Editing Selfish genetic element (section)

== Logic ==
Though selfish genetic elements show a remarkable diversity in the way they promote their own transmission, some generalizations about their biology can be made. In a classic 2001 review, Gregory D.D. Hurst and John H. Werren proposed two ‘rules' of selfish genetic elements.<ref name=":1" />

=== Rule 1: Spread requires sex and outbreeding ===
Sexual reproduction involves the mixing of genes from two individuals. According to [[Mendelian inheritance|Mendel's Law of Segregation]], alleles in a sexually reproducing organism have a 50% chance of being passed from parent to offspring. Meiosis is therefore sometimes referred to as "fair".<ref>{{Cite journal|last=Levinton|first=Jeffrey | name-list-style = vanc |date= June 1972 |title=Adaptation and Diversity. Natural History and the Mathematics of Evolution. Egbert Giles Leigh |journal=The Quarterly Review of Biology|volume=47|issue=2|pages=225–226|doi=10.1086/407257 | department = Book Review |title-link=Egbert Giles Leigh }}</ref>

Highly self-fertilizing or asexual genomes are expected to experience less conflict between selfish genetic elements and the rest of the host genome than outcrossing sexual genomes.<ref>{{Cite journal |last=Hickey |first=Donal A. | name-list-style = vanc |date=October 1984 |title=DNA can be a selfish parasite |journal=Nature|volume=311|issue=5985|pages=417–418|doi=10.1038/311417d0|bibcode=1984Natur.311..417H |s2cid=4362210 }}</ref><ref>{{cite journal | vauthors = Wright S, Finnegan D | title = Genome evolution: sex and the transposable element | journal = Current Biology | volume = 11 | issue = 8 | pages = R296–9 | date = April 2001 | pmid = 11369217 | doi = 10.1016/s0960-9822(01)00168-3 | s2cid = 2088287 | doi-access = free | bibcode = 2001CBio...11.R296W }}</ref><ref>{{cite book |last1=Wright |first1=Stephen I. |last2=Schoen |first2=Daniel J. | name-list-style = vanc |title=Transposon dynamics and the breeding system|date=2000| work=Transposable Elements and Genome Evolution|volume=107 |issue=1–3 |pages=139–148|publisher=Springer Netherlands|pmid=10952207 |isbn=9789401058124 }}</ref> There are several reasons for this. First, sex and outcrossing put selfish genetic elements into new genetic lineages. In contrast, in a highly selfing or asexual lineage, any selfish genetic element is essentially stuck in that lineage, which should increase variation in fitness among individuals. The increased variation should result in stronger purifying selection in selfers/asexuals, as a lineage without the selfish genetic elements should out-compete a lineage with the selfish genetic element. Second, the increased homozygosity in selfers removes the opportunity for competition among homologous alleles. Third, theoretical work has shown that the greater linkage disequilibrium in selfing compared to outcrossing genomes may in some, albeit rather limited, cases cause selection for reduced transposition rates.<ref name=":13">{{cite journal | vauthors = Charlesworth B, Langley CH | title = The evolution of self-regulated transposition of transposable elements | journal = Genetics | volume = 112 | issue = 2 | pages = 359–83 | date = February 1986 | doi = 10.1093/genetics/112.2.359 | pmid = 3000868 | pmc = 1202706 }}</ref> Overall, this reasoning leads to the prediction that asexuals/selfers should experience a lower load of selfish genetic elements. One caveat to this is that the evolution of selfing is associated with a reduction in the [[effective population size]].<ref>{{cite journal | vauthors = Nordborg M | title = Linkage disequilibrium, gene trees and selfing: an ancestral recombination graph with partial self-fertilization | journal = Genetics | volume = 154 | issue = 2 | pages = 923–9 | date = February 2000 | doi = 10.1093/genetics/154.2.923 | pmid = 10655241 | pmc = 1460950 }}</ref> A reduction in the effective population size should reduce the efficacy of selection and therefore leads to the opposite prediction: higher accumulation of selfish genetic elements in selfers relative to outcrossers.

Empirical evidence for the importance of sex and outcrossing comes from a variety of selfish genetic elements, including transposable elements,<ref>{{cite journal | vauthors = Arkhipova I, Meselson M | title = Transposable elements in sexual and ancient asexual taxa | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 97 | issue = 26 | pages = 14473–7 | date = December 2000 | pmid = 11121049 | pmc = 18943 | doi = 10.1073/pnas.97.26.14473 | bibcode = 2000PNAS...9714473A | doi-access = free }}</ref><ref>{{cite journal | vauthors = Agren JÅ, Wang W, Koenig D, Neuffer B, Weigel D, Wright SI | title = Mating system shifts and transposable element evolution in the plant genus Capsella | journal = BMC Genomics | volume = 15 | issue = 1 | pages = 602 | date = July 2014 | pmid = 25030755 | pmc = 4112209 | doi = 10.1186/1471-2164-15-602 | doi-access = free }}</ref> self-promoting plasmids,<ref>{{cite journal | vauthors = Harrison E, MacLean RC, Koufopanou V, Burt A | title = Sex drives intracellular conflict in yeast | journal = Journal of Evolutionary Biology | volume = 27 | issue = 8 | pages = 1757–63 | date = August 2014 | pmid = 24825743 | doi = 10.1111/jeb.12408 | s2cid = 23049054 | doi-access = free }}</ref> and B chromosomes.<ref>{{Cite journal| vauthors = Burt A, Trivers R | date=1998-01-22|title=Selfish DNA and breeding system in flowering plants |journal=Proceedings of the Royal Society B: Biological Sciences|volume=265|issue=1391|pages=141–146|doi=10.1098/rspb.1998.0275| pmc=1688861}}</ref>

=== Rule 2: Presence is often revealed in hybrids ===
The presence of selfish genetic elements can be difficult to detect in natural populations. Instead, their phenotypic consequences often become apparent in hybrids. The first reason for this is that some selfish genetic elements rapidly sweep to fixation, and the phenotypic effects will therefore not be segregating in the population. Hybridization events, however, will produce offspring with and without the selfish genetic elements and so reveal their presence. The second reason is that host genomes have evolved mechanisms to suppress the activity of the selfish genetic elements, for example the small RNA administered silencing of transposable elements.<ref>{{cite journal | vauthors = Aravin AA, Hannon GJ, Brennecke J | title = The Piwi-piRNA pathway provides an adaptive defense in the transposon arms race | journal = Science | volume = 318 | issue = 5851 | pages = 761–4 | date = November 2007 | pmid = 17975059 | doi = 10.1126/science.1146484 | bibcode = 2007Sci...318..761A | s2cid = 8532459 | doi-access =  | url = https://resolver.caltech.edu/CaltechAUTHORS:20190509-083948927 }}</ref> The co-evolution between selfish genetic elements and their suppressors can be rapid, and follow a [[Red Queen hypothesis|Red Queen dynamics]], which may mask the presence of selfish genetic elements in a population. Hybrid offspring, on the other hand, may &nbsp;inherit a given selfish genetic element, but not the corresponding suppressor and so reveal the phenotypic effect of the selfish genetic element.<ref name=":9">{{cite journal | vauthors = Crespi B, Nosil P | title = Conflictual speciation: species formation via genomic conflict | journal = Trends in Ecology & Evolution | volume = 28 | issue = 1 | pages = 48–57 | date = January 2013 | pmid = 22995895 | doi = 10.1016/j.tree.2012.08.015 }}</ref><ref name=":10">{{cite journal | vauthors = Ågren JA | title = Selfish genes and plant speciation. | journal = Evolutionary Biology | date = September 2013 | volume = 40 | issue = 3 | pages = 439–449 | doi = 10.1007/s11692-012-9216-1 | bibcode = 2013EvBio..40..439A | s2cid = 19018593 }}</ref>