Editing Selfish genetic element (section)

== Consequences to the host ==

=== Species extinction ===
Perhaps one of the clearest ways to see that the process of natural selection does not always have organismal fitness as the sole driver is when selfish genetic elements have their way without restriction. In such cases, selfish elements can, in principle, result in species extinction. This possibility was pointed out already in 1928 by Sergey Gershenson<ref name=":5" /> and then in 1967, [[W. D. Hamilton|Bill Hamilton]]<ref>{{cite journal | vauthors = Hamilton WD | title = Extraordinary sex ratios. A sex-ratio theory for sex linkage and inbreeding has new implications in cytogenetics and entomology | journal = Science | volume = 156 | issue = 3774 | pages = 477–88 | date = April 1967 | pmid = 6021675 | doi = 10.1126/science.156.3774.477}}</ref> developed a formal population genetic model for a case of segregation distortion of sex chromosomes driving a population to extinction. In particular, if a selfish element should be able to direct the production of sperm, such that males bearing the element on the Y chromosome would produce an excess of Y-bearing sperm, then in the absence of any countervailing force, this would ultimately result in the Y chromosome going to fixation in the population, producing an extremely male-biased sex ratio. In ecologically challenged species, such biased sex ratios imply that the conversion of resources to offspring becomes very inefficient, to the point of risking extinction.<ref>{{Cite book|title=Allee effects in ecology and conservation|last=Franck.|first=Courchamp|date=2009|publisher=Oxford University Press|isbn=978-0199567553|oclc=929797557}}</ref>

=== Speciation ===
Selfish genetic elements have been shown to play a role in [[speciation]].<ref name=":9" /><ref name=":10" /><ref>{{cite journal | vauthors = Patten MM | title = Selfish X chromosomes and speciation | journal = Molecular Ecology | volume = 27 | issue = 19 | pages = 3772–3782 | date = October 2018 | pmid = 29281152 | doi = 10.1111/mec.14471 | bibcode = 2018MolEc..27.3772P | s2cid = 20779621 }}</ref> This could happen because the presence of selfish genetic elements can result in changes in morphology and/or life history, but ways by which the co-evolution between selfish genetic elements and their suppressors can cause reproductive isolation through so-called [[Bateson–Dobzhansky–Muller model|Bateson–Dobzhansky–Muller incompatibilities]] has received particular attention.

An early striking example of hybrid dysgenesis induced by a selfish genetic element was the ''P'' element in ''Drosophila''.<ref>{{cite journal | vauthors = Engels WR | title = The origin of P elements in Drosophila melanogaster | journal = BioEssays | volume = 14 | issue = 10 | pages = 681–6 | date = October 1992 | pmid = 1285420 | doi = 10.1002/bies.950141007 | s2cid = 20741333 }}</ref><ref>{{cite journal | vauthors = Kidwell MG | title = Evolution of hybrid dysgenesis determinants in Drosophila melanogaster | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 80 | issue = 6 | pages = 1655–9 | date = March 1983 | pmid = 6300863 | pmc = 393661 | doi = 10.1073/pnas.80.6.1655| bibcode = 1983PNAS...80.1655K | doi-access = free }}</ref> If males carrying the ''P'' element were crossed to females lacking it, the resulting offspring suffered from reduced fitness. However, offspring of the reciprocal cross were normal, as would be expected since [[Piwi-interacting RNA|piRNAs]] are maternally inherited. The ''P'' element is typically present only in wild strains, and not in lab strains of ''D. melanogaster'', as the latter were collected before the ''P'' elements were introduced into the species, probably from a closely related ''Drosophila'' species. The ''P'' element story is also a good example of how the rapid co-evolution between selfish genetic elements and their silencers can lead to incompatibilities on short evolutionary time scales, as little as within a few decades.<ref name=":9" />

Several other examples of selfish genetic elements causing reproductive isolation have since been demonstrated. Crossing different species of ''Arabidopsis'' results in both higher activity of transposable elements<ref>Josefsson C, Dilkes B, Comai L. Parent-dependent loss of gene silencing during interspecies hybridization. Curr Biol. 2006;16: 1322–1328.</ref> and disruption in imprinting,<ref>{{cite journal | vauthors = Walia H, Josefsson C, Dilkes B, Kirkbride R, Harada J, Comai L | title = Dosage-dependent deregulation of an AGAMOUS-LIKE gene cluster contributes to interspecific incompatibility | journal = Current Biology | volume = 19 | issue = 13 | pages = 1128–32 | date = July 2009 | pmid = 19559614 | pmc = 6754343 | doi = 10.1016/j.cub.2009.05.068 | bibcode = 2009CBio...19.1128W }}</ref> both of which have been linked to fitness reduction in the resulting hybrids. Hybrid dysgenesis has also been shown to be caused by centromeric drive in barley<ref>{{cite journal | vauthors = Sanei M, Pickering R, Kumke K, Nasuda S, Houben A | title = Loss of centromeric histone H3 (CENH3) from centromeres precedes uniparental chromosome elimination in interspecific barley hybrids | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 108 | issue = 33 | pages = E498–505 | date = August 2011 | pmid = 21746892 | pmc = 3158150 | doi = 10.1073/pnas.1103190108 | doi-access = free }}</ref> and in several species of angiosperms by mito-nuclear conflict.<ref>{{cite journal | vauthors = Rieseberg LH, Blackman BK | title = Speciation genes in plants | journal = Annals of Botany | volume = 106 | issue = 3 | pages = 439–55 | date = September 2010 | pmid = 20576737 | pmc = 2924826 | doi = 10.1093/aob/mcq126 }}</ref>

=== Genome-size variation ===
Attempts to understand the extraordinary variation in genome size ([[C-value]])—animals vary 7,000 fold and land plants some 2,400-fold—has a long history in biology.<ref>{{cite book | last = Ryan | first = Gregory T | title = The Evolution of the Genome | publisher = Academic Press | date =  2005 | isbn = 978-0-12-301463-4 }}</ref> However, this variation is poorly correlated with gene number or any measure of organismal complexity, which led CA Thomas to coin the term C-value paradox in 1971.<ref>{{cite journal | vauthors = Thomas CA | title = The genetic organization of chromosomes | journal = Annu Rev Genet | date = December 1971 | volume = 5 | pages = 237–256 | doi = 10.1146/annurev.ge.05.120171.001321 | pmid = 16097657 }}</ref> The discovery of non-coding DNA resolved some of the paradox, and most current researchers now use the term "C-value enigma".<ref>{{cite journal | vauthors = Gregory TR | title = Macroevolution, hierarchy theory, and the C-value enigma. | journal = Paleobiology | year = 2004 | volume = 30 | issue = 2 | pages = 179–202 | doi = 10.1666/0094-8373(2004)030<0179:MHTATC>2.0.CO;2 | bibcode = 2004Pbio...30..179G | s2cid = 86214775 }}</ref>

Two kinds of selfish genetic elements in particular have been shown to contribute to genome-size variation: B chromosomes and transposable elements.<ref name=":12" /><ref>{{cite journal | vauthors = Ågren JA, Wright SI | title = Selfish genetic elements and plant genome size evolution | journal = Trends in Plant Science | volume = 20 | issue = 4 | pages = 195–6 | date = April 2015 | pmid = 25802093 | doi = 10.1016/j.tplants.2015.03.007 }}</ref> The contribution of transposable elements to the genome is especially well studied in plants.<ref name=":18" /><ref name=":19" /><ref>{{cite journal | vauthors = Wright SI, Agren JA | title = Sizing up Arabidopsis genome evolution | journal = Heredity | volume = 107 | issue = 6 | pages = 509–10 | date = December 2011 | pmid = 21712843 | pmc = 3242632 | doi = 10.1038/hdy.2011.47 }}</ref> A striking example is how the genome of the model organism ''[[Arabidopsis thaliana]]'' contains the same number of genes as that of the Norwegian spruce (''Picea abies''), around 30,000, but accumulation of transposons means that the genome of the latter is some 100 times larger. Transposable element abundance has also been shown to cause the unusually large genomes found in salamanders.<ref>{{cite journal | vauthors = Sun C, Shepard DB, Chong RA, López Arriaza J, Hall K, Castoe TA, Feschotte C, Pollock DD, Mueller RL | title = LTR retrotransposons contribute to genomic gigantism in plethodontid salamanders | journal = Genome Biology and Evolution | volume = 4 | issue = 2 | pages = 168–83 | date = 2012 | pmid = 22200636 | pmc = 3318908 | doi = 10.1093/gbe/evr139 }}</ref>

The presence of an abundance of transposable elements in many eukaryotic genomes was a central theme of the original selfish DNA papers mentioned above (See [[#Conceptual developments|Conceptual developments]]). Most people quickly accepted the central message of those papers, that the existence of transposable elements can be explained by selfish selection at the gene level and there is no need to invoke individual level selection. However, the idea that organisms keep transposable elements around as genetic reservoir to "speed up evolution" or for other regulatory functions persists in some quarters.<ref>{{cite journal | vauthors = Fedoroff NV | title = Presidential address. Transposable elements, epigenetics, and genome evolution | journal = Science | volume = 338 | issue = 6108 | pages = 758–67 | date = November 2012 | pmid = 23145453 | doi = 10.1126/science.338.6108.758| doi-access = free }}</ref> In 2012, when the [[ENCODE|ENCODE Project]] published a paper claiming that 80% of the human genome can be assigned a function, a claim interpreted by many as the death of the idea of [[Non-coding DNA|junk DNA]], this debate was reignited.<ref>{{cite journal | vauthors = Elliott TA, Linquist S, Gregory TR | title = Conceptual and empirical challenges of ascribing functions to transposable elements | journal = The American Naturalist | volume = 184 | issue = 1 | pages = 14–24 | date = July 2014 | pmid = 24921597 | doi = 10.1086/676588 | s2cid = 14549993 | url = http://philsci-archive.pitt.edu/11636/1/Conceptual_and_Empirical_Challenges_%28preprint_version%29.pdf }}</ref><ref>{{cite journal | vauthors = Palazzo AF, Gregory TR | title = The case for junk DNA | journal = PLOS Genetics | volume = 10 | issue = 5 | pages = e1004351 | date = May 2014 | pmid = 24809441 | pmc = 4014423 | doi = 10.1371/journal.pgen.1004351 | doi-access = free }}</ref>