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Phylogenetics

In biology, phylogenetics }}}} ( Greek: φυλή, φῦλον - phylé, phylon = tribe, clan, race + γενετικός - genetikós = origin, source, birth) 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. The tips of a phylogenetic tree can be living organisms or fossils, and represent the "end," or the present, in an evolutionary lineage. 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. 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 other observable traits (i.e. in the phenotype, not the DNA), which was often assumed to approximate phylogenetic relationships. Prior to 1990, 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. .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.

History

The term "phylogeny" derives from the German Phylogenie, introduced by Haeckel in 1866, and the Darwinian approach to classification became known as the "phyletic" approach.

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 – 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

  • 14th century, lex parsimoniae (parsimony principle), William of Ockam, English philosopher, theologian, and Franciscan monk, but the idea actually goes back to Aristotle, precursor concept
  • 1763, Bayesian probability, Rev. Thomas Bayes,Bayes, T. 1763. An Essay towards solving a Problem in the Doctrine of Chances. Phil. Trans. 53: 370–418. 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. 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 tree Darwin's Tree of Life
  • 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.J. David Archibald (2009) 'Edward Hitchcock’s Pre-Darwinian (1840) 'Tree of Life'.', Journal of the History of Biology (2009) page 568.
  • 1858, elaboration of evolutionary theory, Darwin and Wallace,Darwin, C. R. and A. R. Wallace. 1858. 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: 45-50. 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 systemTillyard R. J. 1921. A new classification of the order Perlaria. Canadian Entomologist 53: 35-43
  • 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 formalizationHennig. W. (1950). Grundzuge einer theorie der phylogenetischen systematik. Deutscher Zentralverlag, Berlin.
  • 1952, William Wagner's groundplan divergence methodWagner, W.H. Jr. 1952. The fern genus Diellia: structure, affinities, and taxonomy. Univ. Calif. Publ. Botany 26: 1–212.
  • 1953, "cladogenesis" coinedWebster's 9th New Collegiate Dictionary
  • 1960, "cladistic" coined by Cain and HarrisonCain, A. J., Harrison, G. A. 1960. "Phyletic weighting". Proceedings of the Zoological Society of London 35: 1–31.
  • 1963, first attempt to use ML (maximum likelihood) for phylogenetics, Edwards and Cavalli-SforzaEdwards, A.W.F, Cavalli-Sforza, L.L. (1963). The reconstruction of evolution. Ann. Hum. Genet. 27: 105–106.
  • 1965
  • *Camin-Sokal parsimony, first parsimony (optimization) criterion and first computer program/algorithm for cladistic analysis both by Camin and SokalCamin J.H, Sokal R.R. (1965). A method for deducing branching sequences in phylogeny.Evolution 19: 311–326.
  • *character compatibility method, also called clique analysis, introduced independently by Camin and Sokal (loc. cit.) and E. O. WilsonWilson, E. O. 1965. A consistency test for phylogenies based on contemporaneous species. Systematic Zoology 14: 214-220.
  • 1966
  • *English translation of HennigHennig. W. (1966). Phylogenetic systematics. Illinois University Press, Urbana.
  • *"cladistics" and "cladogram" coined (Webster's, loc. cit.)
  • 1969
  • *dynamic and successive weighting, James FarrisFarris, J.S. 1969. A successive approximations approach to character weighting. Syst. Zool. 18: 374-85.
  • *Wagner parsimony, Kluge and FarrisKluge, A.G, Farris, J.S. (1969). Quantitative phyletics and the evolution of anurans. Syst. Zool. 18: 1–32.
  • *CI (consistency index), Kluge and Farris
  • *introduction of pairwise compatibility for clique analysis, Le QuesneLe Quesne, W. J. 1969. A method of selection of characters in numerical taxonomy. Systematic Zoology 18: 201-205.
  • 1970, Wagner parsimony generalized by FarrisFarris, J.S. (1970). Methods of computing Wagner trees. Syst. Zool. 19: 83–92.
  • 1971
  • *Fitch parsimony, FitchFitch, W.M. (1971). Toward defining the course of evolution: minimum change for a specified tree topology. Syst. Zool. 20: 406–416.
  • *NNI (nearest neighbour interchange), first branch-swapping search strategy, developed independently by RobinsonRobinson. D.F. 1971. Comparison of labeled trees with valency three. Journal of Combinatorial Theory 11:105–119. and Moore et al.
  • *ME (minimum evolution), Kidd and Sgaramella-ZontaKidd, K.K. and Laura Sgaramella-Zonta (1971). Phylogenetic analysis: concepts and methods. Am. J. Human Genet. 23, 235-252. (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, AdamsAdams, E. (1972). Consensus techniques and the comparison of taxonomic trees. Syst. Zool. 21: 390–397.
  • 1974, first successful application of ML to phylogenetics (for nucleotide sequences), NeymanNeyman, J. (1974). Molecular studies: A source of novel statistical problems. In: Gupta SS, Yackel J. (eds), Statistical Decision Theory and Related Topics, pp. 1–27. Academic Press, New York.
  • 1976, prefix system for ranks, FarrisFarris, J.S. (1976). Phylogenetic classification of fossils with recent species. Syst. Zool. 25: 271-282.
  • 1977, Dollo parsimony, FarrisFarris, J.S. (1977). Phylogenetic analysis under Dollo’s Law. Syst. Zool. 26: 77–88.
  • 1979
  • *Nelson consensus, NelsonNelson, G.J. 1979. Cladsitic analysis and synthesis: pronciples and definitions with a historical noteon Adanson's Famille des plantes
(1763-1764). Syst. Zool. 28: 1-21.
  • *MAST (maximum agreement subtree)((GAS)greatest agreement subtree), a consensus method, Gordon Gordon, Aé
  • *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 MacMorrisMargush T, McMorris FR. 1981. Consensus n-trees. Bull. Math .Biol. 43, 239–244.
  • *strict consensus, Sokal and RohlfSokal, R. R., F. J. Rohlf. 1981. Taxonomic congruence in the Leptopodomorpha re-examined. Syst. Zool. 30:309-325.
  • *first computationally efficient ML algorithm, FelsensteinFelsenstein, J. (1981). Evolutionary trees from DNA sequences: A maximum likelihood approach. J. Mol. Evol. 17: 368–376.
  • 1982
  • *PHYSIS, Mikevich and Farris
  • *branch and bound, Hendy and PennyHendy MD, Penny D (1982) Branch and bound algorithms to determine minimal evolutionary trees. Math Biosci 59: 277–290.
  • 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 LanyonLanyon, S.M. (1985). Detecting internal inconsistencies in distance data. Syst. Zool. 34: 397-403.
  • 1986, MacClade, Maddison and Maddison
  • 1987, neighbor-joining method Saitou and NeiSaitou N, Nei M (1987) The Neighbor-joining Method: A New Method for Constructing Phylogenetic Trees. Mol. Biol. Evol. 4:406-425.
  • 1988, Hennig86 (version 1.5), Farris
  • *Bremer support (decay index), Bremer Bremer, K., 1988. The limits of amino acid sequence data in angiosperm phylogenetic reconstruction. Evolution 42, 795–803
  • 1989
  • *RI (retention index), RCI (rescaled consistency index), FarrisFarris, J.S.
(1989). The retention index and rescaled consistency index. Cladistics 5: 417–419.
  • *HER (homoplasy excess ratio), ArchieArchie, J.W. 1989. Homoplasy Excess Ratios: new indices for measuring levels of homoplasy in phylogenetic systematics and a critique of the Consistency Index. Syst. Zool. 38: 253-69.
  • 1990
  • *combinable components (semi-strict) consensus, BremerBremer. Kåre. 1990. Combinable Component Consensus. Cladistics 6: 369–372.
  • *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 andG. Moritz, editors, Molecular Systematics, pages 411–501. Sinauer Associates,
Sunderland, Mass.
  • 1991
  • *DDI (data decisiveness index), GoloboffGoloboff, P. A. (1991). Homoplasy and the choice among cladograms. Cladistics 7:215–232.Goloboff, P. A. (1991b). Random data, homoplasy and information.Cladistics 7:395–406.
  • *first cladistic analysis of eukaryotes based only on phenotypic evidence, Lipscomb
  • 1993, implied weighting GoloboffGoloboff, P. A. 1993. Estimating character weights during tree search. Cladistics 9: 83–91.
  • 1994, reduced consensus: RCC (reduced cladistic consensus) for rooted trees, WilkinsonWilkinson, Mark. 1994. Common cladistic information and its consensus representation: reduced Adams and reduced cladistic consensus trees and profiles. Syst. Biol. 43:343-368.
  • 1995, reduced consensus RPC (reduced partition consensus) for unrooted trees, WilkinsonWilkinson, Mark. 1995. More on reduced consensus methods. Syst. Biol. 44:436-440.
  • 1996, first working methods for BI (Bayesian Inference)independently developed by Li,Li, S. (1996). Phylogenetic tree construction using Markov Chain Monte Carlo. Ph.D. disseration, Ohio State University, Columbus. Mau,Mau B (1996) Bayesian phylogenetic inference via Markov chain Monte Carlo Methods. Ph.D. dissertation, University of Wisconsin, Madison (abstract). and Rannala and YangRannala B, Yang Z. 1996. Probability distribution of molecular evolutionary trees: A new method of phylogenetic inference. J. Mol. Evol. 43: 304–311. 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, GoloboffGoloboff, Pablo; Farris, James; Källersjö, Mari; Oxelman, Bengt; Ramiacuterez, Maria; Szumik, Claudia. 2003. Improvements to resampling measures of group support. Cladistics 19: 324–332.

See also

References

Bibliography

External links

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This article based upon the http://en.wikipedia.org/wiki/Phylogenetics, the free encyclopaedia Wikipedia and is licensed under the GNU Free Documentation License.
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