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Bayesian Inference In Phylogeny
Bayesian Computational phylogenetics, inference of phylogeny combines the information in the prior and in the data likelihood to create the so-called posterior probability of trees, which is the probability that the tree is correct given the data, the prior and the likelihood model. Bayesian inference was introduced into molecular phylogenetics in the 1990s by three independent groups: Bruce Rannala and Ziheng Yang in Berkeley, Bob Mau in Madison, and Shuying Li in University of Iowa, the last two being PhD students at the time. The approach has become very popular since the release of the MrBayes software in 2001, and is now one of the most popular methods in molecular phylogenetics. Bayesian inference of phylogeny background and bases Bayesian inference refers to a probabilistic method developed by Reverend Thomas Bayes based on Bayes' theorem. Published posthumously in 1763 it was the first expression of inverse probability and the basis of Bayesian inference. Independently, una ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Evolutionary Biology
Evolutionary biology is the subfield of biology that studies the evolutionary processes such as natural selection, common descent, and speciation that produced the diversity of life on Earth. In the 1930s, the discipline of evolutionary biology emerged through what Julian Huxley called the Modern synthesis (20th century), modern synthesis of understanding, from previously unrelated fields of biological research, such as genetics and ecology, systematics, and paleontology. The investigational range of current research has widened to encompass the genetic architecture of adaptation, molecular evolution, and the different forces that contribute to evolution, such as sexual selection, genetic drift, and biogeography. The newer field of evolutionary developmental biology ("evo-devo") investigates how embryogenesis is controlled, thus yielding a wider synthesis that integrates developmental biology with the fields of study covered by the earlier evolutionary synthesis. Subfields ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Tiger Phylogenetic Relationships
The tiger (''Panthera tigris'') is a large Felidae, cat and a member of the genus ''Panthera'' native to Asia. It has a powerful, muscular body with a large head and paws, a long tail and orange fur with black, mostly vertical stripes. It is traditionally classified into nine Holocene, recent subspecies, though some recognise only two subspecies, mainland Asian tigers and the island tigers of the Sunda Islands. Throughout the tiger's range, it inhabits mainly forests, from coniferous and temperate broadleaf and mixed forests in the Russian Far East and Northeast China to tropical and subtropical moist broadleaf forests on the Indian subcontinent and Southeast Asia. The tiger is an apex predator and preys mainly on ungulates, which it takes by ambush. It lives a mostly solitary life and occupies home ranges, defending these from individuals of the same sex. The range of a male tiger overlaps with that of multiple females with whom he mates. Females give birth to usually two or ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Cécile Ané
Cécile Ané is an evolutionary biologist, botanist, and statistical geneticist whose research involves the inference of evolutionary trees and the evolution of inherited traits, especially for plant species, as well as the mathematical statistics underlying these methods. Educated in France, she works in the United States as a professor at the University of Wisconsin–Madison, with joint appointments in the departments of botany and statistics. Education Ané is a graduate of the École normale supérieure de Lyon. She completed her Ph.D. in mathematics in 2000, at Toulouse III - Paul Sabatier University. Her dissertation, ''Grandes déviations et inégalités fonctionnelles pour des processus de Markov a temps continu sur un graphe'' 'Large deviations and functional inequalities for continuous-time Markov processes on a graph''concerned probability theory, and was directed by Michel Ledoux. Research After completing a doctorate in mathematics, Ané's research interests ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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BEAST 2
BEAST 2 is a cross-platform program for Bayesian analysis of molecular sequences. Using MCMC, it estimates rooted, timed phylogenies using a range of substitution and clock models, and a variety of tree priors. There is an associated tool, called BEAUTi, for setting up standard analyses (which are specified using XML Extensible Markup Language (XML) is a markup language and file format for storing, transmitting, and reconstructing data. It defines a set of rules for encoding electronic document, documents in a format that is both human-readable and Machine-r ...). BEAST 2 is a complete re-write of the earlier BEAST program (which is still actively developed and has recently been renamed BEASTX). A notable feature of BEAST 2 is the packaging system which has simplified the process of implementing novel models. Taming the BEAST is a community driven resource which teaches the use of BEAST 2 and related phylogenetic software. BEAUti BEAUti stands for "Bayesian Evolutionary ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Nexus File
The extensible NEXUS file format is widely used in phylogenetics, evolutionary biology, and bioinformatics. It stores information about taxa In biology, a taxon (back-formation from ''taxonomy''; : taxa) is a group of one or more populations of an organism or organisms seen by taxonomists to form a unit. Although neither is required, a taxon is usually known by a particular name and ..., morphological character states, DNA and protein sequence alignments, distances, and phylogenetic trees. The NEXUS format also allows the storage of data that can facilitate analyses, such as sets of characters or taxa. Many popular phylogenetic programs, including PAUP*,PAUP* — Phylogenetic Analysis Using Parsimony *and other methods [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Long Branch Attraction
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 ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Bootstrapping
In general, bootstrapping usually refers to a self-starting process that is supposed to continue or grow without external input. Many analytical techniques are often called bootstrap methods in reference to their self-starting or self-supporting implementation, such as bootstrapping (statistics), bootstrapping (finance), or bootstrapping (linguistics). Etymology Tall boots may have a tab, loop or handle at the top known as a bootstrap, allowing one to use fingers or a boot hook tool to help pull the boots on. The saying "to " was already in use during the 19th century as an example of an impossible task. The idiom dates at least to 1834, when it appeared in the ''Workingman's Advocate'': "It is conjectured that Mr. Murphee will now be enabled to hand himself over the Cumberland river or a barn yard fence by the straps of his boots."Jan FreemanBootstraps and Baron Munchausen '' Boston.com'', January 27, 2009 In 1860 it appeared in a comment about philosophy of mind: "The a ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Taxa
In biology, a taxon (back-formation from ''taxonomy''; : taxa) is a group of one or more populations of an organism or organisms seen by taxonomists to form a unit. Although neither is required, a taxon is usually known by a particular name and given a particular ranking, especially if and when it is accepted or becomes established. It is very common, however, for taxonomists to remain at odds over what belongs to a taxon and the criteria used for inclusion, especially in the context of rank-based (" Linnaean") nomenclature (much less so under phylogenetic nomenclature). If a taxon is given a formal scientific name, its use is then governed by one of the nomenclature codes specifying which scientific name is correct for a particular grouping. Initial attempts at classifying and ordering organisms (plants and animals) were presumably set forth in prehistoric times by hunter-gatherers, as suggested by the fairly sophisticated folk taxonomies. Much later, Aristotle, and later st ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Cold Chain
A cold chain is a supply chain that uses refrigeration to maintain perishable goods, such as pharmaceuticals, produce or other goods that are temperature-sensitive. Common goods, sometimes called cool cargo, distributed in cold chains include fresh agricultural produce, seafood, frozen food, photographic film, chemicals, and pharmaceutical products. The objective of a cold chain is to preserve the integrity and quality of goods such as pharmaceutical products or perishable good from production to consumption. A well functioning, or unbroken, cold chain requires uninterrupted sequence of refrigerated production, storage and distribution activities, along with associated equipment and logistics, which maintain a desired low-temperature interval to keep the safety and quality of perishable or sensitive products. Unlike other goods or merchandise, cold chain goods are Decomposition, perishable and always en-route towards end use or destination. Adequate cold storage, in particular, ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Molecular Phylogenetics
Molecular phylogenetics () is the branch of phylogeny that analyzes genetic, hereditary molecular differences, predominantly 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 phylogenetics, 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 (biology), 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 tre ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Metropolis–Hastings Algorithm
In statistics and statistical physics, the Metropolis–Hastings algorithm is a Markov chain Monte Carlo (MCMC) method for obtaining a sequence of random samples from a probability distribution from which direct sampling is difficult. New samples are added to the sequence in two steps: first a new sample is proposed based on the previous sample, then the proposed sample is either added to the sequence or rejected depending on the value of the probability distribution at that point. The resulting sequence can be used to approximate the distribution (e.g. to generate a histogram) or to compute an integral (e.g. an expected value). Metropolis–Hastings and other MCMC algorithms are generally used for sampling from multi-dimensional distributions, especially when the number of dimensions is high. For single-dimensional distributions, there are usually other methods (e.g. adaptive rejection sampling) that can directly return independent samples from the distribution, and these are ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |