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Phylogenesis
Phylogenesis (from Greek φῦλον ''phylon'' "tribe" + γένεσις ''genesis'' "origin") is the biological process by which a taxon (of any rank) appears. The science that studies these processes is called phylogenetics. These terms may be confused with the term phylogenetics, the application of molecular - analytical methods (i.e. molecular biology and genomics), in the explanation of phylogeny and its research. Phylogenetic relationships are discovered through phylogenetic inference methods that evaluate observed heritable traits, such as DNA sequences or overall morpho-anatomical, ethological, and other characteristics. Phylogeny 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. Phylogenetic analyses have become central to understanding biodiversity, evolution, ecological genetics and genomes. Cladistics Cladistics ( Gree ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Ecological Genetics
Ecological genetics is the study of genetics in natural populations. It combines ecology, evolution, and genetics to understand the processes behind adaptation. It is virtually synonymous with the field of molecular ecology. This contrasts with classical genetics, which works mostly on crosses between laboratory strains, and DNA sequence analysis, which studies genes at the molecular level. Research in this field is on traits of ecological significance—traits that affect an organism's fitness, or its ability to survive and reproduce. Examples of such traits include flowering time, drought tolerance, polymorphism, mimicry, and avoidance of attacks by predators.Ruxton G.D. Sherratt T.N. and Speed M.P. 2004. ''Avoiding attack: the evolutionary ecology of crypsis, warning signals & mimicry''. Oxford University Press. Research usually involves a mixture of field and laboratory studies. Samples of natural populations may be taken back to the laboratory for their genetic varia ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Maximum Parsimony (phylogenetics)
In phylogenetics and computational phylogenetics, maximum parsimony is an optimality criterion under which the phylogenetic tree that minimizes the total number of character-state changes (or minimizes the cost of differentially weighted character-state changes). Under the maximum-parsimony criterion, the optimal tree will minimize the amount of homoplasy (i.e., convergent evolution, parallel evolution, and evolutionary reversals). In other words, under this criterion, the shortest possible tree that explains the data is considered best. Some of the basic ideas behind maximum parsimony were presented by James S. Farris in 1970 and Walter M. Fitch in 1971. Maximum parsimony is an intuitive and simple criterion, and it is popular for this reason. However, although it is easy to ''score'' a phylogenetic tree (by counting the number of character-state changes), there is no algorithm to quickly ''generate'' the most-parsimonious tree. Instead, the most-parsimonious tree must be ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Computational Phylogenetics
Computational phylogenetics, phylogeny inference, or phylogenetic inference focuses on computational and optimization algorithms, Heuristic (computer science), heuristics, and approaches involved in Phylogenetics, phylogenetic analyses. The goal is to find a phylogenetic tree representing optimal evolutionary ancestry between a set of genes, species, or taxa. Maximum likelihood estimation, Maximum likelihood, Maximum parsimony (phylogenetics), parsimony, Bayesian inference in phylogeny, Bayesian, and minimum evolution are typical optimality criteria used to assess how well a phylogenetic tree topology describes the sequence data. Nearest Neighbour Interchange (NNI), Subtree Prune and Regraft (SPR), and Tree Bisection and Reconnection (TBR), known as tree rearrangements, are deterministic algorithms to search for optimal or the best phylogenetic tree. The space and the landscape of searching for the optimal phylogenetic tree is known as phylogeny search space. Maximum Likelihood (al ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
DNA Sequencing
DNA sequencing is the process of determining the nucleic acid sequence – the order of nucleotides in DNA. It includes any method or technology that is used to determine the order of the four bases: adenine, thymine, cytosine, and guanine. The advent of rapid DNA sequencing methods has greatly accelerated biological and medical research and discovery. Knowledge of DNA sequences has become indispensable for basic biological research, Genographic Project, DNA Genographic Projects and in numerous applied fields such as medical diagnosis, biotechnology, forensic biology, virology and biological systematics. Comparing healthy and mutated DNA sequences can diagnose different diseases including various cancers, characterize antibody repertoire, and can be used to guide patient treatment. Having a quick way to sequence DNA allows for faster and more individualized medical care to be administered, and for more organisms to be identified and cataloged. The rapid advancements in DNA seque ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Dendrogram
A dendrogram is a diagram representing a Tree (graph theory), tree graph. This diagrammatic representation is frequently used in different contexts: * in hierarchical clustering, it illustrates the arrangement of the clusters produced by the corresponding analyses. * in computational biology, it shows the clustering of genes or samples, sometimes in the margins of heat map, heatmaps. * in phylogenetics, it displays the evolutionary relationships among various biological taxa. In this case, the dendrogram is also called a phylogenetic tree. The name ''dendrogram'' derives from the two ancient greek words (), meaning "tree", and (), meaning "drawing, mathematical figure". Clustering example For a clustering example, suppose that five taxa (a to e) have been clustered by UPGMA based on a matrix of genetic distances. The hierarchical clustering dendrogram would show a column of five nodes representing the initial data (here individual taxa), and the remaining nodes repre ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Tree (graph Theory)
In graph theory, a tree is an undirected graph in which any two vertices are connected by path, or equivalently a connected acyclic undirected graph. A forest is an undirected graph in which any two vertices are connected by path, or equivalently an acyclic undirected graph, or equivalently a disjoint union of trees. A directed tree, oriented tree,See .See . polytree,See . or singly connected networkSee . is a directed acyclic graph (DAG) whose underlying undirected graph is a tree. A polyforest (or directed forest or oriented forest) is a directed acyclic graph whose underlying undirected graph is a forest. The various kinds of data structures referred to as trees in computer science have underlying graphs that are trees in graph theory, although such data structures are generally rooted trees. A rooted tree may be directed, called a directed rooted tree, either making all its edges point away from the root—in which case it is called an arborescence or out-tree� ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Cladogram
A cladogram (from Greek language, Greek ''clados'' "branch" and ''gramma'' "character") is a diagram used in cladistics to show relations among organisms. A cladogram is not, however, an Phylogenetic tree, evolutionary tree because it does not show how ancestors are related to descendants, nor does it show how much they have changed, so many differing evolutionary trees can be consistent with the same 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 e ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Most Recent Common Ancestor
A most recent common ancestor (MRCA), also known as a last common ancestor (LCA), is the most recent individual from which all organisms of a set are inferred to have descended. The most recent common ancestor of a higher taxon is generally assumed to have been a species. The term is also used in reference to the ancestry of groups of genes (haplotypes) rather than organisms. The ancestry of a set of individuals can sometimes be determined by referring to an established pedigree, although this may refer only to patrilineal or matrilineal lines for sexually-reproducing organisms with two parents, four grandparents, etc. However, in general, it is impossible to identify the exact MRCA of a large set of individuals, but an estimate of the time at which the MRCA lived can often be given. Such ''time to most recent common ancestor'' (''TMRCA'') estimates can be given based on DNA test results and established mutation rates as practiced in genetic genealogy, or by reference to a non- ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Organism
An organism is any life, living thing that functions as an individual. Such a definition raises more problems than it solves, not least because the concept of an individual is also difficult. Many criteria, few of them widely accepted, have been proposed to define what an organism is. Among the most common is that an organism has autonomous reproduction, Cell growth, growth, and metabolism. This would exclude viruses, despite the fact that they evolution, evolve like organisms. Other problematic cases include colonial organisms; a colony of eusocial insects is organised adaptively, and has Germ-Soma Differentiation, germ-soma specialisation, with some insects reproducing, others not, like cells in an animal's body. The body of a siphonophore, a jelly-like marine animal, is composed of organism-like zooids, but the whole structure looks and functions much like an animal such as a jellyfish, the parts collaborating to provide the functions of the colonial organism. The evolutiona ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Biological Classification
In biology, taxonomy () is the scientific study of naming, defining ( circumscribing) and classifying groups of biological organisms based on shared characteristics. Organisms are grouped into taxa (singular: taxon), and these groups are given a taxonomic rank; groups of a given rank can be aggregated to form a more inclusive group of higher rank, thus creating a taxonomic hierarchy. The principal ranks in modern use are domain, kingdom, phylum (''division'' is sometimes used in botany in place of ''phylum''), class, order, family, genus, and species. The Swedish botanist Carl Linnaeus is regarded as the founder of the current system of taxonomy, having developed a ranked system known as Linnaean taxonomy for categorizing organisms. With advances in the theory, data and analytical technology of biological systematics, the Linnaean system has transformed into a system of modern biological classification intended to reflect the evolutionary relationships among organisms, ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Online Etymology Dictionary
Etymonline, or ''Online Etymology Dictionary'', sometimes abbreviated as OED (not to be confused with the ''Oxford English Dictionary'', which the site often cites), is a free online dictionary that describes the etymology, origins of English language, English words, written and compiled by Douglas R. Harper. Description Douglas R. Harper is an American Civil War historian and copy editor for LNP Media Group. He compiled the etymology dictionary to record the history and evolution of more than 50,000 words, including slang and technical terms. The core of its etymology information stems from ''The Barnhart Dictionary of Etymology'' by Robert Barnhart, Ernest Klein's ''Comprehensive Etymology Dictionary of the English Language'', ''The Middle English Compendium'', ''The Oxford English Dictionary'', and the 1889–1902 ''Century Dictionary''. Harper also researches on digital archives. On the ''Etymonline'' homepage, Harper says that he considers himself "essentially and for the m ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
