Editing Microevolution (section)

===Mutation===
{{Main|Mutation}}
[[File:Gene-duplication.svg|thumb|100px|left|Duplication of part of a [[chromosome]]]]
Mutations are changes in the [[DNA sequencing|DNA sequence]] of a cell's [[genome]] and are caused by [[Radioactive decay|radiation]], [[virus]]es, [[transposon]]s and [[mutagen|mutagenic chemicals]], as well as errors that occur during [[meiosis]] or [[DNA replication]].<ref name=Bertram>{{cite journal |author=Bertram J |title=The molecular biology of cancer |journal=Mol. Aspects Med. |volume=21 |issue=6 |pages=167–223 |year=2000 |pmid=11173079 |doi=10.1016/S0098-2997(00)00007-8|s2cid=24155688 }}</ref><ref name="transposition764">{{cite journal |author=Aminetzach YT, Macpherson JM, Petrov DA |title=Pesticide resistance via transposition-mediated adaptive gene truncation in Drosophila |journal=Science |volume=309 |issue=5735 |pages=764–7 |year=2005 |pmid=16051794 |doi=10.1126/science.1112699|last2=MacPherson |last3=Petrov |bibcode=2005Sci...309..764A |s2cid=11640993 }}</ref><ref name=Burrus>{{cite journal |author=Burrus V, Waldor M |title=Shaping bacterial genomes with integrative and conjugative elements |journal=Res. Microbiol. |volume=155 |issue=5 |pages=376–86 |year=2004 |pmid=15207870 |doi=10.1016/j.resmic.2004.01.012|last2=Waldor |doi-access=free }}</ref> Errors are introduced particularly often in the process of [[DNA replication]], in the polymerization of the second strand. These errors can also be induced by the organism itself, by [[cellular processes]] such as [[somatic hypermutation|hypermutation]]. Mutations can affect the phenotype of an organism, especially if they occur within the protein coding sequence of a gene. Error rates are usually very low—1 error in every 10–100&nbsp;million bases—due to the [[Proofreading (biology)|proofreading ability]] of [[DNA polymerase]]s.<ref name=griffiths2000sect2706>{{cite book |editor1-first=Anthony J. F. |editor1-last=Griffiths |editor2-first=Jeffrey H. |editor2-last=Miller |editor3-first=David T. |editor3-last=Suzuki |editor4-first=Richard C. |editor4-last=Lewontin |editor5-first=William M. |editor5-last=Gelbart |title=An Introduction to Genetic Analysis |year=2000 |isbn=978-0-7167-3520-5 |edition=7th |publisher=W. H. Freeman |location=New York |chapter-url=https://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=iga.section.2706 |chapter=Spontaneous mutations}}</ref><ref name=Kunkel>{{cite journal |doi=10.1038/sj.emboj.7600158 |pmid=15057282 |year=2004 |last1=Freisinger |first1=E |last2=Grollman |last3=Miller |last4=Kisker |title=Lesion (in)tolerance reveals insights into DNA replication fidelity. |volume=23 |issue=7 |pages=1494–505 |journal=The EMBO Journal|first2=AP |first3=H |first4=C |pmc=391067}}</ref> (Without proofreading error rates are a thousandfold higher; because many viruses rely on DNA and RNA polymerases that lack proofreading ability, they experience higher mutation rates.) Processes that increase the rate of changes in DNA are called [[mutagenic]]: mutagenic chemicals promote errors in DNA replication, often by interfering with the structure of base-pairing, while [[UV radiation]] induces mutations by causing damage to the DNA structure.<ref name=griffiths2000sect2727>{{cite book |editor1-first=Anthony J. F. |editor1-last=Griffiths |editor2-first=Jeffrey H. |editor2-last=Miller |editor3-first=David T. |editor3-last=Suzuki |editor4-first=Richard C. |editor4-last=Lewontin |editor5-first=William M. |editor5-last=Gelbart |title=An Introduction to Genetic Analysis |year=2000 |isbn=978-0-7167-3520-5 |edition=7th |publisher=W. H. Freeman |location=New York |chapter-url=https://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=iga.section.2727 |chapter=Induced mutations}}</ref> Chemical damage to DNA occurs naturally as well, and cells use [[DNA repair]] mechanisms to repair mismatches and breaks in DNA—nevertheless, the repair sometimes fails to return the DNA to its original sequence.

In organisms that use [[chromosomal crossover]] to exchange DNA and recombine genes, errors in alignment during [[meiosis]] can also cause mutations.<ref name=griffiths2000sect2844>{{cite book |editor1-first=Anthony J. F. |editor1-last=Griffiths |editor2-first=Jeffrey H. |editor2-last=Miller |editor3-first=David T. |editor3-last=Suzuki |editor4-first=Richard C. |editor4-last=Lewontin |editor5-first=William M. |editor5-last=Gelbart |title=An Introduction to Genetic Analysis |year=2000 |isbn=978-0-7167-3520-5 |edition=7th |publisher=W. H. Freeman |location=New York |chapter-url=https://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=iga.section.2844 |chapter=Chromosome Mutation I: Changes in Chromosome Structure: Introduction}}</ref> Errors in crossover are especially likely when similar sequences cause partner chromosomes to adopt a mistaken alignment making some regions in genomes more prone to mutating in this way. These errors create large structural changes in DNA sequence—[[gene duplication|duplications]], [[chromosomal inversion|inversions]] or [[gene deletion|deletions]] of entire regions, or the accidental exchanging of whole parts between different chromosomes (called [[chromosomal translocation|translocation]]).

Mutation can result in several different types of change in DNA sequences; these can either have no effect, alter the [[gene product|product of a gene]], or prevent the gene from functioning. Studies in the fly ''[[Drosophila melanogaster]]'' suggest that if a mutation changes a protein produced by a gene, this will probably be harmful, with about 70 percent of these mutations having damaging effects, and the remainder being either neutral or weakly beneficial.<ref>{{cite journal |author=Sawyer SA, Parsch J, Zhang Z, Hartl DL |title=Prevalence of positive selection among nearly neutral amino acid replacements in Drosophila |journal=Proc. Natl. Acad. Sci. U.S.A. |volume=104 |issue=16 |pages=6504–10 |year=2007 |pmid=17409186 |doi=10.1073/pnas.0701572104 |pmc=1871816|last2=Parsch |last3=Zhang |last4=Hartl |bibcode=2007PNAS..104.6504S |doi-access=free }}</ref> Due to the damaging effects that mutations can have on cells, organisms have evolved mechanisms such as [[DNA repair]] to remove mutations.<ref name=Bertram/> Therefore, the optimal mutation rate for a species is a trade-off between costs of a high mutation rate, such as deleterious mutations, and the [[metabolism|metabolic]] costs of maintaining systems to reduce the mutation rate, such as DNA repair enzymes.<ref name=Sniegowski>{{cite journal |author=Sniegowski P, Gerrish P, Johnson T, Shaver A |title=The evolution of mutation rates: separating causes from consequences |journal=BioEssays |volume=22 |issue=12 |pages=1057–66 |year=2000 |pmid=11084621 |doi=10.1002/1521-1878(200012)22:12<1057::AID-BIES3>3.0.CO;2-W|last2=Gerrish |last3=Johnson |last4=Shaver |s2cid=36771934 }}</ref> Viruses that use RNA as their genetic material have rapid mutation rates,<ref>{{cite journal |author=Drake JW, Holland JJ |title=Mutation rates among RNA viruses |journal=Proc. Natl. Acad. Sci. U.S.A. |volume=96 |issue=24 |pages=13910–3 |year=1999 |pmid=10570172 |pmc=24164 |doi=10.1073/pnas.96.24.13910|last2=Holland |bibcode=1999PNAS...9613910D |doi-access=free }}</ref> which can be an advantage since these viruses will evolve constantly and rapidly, and thus evade the defensive responses of e.g. the human [[immune system]].<ref>{{cite journal |author=Holland J, Spindler K, Horodyski F, Grabau E, Nichol S, VandePol S |title=Rapid evolution of RNA genomes |journal=Science |volume=215 |issue=4540 |pages=1577–85 |year=1982 |pmid=7041255 |doi=10.1126/science.7041255|last2=Spindler |last3=Horodyski |last4=Grabau |last5=Nichol |last6=Vandepol |bibcode=1982Sci...215.1577H }}</ref>

Mutations can involve large sections of DNA becoming [[gene duplication|duplicated]], usually through [[genetic recombination]].<ref>{{Cite journal| doi = 10.1038/nrg2593| pmid = 19597530| volume = 10| issue = 8| pages = 551–564| last1 = Hastings| first1 = P J| title = Mechanisms of change in gene copy number| journal = Nature Reviews Genetics| year = 2009| last2 = Lupski| first2 = JR| last3 = Rosenberg| first3 = SM| last4 = Ira| first4 = G| pmc=2864001}}</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|title=From DNA to Diversity: Molecular Genetics and the Evolution of Animal Design. Second Edition |publisher=Blackwell Publishing |year=2005 |location=Oxford |isbn=978-1-4051-1950-4|vauthors=Carroll SB, Grenier J, Weatherbee SD }}</ref> Most genes belong to larger [[gene family|families of genes]] of [[homology (biology)|shared ancestry]].<ref>{{cite journal |author=Harrison P, Gerstein M |title=Studying genomes through the aeons: protein families, pseudogenes and proteome evolution |journal=J Mol Biol |volume=318 |issue=5 |pages=1155–74 |year=2002 |pmid=12083509 |doi=10.1016/S0022-2836(02)00109-2|last2=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 |author=Orengo CA, Thornton JM |title=Protein families and their evolution-a structural perspective |journal=Annu. Rev. Biochem. |volume=74 |pages=867–900 |year=2005 |pmid=15954844 |doi=10.1146/annurev.biochem.74.082803.133029|last2=Thornton |issue=1 |s2cid=7483470 }}</ref><ref>{{cite journal |author=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|last2=Betrán |last3=Thornton |last4=Wang |s2cid=33999892 }}</ref>

Here, [[protein domain|domains]] 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 |author=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 |year=2009 |doi=10.1016/j.str.2008.11.008 |pmid=19141283|last2=Caetano-Anollés |doi-access=free }}</ref> For example, the human eye uses four genes to make structures that sense light: three for [[Cone cell|color vision]] and one for [[Rod cell|night vision]]; all four arose from a single ancestral gene.<ref>{{cite journal |author=Bowmaker JK |title=Evolution of colour vision in vertebrates |journal=Eye |volume=12 |issue=Pt 3b |pages=541–7 |year=1998 |pmid=9775215 |doi=10.1038/eye.1998.143|s2cid=12851209 |doi-access=free }}</ref> Another advantage of duplicating a gene (or even an [[Polyploidy|entire genome]]) is that this increases [[Redundancy (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 |author=Gregory TR, Hebert PD |title=The modulation of DNA content: proximate causes and ultimate consequences |url=http://genome.cshlp.org/content/9/4/317.full |journal=Genome Res. |volume=9 |issue=4 |pages=317–24 |year=1999 |pmid=10207154 |doi=10.1101/gr.9.4.317 |last2=Hebert |s2cid=16791399 |doi-access=free }}</ref><ref>{{cite journal |author=Hurles M |title=Gene duplication: the genomic trade in spare parts |journal=PLOS Biol. |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 | title=The evolution and functional diversification of animal microRNA genes| author=Liu N, Okamura K, Tyler DM| journal=Cell Res.| year=2008| volume=18| pages=985–96| doi=10.1038/cr.2008.278 |pmid=18711447 | issue=10 | pmc=2712117| last2=Okamura| last3=Tyler| last4=Phillips| last5=Chung| last6=Lai}}</ref><ref>{{cite journal |author=Siepel A |title=Darwinian alchemy: Human genes from noncoding DNA |journal=Genome Res. |volume=19 |issue=10 |pages=1693–5 |date=October 2009 |pmid=19797681 |doi=10.1101/gr.098376.109 |pmc=2765273}}</ref>