Editing Mutation (section)

== Overview ==
Mutations can involve the [[gene duplication|duplication]] of large sections of DNA, usually through [[genetic recombination]].<ref>{{cite journal | vauthors = Hastings PJ, Lupski JR, Rosenberg SM, Ira G | title = Mechanisms of change in gene copy number | journal = Nature Reviews. Genetics | volume = 10 | issue = 8 | pages = 551–64 | date = August 2009 | pmid = 19597530 | pmc = 2864001 | doi = 10.1038/nrg2593 | author-link2 = James R. Lupski }}</ref> These duplications are a major source of raw material for evolving new genes, with tens to hundreds of genes duplicated in animal genomes every million years.<ref>{{cite book | vauthors = Carroll SB, Grenier JK, Weatherbee SD |author-link1=Sean B. Carroll |year=2005 |title=From DNA to Diversity: Molecular Genetics and the Evolution of Animal Design |edition=2nd |location=Malden, MA |publisher=[[Wiley-Blackwell|Blackwell Publishing]] |isbn=978-1-4051-1950-4 |lccn=2003027991 |oclc=53972564}}</ref> Most genes belong to larger [[gene family|gene families]] of shared ancestry, detectable by their [[sequence homology]].<ref>{{cite journal | vauthors = Harrison PM, Gerstein M | title = Studying genomes through the aeons: protein families, pseudogenes and proteome evolution | journal = Journal of Molecular Biology | volume = 318 | issue = 5 | pages = 1155–74 | date = May 2002 | pmid = 12083509 | doi = 10.1016/S0022-2836(02)00109-2 | author-link2 = Mark Bender Gerstein }}</ref> Novel genes are produced by several methods, commonly through the duplication and mutation of an ancestral gene, or by recombining parts of different genes to form new combinations with new functions.<ref>{{cite journal | vauthors = Orengo CA, Thornton JM | title = Protein families and their evolution-a structural perspective | journal = Annual Review of Biochemistry | volume = 74 | pages = 867–900 | date = July 2005 | pmid = 15954844 | doi = 10.1146/annurev.biochem.74.082803.133029 | author-link2 = Janet Thornton }}</ref><ref>{{cite journal | vauthors = Long M, Betrán E, Thornton K, Wang W | title = The origin of new genes: glimpses from the young and old | journal = Nature Reviews. Genetics | volume = 4 | issue = 11 | pages = 865–75 | date = November 2003 | pmid = 14634634 | doi = 10.1038/nrg1204 | s2cid = 33999892 }}</ref>

Here, [[protein domain]]s act as modules, each with a particular and independent function, that can be mixed together to produce genes encoding new proteins with novel properties.<ref>{{cite journal | vauthors = Wang M, Caetano-Anollés G | title = The evolutionary mechanics of domain organization in proteomes and the rise of modularity in the protein world | journal = Structure | volume = 17 | issue = 1 | pages = 66–78 | date = January 2009 | pmid = 19141283 | doi = 10.1016/j.str.2008.11.008 | author-link2 = Gustavo Caetano-Anolles | doi-access = free }}</ref> For example, the [[human eye]] uses four genes to make structures that sense light: three for [[cone cell]] or [[colour vision]] and one for [[rod cell]] or night vision; all four arose from a single ancestral gene.<ref>{{cite journal | vauthors = Bowmaker JK | s2cid = 12851209 | title = Evolution of colour vision in vertebrates | journal = Eye | volume = 12 | issue = Pt 3b | pages = 541–7 | date = May 1998 | pmid = 9775215 | doi = 10.1038/eye.1998.143 | doi-access = free }}</ref> Another advantage of duplicating a gene (or even an entire genome) is that this increases [[Redundancy (engineering)|engineering redundancy]]; this allows one gene in the pair to acquire a new function while the other copy performs the original function.<ref>{{cite journal | vauthors = Gregory TR, Hebert PD | title = The modulation of DNA content: proximate causes and ultimate consequences | journal = [[Genome Research]] | volume = 9 | issue = 4 | pages = 317–24 | date = April 1999 | pmid = 10207154 | doi = 10.1101/gr.9.4.317 | s2cid = 16791399 | author-link1 = T. Ryan Gregory | author-link2 = Paul D. N. Hebert | doi-access = free }}</ref><ref>{{cite journal | vauthors = Hurles M | title = Gene duplication: the genomic trade in spare parts | journal = PLOS Biology | volume = 2 | issue = 7 | pages = E206 | date = July 2004 | pmid = 15252449 | pmc = 449868 | doi = 10.1371/journal.pbio.0020206 | doi-access = free }}</ref> Other types of mutation occasionally create new genes from previously [[noncoding DNA]].<ref>{{cite journal | vauthors = Liu N, Okamura K, Tyler DM, Phillips MD, Chung WJ, Lai EC | title = The evolution and functional diversification of animal microRNA genes | journal = Cell Research | volume = 18 | issue = 10 | pages = 985–96 | date = October 2008 | pmid = 18711447 | pmc = 2712117 | doi = 10.1038/cr.2008.278 }}</ref><ref>{{cite journal | vauthors = Siepel A | title = Darwinian alchemy: Human genes from noncoding DNA | journal = Genome Research | volume = 19 | issue = 10 | pages = 1693–5 | date = October 2009 | pmid = 19797681 | pmc = 2765273 | doi = 10.1101/gr.098376.109 | author-link = Adam C. Siepel }}</ref>

Changes in [[chromosome]] number may involve even larger mutations, where segments of the DNA within chromosomes break and then rearrange. For example, in the [[Homininae]], two chromosomes fused to produce human [[chromosome 2 (human)|chromosome 2]]; this fusion did not occur in the [[Lineage (evolution)|lineage]] of the other [[ape]]s, and they retain these separate chromosomes.<ref>{{cite journal | vauthors = Zhang J, Wang X, Podlaha O | title = Testing the chromosomal speciation hypothesis for humans and chimpanzees | journal = Genome Research | volume = 14 | issue = 5 | pages = 845–51 | date = May 2004 | pmid = 15123584 | pmc = 479111 | doi = 10.1101/gr.1891104 }}</ref> In evolution, the most important role of such chromosomal rearrangements may be to accelerate the divergence of a population into [[Speciation|new species]] by making populations less likely to interbreed, thereby preserving genetic differences between these populations.<ref>{{cite journal | vauthors = Ayala FJ, Coluzzi M | title = Chromosome speciation: humans, Drosophila, and mosquitoes | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 102 | issue = Suppl 1 | pages = 6535–42 | date = May 2005 | pmid = 15851677 | pmc = 1131864 | doi = 10.1073/pnas.0501847102 | bibcode = 2005PNAS..102.6535A | author-link1 = Francisco J. Ayala | doi-access = free }}</ref>

Sequences of DNA that can move about the genome, such as [[Transposable element|transposon]]s, make up a major fraction of the genetic material of plants and animals, and may have been important in the evolution of genomes.<ref>{{cite journal | vauthors = Hurst GD, Werren JH | s2cid = 2715605 | title = The role of selfish genetic elements in eukaryotic evolution | journal = Nature Reviews Genetics | volume = 2 | issue = 8 | pages = 597–606 | date = August 2001 | pmid = 11483984 | doi = 10.1038/35084545 }}</ref> For example, more than a million copies of the [[Alu element|Alu sequence]] are present in the [[human genome]], and these sequences have now been recruited to perform functions such as regulating [[gene expression]].<ref>{{cite journal | vauthors = Häsler J, Strub K | title = Alu elements as regulators of gene expression | journal = Nucleic Acids Research | volume = 34 | issue = 19 | pages = 5491–7 | date = November 2006 | pmid = 17020921 | pmc = 1636486 | doi = 10.1093/nar/gkl706 }}</ref> Another effect of these mobile DNA sequences is that when they move within a genome, they can mutate or delete existing genes and thereby produce genetic diversity.<ref name="transposition764" />

Nonlethal mutations accumulate within the [[gene pool]] and increase the amount of genetic variation.<ref name="Eyre-Walker07">{{cite journal | vauthors = Eyre-Walker A, Keightley PD | s2cid = 10868777 | title = The distribution of fitness effects of new mutations | journal = Nature Reviews Genetics | volume = 8 | issue = 8 | pages = 610–8 | date = August 2007 | pmid = 17637733 | doi = 10.1038/nrg2146 | url = http://www.lifesci.sussex.ac.uk/home/Adam_Eyre-Walker/Website/Publications_files/EWNRG07.pdf |author1-link = Adam Eyre-Walker | author2-link = Peter Keightley | url-status = dead | archive-url = https://web.archive.org/web/20160304195010/http://www.lifesci.sussex.ac.uk/home/Adam_Eyre-Walker/Website/Publications_files/EWNRG07.pdf | archive-date = 4 March 2016 | access-date = 6 September 2010 }}</ref> The abundance of some genetic changes within the gene pool can be reduced by [[natural selection]], while other "more favorable" mutations may accumulate and result in adaptive changes.

[[File:Prodryas.png|thumb|right|199px|''[[Prodryas persephone]]'', a Late [[Eocene]] butterfly]]
For example, a [[butterfly]] may produce [[offspring]] with new mutations. The majority of these mutations will have no effect; but one might change the [[colour]] of one of the butterfly's offspring, making it harder (or easier) for predators to see. If this color change is advantageous, the chances of this butterfly's surviving and producing its own offspring are a little better, and over time the number of butterflies with this mutation may form a larger percentage of the population.<ref>{{Cite journal |last=Darwin |first=Charles |last2=Wallace |first2=Alfred |date=August 1858 |title=On the Tendency of Species to form Varieties; and on the Perpetuation of Varieties and Species by Natural Means of Selection. |url=https://academic.oup.com/zoolinnean/article-lookup/doi/10.1111/j.1096-3642.1858.tb02500.x |journal=Journal of the Proceedings of the Linnean Society of London. Zoology |language=en |volume=3 |issue=9 |pages=45–62 |doi=10.1111/j.1096-3642.1858.tb02500.x}}</ref>

[[Neutral mutation]]s are defined as mutations whose effects do not influence the [[Fitness (biology)|fitness]] of an individual. These can increase in frequency over time due to [[genetic drift]]. It is believed that the overwhelming majority of mutations have no significant effect on an organism's fitness.<ref name="Kimura-1983" /><ref>{{cite book | url = https://books.google.com/books?id=ybeLBgAAQBAJ&q=t+is+believed+that+the+overwhelming+majority+of+mutations+have+no+significant+effect+on+an+organism's+fitness.&pg=PA299 | title = Fundamentals of Polymer Physics and Molecular Biophysics | vauthors = Bohidar HB | date = January 2015 | publisher = Cambridge University Press | isbn = 978-1-316-09302-3 }}</ref> Also, DNA repair mechanisms are able to mend most changes before they become permanent mutations, and many organisms have mechanisms, such as [[Apoptosis|apoptotic pathways]], for eliminating otherwise-permanently mutated [[somatic cell]]s.<ref>{{Cite web |last=Grisham |first=Julie |date=16 May 2014 |title=What Is Apoptosis? {{!}} Memorial Sloan Kettering Cancer Center |url=https://www.mskcc.org/news/what-apoptosis |access-date=30 May 2024 |website=www.mskcc.org |language=en}}</ref>

Beneficial mutations can improve reproductive success.<ref>{{Cite book|url=https://books.google.com/books?id=sElrZSzoLYMC&pg=PA107|title=Dear Mr. Darwin: Letters on the Evolution of Life and Human Nature| vauthors = Dover GA, Darwin C |date=2000|publisher=University of California Press|isbn=9780520227903|language=en}}</ref><ref>{{Cite book|url=https://books.google.com/books?id=OwBQCwAAQBAJ&pg=PA108|title=Genetics and Evolution of Infectious Diseases| vauthors = Tibayrenc M | date=12 January 2017|publisher=Elsevier|isbn=9780128001530|language=en}}</ref>