Help with literature review on experimental evidence for mechanisms of eukaryotic HGT

And just 1 in our evolution from common ancestry with the Great Apes. Rare indeed. It might even be a reconstruction error…

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That doesn’t back up your false statement and you should be able to see why. I have no further comment on that.

I’m sure it hinders HGT all things considered, but the thread was about eukaryotes, which include vast numbers of lineages to which “gonad” and “immunologically privileged” don’t apply. If the topic of this thread had been “HGT in mammals” I wouldn’t have bothered to respond.

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Maybe we are reading @pnelson wrong here. I admit I am/was anticipating that @pnelson’s argument would look something like the quote here. In citing Martin’s paper, it would seem as if @pnelson is actually raising questions about the authenticity of supposed phylogenetic anomaly. This is good practice - if the anomaly doesn’t exist, if it is an artifact of the technology and analysis, then there is no reason for anyone to get excited about it. And certainly no reason to start talking about a lack of a mechanism (for something that isn’t real) or problems for evolutionary theory.

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Did you know mammalian and yeast cells can be transformed with Agrobacterium?

4 posts were split to a new topic: Still more Comments on Ewert’s Dependency Graph

:exploding_head:

I did not know that. That’s amazing.

Do you know how to find that discussion?

A review discussing Agrobacterium transformation of fungi:
https://fungalbiolbiotech.biomedcentral.com/articles/10.1186/s40694-017-0035-0

Transformation of Hela cells by Agrobacterium:
https://www.pnas.org/content/98/4/1871

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Thanks, Art! Very helpful.

Patterns of HGT cannot be explained by just the patterns of newly-arisen HGT events in newborns, because there is then still the issue of whether natural selection weeds out the event or helps fix it in the population.

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Sure, but I think the underlying question (for me at least) is how often HGT take place in mammals, which would require transfection of germ-line cells. @sfmatheson provided some papers that show it certainly happens sometimes, but it is rare. @T_aquaticus presented a paper that shows HGT fixed only very rarely in the human lineage, so this isn’t really a fundamental problem. It seems that HGT in extant mammals is likely a black swan event.

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Found this dissertation that describes experiments done to assess the occurrence of HGT in brewer’s yeast during wine making:
http://scholar.sun.ac.za/handle/10019.1/1216

ASSESSING THE OCCURRENCE AND MECHANISMS OF HORIZONTAL GENE TRANSFER DURING WINE MAKING

ENGLISH ABSTRACT: Saccharomyces cerevisiae is the most commonly used organism in many fermentation-based industries including baking and the production of single cell proteins, biofuel and alcoholic beverages. In the wine industry, a consumer driven demand for new and improved products has focussed yeast research on developing strains with new qualities. Tremendous progress in the understanding of yeast genetics has promoted the development of yeast biotechnology and subsequently of genetically modified (GM) wine yeast strains. The potential benefits of such GM wine yeast are numerous, benefitting both wine makers and consumers. However, the safety considerations require intense evaluation before launching such strains into commercial production. Such assessments consider the possibility of the transfer of newly engineered DNA from the originally modified host to an unrelated organism. This process of horizontal gene transfer (HGT) creates a potential hazard in the use of such organisms. Although HGT has been extensively studied within the prokaryotic domain, there is an urgent need for similar studies on their eukaryotic counterparts. This study was therefore undertaken to help improve our understanding of this issue by investigating HGT in a model eukaryotic organism through a step-by-step approach. In a first step, this study attempted to determine whether large DNA fragments are released from fermenting wine yeast strains and, in a second step, to assess the stability of released DNA within such a fermenting background. The third step investigated in this study was to establish whether “free floating” DNA within this fermenting environment could be accepted and functionally expressed by the fermenting yeast cultures. Finally, whole plasmid transfer was also investigated as a unified event. Biofilms were also incorporated into this study as they constitute a possibly conducive environment for the observation of such HGT events. The results obtained during this study help to answer most of the above questions. Firstly, during an investigation into the possible release of large DNA fragments (>500 bp) from a GM commercial wine yeast strain (Parental strain: Vin13), no DNA could be detected within the fermenting background, suggesting that such DNA fragments were not released in large numbers. Secondly, the study revealed remarkable stability of free “floating DNA” under these fermentation conditions, identifying intact DNA of up to ~1kb in fermenting media for up to 62 days after it had been added. Thirdly, the data demonstrate the uptake and functional expression of spiked DNA by fermenting Vin13 cultures in grape must. Here, another interesting discovery was made, since it appears that the fermenting natural grape must favours DNA uptake when compared to synthetic must, suggesting the presence of carrier molecules. Additionally, we found that spiked plasmid DNA was not maintained as a circular unit, but that only the antibiotic resistance marker was maintained through genomic integration. Identification of the sites of integration showed the sites varied from one HGT event to the next, indicating that integration occurred through a process known as illegitimate recombination. Finally, we provide evidence for the direct transfer of whole plasmids between Vin13 strains. The overall outcome of this study is that HGT does indeed occur under the conditions investigated. To our knowledge, this is the first report of direct horizontal DNA transfer between organisms of the same species in eukaryotes. Furthermore, while the occurences of such events appears low in number, it cannot be assumed that HGT will not occur more frequently within an industrial scenario, making industrial scale studies similar to this one paramount before drawing further conclusions.

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Sure, but my point is not about germ cell lineages. It is that even after you have collected information about how often a horizontally-transferred gene pops up in gametes, you still don’t know how often a whole species acquires such a gene. Because after it shows up in someone, it doesn’t get to spread through the whole species unless natural selection permits or encourages that.

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In most cases, the null might be neutral fixation. However, give the rarity of HGT, perhaps positive selection is a more likely explanation…?

That would be the “permits” part in “permits or encourages”. Certainly strong positive selection would make fixation more likely. Whether most fixations are due to selection or drift would presumably depend on the frequency of advantageous HGT events vs. neutral ones and the distribution of selection coefficients of those transfers.

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Yes. I’m just suggesting that the already low substitution rate might be above the neutral rate because of positive selection.

Makes sense. The reason neutral substitutions dominate in most genomes is that the frequency of neutral mutations is vastly higher than the frequency of advantageous ones. It’s not incredible that this might not be the case for HGT.

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To see whether HGT events are neutral, we could compare rates of them in pedigrees to rates of them in phylogenies. Unfortunately these are rare events (per individual reproduction) so that one would have to screen for them in a great many individuals to get the pedigree information. So it is not likely that we will get this type of information soon.