Talk:Horizontal gene transfer
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- 1 Copied from the evolution article talk page
- 2 False Dichotomy: Prokaryotes vs. Eukaryotes
- 3 History of Terminology
- 4 Lead
- 5 Question: Horizontal gene transfer between multicellular organism
- 6 accuracy of "more prevalent"
- 7 Image: :Horizental-gene-transfer.jpg
- 8 Salvaged text
- 9 history
- 10 theobald piece in nature
- 11 All genes have been transfered
- 12 Inferring Benchmarking Lateral Gene Transfer
- 13 Cauliflower Mosaic Virus promoter
- 14 This may be a nice example
- 15 Copyright problem removed
- 16 Lead is WRONG - Edit required
Copied from the evolution article talk page
Common Descent Revisited
I've been reading this with some interest. And, after timne spent searching in the loft, found the issue of Scientific American that contained the article of interest here. Uprooting the Tree of Life by W. Ford Doolitte (Scientific American, February 2000, pp 72-77) contains a discussion of the Last Universal Common Ancestor, and the problems that arose with respect to that concept when one considers horizontal gene transfer. The article covers a wide area - the endosymbiont hypothesis for eukaryotes, the use of small subunit ribosomal RNA (SSU rRNA) as a measure of evolutionary distances (this was the field Carl Woese worked in when formulating the first modern "tree of life", and his research results with SSU rRNA led him to propose the Archaea as a third domain of life) and other relevant topics. Indeed, it was while examining the new three-domain view of life that horizontal gene transfer arose as a complicating issue: Archaeoglobus fulgidus is cited in the article (p.76) as being an anomaly with respect to a phylogenetic tree based upon the encoding for the enzyme HMGCoA reductase - the organism in question is a definite Archaean, with all the cell lipids and transcription machinery that are expected of an Archaean, but whose HMGCoA genes are actually of bacterial origin.
Again on p.76, the article continues with:
- "The weight of evidence still supports the likelihood that mitochondria in eukaryotes derived from alpha-proteobacterial cells and that chloroplasts came from ingested cyanobacteria, but it is no longer safe to assume that those were the only lateral gene transfers that occurred after the first eukaryotes arose. Only in later, multicellular eukaryotes do we know of definite restrictions on horizontal gene exchange, such as the advent of separated (and protected) germ cells."
The article continues with:
- "If there had never been any lateral gene transfer, all these individual gene trees would have the same topology (the same branching order), and the ancestral genes at the root of each tree would have all been present in the last universal common ancestor, a single ancient cell. But extensive transfer means that neither is the case: gene trees will differ (although many will have regions of similar topology) and there would never have been a single cell that could be called the last universal common ancestor.
- "As Woese has written, 'the ancestor cannot have been a particular organism, a single organismal lineage. It was communal, a loosely knit, diverse conglomeration of primitive cells that evolved as a unit, and it eventually developed to a stage where it broke into several distinct communities, which in their turn became the three primary lines of descent (bacteria, archaea and eukaryotes)' In other words, early cells, each haing relatively few genes, differed in many ways. By swapping genes freely, they shared various of their talents with their contemporaries. Eventually this collection of eclectic and changeable cells coalesced into the three basic domains known today. These domains become recognisable because much (though by no means all) of the gene transfer that occurs these days goes on within domains."
If required, I could, on request, scan the altered 'tree of life' given toward the end of the article for perusal by interested parties (even though it may not be directly useful within the article itself for copyright reasons unless the editors of Scientific American choose to release it thus). Given the above references, however, it should not be hard for other editors of this article to track down the relevant material.
The point I am making here is that the hypothetical 'last common universal ancestor' was not, at the time that article was published, regarded with consensus as being a single species of cell. More correctly, one could not reliably point to a possible single species contender because information about that contender may have been obfuscated by multiple horizontal gene transfers. Admittedly the information I am quoting is six years old, but unless someone has alighted upon a means of resurrecting the LUCA as a single species in that time that I've missed, the above should be noted. Calilasseia 11:07, 10 January 2006 (UTC)
False Dichotomy: Prokaryotes vs. Eukaryotes
Jan Sapp, a noted Canadian historian of biology, has recently debunked the false dichotomy represented by the use of the labels "prokaryote" and "eukaryote." A task for this article, therefore, will be to update the relevant sections.
Drawing on documents both published and archival, this paper explains how the prokaryote-eukaryote dichotomy of the 1960s was constructed, the purposes it served, and what it implied in terms of classification and phylogeny. In doing so, I first show how the concept was attributed to Edouard Chatton and the context in which he introduced the terms. Following, I examine the context in which the terms were reintroduced into biology in 1962 by Roger Stanier and C. B. van Niel. I study the discourse over the subsequent decade to understand how the organizational dichotomy took on the form of a natural classification as the kingdom Monera or superkingdom Procaryotae. Stanier and van Niel admitted that, in regard to constructing a natural classification of bacteria, structural characteristics were no more useful than physiological properties. They repeatedly denied that bacterial phylogenetics was possible. I thus examine the great historical irony that the "prokaryote," in both its organizational and phylogenetic senses, was defined (negatively) on the basis of structure. Finally, we see how phylogenetic research based on 16S rRNA led by Carl Woese and his collaborators confronted the prokaryote concept while moving microbiology to the center of evolutionary biology.
Sapp, J. (2005). “The Prokaryote-Eukaryote Dichotomy: Meanings and Mythology,” Microbiology and Molecular Biology Reviews, 69, pp. 101-115. —The preceding unsigned comment was added by JTBurman (talk • contribs) 04:49, 21 December 2006 (UTC).
- Not yet accepted as the mainstream position - not yet suitable for Wikipedia, except as a mention. --18.104.22.168 19:28, 29 December 2006 (UTC)
- This dichotomy may not be phylogenetically meaningful, but it is very relevant to the topic of this article. It is a meaningful dichotomy with regard to cell structure and genetic mechanisms -- the latter being exactly what this article is about. 22.214.171.124 (talk) 05:03, 10 March 2012 (UTC)
History of Terminology
Was HGT previously referred to more frequently as "transposition", (not transposons, TEs, but just transposition)? If so, perhaps the article could mention this. In reading a few articles from the 80s and 90s, it seems the term transpositions was used commonly for LGT. Does anyone know if this is true? --Bob Enyart, Denver radio host at KGOV (talk) 18:55, 28 March 2012 (UTC)
I just noticed that an editor removed the term transposition, claiming that it referred to transfer within an organism, but I'm pretty sure that is incorrect, and that what he was thinking of is transpons (TEs, transposable elements). I took a note on the word "transposition" after reading works from the 80s and 90s, but I can't recall where I saw it, but I do recall it was used repeatedly. Bob Enyart, Denver radio host at KGOV (talk) 16:30, 4 December 2012 (UTC)
I'm the one who made that change, I think. I'm not aware of any uses of 'transposition' in reference to transfers of DNA between organisms, which is always called lateral or horizontal transfer. Transposition and lateral transfer also use very different molecular mechanisms (transposon-encoded transposases for the former, and congugation, transduction or transformation for the latter). Here are the definitions from the current version of Alberts et al Molecular Biology of the Cell.
- Transposition. Movement of a DNA sequence from one genome site to another.
- Horizontal (lateral) transfer. Transmission of a DNA sequence from one cell to another.
Thanks JMB for the help. The Oxford English Dictionary (behind a paywall) agrees with your definition. They include this example of usage, and I'm wondering if it fits into that definition: "1978 Nature 20 July 211/3 The subsequent transposition of tetracycline resistance from this engineered plasmid must therefore be due to the transposition of the toxin gene." In January I'll be traveling to St. Paul MN to meet with an author of a (still) popular book that dealt with this topic back in the 1990s which used the term "transposition". (It's partly for the readers of that book who look up this term that I'm interested in trying to get this right.) I'll ask the author see the papers and texts that he was working from and if relevant, for historical purposes anyway, I'll add a note here. Bob Enyart, Denver KGOV radio host (talk) 17:16, 13 November 2015 (UTC)
Proposing a change from:
"Increasingly, studies of genes and genomes are indicating that considerable horizontal transfer has occurred between prokaryotes."  Horizontal gene transfer is called by some "A New Paradigm for Biology "  and emphasised by others as an important factor in "The Hidden Hazards of Genetic Engineering". "While horizontal gene transfer is well-known among bacteria, it is only within the past 10 years that its occurrence has become recognized among higher plants and animals. The scope for horizontal gene transfer is essentially the entire biosphere, with bacteria and viruses serving both as intermediaries for gene trafficking and as reservoirs for gene multiplication and recombination (the process of making new combinations of genetic material)." .
"Horizontal gene transfer occurs frequently between prokaryotes, and gene studies indicate that it has played a considerable part in their evolution. . It is regarded by some as "a new paradigm for biology" , while others emphasise it as an important factor in the hazards of genetic engineering .
Reasons: avoid (long) quotes in the lead and potentially dubious assertion about higher plants and animals. --126.96.36.199 20:23, 2 January 2007 (UTC)
- I moved it out of the lead. It is sourced and you are free to add quotes from up-to-date reliable published sources that back up your belief that the claims are dubious. Claims that don't directly address the evidence these sources are based on simply reflect prior thinking and are not refutations. WAS 4.250 05:04, 3 January 2007 (UTC)
- The source is not a normal, neutral one - it is Mae-Wan Ho, a scholar who is apparently controversial in several respects and clearly a fierce critic of genetic engineering. She may be a good source for the existence of the ecological and health concerns that she expresses, but not for the nature and scope of horizontal genetic transfer. Thus, I think I am the one who is entitled to request another source for that particular claim, if you insist on including it in the article. Also, maybe I have misundersttod your wording, but let me remind you that it is not our business to "address evidence" or provide "refutations" - we are Wikipedians, not scholars (and even those of us who are scholars in real life may not act as such here). You know, WP:NOR and all that. --188.8.131.52 10:49, 4 January 2007 (UTC)
- Please note as well that in this form the wiki article contradicts itself. While the bulk of the text empasises prokaryotic HGT and only speaks of a couple of marginal examples of HGT involving *primitive* eukaryotes, the quote from Mae-Wan Ho seems to suggest that HGT among (and between?) *higher* plants and animals is common. --184.108.40.206 11:07, 4 January 2007 (UTC)
- Not good enough. These texts are mostly about prokaryotes, sometimes with prokaryotes "borrowing" eukaryote material, and a few exceptions which do not automatically justify the broad generalisation in the Mae-Wan Ho quote.
- As one of the sources cited as reference in the second text states: "Unlike eukaryotes, which evolve principally through the modification of existing genetic information, bacteria have obtained a significant proportion of their genetic diversity through the acquisition of sequences from distantly related organisms." The boundary seems rather clear-cut here.
- While the second text does say that "Comparative genome analysis has revealed major lateral gene transfer between the three primary kingdoms of life, Bacteria, Archaea, and Eukarya", they mean mostly transfer between prokaryotes and from eu- to pro-, as obvious from the four articles cited in support of that statement. --220.127.116.11 16:16, 4 January 2007 (UTC)
If you wish to add sourced data to the article without deleting sourced data, feel free. If you insist on playing expert and insisting on deleting sourced relevant quotes because of your original research then we will have to call in other people to decide between our two points of view in this matter. WAS 4.250 11:01, 5 January 2007 (UTC)
- There is a problem with your source, not mine. Anyway, I was going to answer at length and try to convince you to permit at least slight improvements (which, like most of what I have done or proposed, have nothing to do with the question of "sourced" vs "unsourced"), but upon consideration, I feel a sudden need to terminate all communication with you. The text as it is both very poor in terms of style and somewhat misleading in terms of content, but such is life. I am at least attributing the quote to Mae-Wan Ho (thus distancing the article from the statement a little bit). Feel free to revert that, if it makes you feel better. --18.104.22.168 19:37, 5 January 2007 (UTC)
- Attributing the quotes was an improvement to the article. Thank you for helping to improve the article. Please feel welcome to add more attributed sourced relevent quotes anytime. Perhaps you would like to add a sourced footnote that questions the reliability of Mae-Wan Ho? She does come across as a crusader, but I have no sources indicating she is incompetent or corrupt or a liar. And everyone is biased. ... meh WAS 4.250 09:58, 6 January 2007 (UTC)
- Sorry for flaring up, maybe I was wrong to interpret your attitude as hostility. Now, it is my conviction that most quotes should be replaced with re-wordings, re-arranged and trimmed simply for the sake of style and readability. I don't think Mae-Wan Ho is a liar (the wiki article about her seemed to be rather severe without actual sources, so I "trimmed" it per WP:BLP), but in a polemical text, it is natural to expect some things to be put too strongly, and emphasis to be shifted in a way that could be unsuitable for an encyclopedia, even though there is little or no departure from the truth (whatever that means). I'm adding some more quotes that I consider to be more indicative of the state-of-the-art view. However, this is going to make the text even more awkward. The best thing would be to do away with the quotes and synthesise the information in a coherent, non-repetitive, logical text. I won't do it, because you will probably suspect that it is OR or a deletion of sourced info (what else wouuld you expect from a damn IP), but somebody should. --22.214.171.124 14:55, 6 January 2007 (UTC)
Let's try alternating edits that don't delete quotes but can put some into footnotes. Anything that we wind up just reverting back and forth we can simply revert to the quote being used to source the contested re-wording. Sound like its worth trying? I'll go first. WAS 4.250 16:12, 6 January 2007 (UTC)
- OK, I'll start in a day or two.--126.96.36.199 12:06, 7 January 2007 (UTC)
Question: Horizontal gene transfer between multicellular organism
- The article does cover this and mentions the action of viruses and bacteria. Shyamal 16:02, 13 March 2007 (UTC)
- I am way out of my depth here, but I just read about HERVs at http://en.wikipedia.org/wiki/Endogenous_retrovirus#Human_endogenous_retroviruses which suggests that 8% of human DNA is made up from (defective) endogenous retrovirus fossils - Maybe I'm missing something, and I would love to know what - but isn't this quite clearly evidence of viral horizontal gene transfer? (20040302 (talk) 08:25, 18 October 2011 (UTC))
accuracy of "more prevalent"
"Most thinking in genetics has focused on the more prevalent vertical transfer, but there is a recent awareness that horizontal gene transfer is a significant phenomenon."
I don't think that vertical transfer is the most prevalent. Given that there are more bacteria by count of species, population, and (i'm not sure but possibly) bio mas vertical transfer certainly is not more prevalent. Maybe in the animilia kingdom but certainly not by any real definition I can see. Suggestions? Ucla1989 (talk) 05:09, 2 June 2008 (UTC)
Sorry for misspelling horizontal. I can't seem to change it in Wikimedia Commons. Feel free to do so or make a disambiguation page. The image comes from Barth F. Smets, Ph.D.-Dear Paul,
sorry for the slow reply. I have the following figure which was made internally by us, in preparation for the Nat Reviews article.
With proper citation, this can be used.
Barth F. Smets, Ph.D."
I removed the following from the article. It is interesting, relevant and probably true, but still doesn't really fit in. What should we do?
Gonsalves' team of researchers from academia, industry, and government had isolated and copied a virus gene, then used a device called a gene gun to "shoot" the gene into the cells of the papaya plant. The virus gene in the plant works somewhat like immunization, but the mechanism of resistance is different, says Gonsalves, now director of the U.S. Department of Agriculture's Pacific Basin Agricultural Research Center in Hilo, Hawaii. "By integrating this virus gene into the chromosomes of the papaya, this made the papaya and subsequent generations resistant to the virus."
- It needs editing and sourcing for a start. Maybe the person who added it can be requested to give some cites in support of the paragraph. It could also be added back into the article now with a citation request tag. Does this help? Peter morrell 09:28, 14 February 2009 (UTC)
- I agree. I think this should be considered the first report of HGT. See Miller 1998. Estevezj (talk) 08:51, 13 December 2011 (UTC)
theobald piece in nature
There was a reference to the Theobald May 2010 piece beginning and ending the 'importance for evolution' section. I don't see the relevance of the piece here and there are much deeper discussions available (such as work by gogarten, doolittle, koonin, bapteste) but I left some note of it in. It certainly doesn't belong right at the beginning of the section. I put it at the end since if it is relevant, it would seem to be the idea that even with lots of HGT, we can still infer a LUCA which might be thought to counter the Woese quote which it directly follows. What would seem even more relevant given the rest of the section is if HGT discounts the possibility of a tree of life or of phylogenetics generally. The most natural discussion of 'importance for evolution' would be a discussion of how and when HGT has been involved with the actual transfer of functions and whether it plays a role in evolutionary processes. Many people have argued that it does (here is a recent survey piece with lots of references: http://rspb.royalsocietypublishing.org/content/277/1683/819.full.pdf+html ).
It is also worth noting that the original discussion said that the Theobald piece 'demonstrated' (but lots of people don't like it - so argued is better) that there was a LUCA and not a cluster of organisms. But Theobald's understanding of LUCA is very broad. "Furthermore, UCA [universal common ancestry] does not demand that the last universal common ancestor was a single organism, in accord with the traditional evolutionary view that common ancestors of species are groups, not individuals. Rather, the last universal common ancestor may have comprised a population of organisms with different genotypes that lived in different places at different times." This is far from arguing against the view that it is 'a cluster of organisms'. This doesn't even sound like a population (or a LUCA) to me or to some critics of LUCA like Doolittle. Jdvelasc (talk) 18:58, 11 October 2010 (UTC)
GrahamColm think[] it belongs on Talk Page.
However, in a May 2010 article in Nature, Douglas Theobald argued that there was indeed one Last Universal Common Ancestor to all existing life and that horizontal gene transfer has not destroyed our ability to infer this. Therobal article has 3 citation all citations in English language (citation 1,2) emphasizing role of HTG.
All genes have been transfered
I suggest removing the list of genes for which there is evidence of transfer. To a first approximation, there is evidence that all genes have been transfered. For more info, look up "the tree of one percent" 188.8.131.52 (talk) 05:07, 10 March 2012 (UTC)
Inferring Benchmarking Lateral Gene Transfer
We have noticed that although LGT as phenomenon is already relatively well described in the article, the problems of computational inference and benchmarking are not covered at all. For this reason we are currently working on a new version of article on the form of "Topic Pages: PLoS Computational Biology Meets Wikipedia". For detailed information about Topics Pages see:
We intend to survey methods to identify LGT, with a special emphasis on their respective advantages and limitations, and will summarise approaches to evaluating/benchmarking inferred LGT.
Please contact us if you have any objections or suggestions about the proposed article, or if you think that you could substantially contribute to our efforts.
I am pleased that the Topic Page has now been peer-reviewed and published and that it has been incorporated in Wikipedia here: Inferring horizontal gene transfer. --Cdessimoz (talk) 19:48, 14 June 2015 (UTC)
Cauliflower Mosaic Virus promoter
A mention of a 1999 paper that sounded a warning about genetically modified plants that include the Cauliflower Mosaic Virus promoter region was recently removed on the grounds that it didn't satisfy WP:MEDRS because the journal isn't indexed in pubmed, and the author "is a partisan opponent of GMO". Sorry, but I don't agree that the journal fails MEDRS, pubmed is not the be-all and end-all of medical publishing. Nor do I agree that a scientist being scared by something makes their research ready for the trash bin. A journal about microbial ecology in human health should be able to publish articles by both medical people and non-medical, without the whole journal being said to fail MEDRS.
I do agree that the article is rather old. The following year saw the conclusion that the CMV promoter is probably no more dangerous than conventional plant breeding: R. Hull, S.N.C.P.D. (2000). "Genetically modified plants and the 35S promoter: assessing the risks and enhancing the debate". Microbial Ecology in Health and Disease. 12 (1): 1–5. doi:10.1080/089106000435527. That point doesn't really belong on this page, however; there were several aspects of the CMV promoter that raised concerns, not just horizontal gene transfer. I feel that WP:CENSOR is important here. We shouldn't remove discussion of the fear about the CMV promoter. What is needed is updates to the page, 1999 and 2000 are getting to be too old. Sminthopsis84 (talk) 21:50, 22 May 2013 (UTC)
- Has any work been done on this subject since 2000? That's 13 years, has work on 35S promoters entered stasis in this time period? It's not a matter of censorship, it's a matter of obselete information remaining on the page. Does anyone, now, still worry about this? If not, why are we giving undue weight to someone who has dedicated much of their life to opposing genetic modification? Mae-Wan Ho is an activist who believes homeopathy, organic food and biodynamic farming are the answer to the world's problems. I don't think citing a 14-year-old article on the topic serves our readers, particularly if a subsequent article noted that the issue wasn't actually a problem. My inclination would be to include both, which essentially nets to zero and makes me believe we should simply remove both. WLU (t) (c) Wikipedia's rules:simple/complex 13:15, 23 May 2013 (UTC)
- There's a lot of noise about it in 2013, for example, try a google search for "CAMV35S hazard". I think this would be the paper to cite, from 2005. Because of all the noise, I think this really, really needs to be discussed in wikipedia, it's an issue of basic education, which is what we're trying to achieve, no? I think we should be discussing dihydrogen monoxide, too, but that is clearly an intentional hoax, I'm much less sure that this was intentional. There are examples of some seriously deranged ideas in genetic engineering, such as converting a crop plant into something that sequesters plastic in its vacuoles, or transferring big chunks of DNA from plants that many people are allergic to into plants that those people didn't have a problem with, GM crops that can tolerate huge applications of herbicides and that interbreed readily with related weeds, maize that produces pollen that's toxic to insects ... Sminthopsis84 (talk) 15:35, 23 May 2013 (UTC)
This may be a nice example
Transcriptomic evidence for the expression of horizontally transferred algal nuclear genes in the photosynthetic sea slug, Elysia chlorotica. http://www.ncbi.nlm.nih.gov/pubmed/22319135
- Please go ahead and add it then, I don't think anyone will object, thanks Peter morrell 17:32, 9 October 2013 (UTC)
Copyright problem removed
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Lead is WRONG - Edit required
"... there is a growing awareness that horizontal gene transfer is [...] among single-celled organisms perhaps the dominant form of genetic transfer." [bold is my emphasis] That statement is ridiculous!! No serious scholar of single-celled life believes that HGT dominates vertical gene transfer!! Perhaps the editor meant that it dominates the process of speciation in single-celled organism populations, but not being a mind reader, I have no reason to believe that or several other interpretations. Anyway, as written it is an egregious falsehood and gross error. Please fix it.Abitslow (talk) 17:11, 3 June 2016 (UTC)
- Theobald, Douglas L. (13 May 2010). "A formal test of the theory of universal common ancestry". Nature. 465 (7295): 219–222. PMID 20463738. doi:10.1038/nature09014.
- http://www.biology-direct.com/content/5/1/44 Valas & Bourne propose a duality where we must consider variation of genetic material in terms of networks and selection of cellular function in terms of trees