Editing Phylogenetics (section)

{{short description|Study of evolutionary relationships between organisms}}
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{{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>