In biology, phylogenetics /ˌfaɪloʊdʒəˈnɛtɪks, -lə-/ (Greek: φυλή, φῦλον – phylé, phylon = tribe, clan, race + γενετικός – genetikós = origin, source, birth) is the study of the evolutionary history and relationships among individuals or groups of organisms (e.g. species, or populations). These relationships are discovered through phylogenetic inference methods that evaluate observed heritable traits, such as DNA sequences or morphology under a model of evolution of these traits. The result of these analyses is a phylogeny (also known as a phylogenetic tree) – a diagrammatic hypothesis about the history of the evolutionary relationships of a group of organisms. The tips of a phylogenetic tree can be living organisms or fossils, and represent the "end", or the present, in an evolutionary lineage. Phylogenetic analyses have become central to understanding biodiversity, evolution, ecology, and genomes.
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.
Usual methods of phylogenetic inference involve computational approaches implementing the optimality criteria and methods of parsimony, maximum likelihood (ML), and MCMC-based Bayesian inference. All these depend upon an implicit or explicit mathematical model describing the evolution of characters observed.
Phenetics, popular in the mid-20th century but now largely obsolete, used distance matrix-based methods to construct trees based on overall similarity in morphology or similar observable traits (i.e. in the phenotype or the overall similarity of DNA, not the DNA sequence), which was often assumed to approximate phylogenetic relationships.
During the late 19th century, Ernst Haeckel's recapitulation theory, or "biogenetic fundamental law", was widely accepted. It was often expressed as "ontogeny recapitulates phylogeny", i.e. the development of a single organism during its lifetime, from germ to adult, successively mirrors the adult stages of successive ancestors of the species to which it belongs. But this theory has long been rejected. Instead, ontogeny evolves – the phylogenetic history of a species cannot be read directly from its ontogeny, as Haeckel thought would be possible, but characters from ontogeny can be (and have been) used as data for phylogenetic analyses; the more closely related two species are, the more apomorphies their embryos share.
Phylogenetics is the branch of life science concerned with the analysis of molecular sequencing data to study evolutionary relationships among groups of organisms.
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".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.Cetancodontamorpha
Cetancodontamorpha is a total clade of artiodactyls defined, according to Spaulding et al., as Whippomorpha "plus all extinct taxa more closely related to extant members of Whippomorpha than to any other living species". Attempts have been made to rename the clade Whippomorpha to Cetancodonta, but the former maintains precedent.Whippomorpha is the crown clade containing Cetacea (whales, dolphins, etc.) and hippopotamuses. According to Spaulding et al., members of the whippomorph stem group (i.e., "stem-whippomorphs") include such taxa as the family Entelodontidae and the genus Andrewsarchus.Cetruminantia
The Cetruminantia are a clade made up of the Cetacodontamorpha (or Whippomorpha) and their closest living relatives, the Ruminantia.Clade
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.
Over the last few decades, the cladistic approach has revolutionized biological classification and revealed surprising evolutionary relationships among organisms. Increasingly, taxonomists try to avoid naming taxa that are not clades; that is, taxa that are not monophyletic. Some of the relationships between organisms that the molecular biology arm of cladistics has revealed are that fungi are closer relatives to animals than they are to plants, archaea are now considered different from bacteria, and multicellular organisms may have evolved from archaea.Cladogram
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.Crown group
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.Molecular Phylogenetics and Evolution
Molecular Phylogenetics and Evolution is a peer-reviewed scientific journal of evolutionary biology and phylogenetics. The journal is edited by D.E. Wildman.Molecular phylogenetics
Molecular phylogenetics () 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.Monophyly
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.
These definitions have taken some time to be accepted. When the cladistics school of thought became mainstream in the 1960s, several alternative definitions were in use. Indeed, taxonomists sometimes used terms without defining them, leading to confusion in the early literature, a confusion which persists.The first diagram shows a phylogenetic tree with two monophyletic groups. The several groups and subgroups are particularly situated as branches of the tree to indicate ordered lineal relationships between all the organisms shown. Further, any group may (or may not) be considered a taxon by modern systematics, depending upon the selection of its members in relation to their common ancestor(s); see second and third diagrams.Paraphyly
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.If many subgroups are missing from the named group, it is said to be polyparaphyletic. A paraphyletic group cannot be a clade, or monophyletic group, which is any group of species that includes only a common ancestor and all of its descendants. Formally, a paraphyletic group is the relative complement of one or more subclades within a clade: removing one or more subclades leaves a paraphyletic group.Phylogenetic tree
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 ()—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.Plesiomorphy and symplesiomorphy
In phylogenetics, a plesiomorphy, symplesiomorphy or symplesiomorphic character is an ancestral character (trait state) shared by two or more taxa - but also with other taxa linked earlier in the clade (that is, having an earlier last common ancestor, with them, than theirs).
In this situation, the fact that the taxa under consideration share the trait state may hint strongly that they are closely related. But the fact that the trait state is plesiomorphic means the hint may be entirely misleading. It must be disregarded. The question whether those taxa are closely related must be determined from other evidence.The term symplesiomorphy was first introduced in 1950 by German entomologist Willi Hennig.
Reversal – is the loss of a derived trait state, reestablishing the plesiomorphic trait state present in an ancestor.Pseudoplesiomorphy – is a trait that cannot be identified as a plesiomorphy nor as an apomorphy.Polyphyly
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.Many biologists aim to avoid homoplasies in grouping taxa together and therefore it is frequently a goal to eliminate groups that are found to be polyphyletic. This is often the stimulus for major revisions of the classification schemes.
Researchers concerned more with ecology than with systematics may take polyphyletic groups as legitimate subject matter; the similarities in activity within the fungus group Alternaria, for example, can lead researchers to regard the group as a valid genus while acknowledging its polyphyly.Primitive (phylogenetics)
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.
Cladograms are important for scientists as they allow them to classify and hypothesize the origin and future of organisms. Cladograms allow scientists to propose their evolutionary scenarios about the lineage from a primitive trait to a derived one. By understanding how the trait came to be, scientists can hypothesize the environment that specific organism was in and how that affected the evolutionary adaptations of the trait that came to be.Other, more technical, terms for these two conditions—for example, "plesiomorphic" and "synapomorphic"—are frequently encountered; see the table below.Sister group
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:
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.
The whole clade ABC is itself a subtree of a larger tree, which offers yet more sister group branches that are related but farther removed from the leaf nodes, such as A, B, and C.
In cladistic standards, A, B, and C may represent specimens, species, taxon-groups, etc. If they represent species, the term sister species is sometimes used.
The term "sister group" is used in phylogenetic analysis, and only groups identified in the analysis are labeled as sister groups. An example is in birds, whose sister group is commonly cited as the crocodiles, but that is true only when dealing with extant taxa. The bird family tree is rooted in the dinosaurs, making for a number of extinct groups branching off before coming to the last common ancestor of birds and crocodiles. Thus, the term sister group must be seen as a relative term, with the caveat that the sister group is the closest relative only among the groups/species/specimens that are included in the analysis.Synapomorphy 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.Tree of Life Web Project
The Tree of Life Web Project is an Internet project providing information about the diversity and phylogeny of life on Earth.This collaborative peer reviewed project began in 1995, and is written by biologists from around the world. The site has not been updated since 2011, however the pages are still accessible.The pages are linked hierarchically, in the form of the branching evolutionary tree of life, organized cladistically. Each page contains information about one particular group of organisms and is organized according to a branched tree-like form, thus showing hypothetical relationships between different groups of organisms.
In 2009 the project ran into funding problems from the University of Arizona. Pages and Treehouses submitted took a considerably longer time to be approved as they were being reviewed by a small group of volunteers, and apparently, around 2011, all activities ended.Wikispecies
Wikispecies is a wiki-based online project supported by the Wikimedia Foundation. Its aim is to create a comprehensive free content catalogue of all species; the project is directed at scientists, rather than at the general public. Jimmy Wales stated that editors are not required to fax in their degrees, but that submissions will have to pass muster with a technical audience. Wikispecies is available under the GNU Free Documentation License and CC BY-SA 3.0.
Started in September 2004, with biologists across the world invited to contribute, the project had grown a framework encompassing the Linnaean taxonomy with links to Wikipedia articles on individual species by April 2005.
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