biology, phylogenetics (Greek: "phyle/phylon" (φυλή/φῦλον) "tribe, race" and "genetikos" (γενετικός) "relative to birth" from " genesis" (γένεσις ) "birth") is the study of evolutionary relatedness among various groups of organisms (e.g., species, populations). Taxonomy, the classification of organisms according to similarity, has been richly informed by phylogenetics but remains methodologically and logically distinct. [cite book
A.W.F. Edwards& L.L. Cavalli-Sforza
title=Reconstruction of evolutionary trees
editor=Systematics Assoc. Publ. No. 6: Phenetic and Phylogenetic Classification
pages=67-76] The fields overlap however in the science of
phylogenetic systematicsor cladism, where only phylogenetic trees are used to delimit taxa, each representing a group of lineage-connected individuals [cite web
last = Speer
first = Vrian
title = UCMP Glossary: Phylogenetics
publisher = UC Berkeley
year = 1998
url = http://www.ucmp.berkeley.edu/glossary/glossary_1.html
accessdate = 2008-03-22] .
Evolution is regarded as a branching process, whereby populations are altered over time and may
speciateinto 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 fossilrecords ( osteometricdata) are sporadic and less reliable. Our knowledge of how evolution operates is used to reconstruct the full tree. [cite journal
L.L. Cavalli-Sforzaand A.W.F. Edwards
title=Phylogenetic analysis: Models and estimation procedures
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" (
cyanin 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-bloodedanimals 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. Cladisticsis 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 nowadays 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 modeldescribing the evolution of characters observed in the species included, and are usually used for molecular phylogenywhere the characters are aligned nucleotideor amino acidsequences.
Ernst Haeckel's recapitulation theory
During the late 19th century,
Ernst Haeckel's recapitulation theory, or biogenetic law, was widely accepted. This theory was often expressed as " ontogenyrecapitulates phylogeny", i.e. the development of an organism exactly mirrors the evolutionary development of the species. Haeckel's early version of this hypothesis [that the embryo mirrors "adult" evolutionary ancestors] has since been rejected, and the hypothesis amended as the embryo's development mirroring "embryos" of its evolutionary ancestors. Most modern biologists recognize numerous connections between ontogeny and phylogeny, explain them using evolutionary theory, or view them as supporting evidence for that theory. Donald Williamsonsuggested that larvae and embryos represented adults in other taxa that have been transferred by hybridization (the larval transfer theory) [Williamson, D. I. (2003) "The Origins of Larvae". Kluwer. Dordrecht. xviii + 261 pp.] [Williamson, D. I. (2006) Hybridization in the evolution of animal form and life-cycle. "Zoological Journal of the Linnean Society" 148: 585-602.]
Organisms can generally inherit genes in two ways: from parent to offspring (vertical gene transfer), or by horizontal or lateral gene transfer, in which genes jump between unrelated organisms, a common phenomenon in
prokaryotes. Lateral gene transferhas complicated the determination of phylogenies of organisms since inconsistencies have been reported depending on the gene chosen.
Carl Woese came up with the three-domain theory of life (eubacteria, archaea and eukaryotes) based on his discovery that the genes encoding ribosomal RNA are ancient and distributed over all lineages of life with little or no lateral gene transfer. Therefore rRNA are commonly recommended as molecular clocks for reconstructing phylogenies.
This has been particularly useful for the phylogeny of microorganisms, to which the species concept does not apply and which are too morphologically simple to be classified based on phenotypic traits.
Taxon sampling and phylogenetic signal
Owing to the development of advanced sequencing techniques in
molecular biology, it has become feasible to gather large amounts of data (DNA or amino acid sequences) to estimate phylogenies. For example, it is not rare to find studies with character matrices based on whole mitochondrial genomes. However, it has been proposed that it is more important to increase the number of taxa in the matrix than to increase the number of characters, because the more taxa, the more robust is the resulting phylogeny. This is partly due to the breaking up of long branches. It has been argued that this is an important reason to incorporate data from fossils into phylogenies where possible. Using simulations, Derrick Zwickland Hilliscite journal |author=Zwickl DJ, Hillis DM |title=Increased taxon sampling greatly reduces phylogenetic error |journal=Systematic Biology |volume=51 |pages=588–598 |year=2002 | doi = 10.1080/10635150290102339 ] found that increasing taxon sampling in phylogenetic inference has a positive effect on the accuracy of phylogenetic analyses.
Another important factor that affects the accuracy of tree reconstruction is whether the data analyzed actually contain useful phylogenetic signal, a term that is used generally to denote whether related organisms tend to resemble each other with respect to their genetic material or phenotypic traits.cite journal |author=Blomberg SP, Garland T Jr, Ives AR |title=Testing for phylogenetic signal in comparative data: behavioral traits are more labile |journal=Evolution |volume=57 |pages=717–745 |year=2003]
* [http://tolweb.org/tree/learn/concepts/whatisphylogeny.html The Tree of Life]
* [http://itol.embl.de Interactive Tree of Life]
* [http://www.ohiou.edu/phylocode/ PhyloCode]
* [http://www.ucmp.berkeley.edu/exhibit/phylogeny.html UCMP Exhibit Halls: Phylogeny Wing]
* [http://www.cladistics.org Willi Hennig Society]
* [http://www.filogenetica.org Filogenetica.org in Spanish]
* [http://www.cmbi.ru.nl/phylopat PhyloPat, Phylogenetic Patterns]
* [http://www.trex.uqam.ca Phylogenetic inferring on the T-REX server]
* [http://mesquiteproject.org/mesquite/mesquite.html Mesquite]
* [http://www.ncbi.nlm.nih.gov/About/primer/phylo.html NCBI - Systematics and Molecular Phylogenetics]
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phylogenetics — filogenetika statusas T sritis augalininkystė apibrėžtis Genetikos skyrius, kurio objektas yra istoriniai įvairių grupių raidos dėsniai, jų filogenezė. atitikmenys: angl. phylogenetics rus. филогенетика … Žemės ūkio augalų selekcijos ir sėklininkystės terminų žodynas
phylogenetics — phy·lo·ge·net·ics (fī lō jə nĕtʹĭks) n. (used with a sing. verb) The study of phylogeny. * * * … Universalium
phylogenetics — noun The systematic study of organism relationships based on evolutionary similarities and differences. See Also: phylogenetic, phylogenesis, phylogeny … Wiktionary
phylogenetics — n. study of the ways in which different species are related (through common genes or ancestors, etc.) … English contemporary dictionary
phylogenetics — phy·lo·genetics … English syllables
phylogenetics — /faɪloʊdʒəˈnɛtɪks/ (say fuylohjuh netiks) noun the systematic study of phylogeny … Australian English dictionary
phylogenetics — |fīlō+ noun plural but singular or plural in construction : a branch of science that deals with phylogeny … Useful english dictionary
Computational phylogenetics — is the application of computational algorithms, methods and programs to phylogenetic analyses. The goal is to assemble a phylogenetic tree representing a hypothesis about the evolutionary ancestry of a set of genes, species, or other taxa. For… … Wikipedia
Maximum parsimony (phylogenetics) — Parsimony is a non parametric statistical method commonly used in computational phylogenetics for estimating phylogenies. Under parsimony, the preferred phylogenetic tree is the tree that requires the least evolutionary change to explain some… … Wikipedia
Molecular phylogenetics — (pronounced /məˈlɛkjʊlər faɪlɵdʒɪˈnɛtɪks/) is the analysis of hereditary molecular differences, mainly in DNA sequences, to gain information on an organism s evolutionary relationships. The result of a molecular phylogenetic analysis is… … Wikipedia