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biology Biology is the scientific study of life. It is a natural science with a broad scope but has several unifying themes that tie it together as a single, coherent field. For instance, all organisms are made up of cells that process hereditary i ...
, phylogenetics (; from
Greek Greek may refer to: Greece Anything of, from, or related to Greece, a country in Southern Europe: *Greeks, an ethnic group. *Greek language, a branch of the Indo-European language family. **Proto-Greek language, the assumed last common ancestor ...
φυλή/ φῦλον [] "tribe, clan, race", and wikt:γενετικός, γενετικός [] "origin, source, birth") is the study of the evolutionary history and relationships among or within groups of organisms. These relationships are determined by Computational phylogenetics, phylogenetic inference methods that focus on observed
heritable Heredity, also called inheritance or biological inheritance, is the passing on of traits from parents to their offspring; either through asexual reproduction or sexual reproduction, the offspring cells or organisms acquire the genetic informa ...
traits, such as DNA sequences,
protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respo ...
amino acid Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although hundreds of amino acids exist in nature, by far the most important are the alpha-amino acids, which comprise proteins. Only 22 alpha am ...
sequences, or
morphology Morphology, from the Greek and meaning "study of shape", may refer to: Disciplines * Morphology (archaeology), study of the shapes or forms of artifacts * Morphology (astronomy), study of the shape of astronomical objects such as nebulae, galaxies ...
. The result of such an analysis is a
phylogenetic tree A phylogenetic tree (also phylogeny or evolutionary tree Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, MA.) is a branching diagram or a tree showing the evolutionary relationships among various biological spec ...
—a diagram containing a hypothesis of relationships that reflects the evolutionary history of a group of organisms. The tips of a phylogenetic tree can be living taxa or fossils, and represent the "end" or the present time in an evolutionary lineage. A phylogenetic diagram can be rooted or unrooted. A rooted tree diagram indicates the hypothetical common ancestor of the tree. An unrooted tree diagram (a network) makes no assumption about the ancestral line, and does not show the origin or "root" of the taxa in question or the direction of inferred evolutionary transformations. In addition to their use for inferring phylogenetic patterns among taxa, phylogenetic analyses are often employed to represent relationships among genes or individual organisms. Such uses have become central to understanding biodiversity, evolution, ecology, and genomes. Phylogenetics is part of
systematics Biological systematics is the study of the diversification of living forms, both past and present, and the relationships among living things through time. Relationships are visualized as evolutionary trees (synonyms: cladograms, phylogenetic tre ...
.
Taxonomy Taxonomy is the practice and science of categorization or classification. A taxonomy (or taxonomical classification) is a scheme of classification, especially a hierarchical classification, in which things are organized into groups or types. ...
is the identification, naming and
classification Classification is a process related to categorization, the process in which ideas and objects are recognized, differentiated and understood. Classification is the grouping of related facts into classes. It may also refer to: Business, organizat ...
of organisms. Classifications are now usually based on phylogenetic data, and many systematists contend that only
monophyletic In cladistics for a group of organisms, monophyly is the condition of being a clade—that is, a group of taxa composed only of a common ancestor (or more precisely an ancestral population) and all of its lineal descendants. Monophyletic gro ...
taxa should be recognized as named groups. The degree to which classification depends on inferred evolutionary history differs depending on the school of taxonomy:
phenetics In biology, phenetics ( el, phainein – to appear) , also known as taximetrics, is an attempt to classify organisms based on overall similarity, usually in morphology or other observable traits, regardless of their phylogeny or evolutionary rel ...
ignores phylogenetic speculation altogether, trying to represent the similarity between organisms instead;
cladistics Cladistics (; ) is an approach to biological classification in which organisms are categorized in groups (" clades") based on hypotheses of most recent common ancestry. The evidence for hypothesized relationships is typically shared derived char ...
(phylogenetic systematics) tries to reflect phylogeny in its classifications by only recognizing groups based on shared, derived characters (
synapomorphies In phylogenetics, an apomorphy (or derived trait) is a novel character or character state that has evolved from its ancestral form (or plesiomorphy). A synapomorphy is an apomorphy shared by two or more taxa and is therefore hypothesized to have ...
);
evolutionary taxonomy Evolutionary taxonomy, evolutionary systematics or Darwinian classification is a branch of biological classification that seeks to classify organisms using a combination of Phylogenetics, phylogenetic relationship (shared descent), progenitor-de ...
tries to take into account both the branching pattern and "degree of difference" to find a compromise between them.


Inference of a phylogenetic tree

Usual methods of
phylogenetic inference Computational phylogenetics is the application of computational algorithms, methods, and programs to phylogenetic
involve computational approaches implementing the optimality criteria and methods of parsimony,
maximum likelihood In statistics, maximum likelihood estimation (MLE) is a method of estimation theory, estimating the Statistical parameter, parameters of an assumed probability distribution, given some observed data. This is achieved by Mathematical optimization, ...
(ML), and MCMC-based
Bayesian inference Bayesian inference is a method of statistical inference in which Bayes' theorem is used to update the probability for a hypothesis as more evidence or information becomes available. Bayesian inference is an important technique in statistics, a ...
. All these depend upon an implicit or explicit
mathematical model A mathematical model is a description of a system using mathematical concepts and language. The process of developing a mathematical model is termed mathematical modeling. Mathematical models are used in the natural sciences (such as physics, ...
describing the evolution of characters observed.
Phenetics In biology, phenetics ( el, phainein – to appear) , also known as taximetrics, is an attempt to classify organisms based on overall similarity, usually in morphology or other observable traits, regardless of their phylogeny or evolutionary rel ...
, popular in the mid-20th century but now largely obsolete, used
distance matrix In mathematics, computer science and especially graph theory, a distance matrix is a square matrix (two-dimensional array) containing the distances, taken pairwise, between the elements of a set. Depending upon the application involved, the ''dist ...
-based methods to construct trees based on overall similarity in
morphology Morphology, from the Greek and meaning "study of shape", may refer to: Disciplines * Morphology (archaeology), study of the shapes or forms of artifacts * Morphology (astronomy), study of the shape of astronomical objects such as nebulae, galaxies ...
or similar observable traits (i.e. in the
phenotype In genetics, the phenotype () is the set of observable characteristics or traits of an organism. The term covers the organism's morphology or physical form and structure, its developmental processes, its biochemical and physiological proper ...
or the overall similarity of DNA, not the
DNA sequence DNA sequencing is the process of determining the nucleic acid sequence – the order of nucleotides in DNA. It includes any method or technology that is used to determine the order of the four bases: adenine, guanine, cytosine, and thymine. Th ...
), which was often assumed to approximate phylogenetic relationships. Prior to 1950, phylogenetic inferences were generally presented as
narrative A narrative, story, or tale is any account of a series of related events or experiences, whether nonfictional (memoir, biography, news report, documentary, travel literature, travelogue, etc.) or fictional (fairy tale, fable, legend, thriller (ge ...
scenarios. Such methods are often ambiguous and lack explicit criteria for evaluating alternative hypotheses.


History

The term "phylogeny" derives from the German , introduced by Haeckel in 1866, and the
Darwinian Darwinism is a theory of biological evolution developed by the English naturalist Charles Darwin (1809–1882) and others, stating that all species of organisms arise and develop through the natural selection of small, inherited variations that ...
approach to classification became known as the "phyletic" approach.


Ernst Haeckel's recapitulation theory

During the late 19th century,
Ernst Haeckel Ernst Heinrich Philipp August Haeckel (; 16 February 1834 – 9 August 1919) was a German zoologist, naturalist, eugenicist, philosopher, physician, professor, marine biologist and artist. He discovered, described and named thousands of new sp ...
's
recapitulation theory The theory of recapitulation, also called the biogenetic law or embryological parallelism—often expressed using Ernst Haeckel's phrase "ontogeny recapitulates phylogeny"—is a historical hypothesis that the development of the embryo of an ani ...
, or "biogenetic fundamental law", was widely accepted. It was often expressed as "
ontogeny Ontogeny (also ontogenesis) is the origination and development of an organism (both physical and psychological, e.g., moral development), usually from the time of fertilization of the egg to adult. The term can also be used to refer to the stu ...
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 In phylogenetics, an apomorphy (or derived trait) is a novel character or character state that has evolved from its ancestral form (or plesiomorphy). A synapomorphy is an apomorphy shared by two or more taxa and is therefore hypothesized to have ...
their embryos share.


Timeline of key points

*14th century, ''lex parsimoniae'' (parsimony principle),
William of Ockam William of Ockham, OFM (; also Occam, from la, Gulielmus Occamus; 1287 – 10 April 1347) was an English Franciscan friar, scholastic philosopher, apologist, and Catholic theologian, who is believed to have been born in Ockham, a small vil ...
, English philosopher, theologian, and Franciscan friar, but the idea actually goes back to
Aristotle Aristotle (; grc-gre, Ἀριστοτέλης ''Aristotélēs'', ; 384–322 BC) was a Greek philosopher and polymath during the Classical period in Ancient Greece. Taught by Plato, he was the founder of the Peripatetic school of phil ...
, precursor concept *1763, Bayesian probability, Rev. Thomas Bayes, 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 Jean-Baptiste Pierre Antoine de Monet, chevalier de Lamarck (1 August 1744 – 18 December 1829), often known simply as Lamarck (; ), was a French naturalist, biologist, academic, and soldier. He was an early proponent of the idea that biolog ...
, 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 Anaximander (; grc-gre, Ἀναξίμανδρος ''Anaximandros''; ) was a pre-Socratic Greek philosopher who lived in Miletus,"Anaximander" in ''Chambers's Encyclopædia''. London: George Newnes, 1961, Vol. 1, p. 403. a city of Ionia (in moder ...
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 Homology may refer to: Sciences Biology *Homology (biology), any characteristic of biological organisms that is derived from a common ancestor * Sequence homology, biological homology between DNA, RNA, or protein sequences *Homologous chrom ...
and
analogy Analogy (from Greek ''analogia'', "proportion", from ''ana-'' "upon, according to" lso "against", "anew"+ ''logos'' "ratio" lso "word, speech, reckoning" is a cognitive process of transferring information or meaning from a particular subject ( ...
(the latter now referred to as
homoplasy Homoplasy, in biology and phylogenetics, is the term used to describe a Phenotypic trait, feature that has been gained or lost independently in separate lineages over the course of evolution. This is different from Homology (biology), homology, w ...
), 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 Ernst Heinrich Philipp August Haeckel (; 16 February 1834 – 9 August 1919) was a German zoologist, naturalist, eugenicist, philosopher, physician, professor, marine biologist and artist. He discovered, described and named thousands of new sp ...
, 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 A clade (), also known as a monophyletic group or natural group, is a group of organisms that are monophyletic – that is, composed of a common ancestor and all its lineal descendants – on a phylogenetic tree. Rather than the English term, ...
" coined by Lucien Cuénot *1949,
Jackknife resampling In statistics, the jackknife (jackknife cross-validation) is a cross-validation technique and, therefore, a form of resampling. It is especially useful for bias and variance estimation. The jackknife pre-dates other common resampling methods suc ...
, 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, first attempt to use ML (maximum likelihood) for phylogenetics, Edwards and Cavalli-Sforza *1965 **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 Edward Osborne Wilson (June 10, 1929 – December 26, 2021) was an American biologist, naturalist, entomologist and writer. According to David Attenborough, Wilson was the world's leading expert in his specialty of myrmecology, the study of an ...
*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 **first successful application of ML to phylogenetics (for protein sequences), Neyman **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 *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, first software package for phylogenetic analysis, Felsenstein *1981 **majority consensus, Margush and MacMorris **strict consensus, Sokal and Rohlf **first computationally efficient ML algorithm, Felsenstein *1982 **PHYSIS, Mikevich and Farris **branch and bound, Hendy and Penny *1985 **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 *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 **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 *2004,2005, symmilarity metric (using an approximation to Kolmogorov complexity) or NCD (normalized compression distance), Li et al., Cilibrasi and Vitanyi.


Outside biology

Phylogenetic tools and representations (trees and networks) can also be applied to studying the evolution of languages, in the field of
quantitative comparative linguistics Quantitative comparative linguistics is the use of quantitative analysis as applied to comparative linguistics. Examples include the statistical fields of lexicostatistics and glottochronology, and the borrowing of phylogenetics from biology. Hi ...
.


See also

*
Angiosperm Phylogeny Group The Angiosperm Phylogeny Group (APG) is an informal international group of systematic botanists who collaborate to establish a consensus on the taxonomy of flowering plants (angiosperms) that reflects new knowledge about plant relationships disco ...
*
Bauplan A body plan, ( ), or ground plan is a set of morphological features common to many members of a phylum of animals. The vertebrates share one body plan, while invertebrates have many. This term, usually applied to animals, envisages a "bluepr ...
*
Bioinformatics Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combi ...
*
Biomathematics Mathematical and theoretical biology, or biomathematics, is a branch of biology which employs theoretical analysis, mathematical models and abstractions of the living organisms to investigate the principles that govern the structure, development a ...
*
Coalescent theory Coalescent theory is a model of how alleles sampled from a population may have originated from a common ancestor. In the simplest case, coalescent theory assumes no recombination, no natural selection, and no gene flow or population structure, m ...
*
EDGE of Existence programme The ''EDGE of Existence programme'' is a research and conservation initiative that focuses on species deemed to be the world’s most "Evolutionarily Distinct and Globally Endangered" (EDGE). Developed by the Zoological Society of London (ZSL), the ...
*
Evolutionary taxonomy Evolutionary taxonomy, evolutionary systematics or Darwinian classification is a branch of biological classification that seeks to classify organisms using a combination of Phylogenetics, phylogenetic relationship (shared descent), progenitor-de ...
*
Language family A language family is a group of languages related through descent from a common ''ancestral language'' or ''parental language'', called the proto-language of that family. The term "family" reflects the tree model of language origination in hist ...
*
Maximum parsimony In phylogenetics, maximum parsimony is an optimality criterion under which the phylogenetic tree that minimizes the total number of character-state changes (or miminizes the cost of differentially weighted character-state changes) is preferred. ...
*
Microbial phylogenetics Microbial phylogenetics is the study of the manner in which various groups of microorganisms are genetically related. This helps to trace their evolution. To study these relationships biologists rely on comparative genomics, as physiology and compa ...
*
Molecular phylogeny Molecular phylogenetics () is the branch of phylogeny that analyzes genetic, hereditary molecular differences, predominantly in DNA sequences, to gain information on an organism's evolutionary relationships. From these analyses, it is possible to ...
*
Noogenesis The noosphere (alternate spelling noösphere) is a philosophical concept developed and popularized by the Russian-Ukrainian Soviet biogeochemist Vladimir Vernadsky, and the French philosopher and Jesuit priest Pierre Teilhard de Chardin. Vernad ...
*
Ontogeny Ontogeny (also ontogenesis) is the origination and development of an organism (both physical and psychological, e.g., moral development), usually from the time of fertilization of the egg to adult. The term can also be used to refer to the stu ...
*
PhyloCode The ''International Code of Phylogenetic Nomenclature'', known as the ''PhyloCode'' for short, is a formal set of rules governing phylogenetic nomenclature. Its current version is specifically designed to regulate the naming of clades, leaving the ...
*
Phylodynamics Viral phylodynamics is defined as the study of how epidemiological, immunological, and evolutionary processes act and potentially interact to shape viral phylogenies. Since the coining of the term in 2004, research on viral phylodynamics has focuse ...
*
Phylogenesis Phylogenesis (from Greek φῦλον ''phylon'' "tribe" + γένεσις ''genesis'' "origin") is the biological process by which a taxon (of any rank) appears. The science that studies these processes is called phylogenetics. These terms may be ...
*
Phylogenetic comparative methods Phylogenetic comparative methods (PCMs) use information on the historical relationships of lineages (phylogenies) to test evolutionary hypotheses. The comparative method has a long history in evolutionary biology; indeed, Charles Darwin used diffe ...
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Phylogenetic network A phylogenetic network is any graph used to visualize evolutionary relationships (either abstractly or explicitly) between nucleotide sequences, genes, chromosomes, genomes, or species. They are employed when reticulation events such as hybridi ...
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Phylogenetic nomenclature Phylogenetic nomenclature is a method of nomenclature for taxa in biology that uses phylogenetic definitions for taxon names as explained below. This contrasts with the traditional approach, in which taxon names are defined by a '' type'', which ...
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Phylogenetic tree viewers This list of phylogenetic tree viewing software is a compilation of software tools and web portals used in visualizing phylogenetic trees. Online software Desktop software 1 "All" refers to Microsoft Windows, Apple OSX and Linux; L=Linux, M=Ap ...
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Phylogenetics software This list of phylogenetics software is a compilation of computational phylogenetics software used to produce phylogenetic trees. Such tools are commonly used in comparative genomics, cladistics, and bioinformatics. Methods for estimating phylogenie ...
*
Phylogenomics Phylogenomics is the intersection of the fields of evolution and genomics. The term has been used in multiple ways to refer to analysis that involves genome data and evolutionary reconstructions. It is a group of techniques within the larger field ...
*
Phylogeny (psychoanalysis) Phylogeny in psychoanalysis is the study of the whole family or species of an organism in order to better understand the pre-history of it. It might have an unconscious influence on a patient, according to Sigmund Freud. After the possibilities of o ...
*
Phylogeography Phylogeography is the study of the historical processes that may be responsible for the past to present geographic distributions of genealogical lineages. This is accomplished by considering the geographic distribution of individuals in light of ge ...
*
Systematics Biological systematics is the study of the diversification of living forms, both past and present, and the relationships among living things through time. Relationships are visualized as evolutionary trees (synonyms: cladograms, phylogenetic tre ...


References


Bibliography

* * * *


External links

* {{Authority control