Talk:PLOS/Selfish Genetic Elements

Initial editorial comments

T Shafee

Whilst this is in peer review, I would suggest the authors consider putting together some summary image(s) For example, similarities& differences between the example SGEs given (e.g. scale, abundance, propagation mechanism). This is only a suggestion though, and not vital. T Shafee (talk) 20:53, 7 March 2018 (PST)

Ågren and Clark

We have now prepared figures for all seven examples of selfish genetic elements discussed in the review.

Reviewer 1: Dag Olav Hessen

Dag Olav Hessen

This is a very competent and timely introduction to a topic that, despite having been around for a long time, just recently has attended the proper interest. Over a brief space it captures well the historic development and current discussions, yet there are some issues that could have deserved a better coverage. This may be a matter of space for this Wiki-related format, but I provide my comments on the different parts below for a judgement:

Ågren and Clark

We thank Dag Olav Hessen for the kind words and for the suggestions, most which we have incorporated.

Dag Olav Hessen

The intro with the historical part is fine – the history of science is always interesting, and in this context we have a good example on how long it actually may take before a topic is recognized until it receives full attention. I would however believe that Selfish DNA papers would be a natural part of the history and conceptual developments, not really a section on its own.

Ågren and Clark

We have merged the Selfish DNA papers section with the general history section.

Dag Olav Hessen

Under Current views, I believe the heated debate on this could deserve some more insights (cf. Graur et al., 2013; Koonin, 2016). While I share the opinions that selfish elements indeed are “selfish”, the fact that large chunks of noncoding DNA also are transcribed could indicate both costs and some functions of this DNA. For example, the ENCyclopedia Of DNA Elements (ENCODE) project argues that although protein-coding genes constitute <2% of the human genome, 80% of the genome either is transcribed, binds to regulatory proteins or is somehow involved in biochemical pathways and must therefore serve a fitness-promoting purposes. On the other hand, the classical counterargument is the ‘onion test’ (cf. Palazzo and Gregory, 2014), and the non-resolved issue of why some organisms have very bulky genomes while other, and even closely related species, have streamlined genomes.

Ågren and Clark

We have added a short paragraph addressing the ENCODE debate and its relationship to selfish genetic elements. We decided to keep this discussion in the “Genome size” section.

The new text (added to the “Genome Size” section) reads as follows:

“The presence of large amounts of transposable elements present in many eukaryotic genomes were at the heart of the original selfish DNA papers mentioned above (See 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. (Fedoroff 2012)

In 2012, when the ENCODE Project (https://en.wikipedia.org/wiki/ENCODE) 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 junk DNA (https://en.wikipedia.org/wiki/Non-coding_DNA#Junk_DNA) (Pennisi 2012), this debate was reignited. (Elliott et al. 2014; Palazzo and Gregory 2014)

Dag Olav Hessen

This leads to Genome size variation, a topic that now appears late in the paper, but which perhaps better could be presented early on, and in context with the C-value enigma. I also think the authors here should provide more examples. There is some very interesting examples on striking differences in related plants and animals (especially ectotherms like fish, crustaceans, insects) that could be provided without going to details.

Ågren and Clark

In the interest of space and because the stand-alone “Genome size” entry on Wikipedia is already quite extensive and includes many empirical examples illustrating the vast variation in genome size, we chose to focus our discussion on the role of selfish genetic elements in driving this variation.

Dag Olav Hessen

Speciation is also a very interesting issue, and in fact not only transposition, but accumulation of selfish elements per se could promote fast speciation by affecting phenotype, size, life cycle etc.

Ågren and Clark

We have re-written the opening paragraph of the Speciation section to reflect this:

“Selfish genetic elements have been shown to play a role in speciation. 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 incompatibilities has received particular attention.”

Reviewer 2: Andy Gardner

(Review of 08:58 9 February 2018 version.)

Andy Gardner

This is a very nicely written and informative article. Some comments:

Ågren and Clark

Thanks to Andy Gardner for the endorsements and for the comments, which we address below.

Andy Gardner

1. "In 1988 John H. Werren and colleagues wrote the first major review of the topic" -- it really depends on what one means by "major review", but I wonder if a nod to Cosmides & Tooby 1981 (ref 71) would also be appropriate here. Also, "... the first time all different kinds of selfish genetic elements were brought together in one paper..." -- perhaps clarify that they could only review those that were known at the time as, for example, genomic imprinting was not discussed in their article.

Ågren and Clark

We have re-written the section to reflect this comment. It now reads:

“Leda Cosmides and John Tooby wrote a landmark review about the conflict between maternally inherited cytoplasmic genes and biparentally inherited nuclear genes. 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. (…) 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).”

Andy Gardner

2. It may be helpful to mention Gershenson again, briefly, in the "Species extinction" section.

Ågren and Clark

We have added a reference to Gershenson. The sentence now reads:

“ This possibility was pointed out already in 1928 by Sergey Gershenson and then in 1967, Bill Hamilton developed a formal population genetic model for a case of segregation distortion of sex chromosomes driving a population to extinction.”

Andy Gardner

3. Greenbeard genes are not mentioned, and I wonder if they should be. I don't have a strong opinion on whether they constitute "selfish genetic elements", but they are clearly relevant to the topic of intragenomic conflict.

Ågren and Clark

This is a good suggestions and we have now added a new section (4.7) called “Greenbeards”:

“A greenbeard gene is a gene, or set of tightly linked genes, that have the ability to recognize copies of itself in another individuals and then make its carrier act preferentially toward such individuals. The name itself comes from thought-experiment first presented by Bill Hamilton (Hamilton 1964) and then developed and given its current name by Richard Dawkins in The Selfish Gene.

The point of the thought experiment was to highlight that from a gene’s-eye view, it is not the genome wide relatedness that matters (which is usually how kin selection operates, i.e. cooperative behavior is directed towards relatives), but the relatedness at the particular locus that underlies the social behavior.

Following Dawkins (1976), a greenbeard is usually defined as a gene, or set of closely linked genes, that has three effects (Gardner and West 2010; West and Gardner 2010):

1. It gives carriers of the gene a phenotypic label, such as a greenbeard.

2. The carrier is able to recognize other individuals with the same label.

3. The carrier then behaves altruistically towards individuals with the same label

Greenbeards where long thought to be a fun theoretical idea with limited possibility of actually existing in nature. However, since its conception several examples have been identified, including in yeast (Smukalla et al. 2008), slime moulds (Queller et al. 2003), and fire ants (Keller and Ross 1998).

There has been some debate whether greenbeard genes should be considered selfish genetic elements (Alexander and Bargia 1978; Ridley and Grafen 1981; Biernaskie et al. 2011). Conflict between a greenbeard locus and the rest of the genome can arise because during a given social interaction between two individuals, the relatedness at the greenbeard locus can be higher than at other loci in the genome. As a consequence, there may in the interest of the greenbeard locus to perform a costly social act, but not in the interest of the rest of the genome.”

Final wikification

As a last step, please look though and see if there are any additional hyperlinks that could usefully be added. Please also check that abbreviations (such as CMS) are defined when first used.

I also recommend the (optional) aesthetic change to use a more obvious beard style in fig 7, just to make it more immediately clear (example).

The version added to Wikipedia will omit the final "future directions" section and subheadings will be shortened (e.g. from "Examples of Selfish Genetic Elements" to just "Examples"). T Shafee (talk) 18:28, 25 July 2018 (PDT)