In biology, phylogenetics/ˌfaɪloʊdʒəˈnɛtɪks, -lə-/ (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 classification, identification and naming 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.
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.
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. 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.
Branching tree diagram from Heinrich Georg Bronn's work (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, 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, 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
1837, Darwin's notebooks show an evolutionary tree
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.
1858, elaboration of evolutionary theory, Darwin and Wallace, 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, 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
^Edwards AWF; Cavalli-Sforza LL (1964). "Reconstruction of evolutionary trees". In Heywood, Vernon Hilton; McNeill, J. Phenetic and Phylogenetic Classification. pp. 67–76. OCLC733025912. Phylogenetics is the branch of life science concerned with the analysis of molecular sequencing data to study evolutionary relationships among groups of organisms.
^Richard C. Brusca & Gary J. Brusca (2003). Invertebrates (2nd ed.). Sunderland, Massachusetts: Sinauer Associates. ISBN978-0-87893-097-5.
^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.
^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."
^Bayes, T. 1763. An Essay towards solving a Problem in the Doctrine of Chances. Phil. Trans. 53: 370–418.
^Strickberger, Monroe. 1996. Evolution, 2nd. ed. Jones & Bartlett.
^The Theory of Evolution, Teaching Company course, Lecture 1
^J. David Archibald (2009) 'Edward Hitchcock’s Pre-Darwinian (1840) 'Tree of Life'.', Journal of the History of Biology (2009) page 568.
^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.
^Dollo, Louis. 1893. Les lois de l'évolution. Bull. Soc. Belge Géol. Paléont. Hydrol. 7: 164-66.
^Tillyard R. J. 1921. A new classification of the order Perlaria. Canadian Entomologist 53: 35-43
^Hennig. W. (1950). Grundzuge einer theorie der phylogenetischen systematik. Deutscher Zentralverlag, Berlin.
^Wagner, W.H. Jr. 1952. The fern genus Diellia: structure, affinities, and taxonomy. Univ. Calif. Publ. Botany 26: 1–212.
Lents, N. H.; Cifuentes, O. E.; Carpi, A. (2010). "Teaching the Process of Molecular Phylogeny and Systematics: A Multi-Part Inquiry-Based Exercise". Cell Biology Education. 9 (4): 513. doi:10.1187/cbe.09-10-0076.
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