Editing Phylogenetics (section)

== History ==

=== Overview ===
The term "phylogeny" derives from the German {{lang|de|Phylogenie}}, introduced by Haeckel in 1866,<ref>{{cite encyclopedia |last=Harper |first=Douglas |encyclopedia=[[Online Etymology Dictionary]] |title=Phylogeny |url=http://www.etymonline.com/index.php?allowed_in_frame=0&search=Phylogeny&searchmode=term |year=2010}}</ref> and the [[Darwinian]] approach to classification became known as the "phyletic" approach.{{sfn|Stuessy|2009}} It can be traced back to [[Aristotle]], who wrote in his ''[[Posterior Analytics]]'', "We may assume the superiority ceteris paribus [other things being equal] of the demonstration which derives from fewer postulates or hypotheses."

=== Ernst Haeckel's recapitulation theory ===

The modern concept of phylogenetics evolved primarily as a disproof of a previously widely accepted theory. During the late 19th century, [[Ernst Haeckel]]'s [[recapitulation theory]], or "biogenetic fundamental law", was widely popular.<ref>{{cite web| title=Early Evolution and Development: Ernst Haeckel| publisher=UC Museum of Paleontology| url=https://evolution.berkeley.edu/the-history-of-evolutionary-thought/1800s/early-evolution-and-development-ernst-haeckel/}}</ref> 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.<ref>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."</ref><ref>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."</ref> Instead, [[Evolutionary developmental biology|ontogeny evolves]]&nbsp;– 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 [[Cladistics#apomorphy|apomorphies]] their embryos share.

=== Timeline of key points ===
[[File:Bronn tree.gif|right|250px|thumb|Branching tree diagram from Heinrich Georg Bronn's work (1858)]]
[[File:Haeckel arbol bn.png|right|250px|thumb|Phylogenetic tree suggested by Haeckel (1866)]]
* 14th century, ''lex parsimoniae'' ([[Maximum parsimony (phylogenetics)|parsimony principle]]), [[William of Ockam]], English philosopher, theologian, and Franciscan friar, but the idea actually goes back to [[Aristotle]], as a precursor concept. He introduced the concept of [[Occam's razor]], which is the problem solving principle that recommends searching for explanations constructed with the smallest possible set of elements. Though he did not use these exact words, the principle can be summarized as "Entities must not be multiplied beyond necessity." The principle advocates that when presented with competing hypotheses about the same prediction, one should prefer the one that requires fewest assumptions.
* 1763, [[Bayesian probability]], Rev. Thomas Bayes,<ref>{{cite journal |doi=10.1098/rstl.1763.0053 |title=An Essay towards Solving a Problem in the Doctrine of Chances. By the Late Rev. Mr. Bayes, F. R. S. Communicated by Mr. Price, in a Letter to John Canton, A. M. F. R. S |journal=Philosophical Transactions of the Royal Society of London |volume=53 |pages=370–418 |year=1763 |last1=Bayes |first1=Mr |last2=Price |first2=Mr |doi-access=free }}</ref> a precursor concept. Bayesian probability began a resurgence in the 1950s, allowing scientists in the computing field to pair traditional Bayesian statistics with other more modern techniques. It is now used as a blanket term for several related interpretations of probability as an amount of epistemic confidence.
* 18th century, Pierre Simon (Marquis de Laplace), perhaps first to use ML (maximum likelihood), precursor concept. His work gave way to the [[Laplace distribution]], which can be directly linked to [[least absolute deviations]].
* 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,<ref>Strickberger, Monroe. 1996. Evolution, 2nd. ed. Jones & Bartlett.{{page needed|date=June 2018}}</ref> 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<ref>The Theory of Evolution, Teaching Company course, Lecture 1</ref>
* 1837, Darwin's notebooks show an evolutionary tree<ref>[http://www.nhm.ac.uk/nature-online/evolution/tree-of-life/darwin-tree/ Darwin's Tree of Life] {{webarchive|url=https://web.archive.org/web/20140313124644/http://www.nhm.ac.uk/nature-online/evolution/tree-of-life/darwin-tree/ |date=13 March 2014 }}</ref>
* 1840, American Geologist Edward Hitchcock published what is considered to be the first paleontological "Tree of Life". Many critiques, modifications, and explanations would follow.<ref>{{Cite journal |last=Archibald |first=J. David |date=2009-08-01 |title=Edward Hitchcock's Pre-Darwinian (1840) "Tree of Life" |url=https://doi.org/10.1007/s10739-008-9163-y |journal=Journal of the History of Biology |language=en |volume=42 |issue=3 |pages=561–592 |doi=10.1007/s10739-008-9163-y |pmid=20027787 |s2cid=16634677 |issn=1573-0387}}</ref>[[File:Edward Hitchcock Paleontological Chart.jpg|thumb|This chart displays one of the first published attempts at a paleontological "Tree of Life" by Geologist Edward Hitchcock. (1840)]]
* 1843, distinction between [[Homology (biology)|homology]] and [[Analogy (biology)|analogy]] (the latter now referred to as [[homoplasy]]), Richard Owen, precursor concept. Homology is the term used to characterize the similarity of features that can be parsimoniously explained by common ancestry. Homoplasy is the term used to describe a feature that has been gained or lost independently in separate lineages over the course of evolution.
* 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.<ref>{{cite journal |doi=10.1007/s10739-008-9163-y |pmid=20027787 |title=Edward Hitchcock's Pre-Darwinian (1840) 'Tree of Life' |journal=Journal of the History of Biology |volume=42 |issue=3 |pages=561–92 |year=2008 |last1=Archibald |first1=J. David |citeseerx=10.1.1.688.7842 |s2cid=16634677 }}</ref>
* 1858, elaboration of evolutionary theory, Darwin and Wallace,<ref>{{cite journal |doi=10.1111/j.1096-3642.1858.tb02500.x |title=On the Tendency of Species to form Varieties; and on the Perpetuation of Varieties and Species by Natural Means of Selection |journal=Journal of the Proceedings of the Linnean Society of London. Zoology |volume=3 |issue=9 |pages=45–62 |year=1858 |last1=Darwin |first1=Charles |last2=Wallace |first2=Alfred |doi-access=free }}</ref> also in Origin of Species by Darwin the following year, precursor concept.
* 1866, [[Ernst Haeckel]], first publishes his phylogeny-based evolutionary tree, precursor concept. Haeckel introduces the now-disproved recapitulation theory. He introduced the term "Cladus" as a taxonomic category just below subphylum.<ref>{{Cite journal |last=Cavalier-Smith |first=Thomas |date=2010-01-12 |title=Deep phylogeny, ancestral groups and the four ages of life |journal=Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences |volume=365 |issue=1537 |pages=111–132 |doi=10.1098/rstb.2009.0161 |issn=1471-2970 |pmc=2842702 |pmid=20008390}}</ref>
* 1893, [[Dollo's law of irreversibility|Dollo's Law of Character State Irreversibility]],<ref>Dollo, Louis. 1893. Les lois de l'évolution. Bull. Soc. Belge Géol. Paléont. Hydrol. 7: 164–66.</ref> precursor concept. Dollo's Law of Irreversibility states that "an organism never comes back exactly to its previous state due to the indestructible nature of the past, it always retains some trace of the transitional stages through which it has passed."<ref>{{Cite journal |url=https://academic.oup.com/evolut/article/64/8/2466/6854198 |access-date=2023-04-23 |journal=Evolution |doi=10.1111/j.1558-5646.2010.01041.x |title=Dollo's Law and the Irreversibility of Digit Loss in Bachia |year=2010 |last1=Galis |first1=Frietson |last2=Arntzen |first2=Jan W. |last3=Lande |first3=Russell |volume=64 |issue=8 |pages=2466–76; discussion 2477–85 |pmid=20500218 |s2cid=24520027 }}</ref>
* 1912, ML (maximum likelihood recommended, analyzed, and popularized by [[Ronald Fisher]], precursor concept. Fisher is one of the main contributors to the early 20th-century revival of Darwinism, and has been called the "greatest of Darwin's successors" for his contributions to the revision of the theory of evolution and his use of mathematics to combine [[Mendelian inheritance|Mendelian genetics]] and [[natural selection]] in the [[Modern synthesis (20th century)|20th century "modern synthesis"]].
* 1921, Tillyard uses term "phylogenetic" and distinguishes between archaic and specialized characters in his classification system.<ref>{{cite journal |doi=10.4039/Ent5335-2 |title=A New Classification of the Order Perlaria |journal=The Canadian Entomologist |volume=53 |issue=2 |pages=35–43 |year=2012 |last1=Tillyard |first1=R. J |s2cid=90171163 }}</ref>
* 1940, Lucien Cuénot coined the term "[[clade]]" in 1940: "''terme nouveau de clade'' (''du grec κλάδοςç, branche'') [A new term clade (from the Greek word ''klado''s, meaning branch)]".<ref>{{Cite book |last=Cuénot |first=Lucien |url=https://archive.org/stream/ComptesRendusAcademieDesSciences0210/ComptesRendusAcadmieDesSciences-Tome210-Janvier-juin1940_djvu.txt |title=Comptes rendus Academie des sciences 0210 |date=1940 |publisher=Académie des sciences (France) |location=Paris (France) |page=24 |language=French |chapter=Remarques sur un essai d'arbre genealogique du regne animal}}</ref> He used it for evolutionary branching.<ref name="Tassy-2021">{{Cite journal |last1=Tassy |first1=P. |last2=Fischer |first2=M. S. |date=2021 |title="Cladus" and clade: a taxonomic odyssey |journal=Theory in Biosciences |language=en |volume=140 |issue=1 |pages=77–85 |doi=10.1007/s12064-020-00326-2 |pmid=33095417 |issn=1431-7613|pmc=7583691 }}</ref>
* 1947, [[Bernhard Rensch]] introduced the term ''Kladogenesis'' in his German book ''Neuere Probleme der Abstammungslehre Die transspezifische Evolution,''<ref>{{Cite journal |last=Waddington |first=C. H. |date=1948 |title=Neuere Probleme der Abstammungslehre Die Transspezifische Evolution |url=https://www.nature.com/articles/162979a0 |journal=Nature |language=en |volume=162 |issue=4130 |pages=979–980 |doi=10.1038/162979a0 |bibcode=1948Natur.162..979W |issn=1476-4687}}</ref> translated into English in 1959 as ''Evolution Above the Species Level'' (still using the same spelling)''.''<ref>{{Cite journal |last=Elton |first=C. S. |date=1960 |title=Evolutionary Divergence |url=https://www.nature.com/articles/187446a0 |journal=Nature |language=en |volume=187 |issue=4736 |pages=446 |doi=10.1038/187446a0 |bibcode=1960Natur.187..446E |issn=1476-4687}}</ref>
* 1949, [[Jackknife resampling]], Maurice Quenouille (foreshadowed in '46 by Mahalanobis and extended in '58 by Tukey), precursor concept.
* 1950, [[Willi Hennig|Willi Hennig's]] classic formalization.<ref>{{cite book |last1=Hennig |first1=Willi |year=1950 |title=Grundzüge einer Theorie der Phylogenetischen Systematik |trans-title=Basic features of a theory of phylogenetic systematics |language=de |publisher=Deutscher Zentralverlag |location=Berlin |oclc=12126814 }}{{page needed|date=June 2018}}</ref> Hennig is considered the founder of phylogenetic systematics, and published his first works in German of this year. He also asserted a version of the parsimony principle, stating that the presence of amorphous characters in different species 'is always reason for suspecting kinship, and that their origin by convergence should not be presumed a priori'. This has been considered a foundational view of [[Computational phylogenetics|phylogenetic inference]].
* 1952, William Wagner's ground plan divergence method.<ref>{{cite journal |last1=Wagner |first1=Warren Herbert |year=1952 |title=The fern genus Diellia: structure, affinities, and taxonomy |journal=University of California Publications in Botany |volume=26 |issue=1–6 |pages=1–212 |oclc=4228844 }}</ref>
* 1957, [[Julian Huxley]] adopted Rensch's terminology as "cladogenesis" with a full definition: "''Cladogenesis'' I have taken over directly from Rensch, to denote all splitting, from subspeciation through adaptive radiation to the divergence of phyla and kingdoms." With it he introduced the word "clades", defining it as: "Cladogenesis results in the formation of delimitable monophyletic units, which may be called clades."<ref>{{Cite journal |last=Huxley |first=Julian |date=1957 |title=The Three Types of Evolutionary Process |url=https://www.nature.com/articles/180454a0 |journal=Nature |language=en |volume=180 |issue=4584 |pages=454–455 |doi=10.1038/180454a0 |bibcode=1957Natur.180..454H |issn=1476-4687}}</ref><ref name="Tassy-2021" />
* 1960, [[Arthur Cain]] and [[Geoffrey Ainsworth Harrison]] coined "cladistic" to mean evolutionary relationship,<ref>{{cite journal |doi=10.1111/j.1469-7998.1960.tb05828.x |title=Phyletic Weighting |journal=Proceedings of the Zoological Society of London |volume=135 |issue=1 |pages=1–31 |year=2009 |last1=Cain |first1=A. J |last2=Harrison |first2=G. A }}</ref>
* 1963, first attempt to use ML (maximum likelihood) for phylogenetics, Edwards and Cavalli-Sforza.<ref>"The reconstruction of evolution" in {{cite journal |doi=10.1111/j.1469-1809.1963.tb00786.x |title=Abstracts of Papers |journal=Annals of Human Genetics |volume=27 |issue=1 |pages=103–5 |year=1963 }}</ref>
* 1965
** Camin-Sokal parsimony, first parsimony (optimization) criterion and first computer program/algorithm for cladistic analysis both by Camin and Sokal.<ref>{{cite journal |doi=10.1111/j.1558-5646.1965.tb01722.x |title=A Method for Deducing Branching Sequences in Phylogeny |journal=Evolution |volume=19 |issue=3 |pages=311–26 |year=1965 |last1=Camin |first1=Joseph H |last2=Sokal |first2=Robert R |s2cid=20957422 |doi-access=free }}</ref>
** Character compatibility method, also called clique analysis, introduced independently by Camin and Sokal (loc. cit.) and [[E. O. Wilson]].<ref>{{cite journal |doi=10.2307/2411550 |jstor=2411550 |title=A Consistency Test for Phylogenies Based on Contemporaneous Species |journal=Systematic Zoology |volume=14 |issue=3 |pages=214–20 |year=1965 |last1=Wilson |first1=Edward O }}</ref>
* 1966
** English translation of Hennig.<ref>Hennig. W. (1966). Phylogenetic systematics. Illinois University Press, Urbana.{{page needed|date=June 2018}}</ref>
** "Cladistics" and "cladogram" coined (Webster's, loc. cit.)
* 1969
** Dynamic and successive weighting, James Farris.<ref>{{cite journal |doi=10.2307/2412182 |jstor=2412182 |title=A Successive Approximations Approach to Character Weighting |journal=Systematic Zoology |volume=18 |issue=4 |pages=374–85 |year=1969 |last1=Farris |first1=James S }}</ref>
** Wagner parsimony, Kluge and Farris.<ref name="Kluge">{{cite journal |doi=10.1093/sysbio/18.1.1 |title=Quantitative Phyletics and the Evolution of Anurans |journal=Systematic Biology |volume=18 |issue=1 |pages=1–32 |year=1969 |last1=Kluge |first1=A. G |last2=Farris |first2=J. S }}</ref>
** CI (consistency index), Kluge and Farris.<ref name="Kluge" />
** Introduction of pairwise compatibility for clique analysis, Le Quesne.<ref>{{cite journal |doi=10.2307/2412604 |jstor=2412604 |title=A Method of Selection of Characters in Numerical Taxonomy |journal=Systematic Zoology |volume=18 |issue=2 |pages=201–205 |year=1969 |last1=Quesne |first1=Walter J. Le }}</ref>
* 1970, Wagner parsimony generalized by Farris.<ref>{{cite journal |doi=10.1093/sysbio/19.1.83 |title=Methods for Computing Wagner Trees |journal=Systematic Biology |volume=19 |pages=83–92 |year=1970 |last1=Farris |first1=J. S }}</ref>
* 1971
** First successful application of ML (maximum likelihood) to phylogenetics (for protein sequences), Neyman.<ref>{{cite book |doi=10.1016/B978-0-12-307550-5.50005-8 |chapter=Molecular studies of evolution: a source of novel statistical problems |title=Statistical Decision Theory and Related Topics |year=1971 |last1=Neyman |first1=Jerzy |pages=1–27 |isbn=978-0-12-307550-5 }}</ref>
** Fitch parsimony, Walter M. Fitch.<ref>{{cite journal |doi=10.1093/sysbio/20.4.406 |jstor=2412116 |title=Toward Defining the Course of Evolution: Minimum Change for a Specific Tree Topology |journal=Systematic Biology |volume=20 |issue=4 |pages=406–16 |year=1971 |last1=Fitch |first1=W. M }}</ref> These gave way to the most basic ideas of [[Maximum parsimony (phylogenetics)|maximum parsimony]]. Fitch is known for his work on reconstructing phylogenetic trees from protein and DNA sequences. His definition of [[Sequence homology|orthologous sequences]] has been referenced in many research publications.
** NNI (nearest neighbour interchange), first branch-swapping search strategy, developed independently by Robinson<ref>{{cite journal |doi=10.1016/0095-8956(71)90020-7 |title=Comparison of labeled trees with valency three |journal=[[Journal of Combinatorial Theory]] | series=Series B |volume=11 |issue=2 |pages=105–19 |year=1971 |last1=Robinson |first1=D.F |doi-access=free }}</ref> and Moore et al.
** ME (minimum evolution), Kidd and Sgaramella-Zonta<ref>{{cite journal |pmid=5089842 |pmc=1706731 |year=1971 |last1=Kidd |first1=K. K |title=Phylogenetic analysis: Concepts and methods |journal=American Journal of Human Genetics |volume=23 |issue=3 |pages=235–52 |last2=Sgaramella-Zonta |first2=L. A }}</ref> (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.<ref>{{cite journal |doi=10.1093/sysbio/21.4.390 |title=Consensus Techniques and the Comparison of Taxonomic Trees |journal=Systematic Biology |volume=21 |issue=4 |pages=390–397 |year=1972 |last1=Adams |first1=E. N }}</ref>
* 1976, prefix system for ranks, Farris.<ref>{{cite journal |doi=10.2307/2412495 |jstor=2412495 |title=Phylogenetic Classification of Fossils with Recent Species |journal=Systematic Zoology |volume=25 |issue=3 |pages=271–282 |year=1976 |last1=Farris |first1=James S }}</ref>
* 1977, Dollo parsimony, Farris.<ref>{{cite journal |doi=10.1093/sysbio/26.1.77 |title=Phylogenetic Analysis Under Dollo's Law |journal=Systematic Biology |volume=26 |pages=77–88 |year=1977 |last1=Farris |first1=J. S }}</ref>
* 1979
** Nelson consensus, Nelson.<ref>{{cite journal |doi=10.1093/sysbio/28.1.1 |title=Cladistic Analysis and Synthesis: Principles and Definitions, with a Historical Note on Adanson's Familles Des Plantes (1763-1764) |journal=Systematic Biology |volume=28 |pages=1–21 |year=1979 |last1=Nelson |first1=G }}</ref>
** MAST ([[Maximum agreement subtree problem|maximum agreement subtree]])((GAS) greatest agreement subtree), a consensus method, Gordon.<ref>{{cite journal |doi= 10.1093/biomet/66.1.7|jstor=2335236 |title=A Measure of the Agreement between Rankings |journal=Biometrika |volume=66 |issue=1 |pages=7–15 |year=1979 |last1=Gordon |first1=A. D }}</ref>
** Bootstrap, Bradley Efron, precursor concept.<ref>Efron B. (1979). Bootstrap methods: another look at the jackknife. Ann. Stat. 7: 1–26.</ref>
* 1980, [[PHYLIP]], first software package for phylogenetic analysis, [[Joseph Felsenstein]]. A free computational phylogenetics package of programs for inferring evolutionary trees ([[Phylogenetic tree|phylogenies]]). One such example tree created by PHYLIP, called a "drawgram", generates rooted trees. This image shown in the figure below shows the evolution of phylogenetic trees over time.
* 1981
** Majority consensus, Margush and MacMorris.<ref>{{cite journal |doi=10.1016/S0092-8240(81)90019-7 |title=Consensus-trees |journal=Bulletin of Mathematical Biology |volume=43 |issue=2 |pages=239 |year=1981 |last1=Margush |first1=T |last2=McMorris |first2=F |doi-broken-date=1 November 2024 }}</ref>
** Strict consensus, Sokal and Rohlf<ref>{{cite journal |doi=10.2307/2413252 |jstor=2413252 |title=Taxonomic Congruence in the Leptopodomorpha Re-Examined |journal=Systematic Zoology |volume=30 |issue=3 |pages=309 |year=1981 |last1=Sokal |first1=Robert R |last2=Rohlf |first2=F. James }}</ref>[[File:PHILYP drawgram.gif|thumb|This image depicts a PHYLIP generated drawgram. This drawgram is an example of one of the possible trees the software is capable of generating.]]first computationally efficient ML (maximum likelihood) algorithm.<ref>{{cite journal |doi=10.1007/BF01734359 |pmid=7288891 |title=Evolutionary trees from DNA sequences: A maximum likelihood approach |journal=Journal of Molecular Evolution |volume=17 |issue=6 |pages=368–76 |year=1981 |last1=Felsenstein |first1=Joseph |bibcode=1981JMolE..17..368F |s2cid=8024924 }}</ref> Felsenstein created the Felsenstein Maximum Likelihood method, used for the inference of phylogeny which evaluates a hypothesis about evolutionary history in terms of the probability that the proposed model and the hypothesized history would give rise to the observed data set.
* 1982
** PHYSIS, Mikevich and Farris
** Branch and bound, Hendy and Penny<ref>{{cite journal |doi=10.1016/0025-5564(82)90027-X |title=Branch and bound algorithms to determine minimal evolutionary trees |journal=Mathematical Biosciences |volume=59 |issue=2 |pages=277 |year=1982 |last1=Hendy |first1=M.D |last2=Penny |first2=David }}</ref>
* 1985
** First cladistic analysis of eukaryotes based on combined phenotypic and genotypic evidence Diana Lipscomb.<ref>{{cite journal | last1 = Lipscomb | first1 = Diana | year = 1985 | title = The Eukaryotic Kingdoms | journal = Cladistics | volume = 1 | issue = 2 | pages = 127–40 | doi = 10.1111/j.1096-0031.1985.tb00417.x | pmid = 34965673 | s2cid = 84151309 }}</ref>
** First issue of ''Cladistics.''
** First phylogenetic application of bootstrap, Felsenstein.<ref>{{cite journal | last1 = Felsenstein | first1 = J | year = 1985 | title = Confidence limits on phylogenies: an approach using the bootstrap | journal = Evolution | volume = 39 | issue = 4 | pages = 783–791 | doi = 10.2307/2408678 | jstor = 2408678 | pmid = 28561359 }}</ref>
** First phylogenetic application of jackknife, Scott Lanyon.<ref>{{cite journal |doi=10.1093/sysbio/34.4.397 |title=Detecting Internal Inconsistencies in Distance Data |journal=Systematic Biology |volume=34 |issue=4 |pages=397–403 |year=1985 |last1=Lanyon |first1=S. M |citeseerx=10.1.1.1000.3956 }}</ref>
* 1986, MacClade, Maddison and Maddison.
* 1987, neighbor-joining method Saitou and Nei<ref>{{cite journal |doi=10.1093/oxfordjournals.molbev.a040454 |pmid=3447015 |title=The neighbor-joining method: A new method for reconstructing phylogenetic trees |journal=Molecular Biology and Evolution |volume=4 |issue=4 |pages=406–25 |year=1987 |last1=Saitou |first1=N. |last2=Nei |first2=M. |doi-access=free }}</ref>
* 1988, Hennig86 (version 1.5), Farris
** Bremer support (decay index), Bremer.<ref>{{cite journal |doi=10.1111/j.1558-5646.1988.tb02497.x |pmid=28563878 |title=The Limits of Amino Acid Sequence Data in Angiosperm Phylogenetic Reconstruction |journal=Evolution |volume=42 |issue=4 |pages=795–803 |year=1988 |last1=Bremer |first1=Kåre |s2cid=13647124 }}</ref>
* 1989
** RI (retention index), RCI (rescaled consistency index), Farris.<ref>{{cite journal |doi=10.1111/j.1096-0031.1989.tb00573.x |title=The Retention Index and the Rescaled Consistency Index |journal=Cladistics |volume=5 |issue=4 |pages=417–419 |year=1989 |last1=Farris |first1=James S |pmid=34933481 |s2cid=84287895 }}</ref>
** HER (homoplasy excess ratio), Archie.<ref>{{cite journal |doi=10.2307/2992286 |jstor=2992286 |title=Homoplasy Excess Ratios: New Indices for Measuring Levels of Homoplasy in Phylogenetic Systematics and a Critique of the Consistency Index |journal=Systematic Zoology |volume=38 |issue=3 |pages=253–269 |year=1989 |last1=Archie |first1=James W }}</ref>
* 1990
** combinable components (semi-strict) consensus, Bremer.<ref>{{cite journal |doi=10.1111/j.1096-0031.1990.tb00551.x |title=Combinable Component Consensus |journal=Cladistics |volume=6 |issue=4 |pages=369–372 |year=1990 |last1=Bremer |first1=Kåre |pmid=34933485 |s2cid=84151348 |doi-access=free }}</ref>
** SPR (subtree pruning and regrafting), TBR (tree bisection and reconnection), Swofford and Olsen.<ref>D. L. Swofford and G. J. Olsen. 1990. Phylogeny reconstruction. In D. M. Hillis and G. Moritz (eds.), Molecular Systematics, pages 411–501. Sinauer Associates, Sunderland, Mass.</ref>
* 1991
** DDI (data decisiveness index), Goloboff.<ref>{{cite journal |doi=10.1111/j.1096-0031.1991.tb00035.x |title=Homoplasy and the Choice Among Cladograms |journal=Cladistics |volume=7 |issue=3 |pages=215–232 |year=1991 |last1=Goloboff |first1=Pablo A |pmid=34933469 |s2cid=85418697 |doi-access=free }}</ref><ref>{{cite journal |doi=10.1111/j.1096-0031.1991.tb00046.x |title=Random Data, Homoplasy and Information |journal=Cladistics |volume=7 |issue=4 |pages=395–406 |year=1991 |last1=Goloboff |first1=Pablo A |s2cid=85132346 }}</ref>
** First cladistic analysis of eukaryotes based only on phenotypic evidence, Lipscomb.
* 1993, implied weighting Goloboff.<ref>{{cite journal |doi=10.1111/j.1096-0031.1993.tb00209.x |title=Estimating Character Weights During Tree Search |journal=Cladistics |volume=9 |pages=83–91 |year=1993 |last1=Goloboff |first1=Pablo A |issue=1 |pmid=34929936 |s2cid=84231334 |doi-access=free }}</ref>
* 1994, reduced consensus: RCC (reduced cladistic consensus) for rooted trees, Wilkinson.<ref>{{cite journal |doi=10.1093/sysbio/43.3.343 |title=Common Cladistic Information and its Consensus Representation: Reduced Adams and Reduced Cladistic Consensus Trees and Profiles |journal=Systematic Biology |volume=43 |issue=3 |pages=343–368 |year=1994 |last1=Wilkinson |first1=M }}</ref>
* 1995, reduced consensus RPC (reduced partition consensus) for unrooted trees, Wilkinson.<ref>{{cite journal |doi=10.2307/2413604 |jstor=2413604 |title=More on Reduced Consensus Methods |journal=Systematic Biology |volume=44 |issue=3 |pages=435–439 |year=1995 |last1=Wilkinson |first1=Mark }}</ref>
* 1996, first working methods for BI (Bayesian Inference) independently developed by Li,<ref>{{cite journal |doi=10.1080/01621459.2000.10474227 |jstor=2669394 |title=Phylogenetic Tree Construction Using Markov Chain Monte Carlo |journal=Journal of the American Statistical Association |volume=95 |issue=450 |pages=493 |year=2000 |last1=Li |first1=Shuying |last2=Pearl |first2=Dennis K |last3=Doss |first3=Hani |citeseerx=10.1.1.40.4461 |s2cid=122459537 }}</ref> Mau,<ref>{{cite journal |doi=10.1111/j.0006-341X.1999.00001.x |pmid=11318142 |jstor=2533889 |title=Bayesian Phylogenetic Inference via Markov Chain Monte Carlo Methods |journal=Biometrics |volume=55 |issue=1 |pages=1–12 |year=1999 |last1=Mau |first1=Bob |last2=Newton |first2=Michael A |last3=Larget |first3=Bret |citeseerx=10.1.1.139.498 |s2cid=932887 }}</ref> and Rannala and Yang<ref>{{cite journal |doi=10.1007/BF02338839 |pmid=8703097 |title=Probability distribution of molecular evolutionary trees: A new method of phylogenetic inference |journal=Journal of Molecular Evolution |volume=43 |issue=3 |pages=304–11 |year=1996 |last1=Rannala |first1=Bruce |last2=Yang |first2=Ziheng |bibcode=1996JMolE..43..304R |s2cid=8269826 }}</ref> 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.<ref>{{cite journal |doi= 10.1111/j.1096-0031.2003.tb00376.x|title=Improvements to resampling measures of group support |journal=Cladistics |volume=19 |issue=4 |pages=324–32 |year=2003 |last1=Goloboff |first1=P |s2cid=55516104 |hdl=11336/101057 |hdl-access=free }}</ref>
* 2004, 2005, similarity metric (using an approximation to Kolmogorov complexity) or NCD (normalized compression distance), Li et al.,<ref>{{cite journal |last1=Li |first1=M. |last2=Chen |first2=X. |last3=Li |first3=X. |last4=Ma |first4=B. |last5=Vitanyi |first5=P.M.B. |title=The Similarity Metric |journal=IEEE Transactions on Information Theory |date=December 2004 |volume=50 |issue=12 |pages=3250–3264 |doi=10.1109/TIT.2004.838101 |s2cid=221927 }}</ref> Cilibrasi and Vitanyi.<ref>{{cite journal |last1=Cilibrasi |first1=R. |last2=Vitanyi |first2=P.M.B. |title=Clustering by Compression |journal=IEEE Transactions on Information Theory |date=April 2005 |volume=51 |issue=4 |pages=1523–1545 |doi=10.1109/TIT.2005.844059 |arxiv=cs/0312044 |s2cid=911 }}</ref>