient greek words φῦλον ( phûlon ), meaning "race, lineage", and γένεσις ( génesis ), meaning "origin, source". A rooted phylogenetic tree (see two graphics at top) is a directed tree with a unique node — the root — corresponding to the (usually imputed ) most recent common ancestor of all the entities at the leaves of the tree. The root node does not have a parent node, but serves as

1156-404: The variation of abundance of various taxa through time. A spindle diagram is not an evolutionary tree: the taxonomic spindles obscure the actual relationships of the parent taxon to the daughter taxon and have the disadvantage of involving the paraphyly of the parental group. This type of diagram is no longer used in the form originally proposed. Darwin also mentioned that the coral may be

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