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Tip Dating
Tip dating is a technique used in molecular dating that allows the inference of time-calibrated phylogenetic trees. Its defining feature is that it uses the ages of the samples to provide time information for the analysis, in contrast with traditional ' node dating' methods that require age constraints to be applied to the internal nodes of the evolutionary tree. In tip dating, morphological data and molecular data are typically analysed together to estimate the evolutionary relationships (tree topology) and the divergence times among lineages (node times); this approach is also known as 'total-evidence dating'. However, tip dating can also be used to analyse data sets that only comprise morphological characters or that only comprise molecular characters (e.g., data sets that include samples of ancient DNA or of serially sampled viruses). Tip dating has been implemented in Bayesian phylogenetic software and typically draws on the fossilised birth-death model for evolution. This ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecular Clock
The molecular clock is a figurative term for a technique that uses the mutation rate of biomolecules to deduce the time in prehistory when two or more life forms diverged. The biomolecular data used for such calculations are usually nucleotide sequences for DNA, RNA, or amino acid sequences for proteins. Early discovery and genetic equidistance The notion of the existence of a so-called "molecular clock" was first attributed to Émile Zuckerkandl and Linus Pauling who, in 1962, noticed that the number of amino acid differences in hemoglobin between different lineages changes roughly linearly with time, as estimated from fossil evidence. They generalized this observation to assert that the rate of evolutionary change of any specified protein was approximately constant over time and over different lineages (known as the molecular clock hypothesis). The genetic equidistance phenomenon was first noted in 1963 by Emanuel Margoliash, who wrote: "It appears that the number ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Phylogenetic Tree
A phylogenetic tree or phylogeny is a graphical representation which shows the evolutionary history between a set of species or taxa during a specific time.Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, MA. In other words, it is a branching diagram or a tree showing the evolutionary relationships among various biological species or other entities based upon similarities and differences in their physical or genetic characteristics. In evolutionary biology, all life on Earth is theoretically part of a single phylogenetic tree, indicating common ancestry. Phylogenetics is the study of phylogenetic trees. The main challenge is to find a phylogenetic tree representing optimal evolutionary ancestry between a set of species or taxa. Computational phylogenetics (also phylogeny inference) focuses on the algorithms involved in finding optimal phylogenetic tree in the phylogenetic landscape. Phylogenetic trees may be rooted or unrooted. In a ''rooted'' p ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Node Dating
In general, a node is a localized swelling (a "knot") or a point of intersection (a Vertex (graph theory), vertex). Node may refer to: In mathematics *Vertex (graph theory), a vertex in a mathematical graph *Vertex (geometry), a point where two or more curves, lines, or edges meet. *Node (autonomous system), behaviour for an ordinary differential equation near a critical point *Singular point of an algebraic variety#Nodes, Singular point of an algebraic variety, a type of singular point of a curve In science and engineering Spherical geometry * node, the points where a great circle crosses a plane of reference, or the equator of a sphere Astronomy *Orbital node, the points where an orbit crosses a plane of reference ** Lunar node, where the orbits of the Sun and Moon intersect ** Longitude of the ascending node, how orbital nodes are parameterized Biology *Lymph node, an immune system organ used to store white blood cells *Node of Ranvier, periodic gaps in the insulating myeli ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Morphology (biology)
Morphology (from Ancient Greek μορφή (morphḗ) "form", and λόγος (lógos) "word, study, research") is the study of the form and structure of organisms and their specific structural features. This includes aspects of the outward appearance (shape, structure, color, pattern, size), as well as the form and structure of internal parts like bones and organs, i.e., anatomy. This is in contrast to physiology, which deals primarily with function. Morphology is a branch of life science dealing with the study of the overall structure of an organism or taxon and its component parts. History The etymology of the word "morphology" is from the Ancient Greek (), meaning "form", and (), meaning "word, study, research". While the concept of form in biology, opposed to function, dates back to Aristotle (see Aristotle's biology), the field of morphology was developed by Johann Wolfgang von Goethe (1790) and independently by the German anatomist and physiologist Karl Fried ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Tree Topology
A tree topology, or star-bus topology, is a hybrid network topology in which star networks are interconnected via bus networks. Tree networks are hierarchical, and each node can have an arbitrary number of child nodes. Regular tree networks A regular tree network's topology is characterized by two parameters: the branching, d, and the number of generations, G. The total number of the nodes, N, and the number of peripheral nodes N_p, are given by : N= \frac,\quad N_p=d^G Random tree networks Three parameters are crucial in determining the statistics of random tree networks, first, the branching probability, second the maximum number of allowed progenies at each branching point, and third the maximum number of generations, that a tree can attain. There are a lot of studies that address the large tree networks, however small tree networks are seldom studied. Tools to deal with networks A group at MIT has developed a set of functions for Matlab MATLAB (an abb ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Virus
A virus is a submicroscopic infectious agent that replicates only inside the living Cell (biology), cells of an organism. Viruses infect all life forms, from animals and plants to microorganisms, including bacteria and archaea. Viruses are found in almost every ecosystem on Earth and are the most numerous type of biological entity. Since Dmitri Ivanovsky's 1892 article describing a non-bacterial pathogen infecting tobacco plants and the discovery of the tobacco mosaic virus by Martinus Beijerinck in 1898, more than 16,000 of the millions of List of virus species, virus species have been described in detail. The study of viruses is known as virology, a subspeciality of microbiology. When infected, a host cell is often forced to rapidly produce thousands of copies of the original virus. When not inside an infected cell or in the process of infecting a cell, viruses exist in the form of independent viral particles, or ''virions'', consisting of (i) genetic material, i.e., long ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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] |
Birth–death Process
The birth–death process (or birth-and-death process) is a special case of continuous-time Markov process where the state transitions are of only two types: "births", which increase the state variable by one and "deaths", which decrease the state by one. It was introduced by William Feller. The model's name comes from a common application, the use of such models to represent the current size of a population where the transitions are literal births and deaths. Birth–death processes have many applications in demography, queueing theory, performance engineering, epidemiology, biology and other areas. They may be used, for example, to study the evolution of bacteria, the number of people with a disease within a population, or the number of customers in line at the supermarket. Definition When a birth occurs, the process goes from state ''n'' to ''n'' + 1. When a death occurs, the process goes from state ''n'' to state ''n'' − 1. The process is speci ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Speciation
Speciation is the evolutionary process by which populations evolve to become distinct species. The biologist Orator F. Cook coined the term in 1906 for cladogenesis, the splitting of lineages, as opposed to anagenesis, phyletic evolution within lineages. Charles Darwin was the first to describe the role of natural selection in speciation in his 1859 book ''On the Origin of Species''. He also identified sexual selection as a likely mechanism, but found it problematic. There are four geographic modes of speciation in nature, based on the extent to which speciating populations are isolated from one another: allopatric speciation, allopatric, peripatric speciation, peripatric, parapatric speciation, parapatric, and sympatric speciation, sympatric. Whether genetic drift is a minor or major contributor to speciation is the subject of much ongoing discussion. Rapid sympatric speciation can take place through polyploidy, such as by doubling of chromosome number; the result is progeny wh ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Fossil
A fossil (from Classical Latin , ) is any preserved remains, impression, or trace of any once-living thing from a past geological age. Examples include bones, shells, exoskeletons, stone imprints of animals or microbes, objects preserved in amber, hair, petrified wood and DNA remnants. The totality of fossils is known as the ''fossil record''. Though the fossil record is incomplete, numerous studies have demonstrated that there is enough information available to give a good understanding of the pattern of diversification of life on Earth. In addition, the record can predict and fill gaps such as the discovery of '' Tiktaalik'' in the arctic of Canada. Paleontology includes the study of fossils: their age, method of formation, and evolutionary significance. Specimens are sometimes considered to be fossils if they are over 10,000 years old. The oldest fossils are around 3.48 billion years to 4.1 billion years old. Early edition, published online before prin ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Extant Taxa
Neontology is a part of biology that, in contrast to paleontology, studies and deals with living (or, more generally, '' recent'') organisms. It is the study of extant taxa (singular: extant taxon): taxa (such as species, genera and families) with members still alive, as opposed to (all) being extinct. For example: * The Indian elephant (''Elephas maximus'') is an extant species, and the woolly mammoth (''Mammuthus primigenius'') is an extinct species. * The moose (''Alces alces'') is an extant species, and the Irish elk (''Megaloceros giganteus'') is an extinct species. * In the group of molluscs known as the cephalopods, there were approximately 600 extant species and 7,500 extinct species. A taxon can be classified as extinct if it is broadly agreed or certified that no members of the group are still alive. Conversely, an extinct taxon can be reclassified as extant if there are new discoveries of living species (" Lazarus species"), or if previously known extant species are ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
