Editing Phylogenetics (section)

== Uses of phylogenetic analysis ==

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=== 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 ===
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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>