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( Phylogeny)
Adaptation
Genetic drift
Gene flow
Mutation
Natural selection
Speciation In biology, phylogenetics is the study of evolutionary relatedness among various groups of organisms (e.g., species, populations), which is discovered through molecular sequencing data. The term phylogenetics is of Greek origin from the terms phyle/phylon (f???/f????), meaning "tribe, race," and genetikos (?e?et????), meaning "relative to birth" from genesis (???es?? ) "birth"). Taxonomy, the classification of organisms according to similarity, has been richly informed by phylogenetics but remains methodologically and logically distinct.[1] The fields overlap however in the science of phylogenetic systematics or cladism, where only phylogenetic trees are used to delimit taxa, each representing a group of lineage-connected individuals[2]. Evolution is regarded as a branching process, whereby populations are altered over time and may speciate into separate branches, hybridize together, or terminate by extinction. This may be visualized as a multidimensional character-space that a population moves through over time. The problem posed by phylogenetics is that genetic data are only available for the present, and fossil records (osteometric data) are sporadic and less reliable. Our knowledge of how evolution operates is used to reconstruct the full tree.[3] There are some terms that describe the nature of a grouping in such trees. For instance, all birds and reptiles are believed to have descended from a single common ancestor, so this taxonomic grouping (yellow in the diagram) is called monophyletic. "Modern reptile" (cyan in the diagram) is a grouping that contains a common ancestor, but does not contain all descendents of that ancestor (birds are excluded). This is an example of a paraphyletic group. A grouping such as warm-blooded animals would include only mammals and birds (red/orange in the diagram) and is called polyphyletic because the members of this grouping do not include the most recent common ancestor. Thus, a phylogenetic tree is based on a hypothesis of the order in which evolutionary events are assumed to have occured. [4] Cladistics is today the method of choice to infer phylogenetic trees. The most commonly used methods to infer phylogenies include parsimony, maximum likelihood, and MCMC-based Bayesian inference. Phenetics, popular in the mid-20th century but now largely obsolete, uses distance matrix-based methods to construct trees based on overall similarity which is often assumed to approximate phylogenetic relationships. All methods depend upon an implicit or explicit mathematical model describing the evolution of characters observed in the species included, and are usually used for molecular phylogeny where the characters are aligned nucleotide or amino acid sequences.
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