In biology, phylogenetics /ˌfaɪloʊdʒəˈnɛtɪks, -lə-/ is the study of the evolutionary history and relationships among individuals or groups of organisms. These relationships are discovered through phylogenetic inference methods that evaluate observed heritable traits, the result of these analyses is a phylogeny – a diagrammatic hypothesis about the history of the evolutionary relationships of a group of organisms. The tips of a tree can be living organisms or fossils. Phylogenetic analyses have become central to understanding biodiversity, ecology, taxonomy is the classification and naming of organisms. It is usually richly informed by phylogenetics, but remains a methodologically and logically distinct discipline, usual methods of phylogenetic inference involve computational approaches implementing the optimality criteria and methods of parsimony, maximum likelihood, and MCMC-based Bayesian inference. All these depend upon an implicit or explicit mathematical model describing the evolution of characters observed, prior to 1990, phylogenetic inferences were generally presented as narrative scenarios.
Such methods are often ambiguous and lack explicit criteria for evaluating alternative hypotheses, the term phylogeny derives from the German Phylogenie, introduced by Haeckel in 1866, and the Darwinian approach to classification became known as the phyletic approach. During the late 19th century, Ernst Haeckels recapitulation theory, or biogenetic fundamental law, was widely accepted, but this theory has long been rejected. O. See, Huerta-Cepas, Dopazo, Joaquín, Gabaldón, ETE, A python Environment for Tree Exploration. PhylomeDB, A public database hosting thousands of gene phylogenies ranging many different species, Huerta-Cepas, J. Capella-Gutierrez, S. Pryszcz, L. P. Denisov, I. Kormes, D. Marcet-Houben, M. Gabaldón, T. PhylomeDB v3.0, An expanding repository of genome-wide collections of trees, lents, N. H. Cifuentes, O. E. Carpi, A. Teaching the Process of Molecular Phylogeny and Systematics, A Multi-Part Inquiry-Based Exercise
In taxonomy, a group is paraphyletic if it consists of the groups 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 term is commonly used in phylogenetics and in linguistics. The term was coined to apply to well-known taxa like 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 all extant reptiles as well as the extinct synapsids—except for mammals. Other commonly recognized paraphyletic groups include fish and lizards, if many subgroups are missing from the named group, it is said to be polyparaphyletic. A paraphyletic group cannot be a clade, which is a monophyletic group, groups that include all the descendants of a common ancestor are said to be monophyletic. A paraphyletic group is a group from which one or more subsidiary clades is excluded to form a separate group.
Ereshefsky has argued that paraphyletic taxa are the result of anagenesis in the group or groups. For example, dinosaurs are paraphyletic with respect to birds because birds possess many features that dinosaurs lack, a group whose identifying features evolved convergently in two or more lineages is polyphyletic. More broadly, any taxon that is not paraphyletic or monophyletic can be called polyphyletic and these terms were developed during the debates of the 1960s and 70s accompanying the rise of cladistics. The prokaryotes, because they exclude the eukaryotes, a descendant group and Archaea are prokaryotes, but archaea and eukaryotes share a common ancestor that is not ancestral to the bacteria. The prokaryote/eukaryote distinction was proposed by Edouard Chatton in 1937 and was accepted after being adopted by Roger Stanier. The botanical code abandoned consideration of bacterial nomenclature in 1975, dicotyledons are paraphyletic because the group excludes monocotyledons. Dicotyledon has not been used as an ICBN classification for decades, phylogenetic analysis indicates that the monocots are a development from a dicot ancestor.
Excluding monocots from the dicots makes the latter a paraphyletic group, the order Artiodactyla, because it excludes Cetaceans. In the ICZN Code, the two taxa are orders of equal rank, molecular studies, have shown that the Cetacea descend from the Artiodactyl ancestors, although the precise phylogeny within the order remains uncertain. Without the Cetacean descendants the Artiodactyls must be paraphyletic, the class Reptilia as traditionally defined, because it excludes birds and mammals. In the ICZN Code, the three taxa are classes of equal rank, mammals hail from the synapsids and birds are descended from the dinosaurs, both of which are reptiles
Long branch attraction
In phylogenetics, long branch attraction is a form of systematic error whereby distantly related lineages are incorrectly inferred to be closely related. Such bias is more common when the overall divergence of some results in long branches within a phylogeny. Long-branches are often attracted to the base of a phylogenetic tree, the frequency of true LBA is unclear and often debated. Although often viewed as a failing of parsimony-based methodology, LBA can result from a variety of scenarios, often this is because convergent evolution of one or more characters included in the analysis has occurred in multiple taxa. Although they were derived independently, these traits can be misinterpreted in the analysis as being shared due to common ancestry. A phylogenetic analysis will group these together as a clade unless other synapomorphies outweigh the homoplastic features to group together true sister taxa. The result of LBA in evolutionary analyses is that rapidly evolving lineages may be inferred to be closely related, for example, in DNA sequence-based analyses, the problem arises when sequences from two lineages evolve rapidly.
There are only four possible nucleotides and when DNA substitution rates are high, when this happens, parsimony may erroneously interpret this homoplasy as a synapomorphy. The opposite effect may be observed, in that if two branches exhibit particularly slow evolution among a wider, fast evolving group, those branches may be misinterpreted as closely related, as such, long branch attraction can in some ways be better expressed as branch length attraction. However, it is typically long branches that exhibit attraction, the recognition of long-branch attraction implies that there is some other evidence that suggests that the phylogeny is incorrect. For example, morphological data may suggest that taxa marked as closely related are not truly sister taxa, hennigs Auxiliary Principle suggests that synapomorphies should be viewed as de facto evidence of grouping unless there is specific contrary evidence. A simple and effective method for determining whether or not long branch attraction is affecting tree topology is the SAW method, named for Siddal, if long branch attraction is suspected in a pair of taxa, simply remove taxon A and re-run the analysis.
Then remove A and replace B, running the analysis again, if either of the taxa appear at different branch points in the absence of the other, there is evidence of long branch attraction. Since long branches cant possibly attract one another when one is in the analysis. Assume for simplicity that we are considering a single binary character, because the distance from B to D is small, in the vast majority of all cases, B and D will be the same. Here, we assume that they are both +. If this is the case, there are four remaining possibilities, a and C can both be +, in which case all taxa are the same and all the trees have the same length. A can be + and C can be -, in which only one character is different
Hybrid speciation is a form of speciation where hybridization between two different species leads to a new species, reproductively isolated from the parent species. From the 1940s, reproductive isolation between hybrids and their parents was thought to be difficult to achieve and thus hybrid species were thought to be extremely rare. With DNA analysis becoming more accessible in the 1990s, hybrid speciation has been shown to be a common phenomenon. In botanical nomenclature, a species is called a nothospecies. Hybrid species are by their nature polyphyletic, a hybrid may occasionally be better fitted to the local environment than the parental lineage and as such natural selection may favor these individuals. If reproductive isolation is achieved, a separate species may arise. Reproductive isolation may be genetic, behavioural, spatial, if reproductive isolation fails to establish, the hybrid population may merge with either or both parent species. This will lead to an influx of foreign genes in the parent population, introgression is a source of genetic variation, and can in itself facilitate speciation.
For a hybrid form to persist, it must be able to exploit the available resources better than either parent species, while grizzly bears and polar bears may have offspring, a grizzly–polar bear hybrid will likely be less suited in either of the ecological roles than the parents themselves. Although the hybrid is fertile, this poor adaptation would prevent the establishment of a permanent population, in both ligers and tigons, the females are fertile and the males are sterile. The other hybrid, the liger, ends up larger than either of its parents, no tiger-lion hybrids are known from the wild, particularly because each species is confined to geographically separated ranges. Some situations may favour hybrid population, one example is rapid turnover of available environment types, like the historical fluctuation of water level in Lake Malawi, a situation that generally favors speciation. A similar situation can be found where closely related species occupy a chain of islands and this will allow any present hybrid population to move into a new unoccupied habitats, avoiding direct competition with parent species and giving a hybrid population time and space to establish.
Genetics too can occasionally favour hybrids, in the Amboseli National Park in Kenya, yellow baboons and anubis baboons regularly interbreed. The hybrid males reach maturity earlier than their pure bred cousins, genetics are more variable and malleable in plants than in animals, probably reflecting the higher activity level in animals. Hybrids genetics will necessarily be less stable than those of species evolving through isolation, many agricultural crops are hybrids with double or even triple chromosome sets. Having multiple sets of chromosomes is called polyploidy, polyploidy is usually fatal in animals where extra chromosome sets upset fetal development, but is often found in plants. A form of hybrid speciation that is common in plants
Therefore, members of a group are assumed to share a common history and are considered to be closely related. The techniques and nomenclature of cladistics have been applied to other disciplines, Cladistics in the original sense refers to a particular set of methods used in phylogenetic analysis, although it is now sometimes used to refer to the whole field. What is now called the cladistic method appeared as early as 1901 with a work by Peter Chalmers Mitchell for birds and subsequently by Robert John Tillyard in 1921, Hennig referred to his own approach as phylogenetic systematics. Phenetics was championed at this time by the numerical taxonomists Peter Sneath and Robert Sokal, originally conceived, if only in essence, by Willi Hennig in a book published in 1950, cladistics did not flourish until its translation into English in 1966. Today, cladistics is the most popular method for constructing phylogenies from morphological, unlike phenetics, cladistics is specifically aimed at reconstructing evolutionary histories.
The way for computational phylogenetics was paved by phenetics, a set of commonly used from the 1950s to 1980s. Phenetics did not try to reconstruct phylogenetic trees, rather, it tried to build dendrograms from similarity data, the cladistic method interprets each character state transformation implied by the distribution of shared character states among taxa as a potential piece of evidence for grouping. The outcome of an analysis is a cladogram – a tree-shaped diagram that is interpreted to represent the best hypothesis of phylogenetic relationships. Cladists contend that these models are unjustified, every cladogram is based on a particular dataset analyzed with a particular method. Different datasets and different methods, not to mention violations of the mentioned assumptions, only scientific investigation can show which is more likely to be correct. Since the cladograms provide competing accounts of events, at most one of them is correct. Within the primates, all anthropoids are hypothesized to have had a common ancestor all of whose descendants were anthropoids, the prosimians, on the other hand, form a paraphyletic taxon.
When two or more taxa that are not nested within each other share a plesiomorphy, it is a symplesiomorphy, symplesiomorphies do not mean that the taxa that exhibit that character state are necessarily closely related. For example, Reptilia is traditionally characterized by being cold-blooded, whereas birds are warm-blooded, an apomorphy or derived state is an innovation. It can thus be used to diagnose a clade – or even to help define a clade name in phylogenetic nomenclature, features that are derived in individual taxa are called autapomorphies. Autapomorphies express nothing about relationships among groups, clades are identified by synapomorphies, for example, the possession of digits that are homologous with those of Homo sapiens is a synapomorphy within the vertebrates. The tetrapods can be singled out as consisting of the first vertebrate with such digits homologous to those of Homo sapiens together with all descendants of this vertebrate and it is therefore inferred to have evolved by convergence or reversal.
Both mammals and birds are able to maintain a constant body temperature
Cladogenesis is an evolutionary splitting event where a parent species splits into two distinct species, forming a clade. This event usually occurs when a few end up in new, often distant areas or when environmental changes cause several extinctions. Note that here the lineage in a tree does not split. To determine whether an event is cladogenesis, researchers may use simulation, evidence from fossils, molecular evidence from the DNA of different living species. It has however been questioned whether the distinction between cladogenesis and anagenesis is necessary at all in evolutionary theory, anagenesis Evolutionary biology Speciation Korotayev, Andrey. World Religions and Social Evolution of the Old World Oikumene Civilizations, New York, Edwin Mellen Press
Convergent evolution is the independent evolution of similar features in species of different lineages. Convergent evolution creates analogous structures that have similar form or function but were not present in the last common ancestor of those groups, the cladistic term for the same phenomenon is homoplasy. The recurrent evolution of flight is an example, as flying insects, birds. Functionally similar features that have arisen through convergent evolution are analogous, whereas homologous structures or traits have a common origin, bird and pterosaur wings are analogous structures, but their forelimbs are homologous, sharing an ancestral state despite serving different functions. The opposite of convergence is divergent evolution, where related species evolve different traits, convergent evolution is similar to but different from parallel evolution. Many instances of convergent evolution are known in plants, including the development of C4 photosynthesis, seed dispersal by fleshy fruits adapted to be eaten by animals.
In morphology, analogous traits arise when different species live in similar ways and/or a similar environment, when occupying similar ecological niches similar problems can lead to similar solutions. The British anatomist Richard Owen was the first to identify the difference between analogies and homologies. In biochemistry and chemical constraints on mechanisms have caused some active site arrangements such as the triad to evolve independently in separate enzyme superfamilies. In his 1989 book Wonderful Life, Stephen Jay Gould argued that if one could rewind the tape of life the same conditions were encountered again, evolution could take a very different course. In cladistics, a homoplasy is a trait shared by two or more taxa for any other than that they share a common ancestry. Taxa which do share ancestry are part of the same clade, homoplastic traits caused by convergence are therefore, from the point of view of cladistics, confounding factors which could lead to an incorrect analysis.
In some cases, it is difficult to tell whether a trait has been lost and re-evolved convergently, or whether a gene has simply been switched off, such a re-emerged trait is called an atavism. From a mathematical standpoint, a gene has a steadily decreasing probability of retaining potential functionality over time. When two species are similar in a character, evolution is defined as parallel if the ancestors were similar. When the ancestral forms are unspecified or unknown, or the range of traits considered is not clearly specified, the enzymology of proteases provides some of the clearest examples of convergent evolution. These examples reflect the intrinsic chemical constraints on enzymes, leading evolution to converge on equivalent solutions independently and repeatedly and cysteine proteases use different amino acid functional groups as a nucleophile. In order to activate that nucleophile, they orient an acidic, the chemical and physical constraints on enzyme catalysis have caused identical triad arrangements to evolve independently more than 20 times in different enzyme superfamilies
It is thus a clade, a group consisting of a species and all its descendants. Though formulated in the 1970s, the term was not commonly used until its reintroduction in 2000 by Graham Budd and it is not necessary for a species to have living descendants in order for it to be included in the crown group. Extinct side branches on the tree that are descended from the most recent common ancestor of living members will still be part of a crown group. Although considered to be birds and other groups are not included in the crown group, as they fall outside the Neornithes clade. An alternative definition does not require any members of a group to be extant. The first definition forms the basis of this article, the crown group is given the designation crown-, to separate it from the group as commonly defined. Crown-Aves and Crown-Mammalia therefore differ slightly in content from the definition of Aves. This has caused confusion in the literature. Thus, a host of prefixes have been defined to describe various branches of the phylogenetic tree relative to extant organisms, a pan-group or total group is the crown group and all organisms more closely related to it than to any other extant organisms.
In a tree analogy, it is the group and all branches back to the split with the closest branch to have living members. The Pan-Aves thus contain the living birds and all more closely related to birds than to crocodilians. The phylogenetic lineage leading back from Neornithes to the point where it merges with the crocodilian lineage, pan-Mammalia consists of all mammals and their fossil ancestors back to the phylogenetic split from the remaining amniotes. Pan-Mammalia is thus a name for Synapsida. A stem group is a group composed of a pan-group or total group, above. This leaves primitive relatives of the groups, back along the phylogenetic line to the last common ancestor of the crown group. It follows from the definition that all members of a group are extinct. Alternatively, the stem group is sometimes used in a narrower sense to cover just the members of the traditional taxon falling outside the crown group. Permian synapsids like Dimetrodon and Anteosaurus are stem mammals in the wider sense, stem birds perhaps constitute the most cited example of a stem group, as the phylogeny of this group is fairly well known
Emil Hans Willi Hennig was a German biologist who is considered the founder of phylogenetic systematics, known as cladistics. In 1945 as a prisoner of war, Hennig began work on his theory of cladistics, with his works on evolution and systematics he revolutionised the view of the natural order of beings. As a taxonomist, he specialised in dipterans, Hennig was born in Dürrhennersdorf, Upper Lusatia. His mother Marie Emma, née Groß, worked as a maid and, and his father Karl Ernst Emil Hennig was a rail worker. Willi had two brothers, Fritz Rudolf Hennig, who became a minister, and Karl Herbert, who went missing at Stalingrad in 1943, in the spring of 1919, Willi Hennig started school in Dürrhennersdorf, and subsequently was at school in Taubenheim an der Spree and Oppach. Rudolf Hennig described the family as calm, his father possessed an even temperament, as of 1927, Willi Hennig continued his education at the Realgymnasium and boarding school in Klotzsche near Dresden. Here he met his first mentor M.
Rost, a science teacher, Rost had an interest in insects and introduced Hennig to Wilhelm Meise, who worked as a scientist at the Dresdener Museum für Tierkunde. In 1930, Hennig skipped a year, and graduated on February 26,1932, as early as 1931, Willi Hennig composed an essay entitled Die Stellung der Systematik in der Zoologie as part of his school work, published posthumously in 1978. It showed his interest as well as his treatment of systematic problems. From the summer semester of 1932 onwards, Hennig read zoology, botany and he would continue to visit the Museum in Dresden. There, he met the curator of the collection, the Dipteran expert Fritz Isidor van Emden. Hennig saw him regularly until van Emden was expelled from National Socialist Germany for having a Jewish mother, Hennig developed a deep friendship with Emdens successor, Klaus Günther. Hennig concluded his studies with a dissertation entitled, Beiträge zur Kenntnis des Kopulationsapparates der cyclorrhaphen Dipteren, by this time, Hennig had published eight scientific papers.
Besides his 300-page revision of the Tylidae, there were papers on Diptera. After his studies, Hennig was Volontär at the State Museum for Zoology in Dresden, on January 1,1937, he obtained a scholarship from the Deutsche Forschungsgemeinschaft to work at the German Entomological Institute of the Kaiser-Wilhelm-Gesellschaft in Berlin-Dahlem. On May 13,1939, Hennig married his fellow student Irma Wehnert. By 1945, they had three sons, Wolfgang and Gerd, Willi Hennig was drafted in 1938 to train for the infantry and concluded this course in 1939. As of the start of World War II, he was deployed in the infantry in Poland, France and Russia
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