Editing Selfish genetic element (section)

==History==
===Early observations ===
Observations of what is now referred to as selfish genetic elements go back to the early days in the [[history of genetics]]. Already in 1928, Russian geneticist [[Sergey Gershenson]] reported the discovery of a driving [[X chromosome]] in ''Drosophila obscura''.<ref name=":5">{{cite journal | vauthors = Gershenson S | title = A New Sex-Ratio Abnormality in DROSOPHILA OBSCURA | journal = Genetics | volume = 13 | issue = 6 | pages = 488–507 | date = November 1928 | doi = 10.1093/genetics/13.6.488 | pmid = 17246563 | pmc = 1200995 }}</ref> Crucially, he noted that the resulting female-biased sex ratio may drive a population extinct (see [[#Species extinction|Species extinction]]). The earliest clear statement of how chromosomes may spread in a population not because of their positive fitness effects on the individual organism, but because of their own "parasitic" nature came from the Swedish botanist and cytogeneticist [[Gunnar Östergren]] in 1945.<ref name=":6">{{cite journal | vauthors = Östergren G | title = Parasitic nature of extra fragment chromosomes. | journal = Botaniska Notiser | date = 1945 | volume = 2 | pages = 157–163 }}</ref> Discussing [[B chromosome]]s in plants he wrote:<ref name=":6" />

<blockquote>In many cases these chromosomes have no useful function at all to the species carrying them, but that they often lead an exclusively parasitic existence ... [B chromosomes] need not be useful for the plants. They need only be useful to themselves.</blockquote>

Around the same time, several other examples of selfish genetic elements were reported. For example, the American maize geneticist [[Marcus Morton Rhoades|Marcus Rhoades]] described how chromosomal knobs led to female [[meiotic drive]] in maize.<ref>{{cite journal | vauthors = Rhoades MM | title = Preferential Segregation in Maize | journal = Genetics | volume = 27 | issue = 4 | pages = 395–407 | date = July 1942 | doi = 10.1093/genetics/27.4.395 | pmid = 17247049 | pmc = 1209167 }}</ref> Similarly, this was also when it was first suggested that an [[intragenomic conflict]] between [[uniparental inheritance|uniparentally inherited]] mitochondrial genes and biparentally inherited nuclear genes could lead to [[cytoplasmic male sterility]] in plants.<ref name=":7">{{cite journal | vauthors = Lewis D | title = Male sterility in natural populations of hermaphrodite plants the equilibrium between females and hermaphrodites to be expected with different types of inheritance. | journal = New Phytologist | date = April 1941 | volume = 40 | issue = 1 | pages = 56–63 | doi = 10.1111/j.1469-8137.1941.tb07028.x | doi-access = free }}</ref> Then, in the early 1950s, [[Barbara McClintock]] published a series of papers describing the existence of [[transposable element]]s, which are now recognized to be among the most successful selfish genetic elements.<ref name=":8">{{cite journal | vauthors = McClintock B | title = The origin and behavior of mutable loci in maize | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 36 | issue = 6 | pages = 344–55 | date = June 1950 | pmid = 15430309 | pmc = 1063197 | doi = 10.1073/pnas.36.6.344 | bibcode = 1950PNAS...36..344M | doi-access = free }}</ref> The discovery of transposable elements led to her being awarded the [[Nobel Prize in Physiology or Medicine|Nobel Prize in Medicine or Physiology in 1983]].

=== Conceptual developments ===
The empirical study of selfish genetic elements benefited greatly from the emergence of the so-called gene-centred view of evolution in the nineteen sixties and seventies.<ref name=":25">{{cite journal | vauthors = Ågren JA | title = Selfish genetic elements and the gene's-eye view of evolution | journal = Current Zoology | volume = 62 | issue = 6 | pages = 659–665 | date = December 2016 | pmid = 29491953 | pmc = 5804262 | doi = 10.1093/cz/zow102  }}</ref> In contrast with Darwin's original formulation of the theory of evolution by natural selection that focused on individual organisms, the gene's-eye view takes the gene to be the central unit of selection in evolution.<ref>{{citation |title=Selfish Genes |last1= Ågren |first1=Jon Arvid |last2=Hurst |first2=Greg | name-list-style = vanc |date=2017-10-25 |website=Oxford Bibliographies Online Datasets |doi=10.1093/obo/9780199941728-0094 }}</ref> It conceives evolution by natural selection as a process involving two separate entities: replicators (entities that produce faithful copies of themselves, usually genes) and vehicles (or interactors; entities that interact with the ecological environment, usually organisms).<ref>{{Cite book|title=The extended phenotype : the long reach of the gene|last=Dawkins |first=Richard | name-list-style = vanc |author-link=Richard Dawkins|publisher=Oxford University Press|year=1982|oclc=610269469}}</ref><ref>{{cite book | vauthors = Dawkins R | chapter = Replicators and vehicles | editor = King's College Sociobiology Group, Cambridge | title =  Current Problems in Sociobiology. | publisher = Cambridge University Press | date = June 1982 | pages = 45–64 | isbn = 978-0-521-28520-9 }}</ref><ref>{{cite book | vauthors = Hull DL | chapter = Units of Evolution: A Metaphysical Essay | veditors = Jensen UJ, Harré R | title = The Philosophy of Evolution | publisher = St. Martin's Press | date = 1981 | pages = 23–44 }}</ref>

Since organisms are temporary occurrences, present in one generation and gone in the next, genes (replicators) are the only entity faithfully transmitted from parent to offspring. Viewing evolution as a struggle between competing replicators made it easier to recognize that not all genes in an organism would share the same evolutionary fate.<ref name=":25" />

The gene's-eye view was a synthesis of the population genetic models of the modern synthesis, in particular the work of [[RA Fisher]], and the social evolution models of [[W. D. Hamilton]]. The view was popularized by  [[George C. Williams (biologist)|George Williams]]'s ''[[Adaptation and Natural Selection]]''<ref name=":2" /> and [[Richard Dawkins]]'s best seller ''[[The Selfish Gene]]''.<ref name="TSG"/> Dawkins summarized a key benefit from the gene's-eye view as follows:

<blockquote>"If we allow ourselves the license of talking about genes as if they had conscious aims, always reassuring ourselves that we could translate our sloppy language back into respectable terms if we wanted to, we can ask the question, what is a single selfish gene trying to do?"  — Richard Dawkins, ''The Selfish Gene''<ref name="TSG"/>{{rp|p. 88}}</blockquote>

In 1980, two high-profile papers published back-to-back in ''Nature'' by Leslie Orgel and Francis Crick, and by Ford Doolittle and Carmen Sapienza, brought the study of selfish genetic elements to the centre of biological debate.<ref name=":3" /><ref name=":4" /> The papers took their starting point in the contemporary debate of the so-called [[C-value|C-value paradox]], the lack of correlation between genome size and perceived complexity of a species. Both papers attempted to counter the prevailing view of the time that the presence of differential amounts of non-coding DNA and transposable elements is best explained from the perspective of individual fitness, described as the "phenotypic paradigm" by Doolittle and Sapienza. Instead, the authors argued that much of the genetic material in eukaryotic genomes persists, not because of its phenotypic effects, but can be understood from a gene's-eye view, without invoking individual-level explanations. The two papers led to a series of exchanges in ''Nature''.<ref>{{cite journal | vauthors = Cavalier-Smith T | title = How selfish is DNA? | journal = Nature | volume = 285 | issue = 5767 | pages = 617–8 | date = June 1980 | pmid = 7393317 | doi = 10.1038/285617a0 | bibcode = 1980Natur.285..617C | s2cid = 27111068 | doi-access = free }}</ref><ref>{{cite journal | vauthors = Dover G | title = Ignorant DNA? | journal = Nature | volume = 285 | issue = 5767 | pages = 618–20 | date = June 1980 | pmid = 7393318 | doi = 10.1038/285618a0 | bibcode = 1980Natur.285..618D | s2cid = 4261755 | doi-access = free }}</ref><ref>{{cite journal | vauthors = Dover G, Doolittle WF | title = Modes of genome evolution | journal = Nature | volume = 288 | issue = 5792 | pages = 646–7 | date = December 1980 | pmid = 6256636 | doi = 10.1038/288646a0 | bibcode = 1980Natur.288..646D | s2cid = 8938434 | doi-access = free }}</ref><ref>{{cite journal | vauthors = Orgel LE, Crick FH, Sapienza C | title = Selfish DNA | journal = Nature | volume = 288 | issue = 5792 | pages = 645–6 | date = December 1980 | pmid = 7453798 | doi = 10.1038/288645a0 | bibcode = 1980Natur.288..645O | s2cid = 4370178 }}</ref>

=== Current views ===
If the selfish DNA papers marked the beginning of the serious study of selfish genetic elements, the subsequent decades have seen an explosion in theoretical advances and empirical discoveries. [[Leda Cosmides]] and [[John Tooby]] wrote a landmark review about the conflict between maternally inherited cytoplasmic genes and biparentally inherited nuclear genes.<ref name=":20">{{cite journal | vauthors = Cosmides LM, Tooby J | title = Cytoplasmic inheritance and intragenomic conflict | journal = Journal of Theoretical Biology | volume = 89 | issue = 1 | pages = 83–129 | date = March 1981 | pmid = 7278311 | doi = 10.1016/0022-5193(81)90181-8 | bibcode = 1981JThBi..89...83M | s2cid = 36815174 }}</ref> The paper also provided a comprehensive introduction to the logic of genomic conflicts, foreshadowing many themes that would later be subject of much research. Then in 1988 [[John H. Werren]] and colleagues wrote the first major empirical review of the topic.<ref name=":0" /> This paper achieved three things. First, it coined the term selfish genetic element, putting an end to a sometimes confusingly diverse terminology (selfish genes, ultra-selfish genes, selfish DNA, parasitic DNA, genomic outlaws). Second, it formally defined the concept of selfish genetic elements. Finally, it was the first paper to bring together all different kinds of selfish genetic elements known at the time ([[genomic imprinting]], for example, was not covered).<ref name=":0" />

In the late 1980s, most molecular biologists considered selfish genetic elements to be the exception, and that genomes were best thought of as highly integrated networks with a coherent effect on organismal fitness.<ref name=":0" /><ref name=":30" /> In 2006, when [[Austin Burt]] and [[Robert Trivers]] published the first book-length treatment of the topic, the tide was changing.<ref name=":30" /> While their role in evolution long remained controversial, in a review published a century after their first discovery, [[William R. Rice]] concluded that "nothing in genetics makes sense except in the light of genomic conflicts".<ref>{{Cite journal|last=Rice|first=William R. | name-list-style = vanc |date=2013-11-23|title=Nothing in Genetics Makes Sense Except in Light of Genomic Conflict |journal=Annual Review of Ecology, Evolution, and Systematics|volume=44|issue=1|pages=217–237|doi=10.1146/annurev-ecolsys-110411-160242|issn=1543-592X}}</ref>