Phylogenetics (Greek: φυλή, φῦλον - ''phylé'', ''phylon'' = tribe, clan, race + γενετικός - ''genetikós'' = origin, source, birth) – in biology – is the study of phylogenesis, or the evolutionary history, development and relationships among groups of organisms (e.g. species, or populations). These are discovered mainly through molecular data matrices, based on nucleic acids sequences and protein structures. The result of a phylogenetic study is a phylogeny – a hypothesis about the evolutionary history of taxonomic groups.〔(【引用サイトリンク】 publisher=Biology online )〕
Evolution is a process whereby populations are altered over time and may split into separate branches, hybridize together, or terminate by extinction. The evolutionary branching process may be depicted as a phylogenetic tree, and the place of each of the various organisms on the tree is based on a hypothesis about the sequence in which evolutionary branching events occurred. In historical linguistics, similar concepts are used with respect to relationships between languages; and in textual criticism with stemmatics.
Phylogenetic analyses have become essential to research on the evolutionary tree of life. For example, the RedToL aims at reconstructing the red algae tree of life. The National Science Foundation sponsors a project called the ''Assembling the Tree of Life'' (AToL). The goal of this project is to determine evolutionary relationships across large groups of organisms throughout the history of life. The research on this project often involves large teams working across institutions and disciplines, and typically provides support to investigators working on computational phylogenetics and phyloinformatics tasks, including data acquisition, analysis, and algorithm development and dissemination.
Taxonomy is the classification, identification and naming of organisms. It is usually richly informed by phylogenetics, but remains a methodologically and logically distinct discipline.
The degree to which taxonomies depend on phylogenies (or classification depends on evolutionary development) differs depending on the school of taxonomy: phenetics ignores phylogeny altogether, trying to represent the similarity between organisms instead; cladistics (phylogenetic systematics) tries to reproduce phylogeny in its classification without loss of information; evolutionary taxonomy tries to find a compromise between them in order to represent stages of evolution.
== Construction of a phylogenetic tree ==
The scientific methods of phylogenetics are often grouped under the term cladistics. The most common ones are parsimony, maximum likelihood (ML), and MCMC-based Bayesian inference. All methods depend upon an implicit or explicit mathematical model describing the evolution of characters observed in the species included; all can be, and are, used for molecular data, wherein the characters are aligned nucleotide or amino acid sequences, and all but maximum likelihood (see below) can be, and are, used for phenotypic (morphological, chemical, and physiological) data (also called classical or traditional data).
Phenetics, popular in the mid-20th century but now largely obsolete, uses distance matrix-based methods to construct trees based on overall similarity in morphology or other observable traits (i.e. in the phenotype, not the DNA), which was often assumed to approximate phylogenetic relationships.
A comprehensive step-by-step protocol on constructing phylogenetic tree, including DNA/Amino Acid contiguous sequence assembly, multiple sequence alignment, model-test (testing best-fitting substitution models) and phylogeny reconstruction using Maximum Likelihood and Bayesian Inference, is available at Nature Protocol〔Bast, F. 2013. Sequence Similarity Search, Multiple Sequence Alignment, Model Selection, Distance Matrix and Phylogeny Reconstruction. Nature Protocol Exchange. doi:(10.1038/protex.2013.065 )〕
Prior to 1990, phylogenetic inferences were generally presented as narrative scenarios. Such methods are legitimate, but often ambiguous and hard to test.〔Richard C. Brusca & Gary J. Brusca (2003). ''Invertebrates'' (2nd ed.). Sunderland, Massachusetts: Sinauer Associates. ISBN 978-0-87893-097-5.〕〔Bock, W.J. (2004). Explanations in systematics. Pp. 49-56. In Williams, D.M. and Forey, P.L. (eds) Milestones in Systematics. London: Systematics Association Special Volume Series 67. CRC Press, Boca Raton, Florida.〕〔Auyang, Sunny Y. (1998). ''Narratives and Theories in Natural History.'' In: ''Foundations of complex-system theories: in economics, evolutionary biology, and statistical physics.'' Cambridge, U.K.; New York: Cambridge University Press.〕
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