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phylogenetics
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{{short description|Study of the evolutionary history and relationships among individuals or groups of organisms}}{{Use dmy dates|date=July 2012}}{{Evolutionary biology|expanded=Fields}}In biology, phylogenetics {{IPAc-en|ˌ|f|aɪ|l|oʊ|dʒ|ə|ˈ|n|ɛ|t|ɪ|k|s|,_|-|l|ə|-}}{{refn|{{Dictionary.com|phylogenetic}}}}{{refn|{{MerriamWebsterDictionary|phylogenetic}}}} (Greek: φυλή, φῦλον – phylé, phylon = tribe, clan, race + γενετικός – genetikós = origin, source, birth)BOOK, Liddell, Henry George, Henry George Liddell, Scott, Robert, Robert Scott (philologist), Jones, Henry Stuart, Henry Stuart-Jones, A Greek-English lexicon, 1968, Clarendon Press, Oxford, 9, 1961,weblink is the study of the evolutionary history and relationships among individuals or groups of organisms (e.g. species, or populations). These relationships are discovered through phylogenetic inference methods that evaluate observed heritable traits, such as DNA sequences or morphology under a model of evolution of these traits. The result of these analyses is a phylogeny (also known as a phylogenetic tree) – a diagrammatic hypothesis about the history of the evolutionary relationships of a group of organisms.WEB, phylogeny, Biology online,weblink 2013-02-15, The tips of a phylogenetic tree can be living organisms or fossils, and represent the "end", or the present, in an evolutionary lineage. A phylogenetic tree can be rooted or unrooted. A rooted tree indicates the common ancestor, or ancestral lineage, of the tree. An unrooted tree makes no assumption about the ancestral line, and does not show the origin or "root" of the gene or organism in question.WEB,weblink Phylogenetic Trees, www.cs.tau.ac.il, 2019-04-27, Phylogenetic analyses have become central to understanding biodiversity, evolution, ecology, and genomes.Taxonomy is the identification, naming and classification of organisms. It is usually richly informed by phylogenetics, but remains a methodologically and logically distinct discipline.BOOK, A. W. F. Edwards, Edwards AWF, Luigi Luca Cavalli-Sforza, Cavalli-Sforza LL, Phylogenetics is the branch of life science concerned with the analysis of molecular sequencing data to study evolutionary relationships among groups of organisms., 1964, Reconstruction of evolutionary trees, Vernon Hilton, Heywood, J., McNeill, Phenetic and Phylogenetic Classification, 67–76, 733025912, 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.

Construction of a phylogenetic tree

Usual methods of phylogenetic inference involve computational approaches implementing the optimality criteria and methods of parsimony, maximum likelihood (ML), and MCMC-based Bayesian inference. All these depend upon an implicit or explicit mathematical model describing the evolution of characters observed.Phenetics, popular in the mid-20th century but now largely obsolete, used distance matrix-based methods to construct trees based on overall similarity in morphology or similar observable traits (i.e. in the phenotype or the overall similarity of DNA, not the DNA sequence), which was often assumed to approximate phylogenetic relationships.Prior to 1950, phylogenetic inferences were generally presented as narrative scenarios. Such methods are often ambiguous and lack explicit criteria for evaluating alternative hypotheses.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.{{page needed|date=June 2018}}

History

The term "phylogeny" derives from the German Phylogenie, introduced by Haeckel in 1866,ENCYCLOPEDIA, Harper, Douglas, Online Etymology Dictionary, Phylogeny,weblink 2010, March 18, 2013, and the Darwinian approach to classification became known as the "phyletic" approach.{{sfn|Stuessy|2009}}

Ernst Haeckel's recapitulation theory

During the late 19th century, Ernst Haeckel's recapitulation theory, or "biogenetic fundamental law", was widely accepted. It was often expressed as "ontogeny recapitulates phylogeny", i.e. the development of a single organism during its lifetime, from germ to adult, successively mirrors the adult stages of successive ancestors of the species to which it belongs. But this theory has long been rejected.Blechschmidt, Erich (1977) The Beginnings of Human Life. Springer-Verlag Inc., p. 32: "The so-called basic law of biogenetics is wrong. No buts or ifs can mitigate this fact. It is not even a tiny bit correct or correct in a different form, making it valid in a certain percentage. It is totally wrong."Ehrlich, Paul; Richard Holm; Dennis Parnell (1963) The Process of Evolution. New York: McGraw–Hill, p. 66: "Its shortcomings have been almost universally pointed out by modern authors, but the idea still has a prominent place in biological mythology. The resemblance of early vertebrate embryos is readily explained without resort to mysterious forces compelling each individual to reclimb its phylogenetic tree." Instead, ontogeny evolves â€“ the phylogenetic history of a species cannot be read directly from its ontogeny, as Haeckel thought would be possible, but characters from ontogeny can be (and have been) used as data for phylogenetic analyses; the more closely related two species are, the more apomorphies their embryos share.

Timeline of key events

(File:Bronn tree.gif|right|250px|thumb|Branching tree diagram from Heinrich Georg Bronn's work (1858))(File:Haeckel arbol bn.png|right|250px|thumb|Phylogenetic tree suggested by Haeckel (1866))
  • 14th century, lex parsimoniae (parsimony principle), William of Ockam, English philosopher, theologian, and Franciscan friar, but the idea actually goes back to Aristotle, precursor concept
  • 1763, Bayesian probability, Rev. Thomas Bayes,JOURNAL, 10.1098/rstl.1763.0053, An Essay towards Solving a Problem in the Doctrine of Chances. By the Late Rev. Mr. Bayes, F. R. S. Communicated by Mr. Price, in a Letter to John Canton, A. M. F. R. S, Philosophical Transactions of the Royal Society of London, 53, 370–418, 1763, Bayes, Mr, Price, Mr, precursor concept
  • 18th century, Pierre Simon (Marquis de Laplace), perhaps first to use ML (maximum likelihood), precursor concept
  • 1809, evolutionary theory, Philosophie Zoologique, Jean-Baptiste de Lamarck, precursor concept, foreshadowed in the 17th century and 18th century by Voltaire, Descartes, and Leibniz, with Leibniz even proposing evolutionary changes to account for observed gaps suggesting that many species had become extinct, others transformed, and different species that share common traits may have at one time been a single race,Strickberger, Monroe. 1996. Evolution, 2nd. ed. Jones & Bartlett.{{page needed|date=June 2018}} also foreshadowed by some early Greek philosophers such as Anaximander in the 6th century BC and the atomists of the 5th century BC, who proposed rudimentary theories of evolutionThe Theory of Evolution, Teaching Company course, Lecture 1
  • 1837, Darwin's notebooks show an evolutionary treeDarwin's Tree of Life {{webarchive|url=https://web.archive.org/web/20140313124644weblink |date=13 March 2014 }}
  • 1843, distinction between homology and analogy (the latter now referred to as homoplasy), Richard Owen, precursor concept
  • 1858, Paleontologist Heinrich Georg Bronn (1800–1862) published a hypothetical tree to illustrating the paleontological "arrival" of new, similar species following the extinction of an older species. Bronn did not propose a mechanism responsible for such phenomena, precursor concept.JOURNAL, 10.1007/s10739-008-9163-y, 20027787, Edward Hitchcock's Pre-Darwinian (1840) 'Tree of Life', Journal of the History of Biology, 42, 3, 561–92, 2008, Archibald, J. David, 10.1.1.688.7842,
  • 1858, elaboration of evolutionary theory, Darwin and Wallace,JOURNAL, 10.1111/j.1096-3642.1858.tb02500.x, 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. Zoology, 3, 9, 45–62, 1858, Darwin, Charles, Wallace, Alfred, also in Origin of Species by Darwin the following year, precursor concept
  • 1866, Ernst Haeckel, first publishes his phylogeny-based evolutionary tree, precursor concept
  • 1893, Dollo's Law of Character State Irreversibility,Dollo, Louis. 1893. Les lois de l'évolution. Bull. Soc. Belge Géol. Paléont. Hydrol. 7: 164–66. precursor concept
  • 1912, ML recommended, analyzed, and popularized by Ronald Fisher, precursor concept
  • 1921, Tillyard uses term "phylogenetic" and distinguishes between archaic and specialized characters in his classification systemJOURNAL, 10.4039/Ent5335-2, A New Classification of the Order Perlaria, The Canadian Entomologist, 53, 2, 35–43, 2012, Tillyard, R. J,
  • 1940, term "clade" coined by Lucien Cuénot
  • 1949, Jackknife resampling, Maurice Quenouille (foreshadowed in '46 by Mahalanobis and extended in '58 by Tukey), precursor concept
  • 1950, Willi Hennig's classic formalizationBOOK, Hennig, Willi, 1950, Grundzüge einer Theorie der Phylogenetischen Systematik, Basic features of a theory of phylogenetic systematics, de, Deutscher Zentralverlag, Berlin, 12126814, {{page needed|date=June 2018}}
  • 1952, William Wagner's groundplan divergence methodJOURNAL, Wagner, Warren Herbert, 1952, The fern genus Diellia: structure, affinities, and taxonomy, University of California Publications in Botany, 26, 1–6, 1–212, 4228844,
  • 1953, "cladogenesis" coinedWebster's 9th New Collegiate Dictionary
  • 1960, "cladistic" coined by Cain and HarrisonJOURNAL, 10.1111/j.1469-7998.1960.tb05828.x, Phyletic Weighting, Proceedings of the Zoological Society of London, 135, 1, 1–31, 2009, Cain, A. J, Harrison, G. A,
  • 1963, first attempt to use ML (maximum likelihood) for phylogenetics, Edwards and Cavalli-Sforza"The reconstruction of evolution" in JOURNAL, 10.1111/j.1469-1809.1963.tb00786.x, Abstracts of Papers, Annals of Human Genetics, 27, 1, 103–5, 1963,
  • 1965
    • Camin-Sokal parsimony, first parsimony (optimization) criterion and first computer program/algorithm for cladistic analysis both by Camin and SokalJOURNAL, 10.1111/j.1558-5646.1965.tb01722.x, A Method for Deducing Branching Sequences in Phylogeny, Evolution, 19, 3, 311–26, 1965, Camin, Joseph H, Sokal, Robert R,
    • character compatibility method, also called clique analysis, introduced independently by Camin and Sokal (loc. cit.) and E. O. WilsonJOURNAL, 10.2307/2411550, 2411550, A Consistency Test for Phylogenies Based on Contemporaneous Species, Systematic Zoology, 14, 3, 214–20, 1965, Wilson, Edward O,
  • 1966
    • English translation of HennigHennig. W. (1966). Phylogenetic systematics. Illinois University Press, Urbana.{{page needed|date=June 2018}}
    • "cladistics" and "cladogram" coined (Webster's, loc. cit.)
  • 1969
    • dynamic and successive weighting, James FarrisJOURNAL, 10.2307/2412182, 2412182, A Successive Approximations Approach to Character Weighting, Systematic Zoology, 18, 4, 374–85, 1969, Farris, James S,
    • Wagner parsimony, Kluge and FarrisJOURNAL, 10.1093/sysbio/18.1.1, Quantitative Phyletics and the Evolution of Anurans, Systematic Biology, 18, 1, 1–32, 1969, Kluge, A. G, Farris, J. S,
    • CI (consistency index), Kluge and Farris
    • introduction of pairwise compatibility for clique analysis, Le QuesneJOURNAL, 10.2307/2412604, 2412604, A Method of Selection of Characters in Numerical Taxonomy, Systematic Zoology, 18, 2, 201–205, 1969, Quesne, Walter J. Le,
  • 1970, Wagner parsimony generalized by FarrisJOURNAL, 10.1093/sysbio/19.1.83, Methods for Computing Wagner Trees, Systematic Biology, 19, 83–92, 1970, Farris, J. S,
  • 1971
    • first successful application of ML to phylogenetics (for protein sequences), NeymanNeyman, J. (1971). Molecular studies: A source of novel statistical problems. In: Gupta S. S., Yackel J. (eds), Statistical Decision Theory and Related Topics, pp. 1–27. Academic Press, New York.
    • Fitch parsimony, FitchJOURNAL, 10.1093/sysbio/20.4.406, 2412116, Toward Defining the Course of Evolution: Minimum Change for a Specific Tree Topology, Systematic Biology, 20, 4, 406–16, 1971, Fitch, W. M,
    • NNI (nearest neighbour interchange), first branch-swapping search strategy, developed independently by RobinsonJOURNAL, 10.1016/0095-8956(71)90020-7, Comparison of labeled trees with valency three, Journal of Combinatorial Theory, Series B, 11, 2, 105–19, 1971, Robinson, D.F, and Moore et al.
    • ME (minimum evolution), Kidd and Sgaramella-ZontaJOURNAL, 5089842, 1706731, 1971, Kidd, K. K, Phylogenetic analysis: Concepts and methods, American Journal of Human Genetics, 23, 3, 235–52, Sgaramella-Zonta, L. A, (it is unclear if this is the pairwise distance method or related to ML as Edwards and Cavalli-Sforza call ML "minimum evolution")
  • 1972, Adams consensus, AdamsJOURNAL, 10.1093/sysbio/21.4.390, Consensus Techniques and the Comparison of Taxonomic Trees, Systematic Biology, 21, 4, 390–397, 1972, Adams, E. N,
  • 1976, prefix system for ranks, FarrisJOURNAL, 10.2307/2412495, 2412495, Phylogenetic Classification of Fossils with Recent Species, Systematic Zoology, 25, 3, 271–282, 1976, Farris, James S,
  • 1977, Dollo parsimony, FarrisJOURNAL, 10.1093/sysbio/26.1.77, Phylogenetic Analysis Under Dollo's Law, Systematic Biology, 26, 77–88, 1977, Farris, J. S,
  • 1979
    • Nelson consensus, NelsonJOURNAL, 10.1093/sysbio/28.1.1, Cladistic Analysis and Synthesis: Principles and Definitions, with a Historical Note on Adanson's Familles Des Plantes (1763-1764), Systematic Biology, 28, 1–21, 1979, Nelson, G,
    • MAST (maximum agreement subtree)((GAS)greatest agreement subtree), a consensus method, Gordon JOURNAL, 10.2307/2335236, 2335236, A Measure of the Agreement between Rankings, Biometrika, 66, 1, 7–15, 1979, Gordon, A. D,
    • bootstrap, Bradley Efron, precursor conceptEfron B. (1979). Bootstrap methods: another look at the jackknife. Ann. Stat. 7: 1–26.
  • 1980, PHYLIP, first software package for phylogenetic analysis, Felsenstein
  • 1981
    • majority consensus, Margush and MacMorrisJOURNAL, 10.1016/S0092-8240(81)90019-7, Consensus-trees, Bulletin of Mathematical Biology, 43, 2, 239, 1981, Margush, T, McMorris, F,
    • strict consensus, Sokal and RohlfJOURNAL, 10.2307/2413252, 2413252, Taxonomic Congruence in the Leptopodomorpha Re-Examined, Systematic Zoology, 30, 3, 309, 1981, Sokal, Robert R, Rohlf, F. James,
    • first computationally efficient ML algorithm, FelsensteinJOURNAL, 10.1007/BF01734359, 7288891, Evolutionary trees from DNA sequences: A maximum likelihood approach, Journal of Molecular Evolution, 17, 6, 368–76, 1981, Felsenstein, Joseph,
  • 1982
    • PHYSIS, Mikevich and Farris
    • branch and bound, Hendy and PennyJOURNAL, 10.1016/0025-5564(82)90027-X, Branch and bound algorithms to determine minimal evolutionary trees, Mathematical Biosciences, 59, 2, 277, 1982, Hendy, M.D, Penny, David,
  • 1985
    • first cladistic analysis of eukaryotes based on combined phenotypic and genotypic evidence Diana LipscombLipscomb, Diana. 1985. The Eukaryotic Kingdoms. Cladistics 1: 127–40.
    • first issue of Cladistics
    • first phylogenetic application of bootstrap, FelsensteinFelsenstein J. (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783–791.
    • first phylogenetic application of jackknife, Scott LanyonJOURNAL, 10.1093/sysbio/34.4.397, Detecting Internal Inconsistencies in Distance Data, Systematic Biology, 34, 4, 397–403, 1985, Lanyon, S. M, 10.1.1.1000.3956,
  • 1986, MacClade, Maddison and Maddison
  • 1987, neighbor-joining method Saitou and NeiJOURNAL, 10.1093/oxfordjournals.molbev.a040454, 3447015, The neighbor-joining method: A new method for reconstructing phylogenetic trees, Molecular Biology and Evolution, 4, 4, 406–25, 1987, Saitou, N., Nei, M.,
  • 1988, Hennig86 (version 1.5), Farris
    • Bremer support (decay index), BremerJOURNAL, 10.1111/j.1558-5646.1988.tb02497.x, 28563878, The Limits of Amino Acid Sequence Data in Angiosperm Phylogenetic Reconstruction, Evolution, 42, 4, 795–803, 1988, Bremer, KÃ¥re,
  • 1989
    • RI (retention index), RCI (rescaled consistency index), FarrisJOURNAL, 10.1111/j.1096-0031.1989.tb00573.x, The Retention Index and the Rescaled Consistency Index, Cladistics, 5, 4, 417–419, 1989, Farris, James S,
    • HER (homoplasy excess ratio), ArchieJOURNAL, 10.2307/2992286, 2992286, Homoplasy Excess Ratios: New Indices for Measuring Levels of Homoplasy in Phylogenetic Systematics and a Critique of the Consistency Index, Systematic Zoology, 38, 3, 253–269, 1989, Archie, James W,
  • 1990
    • combinable components (semi-strict) consensus, BremerJOURNAL, 10.1111/j.1096-0031.1990.tb00551.x, Combinable Component Consensus, Cladistics, 6, 4, 369–372, 1990, Bremer, KÃ¥re,
    • SPR (subtree pruning and regrafting), TBR (tree bisection and reconnection), Swofford and OlsenD. L. Swofford and G. J. Olsen. 1990. Phylogeny reconstruction. In D. M. Hillis and G. Moritz (eds.), Molecular Systematics, pages 411–501. Sinauer Associates, Sunderland, Mass.
  • 1991
    • DDI (data decisiveness index), GoloboffJOURNAL, 10.1111/j.1096-0031.1991.tb00035.x, Homoplasy and the Choice Among Cladograms, Cladistics, 7, 3, 215–232, 1991, Goloboff, Pablo A, JOURNAL, 10.1111/j.1096-0031.1991.tb00046.x, Random Data, Homoplasy and Information, Cladistics, 7, 4, 395–406, 1991, Goloboff, Pablo A,
    • first cladistic analysis of eukaryotes based only on phenotypic evidence, Lipscomb
  • 1993, implied weighting GoloboffJOURNAL, 10.1111/j.1096-0031.1993.tb00209.x, Estimating Character Weights During Tree Search, Cladistics, 9, 83–91, 1993, Goloboff, Pablo A,
  • 1994, reduced consensus: RCC (reduced cladistic consensus) for rooted trees, WilkinsonJOURNAL, 10.1093/sysbio/43.3.343, Common Cladistic Information and its Consensus Representation: Reduced Adams and Reduced Cladistic Consensus Trees and Profiles, Systematic Biology, 43, 3, 343–368, 1994, Wilkinson, M,
  • 1995, reduced consensus RPC (reduced partition consensus) for unrooted trees, WilkinsonJOURNAL, 10.2307/2413604, 2413604, More on Reduced Consensus Methods, Systematic Biology, 44, 3, 435–439, 1995, Wilkinson, Mark,
  • 1996, first working methods for BI (Bayesian Inference)independently developed by Li,JOURNAL, 10.1080/01621459.2000.10474227, 2669394, Phylogenetic Tree Construction Using Markov Chain Monte Carlo, Journal of the American Statistical Association, 95, 450, 493, 2000, Li, Shuying, Pearl, Dennis K, Doss, Hani, 10.1.1.40.4461, Mau,JOURNAL, 10.1111/j.0006-341X.1999.00001.x, 11318142, 2533889, Bayesian Phylogenetic Inference via Markov Chain Monte Carlo Methods, Biometrics, 55, 1, 1–12, 1999, Mau, Bob, Newton, Michael A, Larget, Bret, 10.1.1.139.498, and Rannala and YangJOURNAL, 10.1007/BF02338839, 8703097, Probability distribution of molecular evolutionary trees: A new method of phylogenetic inference, Journal of Molecular Evolution, 43, 3, 304–11, 1996, Rannala, Bruce, Yang, Ziheng, and all using MCMC (Markov chain-Monte Carlo)
  • 1998, TNT (Tree Analysis Using New Technology), Goloboff, Farris, and Nixon
  • 1999, Winclada, Nixon
  • 2003, symmetrical resampling, GoloboffJOURNAL, 10.1016/S0748-3007(03)00060-4, Improvements to resampling measures of group support, Cladistics, 19, 4, 324–32, 2003, Goloboff, P,

See also

{{colbegin||colwidth=20em|rules=yes}} {{colend}}

References

{{Reflist}}

Bibliography

  • BOOK, Schuh, Randall T., Brower, Andrew V.Z., 2009, Biological Systematics: principles and applications, Ithaca, Comstock Pub. Associates/Cornell University Press, 2nd, 978-0-8014-4799-0, 312728177,
  • BOOK, Peter Forster (geneticist), Forster, Peter, Colin Renfrew, Baron Renfrew of Kaimsthorn, Renfrew, Colin, Phylogenetic Methods and the Prehistory of Languages, McDonald Institute Press, University of Cambridge, 2006, 978-1-902937-33-5, 69733654,
  • BOOK, Baum, David A., Smith, Stacey D., Tree Thinking: an introduction to phylogenetic biology, Greenwood Village, CO, Roberts and Company, 2013, 978-1-936221-16-5, 767565978,
  • BOOK, Stuessy, Tod F., Plant Taxonomy: The Systematic Evaluation of Comparative Data, Columbia University Press, 978-0-231-14712-5,weblink 6 February 2014, 2009, harv,

External links

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