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.
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.
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.
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.
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
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 formalization
1952, William Wagner's groundplan divergence method
1953, "cladogenesis" coined
1960, "cladistic" coined by Cain and Harrison
1963, 1st attempt to use ML (maximum likelihood) for phylogenetics, Edwards and Cavalli-Sforza
1965
Camin-Sokal parsimony, 1st parsimony (optimization) criterion and 1st computer program/algorithm for cladistic analysis both by Camin and Sokal
character compatibility method, also called clique analysis, introduced independently by Camin and Sokal (loc. cit.) and E. O. Wilson
1966
English translation of Hennig
"cladistics" and "cladogram" coined (Webster's, loc. cit.)
1969
dynamic and successive weighting, James Farris
Wagner parsimony, Kluge and Farris
CI (consistency index), Kluge and Farris
introduction of pairwise compatibility for clique analysis, Le Quesne
1970, Wagner parsimony generalized by Farris
1971
Fitch parsimony, Fitch
NNI (nearest neighbour interchange), 1st branch-swapping search strategy, developed independently by Robinson and Moore et al.
ME (minimum evolution), Kidd and Sgaramella-Zonta (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
1974, 1st successful application of ML to phylogenetics (for nucleotide sequences), Neyman
1976, prefix system for ranks, Farris
1977, Dollo parsimony, Farris
1979
Nelson consensus, Nelson
MAST (maximum agreement subtree)((GAS)greatest agreement subtree), a consensus method, Gordon
bootstrap, Bradley Efron, precursor concept
1980, PHYLIP, 1st software package for phylogenetic analysis, Felsenstein
1981
majority consensus, Margush and MacMorris
strict consensus, Sokal and Rohlf
1st computationally efficient ML algorithm, Felsenstein
1982
PHYSIS, Mikevich and Farris
branch and bound, Hendy and Penny
1985
1st cladistic analysis of eukaryotes based on combined phenotypic and genotypic evidence Diana Lipscomb
1st issue of Cladistics
1st phylogenetic application of bootstrap, Felsenstein
1st phylogenetic application of jackknife, Scott Lanyon
1986, MacClade, Maddison and Maddison
1987, neighbor-joining method Saitou and Nei
1988, Hennig86 (version 1.5), Farris
Bremer support (decay index), Bremer
1989
RI (retention index), RCI (rescaled consistency index), Farris
HER (homoplasy excess ratio), Archie
1990
combinable components (semi-strict) consensus, Bremer
SPR (subtree pruning and regrafting), TBR (tree bisection and reconnection), Swofford and Olsen
1991
DDI (data decisiveness index), Goloboff
1st cladistic analysis of eukaryotes based only on phenotypic evidence, Lipscomb
1993, implied weighting Goloboff
1994, reduced consensus: RCC (reduced cladistic consensus) for rooted trees, Wilkinson
1995, reduced consensus RPC (reduced partition consensus) for unrooted trees, Wilkinson
1996, 1st working methods for BI (Bayesian Inference)independently developed by Li, Mau, and Rannala and Yang 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
