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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] |
Phylogenetics
In biology, phylogenetics (; from Greek φυλή/ φῦλον [] "tribe, clan, race", and wikt:γενετικός, γενετικός [] "origin, source, birth") is the study of the evolutionary history and relationships among or within groups of organisms. These relationships are determined by Computational phylogenetics, phylogenetic inference methods that focus on observed heritable traits, such as DNA sequences, protein amino acid sequences, or morphology. The result of such an analysis is a phylogenetic tree—a diagram containing a hypothesis of relationships that reflects the evolutionary history of a group of organisms. The tips of a phylogenetic tree can be living taxa or fossils, and represent the "end" or the present time in an evolutionary lineage. A phylogenetic diagram can be rooted or unrooted. A rooted tree diagram indicates the hypothetical common ancestor of the tree. An unrooted tree diagram (a network) makes no assumption about the ancestral line, and do ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Phylogeny
A phylogenetic tree (also phylogeny or evolutionary tree Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, MA.) 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. All life on Earth is part of a single phylogenetic tree, indicating common ancestry. In a ''rooted'' phylogenetic tree, each node with descendants represents the inferred most recent common ancestor of those descendants, and the edge lengths in some trees may be interpreted as time estimates. Each node is called a taxonomic unit. Internal nodes are generally called hypothetical taxonomic units, as they cannot be directly observed. Trees are useful in fields of biology such as bioinformatics, systematics, and phylogenetics. ''Unrooted'' trees illustrate only the relatedness of the leaf nodes and do not require the ancestral r ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Phylogenetic Tree
A phylogenetic tree (also phylogeny or evolutionary tree Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, MA.) 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. All life on Earth is part of a single phylogenetic tree, indicating common ancestry. In a ''rooted'' phylogenetic tree, each node with descendants represents the inferred most recent common ancestor of those descendants, and the edge lengths in some trees may be interpreted as time estimates. Each node is called a taxonomic unit. Internal nodes are generally called hypothetical taxonomic units, as they cannot be directly observed. Trees are useful in fields of biology such as bioinformatics, systematics, and phylogenetics. ''Unrooted'' trees illustrate only the relatedness of the leaf nodes and do not require the ancestral root to ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Outgroup (cladistics)
In cladistics or phylogenetics, an outgroup is a more distantly related group of organisms that serves as a reference group when determining the evolutionary relationships of the ingroup, the set of organisms under study, and is distinct from sociological outgroups. The outgroup is used as a point of comparison for the ingroup and specifically allows for the phylogeny to be rooted. Because the polarity (direction) of character change can be determined only on a rooted phylogeny, the choice of outgroup is essential for understanding the evolution of traits along a phylogeny. History Although the concept of outgroups has been in use from the earliest days of cladistics, the term "outgroup" is thought to have been coined in the early 1970s at the American Museum of Natural History. Prior to the advent of the term, various other terms were used by evolutionary biologists, including "exgroup", "related group", and "outside groups". Choice of outgroup The chosen outgroup is hypothes ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Maximum Parsimony (phylogenetics)
In phylogenetics, maximum parsimony is an optimality criterion under which the phylogenetic tree that minimizes the total number of character-state changes (or miminizes the cost of differentially weighted character-state changes) is preferred. 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 sought in "tree spac ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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 fr ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Convergent Evolution
Convergent evolution is the independent evolution of similar features in species of different periods or epochs in time. 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 a classic example, as flying insects, birds, pterosaurs, and bats have independently evolved the useful capacity of flight. Functionally similar features that have arisen through convergent evolution are ''analogous'', whereas '' homologous'' structures or traits have a common origin but can have dissimilar functions. Bird, bat, 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 para ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Phylogenetic
In biology, phylogenetics (; from Greek φυλή/ φῦλον [] "tribe, clan, race", and wikt:γενετικός, γενετικός [] "origin, source, birth") is the study of the evolutionary history and relationships among or within groups of organisms. These relationships are determined by Computational phylogenetics, phylogenetic inference methods that focus on observed heritable traits, such as DNA sequences, protein amino acid sequences, or morphology. The result of such an analysis is a phylogenetic tree—a diagram containing a hypothesis of relationships that reflects the evolutionary history of a group of organisms. The tips of a phylogenetic tree can be living taxa or fossils, and represent the "end" or the present time in an evolutionary lineage. A phylogenetic diagram can be rooted or unrooted. A rooted tree diagram indicates the hypothetical common ancestor of the tree. An unrooted tree diagram (a network) makes no assumption about the ancestral line, and do ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Hierarchical Clustering
In data mining and statistics, hierarchical clustering (also called hierarchical cluster analysis or HCA) is a method of cluster analysis that seeks to build a hierarchy of clusters. Strategies for hierarchical clustering generally fall into two categories: * Agglomerative: This is a " bottom-up" approach: Each observation starts in its own cluster, and pairs of clusters are merged as one moves up the hierarchy. * Divisive: This is a "top-down" approach: All observations start in one cluster, and splits are performed recursively as one moves down the hierarchy. In general, the merges and splits are determined in a greedy manner. The results of hierarchical clustering are usually presented in a dendrogram. The standard algorithm for hierarchical agglomerative clustering (HAC) has a time complexity of \mathcal(n^3) and requires \Omega(n^2) memory, which makes it too slow for even medium data sets. However, for some special cases, optimal efficient agglomerative methods (of comp ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Synapomorphy
In phylogenetics, an apomorphy (or derived trait) is a novel character or character state that has evolved from its ancestral form (or plesiomorphy). A synapomorphy is an apomorphy shared by two or more taxa and is therefore hypothesized to have evolved in their most recent common ancestor. ) In cladistics, synapomorphy implies homology. Examples of apomorphy are the presence of erect gait, fur, the evolution of three middle ear bones, and mammary glands in mammals but not in other vertebrate animals such as amphibians or reptiles, which have retained their ancestral traits of a sprawling gait and lack of fur. Thus, these derived traits are also synapomorphies of mammals in general as they are not shared by other vertebrate animals. Etymology The word —coined by German entomologist Willi Hennig—is derived from the Ancient Greek words (''sún''), meaning "with, together"; (''apó''), meaning "away from"; and (''morphḗ''), meaning "shape, form". Clade analysis ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Evolution
Evolution is change in the heritable characteristics of biological populations over successive generations. These characteristics are the expressions of genes, which are passed on from parent to offspring during reproduction. Variation tends to exist within any given population as a result of genetic mutation and recombination. Evolution occurs when evolutionary processes such as natural selection (including sexual selection) and genetic drift act on this variation, resulting in certain characteristics becoming more common or more rare within a population. The evolutionary pressures that determine whether a characteristic is common or rare within a population constantly change, resulting in a change in heritable characteristics arising over successive generations. It is this process of evolution that has given rise to biodiversity at every level of biological organisation, including the levels of species, individual organisms, and molecules. The theory of evolut ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Nucleotide
Nucleotides are organic molecules consisting of a nucleoside and a phosphate. They serve as monomeric units of the nucleic acid polymers – deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both of which are essential biomolecules within all life-forms on Earth. Nucleotides are obtained in the diet and are also synthesized from common nutrients by the liver. Nucleotides are composed of three subunit molecules: a nucleobase, a five-carbon sugar (ribose or deoxyribose), and a phosphate group consisting of one to three phosphates. The four nucleobases in DNA are guanine, adenine, cytosine and thymine; in RNA, uracil is used in place of thymine. Nucleotides also play a central role in metabolism at a fundamental, cellular level. They provide chemical energy—in the form of the nucleoside triphosphates, adenosine triphosphate (ATP), guanosine triphosphate (GTP), cytidine triphosphate (CTP) and uridine triphosphate (UTP)—throughout the cell for the many ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
