Talk:Horizontal gene transfer

message: ===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)
thread_title: Copied from the evolution article talk page

message: 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)
thread_title: Common Descent Revisited

message: 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)
replies: text: Not yet accepted as the mainstream position - not yet suitable for Wikipedia, except as a mention. --194.145.161.227 19:28, 29 December 2006 (UTC)

text: 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. 108.203.48.183 (talk) 05:03, 10 March 2012 (UTC)
thread_title:  False Dichotomy: Prokaryotes vs. Eukaryotes 

message: 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)
thread_title: History of Terminology

message: Is there a technique, or even an hypothesized method by which this can happen, and if so are there any examples of it?  Thank you.--Procrastinating@talk2me 13:27, 13 March 2007 (UTC)
replies: text: The article does cover this and mentions the action of viruses and bacteria. Shyamal 16:02, 13 March 2007 (UTC)
replies: text: I'm sorry, I have'nt seen an example on multicellular organism. --Procrastinating@talk2me 10:26, 14 March 2007 (UTC)
replies: text: See sources and notes and further reading for specific examples. WAS 4.250 21:23, 14 March 2007 (UTC)

text: 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)
thread_title:  Question: Horizontal gene transfer between multicellular organism 

message: "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)
replies: text: Find a reliable published source. WAS 4.250 (talk) 06:44, 2 June 2008 (UTC)
replies: text: Fair enough but the claim on the page currently isn't cited from a reliable published source... I'm busy right now but I will look when I get the chance Ucla1989 (talk) 05:26, 5 June 2008 (UTC)
replies: text: That claim exists in many of the sources cited. Read them. Further, most bacteria are created by a process whereby they get all their genes though vertical transfer from a single parent. WAS 4.250 (talk) 20:50, 5 June 2008 (UTC)
thread_title:  accuracy of "more prevalent" 

message: 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."
--Ettrig (talk) 09:08, 14 February 2009 (UTC)
replies: text: 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)
replies: text: It isn't really HGT, it is an artificial genetic modification that would be covered in the article on genetic engineering. Anyway, it is a copyright violation from this article. Tim Vickers (talk) 00:57, 15 February 2009 (UTC)
thread_title:  Salvaged text 

message: Wouldn't Griffith's_experiment in 1928 be an early research on horizontal gene transfer? Hoemaco (talk) 14:59, 14 February 2010 (UTC)
replies: text: I agree. I think this should be considered the first report of HGT. See Miller 1998. Estevezj (talk) 08:51, 13 December 2011 (UTC)
thread_title:  history 

message: 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)
thread_title:  theobald piece in nature 

message: 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" 108.203.48.183 (talk) 05:07, 10 March 2012 (UTC)
thread_title:  All genes have been transfered 

message: 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:
    http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002446
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.
Contact information: --Cdessimoz (talk) 21:32, 29 May 2012 (UTC)
thread_title:  Inferring  Benchmarking Lateral Gene Transfer 

message: 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:  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)
replies: text: 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)
replies: text: 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)
thread_title:  Cauliflower Mosaic Virus promoter 

message: 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
The slug is also quite nice and would make a nice picture for the article. Its leaf-shaped.
217.89.117.154 (talk) 09:19, 9 October 2013 (UTC)
replies: text: Please go ahead and add it then, I don't think anyone will object, thanks Peter morrell 17:32, 9 October 2013 (UTC)
thread_title:  This may be a nice example 

message: Prior content in this article duplicated one or more previously published sources. The material was copied from: http://mbe.oxfordjournals.org/content/27/12/2879.full.pdf. Copied or closely paraphrased material has been rewritten or removed and must not be restored, unless it is duly released under a compatible license. (For more information, please see "using copyrighted works from others" if you are not the copyright holder of this material, or "donating copyrighted materials" if you are.) For legal reasons, we cannot accept copyrighted text or images borrowed from other web sites or published material; such additions will be deleted. Contributors may use copyrighted publications as a source of information, but not as a source of sentences or phrases. Accordingly, the material may be rewritten, but only if it does not infringe on the copyright of the original or plagiarize from that source. Please see our guideline on non-free text for how to properly implement limited quotations of copyrighted text. Wikipedia takes copyright violations very seriously, and persistent violators will be blocked from editing. While we appreciate contributions, we must require all contributors to understand and comply with these policies. Thank you.  Sminthopsis84 (talk) 17:15, 12 December 2013 (UTC)
thread_title:  Copyright problem removed 

message: "... there is a growing awareness that horizontal gene transfer is [...] among single-celled organisms perhaps the dominant form of genetic transfer.[14][15]" [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)
thread_title:  Lead is WRONG - Edit required 

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thread_title:  External links modified 

message: I find a sentence introduced here to be a bit on the fuzzy side for an encyclopedia: 
* Horizontal gene transfer: Difference between revisions
Here is the sentence: 
In other words, HGT is the "power" that "watches over" the universality of the genetic code and forces it into a "lingua franca" of life on Earth.
 
And here is the associated cite:  
 This allows "genetic commerce" or the dissemination of biological novelty through the biosphere.
I'm not actually casting a formal vote here (though I have expressed a sentiment), but mainly moving it into discussion, for others to decide. 
The contributor behind this is fairly new, and might benefit from some helpful feedback. — MaxEnt 21:40, 22 March 2018 (UTC)
thread_title:  Suggestive "language" moved to talk page 

message: The ancestor of the Mitochondria is a Alpghaproteobacterium, not an archeum. Please correct the position of the word "Archaea". Kersti () 16:57, 12 January 2020 (UTC)
thread_title:  Please correct: [[:File:Tree Of Life (with horizontal gene transfer).svg]] 

message: I think some very short information on this study should probably be added to the article. It's currently featured in 2020 in science like so:
Researchers report that antibiotic resistance genes can spread into bacterial populations without the respective selection pressure via horizontal gene transfer.
From the study:
We show that HGT can help antibiotic resistance genes establish at a low frequency in a population, even in the absence of the antibiotic.
...
Together, our findings show how HGT can act as an evolutionary force that facilitates the spread of nonselected genetic variation and expands the adaptive potential of microbial populations.
--Prototyperspective (talk) 17:12, 4 December 2020 (UTC)
thread_title:  Please update with: "Horizontal gene transfer potentiates adaptation by reducing selective constraints on the spread of genetic variation" 

message: — Assignment last updated by Symbiologist (talk) 16:14, 11 December 2022 (UTC)
thread_title: Wiki Education assignment: Introduction to Chemical Ecology

message: This article seems to focus on antibiotic resistance too much. While horizontal gene transfer allows for antibiotic resistance to spread between different species of bacteria, the spread of antibiotic resistance is only one of the many effects caused by horizontal gene transfer. By focusing on antibiotic resistance, the article seems to paint horizontal gene transfer in a negative light even though it is not necessarily a bad thing. 2001:8003:ED34:4000:500E:295:67BC:E2BB (talk) 06:31, 6 May 2023 (UTC)
thread_title:  Too much focus on antibiotic resistance 

message: The section "Mechanisms" should mention electroporation. According to research by Eiichi Hondo and Atsuo Iida (https://www.sciencedaily.com/releases/2023/12/231205114816.htm), electric eeals can trigger transfer of environmental DNA (from a river) into fishes, through a mechanism called electroporation.
Professor Tournesol (talk) 10:37, 10 December 2023 (UTC)
thread_title:  Please mention electroporation as a mechanism