Editing Genetics (section)

== Genetic change ==

=== Mutations ===
{{Main|Mutation}}

[[File:Gene-duplication.png|thumb|upright|Gene duplication allows diversification by providing redundancy: one gene can mutate and lose its original function without harming the organism.]]

During the process of DNA replication, errors occasionally occur in the polymerization of the second strand. These errors, called 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" ability of [[DNA polymerase]]s.<ref name="griffiths2000sect2706">{{cite book | veditors = Griffiths AJ, Miller JH, Suzuki DT, Lewontin RC, 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 | vauthors = Freisinger E, Grollman AP, Miller H, Kisker C | title = Lesion (in)tolerance reveals insights into DNA replication fidelity | journal = The EMBO Journal | volume = 23 | issue = 7 | pages = 1494–1505 | date = April 2004 | pmid = 15057282 | pmc = 391067 | doi = 10.1038/sj.emboj.7600158 }}</ref> 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 | veditors = Griffiths AJ, Miller JH, Suzuki DT, Lewontin RC, 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. The repair does not, however, always restore the original sequence. A particularly important source of DNA damages appears to be [[reactive oxygen species]]<ref name="pmid23378590">{{cite journal | vauthors = Cadet J, Wagner JR | title = DNA base damage by reactive oxygen species, oxidizing agents, and UV radiation | journal = Cold Spring Harbor Perspectives in Biology | volume = 5 | issue = 2 | page = a012559 | date = February 2013 | pmid = 23378590 | pmc = 3552502 | doi = 10.1101/cshperspect.a012559 }}</ref> produced by [[cellular respiration|cellular aerobic respiration]], and these can lead to mutations.<ref name="pmid22750987">{{cite journal | vauthors = Jena NR | title = DNA damage by reactive species: Mechanisms, mutation and repair | journal = Journal of Biosciences | volume = 37 | issue = 3 | pages = 503–517 | date = July 2012 | pmid = 22750987 | doi = 10.1007/s12038-012-9218-2 | s2cid = 14837181 }}</ref>

In organisms that use [[chromosomal crossover]] to exchange DNA and recombine genes, errors in alignment during meiosis can also cause mutations. Errors in crossover are especially likely when similar sequences cause partner chromosomes to adopt a mistaken alignment; this makes 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]], [[Gene deletion|deletions]] of entire regions—or the accidental exchange of whole parts of sequences between different chromosomes, [[chromosomal translocation]].<ref name="griffiths2000sect2844">{{cite book | veditors = Griffiths AJ, Miller JH, Suzuki DT, Lewontin RC, 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>[[File:Mutations.svg|thumb|This is a diagram showing mutations in an RNA sequence. Figure (1) is a normal RNA sequence, consisting of 4 codons. Figure (2) shows a missense, single point, non silent mutation. Figures (3 and 4) both show [[frameshift mutation]]s, which is why they are grouped together. Figure 3 shows a deletion of the second base pair in the second codon. Figure 4 shows an insertion in the third base pair of the second codon. Figure (5) shows a repeat expansion, where an entire codon is duplicated.]]

=== Natural selection and evolution ===

{{Main|Evolution}}
{{further|Natural selection}}

Mutations alter an organism's genotype and occasionally this causes different phenotypes to appear. Most mutations have little effect on an organism's phenotype, health, or reproductive [[fitness (biology)|fitness]].<ref>{{cite book | vauthors = Schaechter M |title=Encyclopedia of Microbiology |url=https://books.google.com/books?id=rLhdW5YzuO4C&pg=RA1-PA551 |year=2009 |publisher=Academic Press |isbn=978-0-12-373944-5 |page=551}}</ref> Mutations that do have an effect are usually detrimental, but occasionally some can be beneficial.<ref name="CalverLymbery2009">{{cite book | vauthors = Calver M, Lymbery A, McComb J, Bamford M |title=Environmental Biology |url=https://books.google.com/books?id=HemnRxzdiFQC&pg=PA118 |year=2009 |publisher=Cambridge University Press |isbn=978-0-521-67982-4 |page=118}}</ref> Studies in the fly ''[[Drosophila melanogaster]]'' suggest that if a mutation changes a protein produced by a gene, about 70 percent of these mutations are harmful with the remainder being either neutral or weakly beneficial.<ref>{{cite journal | vauthors = Sawyer SA, Parsch J, Zhang Z, Hartl DL | title = Prevalence of positive selection among nearly neutral amino acid replacements in Drosophila | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 104 | issue = 16 | pages = 6504–6510 | date = April 2007 | pmid = 17409186 | pmc = 1871816 | doi = 10.1073/pnas.0701572104 | doi-access = free | bibcode = 2007PNAS..104.6504S }}</ref>

[[File:Eukaryote tree.svg|thumb|left|An [[evolutionary tree]] of [[Eukaryote|eukaryotic]] organisms, constructed by the comparison of several [[orthologous gene]] sequences]]

[[Population genetics]] studies the distribution of genetic differences within populations and how these distributions change over time.<ref name="griffiths2000sect3842">{{cite book | veditors = Griffiths AJ, Miller JH, Suzuki DT, Lewontin RC, 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.3842 |chapter=Variation and its modulation}}</ref> Changes in the [[Allele frequency|frequency of an allele]] in a population are mainly influenced by [[natural selection]], where a given allele provides a selective or reproductive advantage to the organism,<ref name="griffiths2000sect3886">{{cite book | veditors = Griffiths AJ, Miller JH, Suzuki DT, Lewontin RC, 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.3886 |chapter=Selection}}</ref> as well as other factors such as [[mutation]], [[genetic drift]], [[genetic hitchhiking]],<ref>{{cite journal | vauthors = Gillespie JH | title = Is the population size of a species relevant to its evolution? | journal = Evolution; International Journal of Organic Evolution | volume = 55 | issue = 11 | pages = 2161–2169 | date = November 2001 | pmid = 11794777 | doi = 10.1111/j.0014-3820.2001.tb00732.x | s2cid = 221735887 | doi-access = free }}</ref> [[artificial selection]] and [[Gene flow|migration]].<ref name="griffiths2000sect3906">{{cite book | veditors = Griffiths AJ, Miller JH, Suzuki DT, Lewontin RC, 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.3906 |chapter=Random events}}</ref>

Over many generations, the genomes of organisms can change significantly, resulting in evolution. In the process called [[adaptation]], selection for beneficial mutations can cause a species to evolve into forms better able to survive in their environment.<ref name="Darwin">{{cite book | vauthors = Darwin C |author-link=Charles Darwin |year=1859 |title=On the Origin of Species |place=London |publisher=John Murray |edition= |page=1 |url=http://darwin-online.org.uk/content/frameset?itemID=F373&viewtype=text&pageseq=16 |isbn=978-0-8014-1319-3 |url-status=live |archive-url=http://archive.wikiwix.com/cache/20061212020054/http://darwin-online.org.uk/content/frameset?itemID=F373&viewtype=text&pageseq=16 |archive-date=12 December 2006 }}<br />Earlier related ideas were acknowledged in {{cite book | vauthors = Darwin C |author-link=Charles Darwin |year=1861 |title=On the Origin of Species |place=London |publisher=John Murray |edition=3rd |page=xiii |url=http://darwin-online.org.uk/content/frameset?itemID=F381&viewtype=text&pageseq=20 |no-pp=true |isbn=978-0-8014-1319-3 |url-status=live |archive-url=http://archive.wikiwix.com/cache/20110223145332/http://darwin-online.org.uk/content/frameset?itemID=F381&viewtype=text&pageseq=20 |archive-date=23 February 2011 }}</ref> New species are formed through the process of [[speciation]], often caused by geographical separations that prevent populations from exchanging genes with each other.<ref name="Gavrilets">{{cite journal | vauthors = Gavrilets S | title = Perspective: models of speciation: what have we learned in 40 years? | journal = Evolution; International Journal of Organic Evolution | volume = 57 | issue = 10 | pages = 2197–2215 | date = October 2003 | pmid = 14628909 | doi = 10.1554/02-727 | s2cid = 198158082 }}</ref>

By comparing the [[Sequence homology|homology]] between different species' genomes, it is possible to calculate the evolutionary distance between them and [[Molecular clock|when they may have diverged]]. Genetic comparisons are generally considered a more accurate method of characterizing the relatedness between species than the comparison of phenotypic characteristics. The evolutionary distances between species can be used to form [[evolutionary tree]]s; these trees represent the [[common descent]] and divergence of species over time, although they do not show the transfer of genetic material between unrelated species (known as [[horizontal gene transfer]] and most common in bacteria).<ref>{{cite journal | vauthors = Wolf YI, Rogozin IB, Grishin NV, Koonin EV | title = Genome trees and the tree of life | journal = Trends in Genetics | volume = 18 | issue = 9 | pages = 472–479 | date = September 2002 | pmid = 12175808 | doi = 10.1016/S0168-9525(02)02744-0 }}</ref>