Editing Phylogenetics (section)

=== 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>