Phylogenetics

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tree of Life

The phylogeny ( retronymes portmanteau word from gr. Φυλή, φῦλον tribe, phylon , tribe, clan, variety 'and γενετικός genetikós , origin') is a discipline of genetics and bioinformatics , dedicated to the research of lineages busy.

properties

Phylogenetics nowadays uses algorithms to determine the degree of relationship between different species or between individuals of a species from DNA sequences that have previously been determined by DNA sequencing . This allows a phylogenetic tree to be created. Phylogenetics is used, among other things, to generate taxonomies . The algorithms used include parsimony , the maximum likelihood method (ML method) and the MCMC -based Bayesian inference . Before the development of DNA sequencing and computers, phylogenetics was derived from phenotypes using a distance matrix ( phenetics ), but the differentiation criteria were sometimes ambiguous, as phenotypes - even viewed over a short period of time - are influenced and change by many other factors .

history

Tree of Life by Heinrich Bronn

In the 14th century, the Franciscan philosopher Wilhelm von Ockham developed the lex parsimoniae principle of descent . In 1763 Pastor Thomas Bayes ' basic work on Bayesian statistics was published. In the 18th century, Pierre Simon Laplace , Marquis de Laplace, introduced a form of the maximum likelihood approach . In 1837 Charles Darwin published the theory of evolution with a representation of a family tree . A distinction between homology and analogy was first made in 1843 by Richard Owen . The paleontologist Heinrich Georg Bronn first published the extinction and reappearance of species in the family tree in 1858 . In the same year the theory of evolution was expanded. The term phylogeny was coined by Ernst Haeckel in 1866 . In his recapitulation theory he postulated a connection between phylogeny and ontogeny , which is no longer tenable today. In 1893, Dollo's Law of Character State Irreversibility was published.

In 1912, Ronald Fisher used the maximum likelihood . In 1921 the name was phylogenetically coined by Robert John Tillyard during his classification. In 1940, Lucien Cuénot introduced the term clade . From 1946 Prasanta Chandra Mahalanobis , from 1949 Maurice Quenouille and from 1958 John Tukey specified the forerunner concept.

A first summary by Willi Hennig followed in 1950, and the English translation in 1966. In 1952, William Wagner developed the divergence method . In 1953 the term cladogenesis was coined. Arthur Cain and Gordon Harrison used the term cladistic from 1960 onwards . From 1963, AWF Edwards and Cavalli-Sforza used maximum likelihood in linguistics. In 1965 JH Camin and Robert R. Sokal developed the Camin-Sokal parsimony and the first computer program for cladistic analyzes. In the same year, the character compatibility method was developed simultaneously by Edward Osborne Wilson and by Camin and Sokal. In 1966 the terms cladistics and cladogram were coined. In 1969 James Farris developed the dynamic and successive weighting, the Wagner parsimony by Kluge and Farris and the CI ( consistency index ) also appeared. as well as the pairwise compatibility of the clique analysis by W. Le Quesne. In 1970 Farris generalized the Wagner parsimony. In 1971 Walter Fitch published the Fitch parsimony and David F. Robinson published the NNI ( nearest neighbor interchange ), at the same time as Moore u. a. The ME ( minimum evolution ) by Kidd and Sgaramella-Zonta was also published in 1971 . In the following year E. Adams developed the Adams consensus.

The first application of the maximum likelihood for nucleic acid sequences was in 1974 by J. Neyman. Farris published the prefix system for ranks in 1976. A year later he developed the dollo parsimony. In 1979 the Nelson consensus was published by Gareth Nelson, as well as the MAST (maximum agreement subtree) and GAS (greatest agreement subtree) by A. Gordon and the bootstrap by Bradley Efron. In 1980 PHYLIP was published as the first software for phylogenetic analyzes by Joseph Felsenstein . In 1981 the majority consensus by Margush and MacMorris, the strict consensus by Sokal and Rohlf, and the first efficient maximum likelihood algorithm by Felsenstein. The following year, PHYSIS were made by Mikevich and Farris and branch and bound. published by Hendy and Penny. In 1985, based on genotype and phenotype , the first cladistic analysis of eukaryotes by Diana Lipscomb published. In the same year bootstrap was first used for phylogenetic studies of Felsenstein, as was jackknife by Scott Lanyon. In 1987 the neighbor-joining method was published by Saitou and Nei. In the following year, Hennig86 version 1.5 was developed by Farris. In 1989 the RI ( retention index ) and the RCI ( rescaled consistency index ) were published by Farris and the HER ( homoplasy excess ratio ) by Archie. In 1990 the combinable components (semi-strict) consensus by Bremer as well as the SPR ( subtree pruning and regrafting ) and the TBR ( tree bisection and reconnection ) by Swofford and Olsen were published. In 1991 Goloboff's DDI ( data decisiveness index ) followed. In 1993 Goloboff published implied weighting . In 1994 the decay index was published by Bremer. From 1994 the reduced cladistic consensus was developed by Mark Wilkinson. In 1996, the first MCMC-based application of Bayesian inference was developed independently from Li, Mau, and Rannalla and Yang. In 1998 the TNT ( Tree Analysis Using New Technology ) was published by Goloboff, Farris and Nixon. In 2003, Goloboff published symmetrical resampling .

Applications

Evolution of cancer

Since the development of Next Generation Sequencing , the evolution of cancer cells can also be followed at the molecular level. As described in the main article Carcinogenesis , a tumor first arises from a mutation in a cell. Under certain conditions, further mutations accumulate, the cell divides indefinitely and further restricts its DNA repair. A tumor develops that consists of different cell populations, each of which can have different mutations. This tumor heterogeneity is of enormous importance for the treatment of cancer patients. Phylogenetic methods make it possible to determine the genealogy of a tumor. This shows which mutations are present in which subpopulation of the tumor.

linguistics

Cavalli-Sforza first described the similarity of the phylogenetics of genes with the evolution of languages from original languages . The methods of phylogenetics are therefore also used to determine the origins of languages. Among other things, this led to the so-called original home of the Indo-European language family being located in Anatolia. In science, however, this transfer of application of phylogenetics is fundamentally controversial, since the spread of languages ​​does not proceed according to biological-evolutionary patterns, but rather follows its own regularities.

literature

Individual evidence

  1. ^ Charles Semple: Phylogenetics. Oxford University Press, 2003, ISBN 0-19-850942-1 .
  2. ↑ David Penny: inferring Phylogenies.-Joseph Felsenstein. 2003. Sinauer Associates, Sunderland, Massachusetts. In: Systematic Biology . tape 53 , no. 4 , August 1, 2004, ISSN  1063-5157 , p. 669–670 , doi : 10.1080 / 10635150490468530 ( oup.com [accessed March 13, 2020]).
  3. ^ AWF Edwards, LL Cavalli-Sforza : Reconstruction of evolutionary trees (PDF) In: Vernon Hilton Heywood, J. McNeill: Phenetic and Phylogenetic Classification . Systematics Association, 1964, pp. 67-76.
  4. ^ Masatoshi Nei: Molecular Evolution and Phylogenetics. Oxford University Press, 2000, ISBN 0-19-513585-7 , p. 3.
  5. ^ EO Wiley: Phylogenetics. John Wiley & Sons, 2011, ISBN 978-1-118-01787-6 .
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  7. ^ J. David Archibald: Edward Hitchcock's Pre-Darwinian (1840) 'Tree of Life'. In: Journal of the History of Biology. 2009, p. 568.
  8. ^ Charles R. Darwin, AR Wallace: On the tendency of species to form varieties; and on the perpetuation of varieties and species by natural means of selection. Journal of the Proceedings of the Linnean Society of London. In: Zoology. Volume 3, 1858, pp. 45-50.
  9. ^ Douglas Harper: Phylogeny . In: Online Etymology Dictionary.
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  13. ^ Robert J. Tillyard: A new classification of the order Perlaria. In: Canadian Entomologist. Volume 53, 1921, pp. 35-43.
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  45. ^ JW Archie: Homoplasy Excess Ratios: new indices for measuring levels of homoplasy in phylogenetic systematics and a critique of the Consistency Index. In: Syst. Zool. Volume 38, 1989, pp. 253-269.
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