Phylogenetics

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"Phylogenesis" redirects here. For the science fiction novel, see Phylogenesis (novel).

Lua error in package.lua at line 80: module 'strict' not found. Phylogenetics /faɪloʊdʒɪˈnɛtɪks/ (Greek: φυλή, φῦλον - phylé, phylon = tribe, clan, race + γενετικός - genetikós = origin, source, birth)[1] – in biology – 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 hypothesis about the history of evolutionary relationships.[2] The tips of a phylogenetic tree can be living organisms or fossils. Phylogenetic analyses have become central to understanding biodiversity, evolution, ecology, and genomes.

Taxonomy is the classification, identification and naming of organisms. It is usually richly informed by phylogenetics, but remains a methodologically and logically distinct discipline.[3] 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

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Main article: Computational phylogenetics

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, 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.

Prior to 1990, phylogenetic inferences were generally presented as narrative scenarios. Such methods are often ambiguous and lack explicit criteria for evaluating alternative hypotheses.[4][5][6]

History

The term "phylogeny" derives from the German Phylogenie, introduced by Haeckel in 1866,[7] and the Darwinian approach to classification became known as the "phyletic" approach.[8]

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 an organism successively mirrors the adult stages of successive ancestors of the species to which it belongs. This theory has long been rejected.[9][10] 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

Branching tree diagram from Heinrich Georg Bronn'swork,(1858)
Phylogenetic tree suggested by Haeckel(1866)
  • 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,[11] precursor concept
  • 18th century, Pierre Simon (Marquis de Laplace), perhaps 1st 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,[12] 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 evolution[13]
  • 1837, Darwin's notebooks show an evolutionary tree[14]
  • 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.[15]
  • 1858, elaboration of evolutionary theory, Darwin and Wallace,[16] 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,[17] 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 system[18]
  • 1940, term "clade" coined by Lucien Cuénot
  • 1949, jackknife, Maurice Quenouille (foreshadowed in '46 by Mahalanobis and extended in '58 by Tukey), precursor concept
  • 1950, Willi Hennig's classic formalization[19]
  • 1952, William Wagner's groundplan divergence method[20]
  • 1953, "cladogenesis" coined[21]
  • 1960, "cladistic" coined by Cain and Harrison[22]
  • 1963, 1st attempt to use ML (maximum likelihood) for phylogenetics, Edwards and Cavalli-Sforza[23]
  • 1965
    • Camin-Sokal parsimony, 1st parsimony (optimization) criterion and 1st computer program/algorithm for cladistic analysis both by Camin and Sokal[24]
    • character compatibility method, also called clique analysis, introduced independently by Camin and Sokal (loc. cit.) and E. O. Wilson[25]
  • 1966
    • English translation of Hennig[26]
    • "cladistics" and "cladogram" coined (Webster's, loc. cit.)
  • 1969
    • dynamic and successive weighting, James Farris[27]
    • Wagner parsimony, Kluge and Farris[28]
    • CI (consistency index), Kluge and Farris[28]
    • introduction of pairwise compatibility for clique analysis, Le Quesne[29]
  • 1970, Wagner parsimony generalized by Farris[30]
  • 1971
    • Fitch parsimony, Fitch[31]
    • NNI (nearest neighbour interchange), 1st branch-swapping search strategy, developed independently by Robinson[32] and Moore et al.
    • ME (minimum evolution), Kidd and Sgaramella-Zonta[33] (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, Adams[34]
  • 1974, 1st successful application of ML to phylogenetics (for nucleotide sequences), Neyman[35]
  • 1976, prefix system for ranks, Farris[36]
  • 1977, Dollo parsimony, Farris[37]
  • 1979
    • Nelson consensus, Nelson[38]
    • MAST (maximum agreement subtree)((GAS)greatest agreement subtree), a consensus method, Gordon [39]
    • bootstrap, Bradley Efron, precursor concept[40]
  • 1980, PHYLIP, 1st software package for phylogenetic analysis, Felsenstein
  • 1981
    • majority consensus, Margush and MacMorris[41]
    • strict consensus, Sokal and Rohlf[42]
    • 1st computationally efficient ML algorithm, Felsenstein[43]
  • 1982
    • PHYSIS, Mikevich and Farris
    • branch and bound, Hendy and Penny[44]
  • 1985
    • 1st cladistic analysis of eukaryotes based on combined phenotypic and genotypic evidence Diana Lipscomb[45]
    • 1st issue of Cladistics
    • 1st phylogenetic application of bootstrap, Felsenstein[46]
    • 1st phylogenetic application of jackknife, Scott Lanyon[47]
  • 1986, MacClade, Maddison and Maddison
  • 1987, neighbor-joining method Saitou and Nei[48]
  • 1988, Hennig86 (version 1.5), Farris
  • 1989
    • RI (retention index), RCI (rescaled consistency index), Farris[49]
    • HER (homoplasy excess ratio), Archie[50]
  • 1990
    • combinable components (semi-strict) consensus, Bremer[51]
    • SPR (subtree pruning and regrafting), TBR (tree bisection and reconnection), Swofford and Olsen[52]
  • 1991
    • DDI (data decisiveness index), Goloboff[53][54]
    • 1st cladistic analysis of eukaryotes based only on phenotypic evidence, Lipscomb
  • 1993, implied weighting Goloboff[55]
  • 1994, Bremer support (decay index), Bremer[56]
  • 1994, reduced consensus: RCC (reduced cladistic consensus) for rooted trees, Wilkinson[57]
  • 1995, reduced consensus RPC (reduced partition consensus) for unrooted trees, Wilkinson[58]
  • 1996, 1st working methods for BI (Bayesian Inference)independently developed by Li,[59] Mau,[60] and Rannalla and Yang[61] 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, Goloboff[62]

See also

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References

  1. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  2. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  3. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  4. ↑ Richard C. Brusca & Gary J. Brusca (2003). Invertebrates (2nd ed.). Sunderland, Massachusetts: Sinauer Associates. ISBN 978-0-87893-097-5.
  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.
  6. ↑ 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.
  7. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  8. ↑ Stuessy 2009.
  9. ↑ 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."
  10. ↑ 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."
  11. ↑ Bayes, T. 1763. An Essay towards solving a Problem in the Doctrine of Chances. Phil. Trans. 53: 370–418.
  12. ↑ Strickberger, Monroe. 1996. Evolution, 2nd. ed. Jones & Bartlett.
  13. ↑ The Theory of Evolution, Teaching Company course, Lecture 1
  14. ↑ Darwin's Tree of Life
  15. ↑ J. David Archibald (2009) 'Edward Hitchcock’s Pre-Darwinian (1840) 'Tree of Life'.', Journal of the History of Biology (2009) page 568.
  16. ↑ 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.
  17. ↑ Dollo, Louis. 1893. Les lois de l'évolution. Bull. Soc. Belge Géol. Paléont. Hydrol. 7: 164-66.
  18. ↑ Tillyard R. J. 1921. A new classification of the order Perlaria. Canadian Entomologist 53: 35-43
  19. ↑ Hennig. W. (1950). Grundzuge einer theorie der phylogenetischen systematik. Deutscher Zentralverlag, Berlin.
  20. ↑ Wagner, W.H. Jr. 1952. The fern genus Diellia: structure, affinities, and taxonomy. Univ. Calif. Publ. Botany 26: 1–212.
  21. ↑ Webster's 9th New Collegiate Dictionary
  22. ↑ Cain, A. J., Harrison, G. A. 1960. "Phyletic weighting". Proceedings of the Zoological Society of London 35: 1–31.
  23. ↑ Edwards, A.W.F, Cavalli-Sforza, L.L. (1963). The reconstruction of evolution. Ann. Hum. Genet. 27: 105–106.
  24. ↑ Camin J.H, Sokal R.R. (1965). A method for deducing branching sequences in phylogeny.Evolution 19: 311–326.
  25. ↑ Wilson, E. O. 1965. A consistency test for phylogenies based on contemporaneous species. Systematic Zoology 14: 214-220.
  26. ↑ Hennig. W. (1966). Phylogenetic systematics. Illinois University Press, Urbana.
  27. ↑ Farris, J.S. 1969. A successive approximations approach to character weighting. Syst. Zool. 18: 374-85.
  28. ↑ 28.0 28.1 Kluge, A.G, Farris, J.S. (1969). Quantitative phyletics and the evolution of anurans. Syst. Zool. 18: 1–32.
  29. ↑ Le Quesne, W. J. 1969. A method of selection of characters in numerical taxonomy. Systematic Zoology 18: 201-205.
  30. ↑ Farris, J.S. (1970). Methods of computing Wagner trees. Syst. Zool. 19: 83–92.
  31. ↑ Fitch, W.M. (1971). Toward defining the course of evolution: minimum change for a specified tree topology. Syst. Zool. 20: 406–416.
  32. ↑ Robinson. D.F. 1971. Comparison of labeled trees with valency three. Journal of Combinatorial Theory 11:105–119.
  33. ↑ Kidd, K.K. and Laura Sgaramella-Zonta (1971). Phylogenetic analysis: concepts and methods. Am. J. Human Genet. 23, 235-252.
  34. ↑ Adams, E. (1972). Consensus techniques and the comparison of taxonomic trees. Syst. Zool. 21: 390–397.
  35. ↑ Neyman, 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.
  36. ↑ Farris, J.S. (1976). Phylogenetic classification of fossils with recent species. Syst. Zool. 25: 271-282.
  37. ↑ Farris, J.S. (1977). Phylogenetic analysis under Dollo’s Law. Syst. Zool. 26: 77–88.
  38. ↑ Nelson, 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.
  39. ↑ Gordon, Aé<.D. 1979. A measure of the agreement between rankings. Biometrika 66: 7-15.
  40. ↑ Efron B. (1979). Bootstrap methods: another look at the jackknife. Ann. Stat. 7: 1–26.
  41. ↑ Margush T, McMorris FR. 1981. Consensus n-trees. Bull. Math .Biol. 43, 239–244.
  42. ↑ Sokal, R. R., F. J. Rohlf. 1981. Taxonomic congruence in the Leptopodomorpha re-examined. Syst. Zool. 30:309-325.
  43. ↑ Felsenstein, J. (1981). Evolutionary trees from DNA sequences: A maximum likelihood approach. J. Mol. Evol. 17: 368–376.
  44. ↑ Hendy MD, Penny D (1982) Branch and bound algorithms to determine minimal evolutionary trees. Math Biosci 59: 277–290.
  45. ↑ Lipscomb, Diana. 1985. The Eukaryotic Kingdoms. Cladistics 1: 127-40.
  46. ↑ Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783–791.
  47. ↑ Lanyon, S.M. (1985). Detecting internal inconsistencies in distance data. Syst. Zool. 34: 397-403.
  48. ↑ Saitou N, Nei M (1987) The Neighbor-joining Method: A New Method for Constructing Phylogenetic Trees. Mol. Biol. Evol. 4:406-425.
  49. ↑ Farris, J.S. (1989). The retention index and rescaled consistency index. Cladistics 5: 417–419.
  50. ↑ Archie, 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.
  51. ↑ Bremer. Kåre. 1990. Combinable Component Consensus. Cladistics 6: 369–372.
  52. ↑ D.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.
  53. ↑ Goloboff, P. A. (1991). Homoplasy and the choice among cladograms. Cladistics 7:215–232.
  54. ↑ Goloboff, P. A. (1991b). Random data, homoplasy and information.Cladistics 7:395–406.
  55. ↑ Goloboff, P. A. 1993. Estimating character weights during tree search. Cladistics 9: 83–91.
  56. ↑ Bremer, K. 1994. Branch support and tree stability.
  57. ↑ Wilkinson, Mark. 1994. Common cladistic information and its consensus representation: reduced Adams and reduced cladistic consensus trees and profiles. Syst. Biol. 43:343-368.
  58. ↑ Wilkinson, Mark. 1995. More on reduced consensus methods. Syst. Biol. 44:436-440.
  59. ↑ Li, S. (1996). Phylogenetic tree construction using Markov Chain Monte Carlo. Ph.D. disseration, Ohio State University, Columbus.
  60. ↑ Mau B (1996) Bayesian phylogenetic inference via Markov chain Monte Carlo Methods. Ph.D. dissertation, University of Wisconsin, Madison (abstract).
  61. ↑ Rannala B, Yang Z. 1996. Probability distribution of molecular evolutionary trees: A new method of phylogenetic inference. J. Mol. Evol. 43: 304–311.
  62. ↑ Goloboff, Pablo; Farris, James; Källersjö, Mari; Oxelman, Bengt; Ramiacuterez, Maria; Szumik, Claudia. 2003. Improvements to resampling measures of group support. Cladistics 19: 324–332.

Bibliography

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External links

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