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In
biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactions, Physiology, physiological mechanisms, Development ...

biology
, phylogenetics (from
Greek#REDIRECT Greek Greek may refer to: Greece Anything of, from, or related to Greece Greece ( el, Ελλάδα, , ), officially the Hellenic Republic, is a country located in Southeast Europe. Its population is approximately 10.7 million as of ...
φυλή/ φῦλον () "tribe, clan, race", and γενετικός () "origin, source, birth") is a part of
systematics Biological Biology is the natural science Natural science is a branch of science Science (from the Latin word ''scientia'', meaning "knowledge") is a systematic enterprise that Scientific method, builds and Taxonomy (general), or ...
that addresses the inference of the
evolution Evolution is change in the heritable Heredity, also called inheritance or biological inheritance, is the passing on of Phenotypic trait, traits from parents to their offspring; either through asexual reproduction or sexual reproduction, ...

evolution
ary history and relationships among or within groups of
organism In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactions, Physiology, physiological me ...

organism
s (e.g.
species In biology, a species is the basic unit of biological classification, classification and a taxonomic rank of an organism, as well as a unit of biodiversity. A species is often defined as the largest group of organisms in which any two individu ...

species
, or more inclusive taxa). These relationships are hypothesized by
phylogenetic inference Computational phylogenetics is the application of computational algorithm In and , an algorithm () is a finite sequence of , computer-implementable instructions, typically to solve a class of problems or to perform a computation. Algorithms ...
methods that evaluate observed
heritable Heredity, also called inheritance or biological inheritance, is the passing on of Phenotypic trait, traits from parents to their offspring; either through asexual reproduction or sexual reproduction, the offspring cell (biology), cells or orga ...
traits, such as
DNA Deoxyribonucleic acid (; DNA) is a molecule File:Pentacene on Ni(111) STM.jpg, A scanning tunneling microscopy image of pentacene molecules, which consist of linear chains of five carbon rings. A molecule is an electrically neutral gro ...

DNA
sequences,
protein Proteins are large biomolecule , showing alpha helices, represented by ribbons. This poten was the first to have its suckture solved by X-ray crystallography by Max Perutz and Sir John Cowdery Kendrew in 1958, for which they received a No ...

protein
amino acid Amino acids are organic compound , CH4; is among the simplest organic compounds. In chemistry, organic compounds are generally any chemical compounds that contain carbon-hydrogen chemical bond, bonds. Due to carbon's ability to Catenation, c ...

amino acid
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 ...
, often under a specified model of evolution of these traits. The result of such an analysis is a
phylogeny A phylogenetic tree (also phylogeny or evolutionary tree Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, MA.) is a branching diagram or a tree (graph theory), tree showing the evolutionary relationships among va ...

phylogeny
(also known as a phylogenetic tree)—a diagrammatic 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, in an evolutionary lineage. A phylogenetic diagram can be rooted or unrooted. A rooted tree diagram indicates the hypothetical common ancestor, or ancestral lineage, 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 proper use for inferring phylogenetic patterns among taxa, phylogenetic analyses are often employed to represent relationships among gene copies or individual organisms. Such uses have become central to understanding biodiversity, evolution, ecology, and genomes. In February 2021, scientists reported, for the first time, the
sequencing In genetics Genetics is a branch of biology concerned with the study of genes, genetic variation, and heredity in organisms.Hartl D, Jones E (2005) Though heredity had been observed for millennia, Gregor Mendel, Moravia, Moravian scientist ...

sequencing
of
DNA Deoxyribonucleic acid (; DNA) is a molecule File:Pentacene on Ni(111) STM.jpg, A scanning tunneling microscopy image of pentacene molecules, which consist of linear chains of five carbon rings. A molecule is an electrically neutral gro ...

DNA
from
animal remains
animal remains
, a
mammoth A mammoth is any species In biology, a species is the basic unit of biological classification, classification and a taxonomic rank of an organism, as well as a unit of biodiversity. A species is often defined as the largest group of organ ...

mammoth
in this instance, over a million years old, the oldest DNA sequenced to date.
Taxonomy Taxonomy (general) is the practice and science of classification of things or concepts, including the principles that underlie such classification. The term may also refer to a specific classification scheme. Originally used only about biological ...
is the identification, naming and
classification Classification is a process related to categorization Categorization is the human ability and activity of recognizing shared features or similarities between the elements of the experience of the world (such as Object (philosophy), objects, eve ...
of organisms. Classifications are now usually based on phylogenetic data, and many systematists contend that only
monophyletic 300px, A cladogram of the primates, showing a ''monophyletic'' taxon: ''the simians'' (in yellow); a ''paraphyletic'' taxon: ''the prosimians'' (in cyan, including the red patch); and a ''polyphyletic'' group: ''the night-active primates, i.e., ...

monophyletic
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 Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactions, Physiology, physiological mechanis ...
ignores phylogenetic speculation altogether, trying to represent the similarity between organisms instead;
cladistics Cladistics (; ) is an approach to biological classification In biology, taxonomy () is the scientific study of naming, defining (Circumscription (taxonomy), circumscribing) and classifying groups of biological organisms based on shared ch ...

cladistics
(phylogenetic systematics) tries to reflect phylogeny in its classifications by only recognizing groups based on shared, derived characters (
synapomorphies 279px, trait states. In phylogenetics, apomorphy and synapomorphy refer to derived characters of a clade A clade (; from grc, , ''klados'', "branch"), also known as a monophyletic group or natural group, is a group of organisms that are mon ...
);
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 algorithm In and , an algorithm () is a finite sequence of , computer-implementable instructions, typically to solve a class of problems or to perform a computation. Algorithms ...
involve computational approaches implementing the optimality criteria and methods of parsimony,
maximum likelihood In statistics, maximum likelihood estimation (MLE) is a method of estimating Estimation (or estimating) is the process of finding an estimate, or approximation An approximation is anything that is intentionally similar but not exactly equa ...
(ML), and MCMC-based
Bayesian inference Bayesian inference is a method of in which is used to update the probability for a hypothesis as more or becomes available. Bayesian inference is an important technique in , and especially in . Bayesian updating is particularly important in th ...
. All these depend upon an implicit or explicit
mathematical model A mathematical model is a description of a system A system is a group of Interaction, interacting or interrelated elements that act according to a set of rules to form a unified whole. A system, surrounded and influenced by its environm ...
describing the evolution of characters observed.
Phenetics In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactions, Physiology, physiological mechanis ...
, popular in the mid-20th century but now largely obsolete, used
distance matrix In mathematics Mathematics (from Ancient Greek, Greek: ) includes the study of such topics as quantity (number theory), mathematical structure, structure (algebra), space (geometry), and calculus, change (mathematical analysis, analysis). It h ...
-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 Genetics is a branch of biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular inter ...

phenotype
or the overall similarity of DNA, not the
DNA sequence DNA sequencing is the process of determining the nucleic acid sequence A nucleic acid sequence is a succession of bases signified by a series of a set of five different letters that indicate the order of nucleotides Nucleotides are organic ...

DNA sequence
), 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 nonfiction Nonfiction (also spelled non-fiction) is any document A document is a written Writing is a medium of human communication Comm ...

narrative
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 A theory is a reason, rational type of abstraction, abstract thinking about a phenomenon, or the results of such thinking. The process of contemplative and rational thinking is often associated with such processes as obser ...
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 Zoology ()The pronunciation of zoology as is typically regarded as nonstandard, though it is not uncommon. is the branch of biology that stu ...

Ernst Haeckel
's
recapitulation theory The theory of recapitulation, also called the biogenetic law or embryological parallelism—often expressed using Ernst Haeckel Ernst Heinrich Philipp August Haeckel (; 16 February 1834 – 9 August 1919) was a German zoologist Zoology ()T ...
, 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 ovum, egg to adult. The term can also be used to refer to th ...
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 points

*14th century, ''lex parsimoniae'' (parsimony principle), William of Ockam, 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 A philosopher is someone who practices philosophy Philosophy (from , ) is the study of general and fundamental questio ...

Aristotle
, 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 Natural history is a domain of inquiry involving organisms, including animals, fu ...

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 Anaximander (; grc-gre, Ἀναξίμανδρος ''Anaximandros''; ) was a who lived in ,"Anaximander" in '. London: , 1961, Vol. 1, p. 403. a city of (in modern-day Turkey). He belonged to the and learned the teachings of his master . He s ...

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 Analogy (from Greek#REDIRECT Greek Greek may refer to: Greece Anything of, from, or related to Greece Greece ( el, Ελλάδα, , ), officially the Hellenic Republic, is a country located in Southeast Europe. Its population is approximate ...
(the latter now referred to as
homoplasy Homoplasy, in biology and phylogenetics, is when a Phenotypic trait, trait has been gained or lost independently in separate lineages over the course of evolution. This is different from Homology (biology), homology, which is the similarity of trait ...

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 Ernst Heinrich Philipp August Haeckel (; 16 February 1834 – 9 August 1919) was a German zoologist Zoology ()The pronunciation of zoology as is typically regarded as nonstandard, though it is not uncommon. is the branch of biology that stu ...

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 A clade (), also known as a monophyletic group or natural group, is a group of organisms that are monophyly, monophyletic – that is, composed of a common ancestor and all its lineage (evolution), lineal descendants - on a phylogenetic tree. R ...

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, 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 (born June 10, 1929), usually cited as E. O. Wilson, is an American biologist Francesco Redi, the founder of biology, is recognized to be one of the greatest biologists of all time A biologist is a professional who has ...
*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, or APG, is an informal international group of systematic botanists who collaborate to establish a consensus on the taxonomy of flowering plant The flowering plants, also known as Angiospermae (), or Magnoliophyt ...
*
Bauplan A body plan, ''Bauplan'' (German plural ''Baupläne''), or ground plan is a set of morphological features common to many members of a phylum In biology, a phylum (; plural The plural (sometimes list of glossing abbreviations, abbreviated ) ...

Bauplan
*
Bioinformatics Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biology, biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformat ...

Bioinformatics
*
Biomathematics Mathematical and theoretical biology or, Biomathematics, is a branch of biology which employs theoretical analysis, mathematical models and abstractions of the Organism, living organisms to investigate the principles that govern the structure, deve ...
*
Coalescent theory Coalescent theory is a model of how gene variants 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 structu ...
* EDGE of Existence programme *
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 ...
*
Joe FelsensteinJoseph "Joe" Felsenstein (born May 9, 1942) is a Professor Emeritus in the Departments of Genome Sciences and Biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemist ...
*
Language family A language family is a group of language A language is a structured system of communication Communication (from Latin ''communicare'', meaning "to share" or "to be in relation with") is "an apparent answer to the painful divisions b ...
*
Maximum parsimony In phylogenetics In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactions, Physiology, physiol ...
*
Microbial phylogeneticsMicrobial phylogenetics is the study of the manner in which various groups of microorganism A microorganism, or microbe,, ''mikros'', "small") and ''organism In biology, an organism (from Ancient Greek, Greek: ὀργανισμός, ''o ...
*
Molecular phylogeny Molecular phylogenetics () is the branch of phylogeny A phylogenetic tree (also phylogeny or evolutionary tree Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, MA.) is a branching diagram A diagram is a symb ...
*
Noogenesis Noogenesis is the emergence In philosophy Philosophy (from , ) is the study of general and fundamental questions, such as those about reason, Metaphysics, existence, Epistemology, knowledge, Ethics, values, Philosophy of mind, mind, ...
*
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 ovum, egg to adult. The term can also be used to refer to th ...
*
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 g ...
* Phylodynamics *
Phylogenesis Phylogenesis (from Greek φῦλον ''phylon'' "tribe" + γένεσις ''genesis'' "origin") is the biological process by which a taxon In biology Biology is the natural science that studies life and living organisms, including their a ...
*
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 C ...
*
Phylogenetic network A phylogenetic network is any graph used to visualize evolutionary relationships (either abstractly or explicitly) between nucleotide sequences, gene In biology, a gene (from ''genos'' "...Wilhelm Johannsen coined the word gene to descri ...
*
Phylogenetic nomenclature In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactions, Physiology, physiological mechanism ...
* Phylogenetic tree viewers * Phylogenetics software *
Phylogenomics Phylogenomics is the intersection of the fields of evolution Evolution is change in the Heredity, heritable Phenotypic trait, characteristics of biological populations over successive generations. These characteristics are the Gene expression, ...
* Phylogeny (psychoanalysis) *
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 Biology is the natural science Natural science is a branch of science Science (from the Latin word ''scientia'', meaning "knowledge") is a systematic enterprise that Scientific method, builds and Taxonomy (general), o ...


References


Bibliography

* * * *


External links

* {{Authority control