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
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.
* 1 Construction of a phylogenetic tree
* 2 History
* 2.1 Ernst Haeckel\'s recapitulation theory * 2.2 Timeline of key events
* 3 See also * 4 References * 5 Bibliography * 6 External links
CONSTRUCTION OF A PHYLOGENETIC TREE
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,
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
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.
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. 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's work (1858)
* 14th century, lex parsimoniae_ (parsimony principle), William of
Ockam , English philosopher, theologian, and Franciscan monk, but the
idea actually goes back to
* Camin-Sokal parsimony, first parsimony (optimization) criterion and first 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
* English translation of Hennig * "cladistics" and "cladogram" coined (Webster's, loc. cit.)
* 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
* Fitch parsimony, Fitch * NNI (nearest neighbour interchange), first 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, first successful application of ML to phylogenetics (for nucleotide sequences), Neyman * 1976, prefix system for ranks, Farris * 1977, Dollo parsimony, Farris
* Nelson consensus, Nelson * MAST (maximum agreement subtree)((GAS)greatest agreement subtree), a consensus method, Gordon * bootstrap, Bradley Efron, precursor concept
* 1980, PHYLIP, first software package for phylogenetic analysis, Felsenstein
* majority consensus, Margush and MacMorris * strict consensus, Sokal and Rohlf * first computationally efficient ML algorithm, Felsenstein
* PHYSIS, Mikevich and Farris * branch and bound, Hendy and Penny
* first cladistic analysis of eukaryotes based on combined phenotypic and genotypic evidence Diana Lipscomb * first issue of _Cladistics_ * first phylogenetic application of bootstrap, Felsenstein * first 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
* RI (retention index), RCI (rescaled consistency index), Farris * HER (homoplasy excess ratio), Archie
* combinable components (semi-strict) consensus, Bremer * SPR (subtree pruning and regrafting), TBR (tree bisection and reconnection), Swofford and Olsen
* DDI (data decisiveness index), Goloboff * first 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, first 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
* ^ "phylogenetic". _
Random House .
* ^ "phylogenetic". _
Merriam-Webster Dictionary _.
* ^ Liddell, Henry George ; Scott, Robert ; Jones, Henry Stuart
(1968). _A Greek-English lexicon_ (9 ed.). Oxford: Clarendon Press. p.
* ^ "phylogeny".