Editing Mutation rate (section)

==Measurement==

An organism's mutation rates can be measured by a number of techniques.

One way to measure the mutation rate is by the fluctuation test, also known as the [[Luria–Delbrück experiment]]. This experiment demonstrated that bacteria mutations occur in the absence of selection instead of the presence of selection.<ref>{{cite book | vauthors = Fry M | date = 2016 | chapter = Chapter 4.5: Luria–Delbrück experiment | title = Landmark Experiments in Molecular Biology | location = Netherlands | publisher = Elsevier Science |isbn=978-0-12-802108-8 | page = 120 | chapter-url = https://books.google.com/books?id=VROKCgAAQBAJ&dq=Luria–Delbrück+experiment&pg=PA120 }}</ref>

This is very important to mutation rates because it proves experimentally mutations can occur without selection being a component—in fact, mutation and selection are completely distinct [https://www.livescience.com/1796-forces-evolution.html evolutionary forces]. Different DNA sequences can have different propensities to mutation (see below) and may not occur randomly.<ref name="pmid35022609">{{cite journal | vauthors = Monroe JG, Srikant T, Carbonell-Bejerano P, Becker C, Lensink M, Exposito-Alonso M, Klein M, Hildebrandt J, Neumann M, Kliebenstein D, Weng ML, Imbert E, Ågren J, Rutter MT, Fenster CB, Weigel D | title = Mutation bias reflects natural selection in Arabidopsis thaliana | journal = Nature | volume = 602 | issue = 7895 | pages = 101–105 | date = February 2022 | pmid = 35022609 | pmc = 8810380 | doi = 10.1038/s41586-021-04269-6 | bibcode = 2022Natur.602..101M }}</ref>

The most commonly measured class of mutations are substitutions, because they are relatively easy to measure with standard analyses of DNA sequence data. However substitutions have a substantially different rate of mutation (10<sup>−8</sup> to 10<sup>−9</sup> per generation for most cellular organisms) than other classes of mutation, which are frequently much higher (~10<sup>−3</sup> per generation for satellite DNA expansion/contraction<ref>{{cite journal | vauthors = Flynn JM, Caldas I, Cristescu ME, Clark AG | title = Selection Constrains High Rates of Tandem Repetitive DNA Mutation in <i>Daphnia pulex</i> | journal = Genetics | volume = 207 | issue = 2 | pages = 697–710 | date = October 2017 | pmid = 28811387 | pmc = 5629333 | doi = 10.1534/genetics.117.300146 | url = https://www.genetics.org/content/207/2/697 | access-date = 2020-03-21 | url-status = live | archive-url = https://web.archive.org/web/20200321203018/https://www.genetics.org/content/207/2/697 | archive-date = 2020-03-21 }}</ref>).

===Substitution rates===
Many sites in an organism's genome may admit mutations with small fitness effects. These sites are typically called neutral sites. Theoretically mutations under no selection become [[Fixation (population genetics)|fixed]] between organisms at precisely the mutation rate. Fixed synonymous mutations, i.e. [[synonymous substitutions]], are changes to the sequence of a gene that do not change the protein produced by that gene. They are often used as estimates of that mutation rate, despite the fact that some synonymous mutations have fitness effects. As an example, mutation rates have been directly inferred from the whole genome sequences of experimentally evolved replicate lines of ''Escherichia coli'' B.<ref name="Wielgoss">{{cite journal | vauthors = Wielgoss S, Barrick JE, Tenaillon O, Cruveiller S, Chane-Woon-Ming B, Médigue C, Lenski RE, Schneider D | title = Mutation Rate Inferred From Synonymous Substitutions in a Long-Term Evolution Experiment With Escherichia coli | journal = G3 | volume = 1 | issue = 3 | pages = 183–186 | date = August 2011 | pmid = 22207905 | pmc = 3246271 | doi = 10.1534/g3.111.000406 }}</ref>

===Mutation accumulation lines===
A particularly labor-intensive way of characterizing the mutation rate is the mutation accumulation line.

Mutation accumulation lines have been used to characterize mutation rates with the [[Bateman-Mukai Method]] and direct sequencing of well-studied experimental organisms ranging from intestinal bacteria (''[[E. coli]]''), roundworms (''[[C. elegans]]''), yeast (''[[S. cerevisiae]]''), fruit flies (''[[D. melanogaster]]''), and small ephemeral plants (''[[A. thaliana]]'').<ref name="Lucas-Lledo">{{cite journal | vauthors = Ossowski S, Schneeberger K, Lucas-Lledó JI, Warthmann N, Clark RM, Shaw RG, Weigel D, Lynch M | title = The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana | journal = Science | volume = 327 | issue = 5961 | pages = 92–94 | date = January 2010 | pmid = 20044577 | pmc = 3878865 | doi = 10.1126/science.1180677 | bibcode = 2010Sci...327...92O }}</ref>