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Bayesian Inference In Phylogeny
Bayesian 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, unaware of Bayes' work, Pierre- ... [...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 (natural selection, common descent, speciation) that produced the diversity of life on Earth. It is also defined as the study of the history of life forms on Earth. Evolution is based on the theory that all species are related and they gradually change over time. In a population, the genetic variations affect the physical characteristics i.e. phenotypes of an organism. These changes in the phenotypes will be an advantage to some organisms, which will then be passed onto their offspring. Some examples of evolution in species over many generations are the Peppered Moth and Flightless birds. In the 1930s, the discipline of evolutionary biology emerged through what Julian Huxley called the modern synthesis of understanding, from previously unrelated fields of biological research, such as genetics and ecology, systematics, and paleontology. The importance of studying Evolutionary biology ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Tiger Phylogenetic Relationships
The tiger (''Panthera tigris'') is the largest living cat species and a member of the genus ''Panthera''. It is most recognisable for its dark vertical stripes on orange fur with a white underside. An apex predator, it primarily preys on ungulates, such as deer and wild boar. It is territorial and generally a solitary but social predator, requiring large contiguous areas of habitat to support its requirements for prey and rearing of its offspring. Tiger cubs stay with their mother for about two years and then become independent, leaving their mother's home range to establish their own. The tiger was first scientifically described in 1758. It once ranged widely from the Eastern Anatolia Region in the west to the Amur River basin in the east, and in the south from the foothills of the Himalayas to Bali in the Sunda Islands. Since the early 20th century, tiger populations have lost at least 93% of their historic range and have been extirpated from Western and Central Asia, the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Divergence Time Estimation And Ancestral Area Reconstruction Of Porcini S
In vector calculus, divergence is a vector operator that operates on a vector field, producing a scalar field giving the quantity of the vector field's source at each point. More technically, the divergence represents the volume density of the outward flux of a vector field from an infinitesimal volume around a given point. As an example, consider air as it is heated or cooled. The velocity of the air at each point defines a vector field. While air is heated in a region, it expands in all directions, and thus the velocity field points outward from that region. The divergence of the velocity field in that region would thus have a positive value. While the air is cooled and thus contracting, the divergence of the velocity has a negative value. Physical interpretation of divergence In physical terms, the divergence of a vector field is the extent to which the vector field flux behaves like a source at a given point. It is a local measure of its "outgoingness" – the extent to ... [...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. 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 arbitrary data. It defines a set of rules for encoding documents in a format that is both human-readable and machine-readable. T ...). BEAST 2 is a complete re-write of the earlier (still actively developed) BEAST program and as such draws on a large body of work. 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 The XML files that specify BEAST computations can be unwield ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Nexus File
The extensible NEXUS file format is widely used in bioinformatics. It stores information about taxa, morphological and molecular characters, distances, genetic codes, assumptions, sets, trees, etc. Several popular phylogenetic programs such as PAUP*,PAUP* — Phylogenetic Analysis Using Parsimony *and other methods MrBayes,MrBayes /ref> Mesquite,Mesquite: A modular system for evolutionary analysis /re ... [...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 resul ... [...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. 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 pulling 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 on philosophy of mind: "The attempt of the mind to analyze itself san effort analogous to one who would lift himself by his own bootstraps." Bootstrap as a metaphor, meaning to better oneself by one's own unaided efforts, was in use in 1922. This metaphor ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Taxa
In biology, a taxon ( back-formation from '' taxonomy''; plural 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. 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 set forth in Carl Linnaeus's system in ''Systema Naturae'', 10th edition (1758), as well as an unpublished work by Bernard and Antoine Laurent de Jussieu. The idea of a unit-based system of biological classification was first made widely available in 1805 in the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Cold Chain
A cold chain is a low temperature-controlled supply chain network. An unbroken cold chain is an uninterrupted series of refrigerated production, storage and distribution activities, along with associated equipment and logistics, which maintain quality via a desired low-temperature range. It is used to preserve and to extend and ensure the shelf life of products, such as fresh agricultural produce, seafood, frozen food, photographic film, chemicals, and pharmaceutical products. Such products, during transport and end-use when in transient storage, are sometimes called cool cargo. Unlike other goods or merchandise, cold chain goods are perishable and always en-route towards end use or destination, even when held temporarily in cold stores and hence commonly referred to as "cargo" during its entire logistics cycle. Adequate cold storage, in particular, can be crucial to prevent quantitative and qualitative food losses. History Mobile refrigeration with ice from the ice trade ... [...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 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. History The theoretical ... [...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. This 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 free from the problem of autocorrelated samples that is inherent in MCMC methods. History The algorithm was named after Nicholas Metropolis and W.K. Hastings. Metropolis was the first author to appear on the list of authors of the 1953 article '' Equatio ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |