Editing Quasispecies model (section)

==Formal background==

The model rests on four assumptions:<ref>{{cite journal | vauthors = Bull JJ, Meyers LA, Lachmann M | title = Quasispecies made simple | journal = PLOS Computational Biology | volume = 1 | issue = 6 | pages = e61 | date = November 2005 | pmid = 16322763 | pmc = 1289388 | doi = 10.1371/journal.pcbi.0010061 | bibcode = 2005PLSCB...1...61B | doi-access = free }}</ref>
# The self-replicating entities can be represented as sequences composed of a small number of building blocks—for example, sequences of RNA consisting of the four bases [[adenine]], [[guanine]], [[cytosine]], and [[uracil]].
# New sequences enter the system solely as the result of a copy process, either correct or erroneous, of other sequences that are already present.
# The substrates, or raw materials, necessary for ongoing replication are always present in sufficient quantity. Excess sequences are washed away in an outgoing flux.
# Sequences may decay into their building blocks. The probability of decay does not depend on the sequences' age; old sequences are just as likely to decay as young sequences.

In the quasispecies model, [[mutation]]s occur through errors made in the process of copying already existing sequences. Further, [[natural selection|selection]] arises because different types of sequences tend to replicate at different rates, which leads to the suppression of sequences that replicate more slowly in favor of sequences that replicate faster. However, the quasispecies model does not predict the ultimate extinction of all but the fastest replicating sequence. Although the sequences that replicate more slowly cannot sustain their abundance level by themselves, they are constantly replenished as sequences that replicate faster mutate into them. At equilibrium, removal of slowly replicating sequences due to decay or outflow is balanced by replenishing, so that even relatively slowly replicating sequences can remain present in finite abundance.<ref>{{cite book|title=Systems Biology: A Textbook|publisher=By Edda Klipp, Wolfram Liebermeister, Christoph Wierling, Axel Kowald}}</ref>

Due to the ongoing production of mutant sequences, selection does not act on single sequences, but on mutational "clouds" of closely related sequences, referred to as ''quasispecies''. In other words, the evolutionary success of a particular sequence depends not only on its own replication rate, but also on the replication rates of the mutant sequences it produces, and on the replication rates of the sequences of which it is a mutant. As a consequence, the sequence that replicates fastest may even disappear completely in selection-mutation equilibrium, in favor of more slowly replicating sequences that are part of a quasispecies with a higher average growth rate.<ref>{{cite journal | vauthors = Schuster P, Swetina J | title = Stationary mutant distributions and evolutionary optimization | journal = Bulletin of Mathematical Biology | volume = 50 | issue = 6 | pages = 635–60 | date = November 1988 | pmid = 3219448 | doi = 10.1007/BF02460094 | s2cid = 189885782 }}</ref>  Mutational clouds as predicted by the quasispecies model have been observed in RNA viruses and in ''in vitro'' RNA replication.<ref>{{cite journal | vauthors = Domingo E, Holland JJ | title = RNA virus mutations and fitness for survival | journal = Annual Review of Microbiology | volume = 51 | pages = 151–78 | date = October 1997 | pmid = 9343347 | doi = 10.1146/annurev.micro.51.1.151 }}</ref><ref>{{cite journal | vauthors = Burch CL, Chao L | title = Evolvability of an RNA virus is determined by its mutational neighbourhood | journal = Nature | volume = 406 | issue = 6796 | pages = 625–8 | date = August 2000 | pmid = 10949302 | doi = 10.1038/35020564 | bibcode = 2000Natur.406..625B | s2cid = 1894386 }}</ref>

The mutation rate and the general fitness of the molecular sequences and their neighbors is crucial to the formation of a quasispecies. If the mutation rate is zero, there is no exchange by mutation, and each sequence is its own species. If the mutation rate is too high, exceeding what is known as the [[Error threshold (evolution)|error threshold]], the quasispecies will break down and be dispersed over the entire range of available sequences.<ref>{{cite journal | vauthors = Manrubia SC, Domingo E, Lázaro E | title = Pathways to extinction: beyond the error threshold | journal = Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences | volume = 365 | issue = 1548 | pages = 1943–52 | date = June 2010 | pmid = 20478889 | pmc = 2880120 | doi = 10.1098/rstb.2010.0076 }}</ref>