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Quasispecies model
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==Simplified explanation== When evolutionary biologists describe competition between species, they generally assume that each species is a single genotype whose descendants are mostly accurate copies. (Such genotypes are said to have a high reproductive ''fidelity''.) In evolutionary terms, we are interested in the behavior and fitness of that one species or genotype over time.<ref>{{cite journal | vauthors = Charlesworth B, Charlesworth D | title = Darwin and genetics | journal = Genetics | volume = 183 | issue = 3 | pages = 757β66 | date = November 2009 | pmid = 19933231 | doi = 10.1534/genetics.109.109991 | pmc = 2778973 }}</ref> Some organisms or genotypes, however, may exist in circumstances of low fidelity, where most descendants contain one or more mutations. A group of such genotypes is constantly changing, so discussions of which single genotype is the most fit become meaningless. Importantly, if many closely related genotypes are only one mutation away from each other, then genotypes in the group can mutate back and forth into each other. For example, with one mutation per generation, a child of the sequence AGGT could be AGTT, and a grandchild could be AGGT again. Thus we can envision a "'''cloud'''" of related genotypes that is rapidly mutating, with sequences going back and forth among different points in the cloud. Though the proper definition is mathematical, that cloud, roughly speaking, is a quasispecies.{{citation needed|date=August 2013}}<ref>{{cite book |last=Eigen |first=Manfred |title=From Strange Simplicity to Complex Familiarity |publisher=Oxford University Press |year=2013 |isbn=978-0-19-857021-9 |pages=404β406 |language=EN}}</ref> Quasispecies behavior exists for large numbers of individuals existing at a certain (high) range of mutation rates.<ref>Martinez, MA, Martus G, Capel E, Parera M, Franco S, Nevot M (2012) Quasispecies Dynamics of RNA Viruses. In: Viruses: Essential Agents of Life, Springer, Dordrecht, pp. 21-42.</ref> ===Quasispecies, fitness, and evolutionary selection=== In a species, though reproduction may be mostly accurate, periodic mutations will give rise to one or more competing genotypes. If a mutation results in greater replication and survival, the mutant genotype may out-compete the parent genotype and come to dominate the species. Thus, the individual genotypes (or species) may be seen as the units on which selection acts and biologists will often speak of a single genotype's [[fitness (biology)|fitness]].<ref>{{cite web|url=https://www.khanacademy.org/science/biology/her|title=Evolution and the tree of life {{!}} Biology {{!}} Science|website=Khan Academy|language=en|access-date=2019-02-20}}</ref> In a quasispecies, however, mutations are ubiquitous and so the fitness of an individual genotype becomes meaningless: if one particular mutation generates a boost in reproductive success, it can't amount to much because that genotype's offspring are unlikely to be accurate copies with the same properties. Instead, what matters is the ''connectedness'' of the cloud. For example, the sequence AGGT has 12 (3+3+3+3) possible single point mutants AGGA, AGGG, and so on. If 10 of those mutants are viable genotypes that may reproduce (and some of whose offspring or grandchildren may mutate back into AGGT again), we would consider that sequence a well-connected node in the cloud. If instead only two of those mutants are viable, the rest being lethal mutations, then that sequence is poorly connected and most of its descendants will not reproduce. The analog of fitness for a quasispecies is the tendency of nearby relatives within the cloud to be well-connected, meaning that more of the mutant descendants will be viable and give rise to further descendants within the cloud.<ref>{{cite journal | first = Francis | last = Heylighen | url=http://pespmc1.vub.ac.be/books/Complexity-Evolution-old.pdf |title=Complexity and Evolution | journal = Entropy | date = 2023 | volume = 25 | issue = 2 | page = 286 | doi = 10.3390/e25020286 | doi-access = free | pmid = 36832653 | pmc = 9955364 | bibcode = 2023Entrp..25..286V | quote = Lecture notes 2014-2015 }}</ref> When the fitness of a single genotype becomes meaningless because of the high rate of mutations, the cloud as a whole or quasispecies becomes the natural unit of selection. ===Application to biological research=== Quasispecies represents the evolution of high-mutation-rate viruses such as [[HIV]] and sometimes single genes or molecules within the genomes of other organisms.<ref>{{cite book | vauthors = Holland JJ, De La Torre JC, Steinhauer DA | title = Genetic Diversity of RNA Viruses | chapter = RNA Virus Populations as Quasispecies | series = Current Topics in Microbiology and Immunology | volume = 176 | pages = 1β20 | pmid = 1600747 | year = 1992 | doi = 10.1007/978-3-642-77011-1_1 | isbn = 978-3-642-77013-5 | s2cid = 46530529 | doi-access = free }}</ref><ref>{{cite journal | vauthors = Shuman LJ, Wolfe H, Whetsell GW, Huber GA | title = Reimbursement alternatives for home health care | journal = Inquiry: A Journal of Medical Care Organization, Provision and Financing| volume = 13 | issue = 3 | pages = 277β87 | date = September 1976 | pmc = | doi = | pmid = 135734 }}</ref><ref>{{cite journal | vauthors = Wilke CO | title = Quasispecies theory in the context of population genetics | journal = BMC Evolutionary Biology | volume = 5 | pages = 44 | date = August 2005 | issue = 1 | pmid = 16107214 | pmc = 1208876 | doi = 10.1186/1471-2148-5-44 | doi-access = free | bibcode = 2005BMCEE...5...44W }}</ref> Quasispecies models have also been proposed by Jose Fontanari and [[Emmanuel David Tannenbaum]] to model the evolution of sexual reproduction.<ref>{{cite journal | vauthors = Tannenbaum E, Fontanari JF | title = A quasispecies approach to the evolution of sexual replication in unicellular organisms | journal = Theory in Biosciences | volume = 127 | issue = 1 | pages = 53β65 | date = March 2008 | pmid = 18286313 | doi = 10.1007/s12064-008-0023-2 | s2cid = 8741998 }}</ref> Quasispecies was also shown in compositional replicators (based on the [[Gard model]] for [[abiogenesis]])<ref>{{cite journal | vauthors = Gross R, Fouxon I, Lancet D, Markovitch O | title = Quasispecies in population of compositional assemblies | journal = BMC Evolutionary Biology | volume = 14 | pages = 265 | date = December 2014 | issue = 1 | pmid = 25547629 | pmc = 4357159 | doi = 10.1186/s12862-014-0265-1 | doi-access = free | bibcode = 2014BMCEE..14..265G }}</ref> and was also suggested to be applicable to describe cell's replication, which amongst other things requires the maintenance and evolution of the internal composition of the parent and bud.
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