Portal:Phylogenetics
Portal maintenance status: (October 2018)
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Introduction
In biology, phylogenetics /ˌfaɪloʊdʒəˈnɛtɪks,
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.
Selected general articles
- Phylogenetic comparative methods (PCMs) use information on the historical relationships of lineages (phylogenies) to test evolutionary hypotheses. The comparative method has a long history in evolutionary biology; indeed, Charles Darwin used differences and similarities between species as a major source of evidence in The Origin of Species. However, the fact that closely related lineages share many traits and trait combinations as a result of the process of descent with modification means that lineages are not independent. This realization inspired the development of explicitly phylogenetic comparative methods. Initially, these methods were primarily developed to control for phylogenetic history when testing for adaptation; however, in recent years the use of the term has broadened to include any use of phylogenies in statistical tests. Although most studies that employ PCMs focus on extant organisms, many methods can also be applied to extinct taxa and can incorporate information from the fossil record.
PCMs can generally be divided into two types of approaches: those that infer the evolutionary history of some character (phenotypic or genetic) across a phylogeny and those that infer the process of evolutionary branching itself (diversification rates), though there are some approaches that do both simultaneously. Typically the tree that is used in conjunction with PCMs has been estimated independently (see computational phylogenetics) such that both the relationships between lineages and the length of branches separating them is assumed to be known. Read more...
Phylogeny of ichthyosaurs. Thick horizontal lines signify the existence of a fossil record for the respective time and taxa. Thin lines represent ghost lineages.
A ghost lineage is a phylogenetic lineage that is inferred to exist (inferred-existence) but has no fossil record. The process of determining a ghost lineage relies on fossilized evidence before and after the hypothetical existence of the lineage and extrapolating relationships between organisms based on phylogenetic analysis.
Ghost lineages are commonly confused with Lazarus taxa, but there is a difference. For example, coelacanths (see below) are a Lazarus taxon, and the gaps in its fossil record are referred to as ghost lineages. Read more...
Molecular phylogenetics (/məˈlɛkjʊlərˌfaɪloʊdʒəˈnɛtɪks, mɒ-, moʊ-/) is the branch of phylogeny that analyzes genetic, hereditary molecular differences, predominately in DNA sequences, to gain information on an organism's evolutionary relationships. From these analyses, it is possible to determine the processes by which diversity among species has been achieved. The result of a molecular phylogenetic analysis is expressed in a phylogenetic tree. Molecular phylogenetics is one aspect of molecular systematics, a broader term that also includes the use of molecular data in taxonomy and biogeography.
Molecular phylogenetics and molecular evolution correlate. Molecular evolution is the process of selective changes (mutations) at a molecular level (genes, proteins, etc.) throughout various branches in the tree of life (evolution). Molecular phylogenetics makes inferences of the evolutionary relationships that arise due to molecular evolution and results in the construction of a phylogenetic tree. The figure displayed on the right depicts the phylogenetic tree of life as one of the first detailed trees, according to information known in the 1870s by Haeckel. Read more...- Evolutionary taxonomy, evolutionary systematics or Darwinian classification is a branch of biological classification that seeks to classify organisms using a combination of phylogenetic relationship (shared descent), progenitor-descendant relationship (serial descent), and degree of evolutionary change. This type of taxonomy may consider whole taxa rather than single species, so that groups of species can be inferred as giving rise to new groups. The concept found its most well-known form in the modern evolutionary synthesis of the early 1940s.
Evolutionary taxonomy differs from strict pre-Darwinian Linnaean taxonomy (producing orderly lists only), in that it builds evolutionary trees. While in phylogenetic nomenclature each taxon must consist of a single ancestral node and all its descendants, evolutionary taxonomy allows for groups to be excluded from their parent taxa (e.g. dinosaurs are not considered to include birds, but to have given rise to them), thus permitting paraphyletic taxa. Read more... - In phylogenetics, a primitive (or ancestral) character, trait, or feature of a lineage or taxon is one that is inherited from the common ancestor of a clade (or clade group) and has undergone little change since. Conversely, a trait that appears within the clade group (that is, is present in any subgroup within the clade but not all) is called advanced or derived. A clade is a group of organisms that consists of a common ancestor and all its lineal descendants.
A primitive trait is the original condition of that trait in the common ancestor; advanced indicates a notable change from the original condition. These terms in biology contain no judgement about the sophistication, superiority, value or adaptiveness of the named trait. "Primitive" in biology means only that the character appeared first in the common ancestor of a clade group and has been passed on largely intact to more recent members of the clade. "Advanced" means the character has evolved within a later subgroup of the clade. Read more... - A sister group or sister taxon is a phylogenetic term denoting the closest relatives of another given unit in an evolutionary tree. The expression is most easily illustrated by a cladogram: A, B, and C each represent a taxon:
The sister group to A is B; conversely, the sister group to B is A. Groups A and B, together with all other descendants of their most recent common ancestor, form the clade AB. The sister group to clade AB is C. Read more... - In phylogenetics, long branch attraction (LBA) is a form of systematic error whereby distantly related lineages are incorrectly inferred to be closely related. LBA arises when the amount of molecular or morphological change accumulated within a lineage is sufficient to cause that lineage to appear similar (thus closely related) to another long-branched lineage, solely because they have both undergone a large amount of change, rather than because they are related by descent. Such bias is more common when the overall divergence of some taxa results in long branches within a phylogeny. Long-branches are often attracted to the base of a phylogenetic tree, because the lineage included to represent an outgroup is often also long-branched. The frequency of true LBA is unclear and often debated, and some authors view it as untestable and therefore irrelevant to empirical phylogenetic inference. Although often viewed as a failing of parsimony-based methodology, LBA could in principle result from a variety of scenarios and be inferred under multiple analytical paradigms. Read more...
- The term phylogenetic niche conservatism has seen increasing use in recent years in the scientific literature, though the exact definition has been a matter of some contention. Fundamentally, phylogenetic niche conservatism refers to the tendency of species to retain their ancestral traits. When defined as such, phylogenetic niche conservatism is therefore nearly synonymous with phylogenetic signal. The point of contention is whether or not "conservatism" refers simply to the tendency of species to resemble their ancestors, or implies that "closely related species are more similar than expected based on phylogenetic relationships". If the latter interpretation is employed, then phylogenetic niche conservatism can be seen as an extreme case of phylogenetic signal, and implies that the processes which prevent divergence are in operation in the lineage under consideration. Despite efforts by Losos to end this habit, however, the former interpretation appears to frequently motivate scientific research. In this case, phylogenetic niche conservatism might best be considered a form of phylogenetic signal reserved for traits with broad-scale ecological ramifications (i.e. related to the Hutchinsonian niche). Thus, phylogenetic niche conservatism is usually invoked with regards to closely related species occurring in similar environments. Read more...
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. Read more...
Phylogenies showing the terminology used to describe different patterns of ancestral and derived character or trait states.
In phylogenetics, an autapomorphy is a distinctive feature, known as a derived trait, that is unique to a given taxon. That is, it is found only in one taxon, but not found in any others or outgroup taxa, not even those most closely related to the focal taxon (which may be a species, family or in general any clade). It can therefore be considered an apomorphy in relation to a single taxon. The word autapomorphy, first introduced in 1950 by German entomologist Willi Hennig, is derived from the Greek words αὐτός, aut- = "self"; ἀπό, apo = "away from"; and μορφή, morphḗ = "shape". Read more...- This list of phylogenetics software is a compilation of computational phylogenetics software used to produce phylogenetic trees. Such tools are commonly used in comparative genomics, cladistics, and bioinformatics. Methods for estimating phylogenies include neighbor-joining, maximum parsimony (also simply referred to as parsimony), UPGMA, Bayesian phylogenetic inference, maximum likelihood and distance matrix methods. Read more...
- In statistics, maximum likelihood estimation (MLE) is a method of estimating the parameters of a statistical model, given observations. MLE attempts to find the parameter values that maximize the likelihood function, given the observations. The resulting estimate is called a maximum likelihood estimate, which is also abbreviated as MLE.
The method of maximum likelihood is used with a wide range of statistical analyses. As an example, suppose that we are interested in the heights of adult female penguins, but are unable to measure the height of every penguin in a population (due to cost or time constraints). Assuming that the heights are normally distributed with some unknown mean and variance, the mean and variance can be estimated with MLE while only knowing the heights of some sample of the overall population. MLE would accomplish that by taking the mean and variance as parameters and finding particular parametric values that make the observed results the most probable given the normal model. Read more... - UPGMA (Unweighted Pair Group Method with Arithmetic Mean) is a simple agglomerative (bottom-up) hierarchical clustering method. The method is generally attributed to Sokal and Michener.
The UPGMA method is similar to its weighted variant, the WPGMA method. Read more... - In phylogenetics, maximum parsimony is an optimality criterion under which the phylogenetic tree that minimizes the total number of character-state changes is to be preferred. Under the maximum-parsimony criterion, the optimal tree will minimize the amount of homoplasy (i.e., convergent evolution, parallel evolution, and evolutionary reversals). In other words, under this criterion, the shortest possible tree that explains the data is considered best. The principle is akin to Occam's razor, which states that—all else being equal—the simplest hypothesis that explains the data should be selected. Some of the basic ideas behind maximum parsimony were presented by James S. Farris in 1970 and Walter M. Fitch in 1971.
Maximum parsimony is an intuitive and simple criterion, and it is popular for this reason. However, although it is easy to score a phylogenetic tree (by counting the number of character-state changes), there is no algorithm to quickly generate the most-parsimonious tree. Instead, the most-parsimonious tree must be found in "tree space" (i.e., amongst all possible trees). For a small number of taxa (i.e., fewer than nine) it is possible to do an exhaustive search, in which every possible tree is scored, and the best one is selected. For nine to twenty taxa, it will generally be preferable to use branch-and-bound, which is also guaranteed to return the best tree. For greater numbers of taxa, a heuristic search must be performed. Read more...
A phylogenetic tree or evolutionary tree is a branching diagram or "tree" showing the evolutionary relationships among various biological species or other entities—their phylogeny (/faɪˈlɒdʒəni/)—based upon similarities and differences in their physical or genetic characteristics. All life on Earth is part of a single phylogenetic tree, indicating common ancestry.
In 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 the relatedness of the leaf nodes and do not require the ancestral root to be known or inferred. Read more...- Taxonomy (from Ancient Greek τάξις (taxis), meaning 'arrangement', and -νομία (-nomia), meaning 'method') is the science of defining and naming groups of biological organisms on the basis of shared characteristics. Organisms are grouped together into taxa (singular: taxon) and these groups are given a taxonomic rank; groups of a given rank can be aggregated to form a super-group of higher rank, thus creating a taxonomic hierarchy. The principal ranks in modern use are domain, kingdom, phylum (division is sometimes used in botany in place of phylum), class, order, family, genus and species. The Swedish botanist Carl Linnaeus is regarded as the father of taxonomy, as he developed a system known as Linnaean taxonomy for categorization of organisms and binomial nomenclature for naming organisms.
With the advent of such fields of study as phylogenetics, cladistics, and systematics, the Linnaean system has progressed to a system of modern biological classification based on the evolutionary relationships between organisms, both living and extinct. Read more... - Least squares inference in phylogeny generates a
phylogenetic tree based on an
observed matrix of pairwise genetic distances and
optionally a weight
matrix. The goal is to find a tree which satisfies the distance constraints as
best as possible. Read more...
An example of cladogenesis today is the Hawaiian archipelago, to which stray organisms traveled across the ocean via ocean currents and winds. Most of the species on the islands are not found anywhere else on Earth due to evolutionary divergence.
Cladogenesis is an evolutionary splitting of a parent species into two distinct species, forming a clade.
This event usually occurs when a few organisms end up in new, often distant areas or when environmental changes cause several extinctions, opening up ecological niches for the survivors and causing population bottlenecks and founder effects changing allele frequencies of diverging populations compared to their ancestral population. The events that cause these species to originally separate from each other over distant areas may still allow both of the species to have equal chances of surviving, reproducing, and even evolving to better suit their environments while still being two distinct species due to subsequent natural selection, mutations and genetic drift. Read more...
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. Read more...
A polyphyletic group is a set of organisms, or other evolving elements, that have been grouped together but do not share an immediate common ancestor. The term is often applied to groups that share characteristics that appear to be similar but have not been inherited from common ancestors; these characteristics are known as homoplasies, and the development and phenomenon of homoplasies is known as convergent evolution. The arrangement of the members of a polyphyletic group is called a polyphyly.
Alternatively, polyphyletic is simply used to describe a group whose members come from multiple ancestral sources, regardless of similarity of characteristics. For example, the biological characteristic of warm-bloodedness evolved separately in the ancestors of mammals and the ancestors of birds. Other polyphyletic groups are for example algae, C4 photosynthetic plants, and edentates. Read more...
Cladogram (family tree) of a biological group, showing the last common ancestor of the composite tree, which is the vertical line 'trunk' (stem) at the bottom, with all descendant branches shown above. The blue and red subgroups (at left and right) are clades, or monophyletic (complete) groups; each shows its common ancestor 'stem' at the bottom of the subgroup 'branch'. The green subgroup is not a clade; it is a paraphyletic group, which is an incomplete clade here because it excludes the blue branch even though it has also descended from the common ancestor stem at the bottom of the green branch. The green subgroup together with the blue one forms a clade again.
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. Read more...
In phylogenetics, the crown group of a collection of species consists of the living representatives of the collection together with their ancestors back to their most recent common ancestor as well as all of that ancestor's descendants. It is thus a clade, a group consisting of a species and all its descendants.
The concept was developed by Willi Hennig, the formulator of phylogenetic systematics, as a way of classifying living organisms relative to their extinct relatives in his "Die Stammesgeschichte der Insekten",
and the "crown" and "stem" group terminology was coined by R. P. S. Jefferies in 1979. Though formulated in the 1970s, the term was not commonly used until its reintroduction in 2000 by Graham Budd and Sören Jensen. Read more...- Phylogeography is the study of the historical processes that may be responsible for the contemporary geographic distributions of individuals. This is accomplished by considering the geographic distribution of individuals in light of genetics, particularly population genetics.
This term was introduced to describe geographically structured genetic signals within and among species. An explicit focus on a species' biogeography/biogeographical past sets phylogeography apart from classical population genetics and phylogenetics. Read more...
Molecular phylogenetics (/məˈlɛkjʊlərˌfaɪloʊdʒəˈnɛtɪks, mɒ-, moʊ-/) is the branch of phylogeny that analyzes genetic, hereditary molecular differences, predominately in DNA sequences, to gain information on an organism's evolutionary relationships. From these analyses, it is possible to determine the processes by which diversity among species has been achieved. The result of a molecular phylogenetic analysis is expressed in a phylogenetic tree. Molecular phylogenetics is one aspect of molecular systematics, a broader term that also includes the use of molecular data in taxonomy and biogeography.
Molecular phylogenetics and molecular evolution correlate. Molecular evolution is the process of selective changes (mutations) at a molecular level (genes, proteins, etc.) throughout various branches in the tree of life (evolution). Molecular phylogenetics makes inferences of the evolutionary relationships that arise due to molecular evolution and results in the construction of a phylogenetic tree. The figure displayed on the right depicts the phylogenetic tree of life as one of the first detailed trees, according to information known in the 1870s by Haeckel. Read more...- Three-taxon analysis (or TTS, three-item analysis, 3ia) is a cladistic based method of phylogenetic reconstruction. Introduced by Nelson and Platnick (1991) to reconstruct organisms' phylogeny, this method can also be applied to biogeographic areas. It attempts to reconstruct complex phylogenetic trees by breaking the problem down into simpler chunks. Rather than try to resolve the relationships of all X taxa at once, it considers taxa 3 at a time. It is relatively easy to generate three-taxon statements (3is); that is, statements of the form "A and B are more closely related to one another than to C". Once each group of three taxa has been considered, the method constructs a tree that is consistent with as many three-item statements as possible. Computer program that implement three-taxon analysis is LisBeth (for systematic and biogeographic studies). LisBeth have been freely released. A recent simulation-based study found that Three-taxon analysis yields good power and an error rate intermediate between parsimony with ordered states and parsimony with unordered states. Read more...
- In phylogenetics, basal is the direction of the base (or root) of a rooted phylogenetic tree or cladogram. Clade C may be described as basal within a larger clade D if its root is directly linked (adjacent) to the root of D. The terms deep-branching or early-branching are similar in meaning. If C is a basal clade within D that has the lowest taxonomic rank of all basal clades within D, C may be described as the basal taxon of that rank within D. While there must always be two or more equally basal clades sprouting from the root of every cladogram, those clades may differ widely in rank and/or species diversity. 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 more 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 of lowest rank within a larger clade. Read more... - DNA barcoding is a taxonomic method that uses a short genetic marker in an organism's DNA to identify it as belonging to a particular species. It differs from molecular phylogeny in that the main goal is not to determine patterns of relationship but to identify an unknown sample in terms of a preexisting classification. Although barcodes are sometimes used in an effort to identify unknown species or assess whether species should be combined or separated, the utility of DNA barcoding for these purposes is subject to debate.
The most commonly used barcode region for animals and some protists is a segment of approximately 600 base pairs of the mitochondrial gene cytochrome oxidase I (COI or COX1). This differs in the case of fungi, where part of Internal Transcribed Spacer 2 (ITS2) between rRNA genes is used, and again in plants, where multiple regions are used.
Applications include, for example, identifying plant leaves even when flowers or fruit are not available, identifying pollen collected on the bodies of pollinating animals, identifying insect larvae (which may have fewer diagnostic characters than adults and are frequently less well-known), identifying the diet of an animal, based on its stomach contents or faeces and identifying products in commerce (for example, herbal supplements, wood, or skins and other animal parts). Read more... - In bioinformatics, neighbor joining is a bottom-up (agglomerative) clustering method for the creation of phylogenetic trees, created by Naruya Saitou and Masatoshi Nei in 1987. Usually used for trees based on DNA or protein sequence data, the algorithm requires knowledge of the distance between each pair of taxa (e.g., species or sequences) to form the tree. Read more...
- Phylogenomics is the intersection of the fields of evolution and genomics. The term has been used in multiple ways to refer to analysis that involves genome data and evolutionary reconstructions. It is a group of techniques within the larger fields of phylogenetics and genomics. Phylogenomics draws information by comparing entire genomes, or at least large portions of genomes. Phylogenetics compares and analyzes the sequences of single genes, or a small number of genes, as well as many other types of data. Four major areas fall under phylogenomics:
- Prediction of gene function
- Establishment and clarification of evolutionary relationships
- Gene family evolution
- Prediction and retracing lateral gene transfer.
- Phylogenetic nomenclature, often called cladistic nomenclature, is a method of nomenclature for taxa in biology that uses phylogenetic definitions for taxon names as explained below. This contrasts with the traditional approach, in which taxon names are defined by a type, which can be a specimen or a taxon of lower rank, and a description in words. Phylogenetic nomenclature is currently not regulated, but the International Code of Phylogenetic Nomenclature (PhyloCode) is intended to regulate it once it is ratified. Read more...
A phylogenetic tree: both blue and red groups are monophyletic. The green group is paraphyletic because it is missing a monophyletic group (the blue group) that shares a common ancestor—the lowest green vertical stem.
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. Read more...- Bayesian inference of phylogeny uses a likelihood function to create a quantity called the posterior probability of trees using a model of evolution, based on some prior probabilities, producing the most likely phylogenetic tree for the given data. The Bayesian approach has become popular due to advances in computing speeds and the integration of Markov chain Monte Carlo (MCMC) algorithms. Bayesian inference has a number of applications in molecular phylogenetics and systematics. Read more...
- An evolutionary lineage is a temporal series of organisms, populations, cells, or genes connected by a continuous line of descent from ancestor to descendent. Lineages are subsets of the evolutionary tree of life. Lineages are often determined by the techniques of molecular systematics. Read more...
Phylogenetic divergence (Phyletic gradualism) (above) shows relatively slow changes during geologic epoch: the broken balance (below) illustrates morphological stability and (rarely) the relatively rapid evolutionary change.
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. Read more...- A ghost population is a population that has been inferred through using statistical techniques. Read more...
- Distance matrices are used in phylogeny as
non-parametric distance methods and were originally applied to phenetic data using a matrix of pairwise distances. These distances are then reconciled to produce a tree (a phylogram, with informative branch lengths). The distance matrix can come from a number of different sources, including measured distance (for example from immunological studies) or morphometric analysis, various pairwise distance formulae (such as euclidean distance) applied to discrete morphological characters, or genetic distance from sequence, restriction fragment, or allozyme data. For phylogenetic character data, raw distance values can be calculated by simply counting the number of pairwise differences in character states (Hamming distance). Read more... - Computational phylogenetics is the application of computational algorithms, methods, and programs to phylogenetic analyses. The goal is to assemble a phylogenetic tree representing a hypothesis about the evolutionary ancestry of a set of genes, species, or other taxa. For example, these techniques have been used to explore the family tree of hominid species and the relationships between specific genes shared by many types of organisms. Traditional phylogenetics relies on morphological data obtained by measuring and quantifying the phenotypic properties of representative organisms, while the more recent field of molecular phylogenetics uses nucleotide sequences encoding genes or amino acid sequences encoding proteins as the basis for classification. Many forms of molecular phylogenetics are closely related to and make extensive use of sequence alignment in constructing and refining phylogenetic trees, which are used to classify the evolutionary relationships between homologous genes represented in the genomes of divergent species. The phylogenetic trees constructed by computational methods are unlikely to perfectly reproduce the evolutionary tree that represents the historical relationships between the species being analyzed. The historical species tree may also differ from the historical tree of an individual homologous gene shared by those species. Read more...
A phylogenetic network or reticulation is any graph used to visualize evolutionary relationships (either abstractly or explicitly) between nucleotide sequences, genes, chromosomes, genomes, or species. They are employed when reticulation events such as hybridization, horizontal gene transfer, recombination, or gene duplication and loss are believed to be involved. They differ from phylogenetic trees by the explicit modeling of richly linked networks, by means of the addition of hybrid nodes (nodes with two parents) instead of only tree nodes (a hierarchy of nodes, each with only one parent). Phylogenetic trees are a subset of phylogenetic networks. Phylogenetic networks can be inferred and visualised with software such as SplitsTree, the R-package, phangorn,
and, more recently, Dendroscope. A standard format for representing phylogenetic networks is a variant of Newick format which is extended to support networks as well as trees.
Many kinds and subclasses of phylogenetic networks have been defined based on the biological phenomenon they represent or which data they are built from (hybridization networks, usually built from rooted trees, recombination networks from binary sequences, median networks from a set of splits, optimal realizations and reticulograms from a distance matrix), or restrictions to get computationally tractable problems (galled trees, and their generalizations level-k phylogenetic networks, tree-child or tree-sibling phylogenetic networks). Read more...
Phylogenies showing the terminology used to describe different patterns of ancestral and derived character or trait states.
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. Read more...- Cladistics (/kləˈdɪstɪks/, from Greek κλάδος, cládos, "branch") 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.
The techniques and nomenclature of cladistics have been applied to other disciplines. (See phylogenetic nomenclature.) Read more...
Phylogenies showing the terminology used to describe different patterns of ancestral and derived character or trait states.
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. Read more...- The International Code of Phylogenetic Nomenclature, known as the PhyloCode for short, is a developing draft for a formal set of rules governing phylogenetic nomenclature. Its current version is specifically designed to regulate the naming of clades, leaving the governance of species names up to the rank-based Nomenclature codes (ICN, ICZN, ICNB, ICTV).
The PhyloCode is associated with the International Society for Phylogenetic Nomenclature (ISPN). Read more...
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