Talk:Horizontal gene transfer

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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. --194.145.161.227 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. 108.203.48.183 (talk) 05:03, 10 March 2012 (UTC)

Lead

Proposing a change from:

"Increasingly, studies of genes and genomes are indicating that considerable horizontal transfer has occurred between prokaryotes." [1] Horizontal gene transfer is called by some "A New Paradigm for Biology " [2] 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)." [3].

To:

"Horizontal gene transfer occurs frequently between prokaryotes, and gene studies indicate that it has played a considerable part in their evolution. [4]. It is regarded by some as "a new paradigm for biology" [5], while others emphasise it as an important factor in the hazards of genetic engineering [6].

Reasons: avoid (long) quotes in the lead and potentially dubious assertion about higher plants and animals. --194.145.161.227 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. --194.145.161.227 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. --194.145.161.227 11:07, 4 January 2007 (UTC)

[7] [8] WAS 4.250 15:04, 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. --194.145.161.227 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. --194.145.161.227 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. --194.145.161.227 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.--194.145.161.227 12:06, 7 January 2007 (UTC)

Question: Horizontal gene transfer between multicellular organism

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)

The article does cover this and mentions the action of viruses and bacteria. Shyamal 16:02, 13 March 2007 (UTC)

I'm sorry, I have'nt seen an example on multicellular organism. --Procrastinating@^talk2me 10:26, 14 March 2007 (UTC)

See sources and notes and further reading for specific examples. WAS 4.250 21:23, 14 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)

Find a reliable published source. WAS 4.250 (talk) 06:44, 2 June 2008 (UTC)

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)

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)

Image: :Horizental-gene-transfer.jpg

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.

Regards,

barth

Barth F. Smets, Ph.D."

Salvaged text

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)

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)

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)

history

Wouldn't Griffith's_experiment in 1928 be an early research on horizontal gene transfer? Hoemaco (talk) 14:59, 14 February 2010 (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[[9]] 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.