Editing Selfish genetic element (section)

=== 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>