Editing Phylogenetics

{{short description|Study of evolutionary relationships between organisms}}
{{refimprove|date=February 2024}}
{{Use dmy dates|date=September 2020}}
{{Evolutionary biology|expanded=Fields}}
In [[biology]], '''phylogenetics''' ({{IPAc-en|ˌ|f|aɪ|l|oʊ|dʒ|ə|ˈ|n|ɛ|t|ɪ|k|s|,_|-|l|ə|-}}){{refn|{{Dictionary.com|phylogenetic}}}}{{refn|{{MerriamWebsterDictionary|phylogenetic}}}}<ref>from [[Greek language|Greek]] [[wikt:φυλή|φυλή]]/[[wikt:φῦλον|φῦλον]] [{{transliteration|el|phylé/phylon}}] "tribe, clan, race", and [[wikt:γενετικός|γενετικός]] [{{transliteration|el|genetikós}}] "origin, source, birth" {{cite book |last1=Liddell |first1=Henry George |author-link1=Henry George Liddell |last2=Scott |first2=Robert |author-link2=Robert Scott (philologist) |last3=Jones |first3=Henry Stuart |author-link3=Henry Stuart-Jones |title=A Greek-English lexicon |year=1968 |publisher=Clarendon Press |location=Oxford |edition=9 |page=1961 |url=https://archive.org/stream/greekenglishlex00lidduoft#page/304/mode/2up}}</ref> is the study of the [[evolution]]ary [[history of life]] using observable characteristics of organisms (or genes), which is known as [[Computational phylogenetics|phylogenetic inference]]. It infers the relationship among [[organism]]s based on empirical data and observed [[heritable]] traits of [[DNA]] sequences, [[protein]] [[amino acid]] sequences, and [[Morphology (biology)|morphology]]. The results are a [[phylogenetic tree]]—a diagram depicting the [[hypothesis|hypothetical]] relationships among the organisms, reflecting their inferred evolutionary history.<ref>{{cite web| title=phylogeny| publisher=Biology online| url=http://www.biology-online.org/dictionary/Phylogeny| access-date=2013-02-15}}</ref>

The tips of a [[phylogenetic tree]] represent the observed entities, which can be living [[Taxon|taxa]] or [[fossil]]s. A phylogenetic diagram can be rooted or unrooted. A rooted tree diagram indicates the hypothetical [[common ancestor]] of the taxa represented on the tree. An unrooted tree diagram (a network) makes no assumption about directionality of character state transformation, and does not show the origin or "root" of the taxa in question.<ref>{{Cite web|url=http://www.cs.tau.ac.il/~rshamir/algmb/00/scribe00/html/lec08/node3.html|title=Phylogenetic Trees|website=www.cs.tau.ac.il|access-date= |first = Peer|last = Itzik|date = 1 January 2001}}</ref>

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 [[genome]]s.

Phylogenetics is a component of [[systematics]] that uses similarities and differences of the characteristics of species to interpret their evolutionary relationships and origins. <ref name="tax&phylog">{{cite book |last1=Harris |first1=Katherine |title=Taxonomy & Phylogeny |date=23 June 2019 |publisher=Biology LibreTexts |url=https://bio.libretexts.org/?title=Learning_Objects%2FWorksheets%2FBiology_Tutorials%2FTaxonomy_%26_Phylogeny |access-date=19 April 2023}}</ref>

In the field of [[cancer]] research, phylogenetics can be used to study the clonal evolution of [[tumors]] and molecular [[chronology]], predicting and showing how cell populations vary throughout the progression of the disease and during treatment, using whole [[Whole genome sequencing|genome sequencing]] techniques.<ref name=Herberts2022>{{Cite journal |last1=Herberts |first1=Cameron |last2=Annala |first2=Matti |last3=Sipola |first3=Joonatan |last4=Ng |first4=Sarah W. S. |last5=Chen |first5=Xinyi E. |last6=Nurminen |first6=Anssi |last7=Korhonen |first7=Olga V. |last8=Munzur |first8=Aslı D. |last9=Beja |first9=Kevin |last10=Schönlau |first10=Elena |last11=Bernales |first11=Cecily Q. |last12=Ritch |first12=Elie |last13=Bacon |first13=Jack V. W. |last14=Lack |first14=Nathan A. |last15=Nykter |first15=Matti |date= August 2022 |title=Deep whole-genome ctDNA chronology of treatment-resistant prostate cancer |url=https://www.nature.com/articles/s41586-022-04975-9 |journal=Nature |language=en |volume=608 |issue=7921 |pages=199–208 |doi=10.1038/s41586-022-04975-9 |pmid=35859180 |bibcode=2022Natur.608..199H |s2cid=250730778 |issn=1476-4687}}</ref> Because cancer cells reproduce mitotically, the evolutionary processes behind cancer progression are quite different from those in sexually-reproducing species. These differences manifest in several areas: the types of aberrations that occur, the rates of [[mutation]], the high heterogeneity (variability) of tumor cell subclones, and the absence of [[genetic recombination]].<ref>{{Cite journal |last1=Schwartz |first1=Russell |last2=Schäffer |first2=Alejandro A. |date=April 2017 |title=The evolution of tumour phylogenetics: principles and practice |journal=Nature Reviews Genetics |language=en |volume=18 |issue=4 |pages=213–229 |doi=10.1038/nrg.2016.170 |issn=1471-0056 |pmc=5886015 |pmid=28190876}}</ref><ref>{{Cite journal |last1=Ní Leathlobhair |first1=Máire |last2=Lenski |first2=Richard E. |date=2022 |title=Population genetics of clonally transmissible cancers |url=https://www.nature.com/articles/s41559-022-01790-3 |journal=Nature Ecology & Evolution |language=en |volume=6 |issue=8 |pages=1077–1089 |doi=10.1038/s41559-022-01790-3 |pmid=35879542 |bibcode=2022NatEE...6.1077N |issn=2397-334X}}</ref>

Phylogenetics can also aid in [[drug design]] and discovery. Phylogenetics allows scientists to organize species and can show which species are likely to have inherited particular traits that are medically useful, such as producing biologically active compounds - those that have effects on the human body. For example, in drug discovery, [[venom]]-producing animals are particularly useful. Venoms from these animals produce several important drugs, e.g., [[ACE inhibitor]]s and Prialt ([[Ziconotide]]). To find new venoms, scientists turn to phylogenetics to screen for closely related species that may have the same useful traits. [[File:Clade of the fish tree of life.png|right|thumb|One small clade of fish, showing how venom has evolved multiple times.<ref name="Drug discovery">{{Cite web |date=2021-07-07 |title=Drug discovery - Understanding Evolution |url=https://evolution.berkeley.edu/the-tree-room/trees-matter/drug-discovery/ |access-date=2023-04-23 |language=en-US}}</ref>]]The phylogenetic tree shows venomous species of [[fish]], and related fish they may also contain the trait. Using this approach, biologists are able to identify the fish,  snake and lizard species that may be venomous. <ref name="Drug discovery" />
In [[forensic science]], phylogenetic tools are useful to assess DNA evidence for court cases. Phylogenetic analysis has been used in criminal trials to exonerate or hold individuals. 

[[HIV]] forensics uses phylogenetic analysis to track the differences in HIV genes and determine the relatedness of two samples. HIV forensics have limitations, i.e., it cannot be the sole proof of transmission between individuals, and phylogenetic analysis which shows transmission relatedness does not indicate direction of transmission.<ref name="Bernard-2007">{{Cite journal |last1=Bernard |first1=EJ |last2=Azad |first2=Y |last3=Vandamme |first3=AM |last4=Weait |first4=M |last5=Geretti |first5=AM |date=2007 |title=HIV forensics: pitfalls and acceptable standards in the use of phylogenetic analysis as evidence in criminal investigations of HIV transmission |journal=HIV Medicine |volume=8 |issue=6 |pages=382–387 |doi=10.1111/j.1468-1293.2007.00486.x |pmid=17661846 |s2cid=38883310 |issn=1464-2662|doi-access=free }}</ref>

== Taxonomy and classification ==
{{main|Taxonomy}}

[[Taxonomy (biology)|Taxonomy]] is the identification, naming, and [[Classification (general theory)|classification]] of organisms. <ref name="tax&phylog"/> The [[Linnaean taxonomy|Linnaean classification]] system developed in the 1700s by [[Carl Linnaeus|Carolus Linnaeus]] is the foundation for modern classification methods. Linnaean classification traditionally relied on the phenotypes or physical characteristics of organisms to group species.<ref name="linnaeanClassification">{{cite book |last1=CK-12 Foundation |title=Linnaean Classification |date=6 March 2021 |publisher=Biology LibreTexts |url=https://bio.libretexts.org/Bookshelves/Introductory_and_General_Biology/Book%3A_Introductory_Biology_(CK-12)/05%3A_Evolution/5.01%3A_Linnaean_Classification |access-date=19 April 2023}}</ref> With the emergence of [[biochemistry]],  classifications of organisms are now often based on DNA sequence data or a combination of DNA and morphology.  Many systematists contend that only [[monophyletic]] taxa should be recognized as named groups.<ref>{{Cite book |last1=Wiley |first1=E.O. |author-link1=Edward O. Wiley |title=Phylogenetics: theory and practice of phylogenetic systematics |last2=Lieberman |first2=Bruce S. |author-link2=Bruce S. Lieberman |date=2011 |publisher=[[Wiley-Blackwell]] |isbn=978-0-470-90596-8 |editor-first= |edition=2nd |location=Hoboken, N.J }}</ref> The degree to which classification depends on inferred evolutionary history differs depending on the school of taxonomy: [[phenetics]] ignores phylogenetic speculation altogether, trying to represent the similarity between organisms instead; [[cladistics]] (phylogenetic systematics) tries to reflect phylogeny in its classifications by only recognizing groups based on shared, derived characters ([[synapomorphies]]); [[evolutionary taxonomy]] tries to take into account both the branching pattern and "degree of difference" to find a compromise between inferred patterns of common ancestry and evolutionary distinctness.

== Inference of a phylogenetic tree ==
{{main|Computational phylogenetics}}

Usual methods of [[phylogenetic inference]] involve computational approaches implementing an [[Optimality criterion|optimality criterion]] and methods of [[Maximum parsimony (phylogenetics)|parsimony]], [[maximum likelihood]] (ML), and [[Markov chain Monte Carlo|MCMC]]-based [[Bayesian inference]]. All these depend upon an implicit or explicit [[mathematical model]] describing the relative probabilities of character state transformation within and among the characters observed.<ref>{{Cite book |title=Phylogenetic Inference |url=https://plato.stanford.edu/entries/phylogenetic-inference/ |website=Stanford Encyclopedia of Philosophy|date=15 February 2024 |publisher=Metaphysics Research Lab, Stanford University }}</ref>

[[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 (biology)|morphology]] or similar observable traits, which was often assumed to approximate phylogenetic relationships.  [[Neighbor joining|Neighbor Joining]] is a phenetic method that is often used for building similarity trees for [[DNA barcoding|DNA barcodes]].

Prior to 1950, phylogenetic inferences were generally presented as [[narrative]] scenarios. Such methods were often ambiguous and lacked explicit criteria for evaluating alternative hypotheses.<ref>Richard C. Brusca & Gary J. Brusca (2003). ''Invertebrates'' (2nd ed.). Sunderland, Massachusetts: Sinauer Associates. {{ISBN|978-0-87893-097-5}}.</ref><ref>Bock, W. J. (2004). Explanations in systematics. Pp. 49–56. In Williams, D. M. and Forey, P. L. (eds) Milestones in Systematics. London: Systematics Association Special Volume Series 67. CRC Press, Boca Raton, Florida.</ref><ref>Auyang, Sunny Y. (1998). ''Narratives and Theories in Natural History.'' In: ''Foundations of complex-system theories: in economics, evolutionary biology, and statistical physics.'' Cambridge, U.K.; New York: Cambridge University Press.{{page needed|date=June 2018}}</ref>

== Impacts of taxon sampling ==
In phylogenetic analysis, taxon sampling selects a small group of exemplar taxa to infer the evolutionary history of a clade.<ref name="incomplete taxon sampling">{{cite journal |last1=Rosenberg |first1=Michael |title=Incomplete taxon sampling is not a problem for phylogenetic inference |journal=Proceedings of the National Academy of Sciences |date=28 August 2001 |volume=98 |issue=19 |pages=10751–10756 |doi=10.1073/pnas.191248498 |pmid=11526218 |pmc=58547 |bibcode=2001PNAS...9810751R |doi-access=free }}</ref> This process is also known as [[stratified sampling]] or clade-based sampling.<ref name="taxonSampling">{{cite journal |last1=Rosenberg |first1=Michael |last2=Kumar |first2=Sudhir |title=Taxon Sampling, Bioinformatics, and Phylogenetics |journal=Systematic Biology|date=1 February 2003 |volume=52 |issue=1 |pages=119–124 |doi=10.1080/10635150390132894 |pmid=12554445 |pmc=2796430 |url=https://doi.org/10.1080/10635150390132894 |access-date=19 April 2023}}</ref> Judicious taxon sampling is important, given limited resources to compare and analyze every species within a diverse clade, and also given the computational limits of phylogenetic software.<ref name="incomplete taxon sampling" /> Poor taxon sampling may result in incorrect phylogenetic inferences.<ref name="taxonSampling" /> [[Long branch attraction]], in which nonrelated branches are incorrectly grouped by shared, homoplastic nucleotide sites, is an theoretical cause for inaccuracy <ref name="incomplete taxon sampling" />

[[File:Accuracy increase sites per taxon.png|thumb|Percentage of inter-ordinal branches reconstructed with a constant number of bases and four phylogenetic tree construction models; neighbor-joining (NJ), minimum evolution (ME), unweighted maximum parsimony (MP), and maximum likelihood (ML). Demonstrates phylogenetic analysis with fewer taxa and more genes per taxon matches more often with the replicable consensus tree. The dotted line demonstrates an equal accuracy increase between the two taxon sampling methods. Figure is property of Michael S. Rosenberg and Sudhir Kumar as presented in the journal article ''Taxon Sampling, Bioinformatics, and Phylogenomics''.<ref name="taxonSampling" />]]
There are debates if increasing the number of taxa sampled improves phylogenetic accuracy more than increasing the number of genes sampled per taxon. Differences in each method's sampling impact the number of nucleotide sites utilized in a sequence alignment, which may contribute to disagreements. For example, phylogenetic trees constructed utilizing a more significant number of total nucleotides are generally more accurate, as supported by phylogenetic trees' bootstrapping replicability from random sampling.

The graphic presented in ''Taxon Sampling, Bioinformatics, and Phylogenomics'', compares the correctness of phylogenetic trees generated using fewer taxa and more sites per taxon on the x-axis to more taxa and fewer sites per taxon on the y-axis. With fewer taxa, more genes are sampled amongst the taxonomic group; in comparison, with more taxa added to the taxonomic sampling group, fewer genes are sampled. Each method has the same total number of nucleotide sites sampled. Furthermore, the dotted line represents a 1:1 accuracy between the two sampling methods. As seen in the graphic, most of the plotted points are located below the dotted line, which indicates gravitation toward increased accuracy when sampling fewer taxa with more sites per taxon. The research performed utilizes four different phylogenetic tree construction models to verify the theory; neighbor-joining (NJ), minimum evolution (ME), unweighted maximum parsimony (MP), and maximum likelihood (ML). In the majority of models, sampling fewer taxon with more sites per taxon demonstrated higher accuracy.

Generally, with the alignment of a relatively equal number of total nucleotide sites, sampling more genes per taxon has higher bootstrapping replicability than sampling more taxa. However, unbalanced datasets within genomic databases make increasing the gene comparison per taxon in uncommonly sampled organisms increasingly difficult.<ref name="taxonSampling" />

== 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>

== Uses of phylogenetic analysis ==

{{tone|date=February 2024|Needs rewriting and citing so as to be helpful, clear, and encyclopedic; the section}}

=== Pharmacology ===
One use of phylogenetic analysis involves the pharmacological examination of closely related groups of organisms. Advances in [[cladistics]] analysis through faster computer programs and improved molecular techniques have increased the precision of phylogenetic determination, allowing for the identification of species with pharmacological potential.

Historically, phylogenetic screens for pharmacological purposes were used in a basic manner, such as studying the [[Apocynaceae]] family of plants, which includes alkaloid-producing species like [[Catharanthus]], known for producing [[vincristine]], an antileukemia drug. Modern techniques now enable researchers to study close relatives of a species to uncover either a higher abundance of important bioactive compounds (e.g., species of [[Taxus]] for taxol) or natural variants of known pharmaceuticals (e.g., species of ''Catharanthus'' for different forms of vincristine or vinblastine).<ref>{{Citation |last1=Alam |first1=M. Masidur |title=Vincristine and Vinblastine Anticancer Catharanthus Alkaloids: Pharmacological Applications and Strategies for Yield Improvement |date=2017 |work=Catharanthus roseus: Current Research and Future Prospects |pages=277–307 |editor-last=Naeem |editor-first=M. |url=https://doi.org/10.1007/978-3-319-51620-2_11 |access-date=2024-07-23 |place=Cham |publisher=Springer International Publishing |language=en |doi=10.1007/978-3-319-51620-2_11 |isbn=978-3-319-51620-2 |last2=Naeem |first2=M. |last3=Khan |first3=M. Masroor A. |last4=Uddin |first4=Moin |editor2-last=Aftab |editor2-first=Tariq |editor3-last=Khan |editor3-first=M. Masroor A.}}</ref>

=== Biodiversity ===
Phylogenetic analysis has also been applied to biodiversity studies within the fungi family. Phylogenetic analysis helps understand the evolutionary history of various groups of organisms, identify relationships between different species, and predict future evolutionary changes. Emerging imagery systems and new analysis techniques allow for the discovery of more genetic relationships in biodiverse fields, which can aid in conservation efforts by identifying rare species that could benefit ecosystems globally.
[[File:Fig. S6. Phylogenetic subtree of P4ATPase in Fungi. Blue- Ascomycota; Red- Basidiomycota; Green- Zygomycota; Cyan- Chytridiomycota; Orange- Entomophthoromycota; Pink- Mucoromycota and Purple- Glomeromycota..jpg|thumb|405x405px|Phylogenetic Subtree of fungi containing different biodiverse sections of the fungi group.|center]]

=== Infectious disease epidemiology ===
{{Confusing|reason=this section includes dense text that might be hard to understand by general audiences|date=February 2024}}
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[[Whole genome sequencing|Whole-genome sequence]] data from outbreaks or epidemics of infectious diseases can provide important insights into transmission dynamics and inform public health strategies. Traditionally, studies have combined genomic and epidemiological data to reconstruct transmission events. However, recent research has explored deducing transmission patterns solely from genomic data using [[phylodynamics]], which involves analyzing the properties of pathogen phylogenies. Phylodynamics uses theoretical models to compare predicted branch lengths with actual branch lengths in phylogenies to infer transmission patterns. Additionally, [[coalescent theory]], which describes probability distributions on trees based on population size, has been adapted for epidemiological purposes. Another source of information within phylogenies that has been explored is "tree shape." These approaches, while computationally intensive, have the potential to provide valuable insights into pathogen transmission dynamics.<ref name="Colijn-2014">{{Cite journal |last1=Colijn |first1=Caroline |last2=Gardy |first2=Jennifer |date=2014-01-01 |title=Phylogenetic tree shapes resolve disease transmission patterns |url=https://academic.oup.com/emph/article/2014/1/96/1845716 |journal=Evolution, Medicine, and Public Health |language=en |volume=2014 |issue=1 |pages=96–108 |doi=10.1093/emph/eou018 |issn=2050-6201 |pmc=4097963 |pmid=24916411}}</ref>
[[File:WebTree.jpg|thumb|320x320px|Pathogen Transmission Trees]]

The structure of the host contact network significantly impacts the dynamics of outbreaks, and management strategies rely on understanding these transmission patterns. Pathogen genomes spreading through different contact network structures, such as chains, homogeneous networks, or networks with super-spreaders, accumulate mutations in distinct patterns, resulting in noticeable differences in the shape of phylogenetic trees, as illustrated in Fig. 1. Researchers have analyzed the structural characteristics of phylogenetic trees generated from simulated bacterial genome evolution across multiple types of contact networks. By examining simple topological properties of these trees, researchers can classify them into chain-like, homogeneous, or super-spreading dynamics, revealing transmission patterns. These properties form the basis of a computational classifier used to analyze real-world outbreaks. Computational predictions of transmission dynamics for each outbreak often align with known epidemiological data.
[[File:GraphRepresentation.jpg|thumb|350x350px|Graphical Representation of Phylogenetic Tree analysis]]
Different transmission networks result in quantitatively different tree shapes. To determine whether tree shapes captured information about underlying disease transmission patterns, researchers simulated the evolution of a bacterial genome over three types of outbreak contact networks—homogeneous, super-spreading, and chain-like. They summarized the resulting phylogenies with five metrics describing tree shape. Figures 2 and 3 illustrate the distributions of these metrics across the three types of outbreaks, revealing clear differences in tree topology depending on the underlying host contact network.

Super-spreader networks give rise to phylogenies with higher Colless imbalance, longer ladder patterns, lower Δw, and deeper trees than those from homogeneous contact networks. Trees from chain-like networks are less variable, deeper, more imbalanced, and narrower than those from other networks.

Scatter plots can be used to visualize the relationship between two variables in pathogen transmission analysis, such as the number of infected individuals and the time since infection. These plots can help identify trends and patterns, such as whether the spread of the pathogen is increasing or decreasing over time, and can highlight potential transmission routes or super-spreader events. [[Box plot]]s displaying the range, median, quartiles, and potential outliers datasets can also be valuable for analyzing pathogen transmission data, helping to identify important features in the data distribution. They may be used to quickly identify differences or similarities in the transmission data.<ref name="Colijn-2014" />
=== Disciplines other than biology ===
[[File:A-phylogeny-of-the-Indo-European-languages-showing-several-of-the-major-groups-and-the.png|thumb|577x577px|Phylogeny of Indo-European languages<ref>{{Cite journal |last=Pagel |first=Mark |date=2017 |title=Darwinian perspectives on the evolution of human languages |journal=Psychonomic Bulletin & Review |language=en |volume=24 |issue=1 |pages=151–157 |doi=10.3758/s13423-016-1072-z |pmid=27368626 |pmc=5325856 |issn=1069-9384}}</ref>]]
Phylogenetic tools and representations (trees and networks) can also be applied to [[philology]], the study of the evolution of oral languages and written text and manuscripts, such as in the field of [[quantitative comparative linguistics]].<ref>{{cite book |last=Heggarty |first=Paul |year=2006 |chapter=Interdisciplinary Indiscipline? Can Phylogenetic Methods Meaningfully Be Applied to Language Data — and to Dating Language? |chapter-url=https://mpi-lingweb.shh.mpg.de/languagesandorigins/All/PapersDownLoad/2006%20%20Heggarty%20-%20Interdisciplinary%20Indiscipline.pdf |title=Phylogenetic Methods and the Prehistory of Languages |editor1=Peter Forster |editor2=Colin Renfrew |series=McDonald Institute Monographs |publisher=McDonald Institute for Archaeological Research |access-date=19 January 2021 |archive-date=28 January 2021 |archive-url=https://web.archive.org/web/20210128030515/https://mpi-lingweb.shh.mpg.de/languagesandorigins/All/PapersDownLoad/2006%20%20Heggarty%20-%20Interdisciplinary%20Indiscipline.pdf |url-status=dead }}</ref>

Computational phylogenetics can be used to investigate a language as an evolutionary system. The evolution of human language closely corresponds with human's biological evolution which allows phylogenetic methods to be applied. The concept of a "tree" serves as an efficient way to represent relationships between languages and language splits. It also serves as a way of testing hypotheses about the connections and ages of language families. For example, relationships among languages can be shown by using [[cognate]]s as characters.<ref name="Bowern-2018">{{Cite journal |last=Bowern |first=Claire |date=2018-01-14 |title=Computational Phylogenetics |journal=Annual Review of Linguistics |language=en |volume=4 |issue=1 |pages=281–296 |doi=10.1146/annurev-linguistics-011516-034142 |issn=2333-9683|doi-access=free }}</ref><ref>{{Cite journal |last1=Retzlaff |first1=Nancy |last2=Stadler |first2=Peter F. |date=2018 |title=Phylogenetics beyond biology |journal=Theory in Biosciences |language=en |volume=137 |issue=2 |pages=133–143 |doi=10.1007/s12064-018-0264-7 |issn=1431-7613 |pmc=6208858 |pmid=29931521}}</ref> The phylogenetic tree of Indo-European languages shows the relationships between several of the languages in a timeline, as well as the similarity between words and word order.

There are three types of criticisms about using phylogenetics in philology, the first arguing that languages and species are different entities, therefore you can not use the same methods to study both. The second being how phylogenetic methods are being applied to linguistic data. And the third, discusses the types of data that is being used to construct the trees.<ref name="Bowern-2018" />

[[Bayesian inference in phylogeny|Bayesian phylogenetic]] methods, which are sensitive to how treelike the data is, allow for the reconstruction of relationships among languages, locally and globally. The main two reasons for the use of Bayesian phylogenetics are that (1) diverse scenarios can be included in calculations and (2) the output is a sample of trees and not a single tree with true claim.<ref>{{Cite journal |last1=Hoffmann |first1=Konstantin |last2=Bouckaert |first2=Remco |last3=Greenhill |first3=Simon J |last4=Kühnert |first4=Denise |date=2021-11-25 |title=Bayesian phylogenetic analysis of linguistic data using BEAST |url=https://academic.oup.com/jole/article/6/2/119/6374521 |journal=Journal of Language Evolution |language=en |volume=6 |issue=2 |pages=119–135 |doi=10.1093/jole/lzab005 |issn=2058-458X|doi-access=free |hdl=1885/311145 |hdl-access=free }}</ref>

The same process can be applied to texts and manuscripts. In [[Palaeography|Paleography]], the study of historical writings and manuscripts, texts were replicated by scribes who copied from their source and alterations - i.e., 'mutations' - occurred when the scribe did not precisely copy the source.<ref>{{Cite journal |last1=Spencer |first1=Matthew |last2=Davidson |first2=Elizabeth A |last3=Barbrook |first3=Adrian C |last4=Howe |first4=Christopher J |date=2004-04-21 |title=Phylogenetics of artificial manuscripts |url=https://www.sciencedirect.com/science/article/pii/S0022519303004442 |journal=Journal of Theoretical Biology |language=en |volume=227 |issue=4 |pages=503–511 |doi=10.1016/j.jtbi.2003.11.022 |pmid=15038985 |bibcode=2004JThBi.227..503S |issn=0022-5193}}</ref>

Phylogenetics has been applied to archaeological artefacts such as the early hominin hand-axes,<ref>{{cite journal |last1=Lycett |first1=Stephen J. |title=Understanding Ancient Hominin Dispersals Using Artefactual Data: A Phylogeographic Analysis of Acheulean Handaxes |journal=PLOS ONE |date=14 October 2009 |volume=4 |issue=10 |pages=e7404 |doi=10.1371/journal.pone.0007404|doi-access=free |pmid=19826473 |pmc=2756619 |bibcode=2009PLoSO...4.7404L }}</ref> late Palaeolithic figurines,<ref>{{cite book |last1=Tripp |first1=Allison |chapter=A Cladistics Analysis Exploring Regional Patterning of the Anthropomorphic Figurines from the Gravettian |title=Cultural Phylogenetics |journal=Cultural Phylogenetics: Concepts and Applications in Archaeology |series=Interdisciplinary Evolution Research |date=2016 |volume=4 |pages=179–202 |doi=10.1007/978-3-319-25928-4_8|isbn=978-3-319-25926-0 }}</ref> Neolithic stone arrowheads,<ref>{{cite journal |last1=Marwick |first1=Ben |last2=Matzig |first2=David |last3=Riede |first3=Felix |title=Bayesian inference of material culture phylogenies using continuous traits: A birth–death model for Late Neolithic/Early Bronze Age arrowheads from Northwestern Europe |journal=Osf.io |doi=10.31235/osf.io/j2kva}}</ref> Bronze Age ceramics,<ref>{{cite journal |last1=Manem |first1=Sébastien |title=Modeling the Evolution of Ceramic Traditions Through a Phylogenetic Analysis of the Chaînes Opératoires: the European Bronze Age as a Case Study |journal=Journal of Archaeological Method and Theory |date=1 December 2020 |volume=27 |issue=4 |pages=992–1039 |doi=10.1007/s10816-019-09434-w}}</ref> and historical-period houses.<ref>{{cite journal |last1=O'Brien |first1=Michael J. |last2=Lyman |first2=R. Lee |title=Darwinian Evolutionism Is Applicable to Historical Archaeology |journal=International Journal of Historical Archaeology |date=1 March 2000 |volume=4 |issue=1 |pages=71–112 |doi=10.1023/A:1009556427520}}</ref> Bayesian methods have also been employed by archaeologists in an attempt to quantify uncertainty in the tree topology and divergence times of stone projectile point shapes in the European Final Palaeolithic and earliest Mesolithic.<ref>{{cite journal |last1=Matzig |first1=David N. |last2=Marwick |first2=Ben |last3=Riede |first3=Felix |last4=Warnock |first4=Rachel C. M. |title=A macroevolutionary analysis of European Late Upper Palaeolithic stone tool shape using a Bayesian phylodynamic framework |journal=Royal Society Open Science |date=August 2024 |volume=11 |issue=8 |doi=10.1098/rsos.240321|pmid=39144489 |pmc=11321859 |bibcode=2024RSOS...1140321M }}</ref>

== See also ==
{{colbegin||colwidth=20em|rules=yes}}
* [[Angiosperm Phylogeny Group]]
* [[Bauplan]]
* [[Bioinformatics]]
* [[Biomathematics]]
* [[Coalescent theory]]
* [[Cytonuclear discordance]]
* [[EDGE of Existence programme]]
* [[Evolutionary taxonomy]]
* [[Language family]]
* [[Maximum parsimony]]
* [[Microbial phylogenetics]]
* [[Molecular evolution]]
* [[Molecular phylogeny]]
* [[Ontogeny]]
* [[PhyloCode]]
* [[Phylodynamics]]
* [[Phylogenesis]]
* [[Phylogenetic comparative methods]]
* [[Phylogenetic network]]
* [[Phylogenetic nomenclature]]
* [[Phylogenetic tree viewers]]
* [[List of phylogenetics software|Phylogenetics software]]
* [[Phylogenomics]]
* [[Phylogeny (psychoanalysis)]]
* [[Phylogeography]]
* [[Systematics]]
{{colend}}

== References ==
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{{Reflist}}

== Bibliography ==
{{refbegin|30em}}
* {{Cite book |last1=Schuh |first1=Randall T. |last2=Brower |first2=Andrew V.Z. |year=2009 |title=Biological Systematics: principles and applications |location=Ithaca |publisher=Comstock Pub. Associates/Cornell University Press |edition=2nd |isbn=978-0-8014-4799-0 |oclc=312728177}}
* {{Cite book|editor1-link=Peter Forster (geneticist)|editor1-last=Forster|editor1-first=Peter|editor2-link=Colin Renfrew, Baron Renfrew of Kaimsthorn|editor2-last=Renfrew|editor2-first=Colin|title=Phylogenetic Methods and the Prehistory of Languages|publisher= McDonald Institute Press, University of Cambridge|year=2006|isbn=978-1-902937-33-5|oclc=69733654}}
* {{Cite book|last1=Baum|first1=David A.|last2=Smith|first2=Stacey D.|title=Tree Thinking: an introduction to phylogenetic biology|location=Greenwood Village, CO|publisher=Roberts and Company|year=2013|isbn=978-1-936221-16-5|oclc=767565978}}
* {{cite book|last=Stuessy|first=Tod F.|title=Plant Taxonomy: The Systematic Evaluation of Comparative Data|publisher=Columbia University Press|isbn=978-0-231-14712-5|url=https://books.google.com/books?id=0bYs8F0Mb9gC|year=2009}}
{{refend}}

== External links ==
* {{Wiktionary-inline|phylogenetics}}

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{{Evolution}}
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